def clear(self):
""" Deletes all items in the TreeView
"""
#logging.debug(__name__ + ": clear")
self._itemDict = {}
self._firstItem = None
QTreeWidget.clear(self)
class Results(QWidget):
def __init__(self, parent):
QWidget.__init__(self, parent)
self._parent = parent
vbox = QVBoxLayout(self)
self._tree = QTreeWidget()
self._tree.setHeaderLabels((self.tr("Content"), self.tr("File"), self.tr("Line")))
self._tree.header().setHorizontalScrollMode(QAbstractItemView.ScrollPerPixel)
self._tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(1, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(2, QHeaderView.ResizeToContents)
self._tree.header().setStretchLastSection(True)
self._tree.sortByColumn(1, Qt.AscendingOrder)
vbox.addWidget(self._tree)
# Signals
self.connect(self._tree, SIGNAL("itemClicked(QTreeWidgetItem*, int)"), self._open_result)
def _open_result(self, item, col):
filename = unicode(item.toolTip(1))
line = int(item.text(2)) - 1
main_container.MainContainer().open_file(fileName=filename, cursorPosition=line, positionIsLineNumber=True)
self._parent.hide()
def update_result(self, items):
self._tree.clear()
for i in items:
item = QTreeWidgetItem(self._tree, (i[3], i[0], QString.number(i[2] + 1)))
item.setToolTip(1, i[1])
def clear(self):
""" Deletes all items in the TreeView
"""
#logging.debug(__name__ + ": clear")
self._itemDict = {}
self._firstItem = None
QTreeWidget.clear(self)
def clear( self ):
" Resets everything "
self.resortEnabled = True
self.openItems = []
self.framenr = 0
QTreeWidget.clear( self )
return
def clear(self):
" Resets everything "
self.resortEnabled = True
self.openItems = []
self.framenr = 0
QTreeWidget.clear(self)
return
class DictWidget(QWidget, NodeWidget):
data_type = "Dict"
two_rows = True
data_class = StructuredNode
def __init__(self, name, data, scheme, parent=None):
QWidget.__init__(self, parent)
NodeWidget.__init__(self, name, data, scheme)
self.layout = QVBoxLayout(self)
self.layout.setMargin(0)
self.layout.setContentsMargins(0,0,0,0)
self._listwidget = QTreeWidget(self)
self._listwidget.setColumnCount(2)
self._listwidget.setHeaderLabels(("Key","Value"))
self.layout.addWidget(self._listwidget)
hlayout = QHBoxLayout()
self.layout.addLayout(hlayout)
self._plus_minus_widget = PlusMinusWidget(self.create_item, self.delete_item, self)
hlayout.addWidget(self._plus_minus_widget)
self.new_data = None
hlayout.addStretch(1)
self.add_widget = WidgetSelector(self)
hlayout.addWidget(self.add_widget)
def delete_item(self):
current_item = self._listwidget.currentItem()
if current_item:
key = current_item.data(1)
new_data = self.data.get()
del new_data[key]
self.data.set(new_data)
def create_item(self):
new_data = self.data.get()
new_item = self.add_widget.get_item()
new_data[new_item["key"]] = Node.create_node(new_item["value"].get())
self.data.set(new_data)
def __createItem(self, itemname, itemvalue):
item = QTreeWidgetItem(self._listwidget, [unicode(itemname), unicode(itemvalue)])
# item.setFlags (Qt.ItemIsSelectable | Qt.ItemIsEditable | Qt.ItemIsEnabled )
def dump(self):
pass
def load(self):
self._listwidget.clear()
for key, value in self.data.iteritems():
self.__createItem(key, value)
@classmethod
def _get_default_data(cls, scheme, data):
return StructuredNode({})
class MemUsageDialog(QDialog):
def __init__(self, parent=None, update=True):
QDialog.__init__(self, parent=parent)
layout = QVBoxLayout()
self.tree = QTreeWidget()
layout.addWidget(self.tree)
self.setLayout(layout)
self._mgr = CacheMemoryManager()
self._tracked_caches = {}
# tree setup code
self.tree.setHeaderLabels(
["cache", "memory", "roi", "dtype", "type", "info", "id"])
self._idIndex = self.tree.columnCount() - 1
self.tree.setColumnHidden(self._idIndex, True)
self.tree.setSortingEnabled(True)
self.tree.clear()
self._root = TreeNode()
# refresh every x seconds (see showEvent())
self.timer = QTimer(self)
if update:
self.timer.timeout.connect(self._updateReport)
def _updateReport(self):
# we keep track of dirty reports so we just have to update the tree
# instead of reconstructing it
reports = []
for c in self._mgr.getFirstClassCaches():
r = MemInfoNode()
c.generateReport(r)
reports.append(r)
self._root.handleChildrenReports(reports,
root=self.tree.invisibleRootItem())
def hideEvent(self, event):
self.timer.stop()
def showEvent(self, show):
# update once so we don't have to wait for initial report
self._updateReport()
# update every 5 sec.
self.timer.start(5 * 1000)
class Results(QWidget):
"""Show results of occurrences in files inside the tools dock."""
def __init__(self, parent):
super(Results, self).__init__(parent)
self._parent = parent
vbox = QVBoxLayout(self)
self._tree = QTreeWidget()
self._tree.setHeaderLabels((self.tr("Content"),
self.tr('File'), self.tr('Line')))
self._tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self._tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(1, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(2, QHeaderView.ResizeToContents)
self._tree.header().setStretchLastSection(True)
self._tree.sortByColumn(1, Qt.AscendingOrder)
vbox.addWidget(self._tree)
#Signals
self.connect(self._tree,
SIGNAL("itemActivated(QTreeWidgetItem*, int)"),
self._open_result)
self.connect(self._tree, SIGNAL("itemClicked(QTreeWidgetItem*, int)"),
self._open_result)
def _open_result(self, item, col):
"""Get the data of the selected item and open the file."""
filename = item.toolTip(1)
line = int(item.text(2)) - 1
main_container = IDE.get_service('main_container')
if main_container:
main_container.open_file(
filename=filename,
cursorPosition=line,
positionIsLineNumber=True)
self._parent.hide()
def update_result(self, items):
"""Update the result tree with the new items."""
self._tree.clear()
for i in items:
item = QTreeWidgetItem(self._tree, (i[3], i[0], str(i[2] + 1)))
item.setToolTip(1, i[1])
class MemUsageDialog(QDialog):
def __init__(self, parent=None, update=True):
QDialog.__init__(self, parent=parent)
layout = QVBoxLayout()
self.tree = QTreeWidget()
layout.addWidget(self.tree)
self.setLayout(layout)
self._mgr = CacheMemoryManager()
self._tracked_caches = {}
# tree setup code
self.tree.setHeaderLabels(
["cache", "memory", "roi", "dtype", "type", "info", "id"])
self._idIndex = self.tree.columnCount() - 1
self.tree.setColumnHidden(self._idIndex, True)
self.tree.setSortingEnabled(True)
self.tree.clear()
self._root = TreeNode()
# refresh every x seconds (see showEvent())
self.timer = QTimer(self)
if update:
self.timer.timeout.connect(self._updateReport)
def _updateReport(self):
# we keep track of dirty reports so we just have to update the tree
# instead of reconstructing it
reports = []
for c in self._mgr.getFirstClassCaches():
r = MemInfoNode()
c.generateReport(r)
reports.append(r)
self._root.handleChildrenReports(
reports, root=self.tree.invisibleRootItem())
def hideEvent(self, event):
self.timer.stop()
def showEvent(self, show):
# update once so we don't have to wait for initial report
self._updateReport()
# update every 5 sec.
self.timer.start(5*1000)
class Results(QWidget):
"""Show results of occurrences in files inside the tools dock."""
def __init__(self, parent):
super(Results, self).__init__(parent)
self._parent = parent
vbox = QVBoxLayout(self)
self._tree = QTreeWidget()
self._tree.setHeaderLabels(
(translations.TR_CONTENT, translations.TR_FILE,
translations.TR_LINE))
self._tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self._tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(1, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(2, QHeaderView.ResizeToContents)
self._tree.header().setStretchLastSection(True)
self._tree.sortByColumn(1, Qt.AscendingOrder)
vbox.addWidget(self._tree)
#Signals
self.connect(self._tree,
SIGNAL("itemActivated(QTreeWidgetItem*, int)"),
self._open_result)
self.connect(self._tree, SIGNAL("itemClicked(QTreeWidgetItem*, int)"),
self._open_result)
def _open_result(self, item, col):
"""Get the data of the selected item and open the file."""
filename = item.toolTip(1)
line = int(item.text(2)) - 1
main_container = IDE.get_service('main_container')
if main_container:
main_container.open_file(filename=filename,
cursorPosition=line,
positionIsLineNumber=True)
self._parent.hide()
def update_result(self, items):
"""Update the result tree with the new items."""
self._tree.clear()
for i in items:
item = QTreeWidgetItem(self._tree, (i[3], i[0], str(i[2] + 1)))
item.setToolTip(1, i[1])
class Results(QWidget):
def __init__(self, parent):
QWidget.__init__(self, parent)
self._parent = parent
vbox = QVBoxLayout(self)
self._tree = QTreeWidget()
self._tree.setHeaderLabels(
(self.tr("Content"), self.tr('File'), self.tr('Line')))
self._tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self._tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(1, QHeaderView.ResizeToContents)
self._tree.header().setResizeMode(2, QHeaderView.ResizeToContents)
self._tree.header().setStretchLastSection(True)
self._tree.sortByColumn(1, Qt.AscendingOrder)
vbox.addWidget(self._tree)
#Signals
self.connect(self._tree,
SIGNAL("itemActivated(QTreeWidgetItem*, int)"),
self._open_result)
self.connect(self._tree, SIGNAL("itemClicked(QTreeWidgetItem*, int)"),
self._open_result)
def _open_result(self, item, col):
filename = unicode(item.toolTip(1))
line = int(item.text(2)) - 1
main_container.MainContainer().open_file(filename=filename,
cursorPosition=line,
positionIsLineNumber=True)
self._parent.hide()
def update_result(self, items):
self._tree.clear()
for i in items:
item = QTreeWidgetItem(self._tree,
(i[3], i[0], QString.number(i[2] + 1)))
item.setToolTip(1, i[1])
class Window(QMainWindow):
def __init__(self):
self.a = 0
QMainWindow.__init__(self)
self.setWindowTitle("Explorador de archivos y carpetas")
self.back_history = []
self.forward_history = []
self.back_button = QPushButton(self)
self.back_button.setIcon(QIcon("images/back.png"))
self.back_button.clicked.connect(self.back_clicked)
self.back_button.setEnabled(False)
self.forward_button = QPushButton(self)
self.forward_button.setIcon(QIcon("images/forward.png"))
self.forward_button.clicked.connect(self.forward_clicked)
self.forward_button.setEnabled(False)
self.up_button = QPushButton(self)
self.up_button.setIcon(QIcon("images/up.png"))
self.up_button.clicked.connect(self.up_button_clicked)
self.address_edit = QLineEdit(self)
self.refresh_button = QPushButton(self)
self.refresh_button.setIcon(QIcon("images/update.png"))
self.refresh_button.clicked.connect(self.refresh_button_clicked)
self.toplayout = QHBoxLayout()
self.toplayout.addWidget(self.back_button)
self.toplayout.addWidget(self.forward_button)
self.toplayout.addWidget(self.up_button)
self.toplayout.addWidget(self.address_edit)
self.toplayout.addWidget(self.refresh_button)
self.main_tree = QTreeWidget(self)
self.main_tree.setRootIsDecorated(False)
self.main_tree.setHeaderLabels(
("Nombre", u"Fecha de modificación", u"Tamaño"))
self.main_tree.itemDoubleClicked.connect(self.item_double_clicked)
self.layout = QVBoxLayout()
self.layout.addLayout(self.toplayout)
self.layout.addWidget(self.main_tree)
self.central_widget = QWidget(self)
self.central_widget.setLayout(self.layout)
self.setCentralWidget(self.central_widget)
self.resize(800, 600)
# Iniciar en el directorio actual.
self.load_path(getcwd())
def back_clicked(self, checked):
if self.back_history and len(self.back_history) > 1:
# Obtener el último elemento.
path = self.back_history[-2]
self.forward_history.append(self.back_history[-1])
# Remover el directorio actual.
del self.back_history[-1]
self.load_path(path, False)
def forward_clicked(self, checked):
if self.forward_history:
path = self.forward_history[-1]
self.back_history.append(path)
del self.forward_history[-1]
self.load_path(path, False)
def item_double_clicked(self, item, column):
filepath = join(self.current_path, unicode(item.text(0)))
if isdir(filepath):
self.load_path(filepath)
else:
# Iniciar archivo con el programa predeterminado.
#startfile(filepath)
a = filepath
parcial.ponfoto(a)
#print self.a
def up_button_clicked(self, checked):
parent = dirname(self.current_path)
if parent != self.current_path:
self.load_path(parent)
def load_path(self, path, use_history=True):
# Obtener archivos y carpetas.
items = listdir(unicode(path))
# Eliminar el contenido anterior.
self.main_tree.clear()
for i in items:
# Omitir archivos ocultos.
if i.startswith("."):
continue
filepath = join(path, i)
# Obtener informacion del archivo.
stats = stat(filepath)
# Crear el control ítem.
item_widget = QTreeWidgetItem(
(i, strftime("%c", localtime(stats.st_mtime)).decode("utf-8"),
size(stats.st_size) if isfile(filepath) else ""))
# Establecer el ícono correspondiente.
item_widget.setIcon(
0,
QIcon("images/%s.png" %
("file" if isfile(filepath) else "folder")))
# Añadir elemento.
self.main_tree.addTopLevelItem(item_widget)
# Ajustar el tamaño de las columnas.
for i in range(3):
self.main_tree.resizeColumnToContents(i)
self.current_path = path
self.address_edit.setText(self.current_path)
# Añadir al historial.
if use_history:
self.back_history.append(self.current_path)
# Habilitar / dehabilitar botones del historial.
if self.back_history and len(self.back_history) > 1:
if not self.back_button.isEnabled():
self.back_button.setEnabled(True)
else:
if self.back_button.isEnabled():
self.forward_history = []
self.back_button.setEnabled(False)
if self.forward_history:
if not self.forward_button.isEnabled():
self.forward_button.setEnabled(True)
else:
if self.forward_button.isEnabled():
self.forward_button.setEnabled(False)
def refresh_button_clicked(self, checked):
self.load_path(self.current_path)
class OWKEGGPathwayBrowser(widget.OWWidget):
name = "KEGG Pathways"
description = "Browse KEGG pathways that include an input set of genes."
icon = "../widgets/icons/KEGGPathways.svg"
priority = 2030
inputs = [("Examples", Orange.data.Table, "SetData", widget.Default),
("Reference", Orange.data.Table, "SetRefData")]
outputs = [("Selected Examples", Orange.data.Table, widget.Default),
("Unselected Examples", Orange.data.Table)]
settingsHandler = settings.DomainContextHandler()
organismIndex = settings.ContextSetting(0)
geneAttrIndex = settings.ContextSetting(0)
useAttrNames = settings.ContextSetting(False)
autoCommit = settings.Setting(False)
autoResize = settings.Setting(True)
useReference = settings.Setting(False)
showOrthology = settings.Setting(True)
Ready, Initializing, Running = 0, 1, 2
def __init__(self, parent=None):
super().__init__(parent)
self.organismCodes = []
self._changedFlag = False
self.__invalidated = False
self.__runstate = OWKEGGPathwayBrowser.Initializing
self.__in_setProgress = False
self.controlArea.setMaximumWidth(250)
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(box, "No data on input\n")
# Organism selection.
box = gui.widgetBox(self.controlArea, "Organism")
self.organismComboBox = gui.comboBox(
box, self, "organismIndex",
items=[],
callback=self.Update,
addSpace=True,
tooltip="Select the organism of the input genes")
# Selection of genes attribute
box = gui.widgetBox(self.controlArea, "Gene attribute")
self.geneAttrCandidates = itemmodels.VariableListModel(parent=self)
self.geneAttrCombo = gui.comboBox(
box, self, "geneAttrIndex", callback=self.Update)
self.geneAttrCombo.setModel(self.geneAttrCandidates)
gui.checkBox(box, self, "useAttrNames",
"Use variable names", disables=[(-1, self.geneAttrCombo)],
callback=self.Update)
self.geneAttrCombo.setDisabled(bool(self.useAttrNames))
gui.separator(self.controlArea)
gui.checkBox(self.controlArea, self, "useReference",
"From signal", box="Reference", callback=self.Update)
gui.separator(self.controlArea)
gui.checkBox(self.controlArea, self, "showOrthology",
"Show pathways in full orthology", box="Orthology",
callback=self.UpdateListView)
gui.checkBox(self.controlArea, self, "autoResize",
"Resize to fit", box="Image",
callback=self.UpdatePathwayViewTransform)
box = gui.widgetBox(self.controlArea, "Cache Control")
gui.button(box, self, "Clear cache",
callback=self.ClearCache,
tooltip="Clear all locally cached KEGG data.")
gui.separator(self.controlArea)
gui.auto_commit(self.controlArea, self, "autoCommit", "Commit")
gui.rubber(self.controlArea)
spliter = QSplitter(Qt.Vertical, self.mainArea)
self.pathwayView = PathwayView(self, spliter)
self.pathwayView.scene().selectionChanged.connect(
self._onSelectionChanged
)
self.mainArea.layout().addWidget(spliter)
self.listView = QTreeWidget(
allColumnsShowFocus=True,
selectionMode=QTreeWidget.SingleSelection,
sortingEnabled=True,
maximumHeight=200)
spliter.addWidget(self.listView)
self.listView.setColumnCount(4)
self.listView.setHeaderLabels(
["Pathway", "P value", "Genes", "Reference"])
self.listView.itemSelectionChanged.connect(self.UpdatePathwayView)
select = QAction(
"Select All", self,
shortcut=QKeySequence.SelectAll
)
select.triggered.connect(self.selectAll)
self.addAction(select)
self.data = None
self.refData = None
self._executor = concurrent.ThreadExecutor()
self.setEnabled(False)
self.setBlocking(True)
progress = concurrent.methodinvoke(self, "setProgress", (float,))
def get_genome():
"""Return a KEGGGenome with the common org entries precached."""
genome = kegg.KEGGGenome()
essential = genome.essential_organisms()
common = genome.common_organisms()
# Remove duplicates of essential from common.
# (essential + common list as defined here will be used in the
# GUI.)
common = [c for c in common if c not in essential]
# TODO: Add option to specify additional organisms not
# in the common list.
keys = list(map(genome.org_code_to_entry_key, essential + common))
genome.pre_cache(keys, progress_callback=progress)
return (keys, genome)
self._genomeTask = task = concurrent.Task(function=get_genome)
task.finished.connect(self.__initialize_finish)
self.progressBarInit()
self.infoLabel.setText("Fetching organism definitions\n")
self._executor.submit(task)
def __initialize_finish(self):
if self.__runstate != OWKEGGPathwayBrowser.Initializing:
return
try:
keys, genome = self._genomeTask.result()
except Exception as err:
self.error(0, str(err))
raise
self.progressBarFinished()
self.setEnabled(True)
self.setBlocking(False)
entries = [genome[key] for key in keys]
items = [entry.definition for entry in entries]
codes = [entry.organism_code for entry in entries]
self.organismCodes = codes
self.organismComboBox.clear()
self.organismComboBox.addItems(items)
self.organismComboBox.setCurrentIndex(self.organismIndex)
self.infoLabel.setText("No data on input\n")
def Clear(self):
"""
Clear the widget state.
"""
self.queryGenes = []
self.referenceGenes = []
self.genes = {}
self.uniqueGenesDict = {}
self.revUniqueGenesDict = {}
self.pathways = {}
self.org = None
self.geneAttrCandidates[:] = []
self.infoLabel.setText("No data on input\n")
self.listView.clear()
self.pathwayView.SetPathway(None)
self.send("Selected Examples", None)
self.send("Unselected Examples", None)
def SetData(self, data=None):
if self.__runstate == OWKEGGPathwayBrowser.Initializing:
self.__initialize_finish()
self.closeContext()
self.data = data
self.warning(0)
self.error(0)
self.information(0)
if data is not None:
vars = data.domain.variables + data.domain.metas
vars = [var for var in vars
if isinstance(var, Orange.data.StringVariable)]
self.geneAttrCandidates[:] = vars
# Try to guess the gene name variable
names_lower = [v.name.lower() for v in vars]
scores = [(name == "gene", "gene" in name)
for name in names_lower]
imax, _ = max(enumerate(scores), key=itemgetter(1))
self.geneAttrIndex = imax
taxid = data_hints.get_hint(data, "taxid", None)
if taxid:
try:
code = kegg.from_taxid(taxid)
self.organismIndex = self.organismCodes.index(code)
except Exception as ex:
print(ex, taxid)
self.useAttrNames = data_hints.get_hint(data, "genesinrows",
self.useAttrNames)
self.openContext(data)
else:
self.Clear()
self.__invalidated = True
def SetRefData(self, data=None):
self.refData = data
self.information(1)
if data is not None and self.useReference:
self.__invalidated = True
def handleNewSignals(self):
if self.__invalidated:
self.Update()
self.__invalidated = False
def UpdateListView(self):
self.bestPValueItem = None
self.listView.clear()
if not self.data:
return
allPathways = self.org.pathways()
allRefPathways = kegg.pathways("map")
items = []
kegg_pathways = kegg.KEGGPathways()
org_code = self.organismCodes[min(self.organismIndex,
len(self.organismCodes) - 1)]
if self.showOrthology:
self.koOrthology = kegg.KEGGBrite("ko00001")
self.listView.setRootIsDecorated(True)
path_ids = set([s[-5:] for s in self.pathways.keys()])
def _walkCollect(koEntry):
num = koEntry.title[:5] if koEntry.title else None
if num in path_ids:
return ([koEntry] +
reduce(lambda li, c: li + _walkCollect(c),
[child for child in koEntry.entries],
[]))
else:
c = reduce(lambda li, c: li + _walkCollect(c),
[child for child in koEntry.entries],
[])
return c + (c and [koEntry] or [])
allClasses = reduce(lambda li1, li2: li1 + li2,
[_walkCollect(c) for c in self.koOrthology],
[])
def _walkCreate(koEntry, lvItem):
item = QTreeWidgetItem(lvItem)
id = "path:" + org_code + koEntry.title[:5]
if koEntry.title[:5] in path_ids:
p = kegg_pathways.get_entry(id)
if p is None:
# In case the genesets still have obsolete entries
name = koEntry.title
else:
name = p.name
genes, p_value, ref = self.pathways[id]
item.setText(0, name)
item.setText(1, "%.5f" % p_value)
item.setText(2, "%i of %i" % (len(genes), len(self.genes)))
item.setText(3, "%i of %i" % (ref, len(self.referenceGenes)))
item.pathway_id = id if p is not None else None
else:
if id in allPathways:
text = kegg_pathways.get_entry(id).name
else:
text = koEntry.title
item.setText(0, text)
if id in allPathways:
item.pathway_id = id
elif "path:map" + koEntry.title[:5] in allRefPathways:
item.pathway_id = "path:map" + koEntry.title[:5]
else:
item.pathway_id = None
for child in koEntry.entries:
if child in allClasses:
_walkCreate(child, item)
for koEntry in self.koOrthology:
if koEntry in allClasses:
_walkCreate(koEntry, self.listView)
self.listView.update()
else:
self.listView.setRootIsDecorated(False)
pathways = self.pathways.items()
pathways = sorted(pathways, key=lambda item: item[1][1])
for id, (genes, p_value, ref) in pathways:
item = QTreeWidgetItem(self.listView)
item.setText(0, kegg_pathways.get_entry(id).name)
item.setText(1, "%.5f" % p_value)
item.setText(2, "%i of %i" % (len(genes), len(self.genes)))
item.setText(3, "%i of %i" % (ref, len(self.referenceGenes)))
item.pathway_id = id
items.append(item)
self.bestPValueItem = items and items[0] or None
self.listView.expandAll()
for i in range(4):
self.listView.resizeColumnToContents(i)
if self.bestPValueItem:
index = self.listView.indexFromItem(self.bestPValueItem)
self.listView.selectionModel().select(
index, QItemSelectionModel.ClearAndSelect
)
def UpdatePathwayView(self):
items = self.listView.selectedItems()
if len(items) > 0:
item = items[0]
else:
item = None
self.commit()
item = item or self.bestPValueItem
if not item or not item.pathway_id:
self.pathwayView.SetPathway(None)
return
def get_kgml_and_image(pathway_id):
"""Return an initialized KEGGPathway with pre-cached data"""
p = kegg.KEGGPathway(pathway_id)
p._get_kgml() # makes sure the kgml file is downloaded
p._get_image_filename() # makes sure the image is downloaded
return (pathway_id, p)
self.setEnabled(False)
self._pathwayTask = concurrent.Task(
function=lambda: get_kgml_and_image(item.pathway_id)
)
self._pathwayTask.finished.connect(self._onPathwayTaskFinshed)
self._executor.submit(self._pathwayTask)
def _onPathwayTaskFinshed(self):
self.setEnabled(True)
pathway_id, self.pathway = self._pathwayTask.result()
self.pathwayView.SetPathway(
self.pathway,
self.pathways.get(pathway_id, [[]])[0]
)
def UpdatePathwayViewTransform(self):
self.pathwayView.updateTransform()
def Update(self):
"""
Update (recompute enriched pathways) the widget state.
"""
if not self.data:
return
self.error(0)
self.information(0)
# XXX: Check data in setData, do not even alow this to be executed if
# data has no genes
try:
genes = self.GeneNamesFromData(self.data)
except ValueError:
self.error(0, "Cannot extract gene names from input.")
genes = []
if not self.useAttrNames and any("," in gene for gene in genes):
genes = reduce(add, (split_and_strip(gene, ",")
for gene in genes),
[])
self.information(0,
"Separators detected in input gene names. "
"Assuming multiple genes per instance.")
self.queryGenes = genes
self.information(1)
reference = None
if self.useReference and self.refData:
reference = self.GeneNamesFromData(self.refData)
if not self.useAttrNames \
and any("," in gene for gene in reference):
reference = reduce(add, (split_and_strip(gene, ",")
for gene in reference),
[])
self.information(1,
"Separators detected in reference gene "
"names. Assuming multiple genes per "
"instance.")
org_code = self.SelectedOrganismCode()
def run_enrichment(org_code, genes, reference=None, progress=None):
org = kegg.KEGGOrganism(org_code)
if reference is None:
reference = org.get_genes()
# Map 'genes' and 'reference' sets to unique KEGG identifiers
unique_genes, _, _ = org.get_unique_gene_ids(set(genes))
unique_ref_genes, _, _ = org.get_unique_gene_ids(set(reference))
taxid = kegg.to_taxid(org.org_code)
# Map the taxid back to standard 'common' taxids
# (as used by 'geneset') if applicable
r_tax_map = dict((v, k) for k, v in
kegg.KEGGGenome.TAXID_MAP.items())
if taxid in r_tax_map:
taxid = r_tax_map[taxid]
# We use the kegg pathway gene sets provided by 'geneset' for
# the enrichment calculation.
# Ensure we are using the latest genesets
# TODO: ?? Is updating the index enough?
serverfiles.update(geneset.sfdomain, "index.pck")
kegg_gs_collections = geneset.collections(
(("KEGG", "pathways"), taxid)
)
pathways = pathway_enrichment(
kegg_gs_collections, unique_genes.keys(),
unique_ref_genes.keys(),
callback=progress
)
# Ensure that pathway entries are pre-cached for later use in the
# list/tree view
kegg_pathways = kegg.KEGGPathways()
kegg_pathways.pre_cache(
pathways.keys(), progress_callback=progress
)
return pathways, org, unique_genes, unique_ref_genes
self.progressBarInit()
self.setEnabled(False)
self.infoLabel.setText("Retrieving...\n")
progress = concurrent.methodinvoke(self, "setProgress", (float,))
self._enrichTask = concurrent.Task(
function=lambda:
run_enrichment(org_code, genes, reference, progress)
)
self._enrichTask.finished.connect(self._onEnrichTaskFinished)
self._executor.submit(self._enrichTask)
def _onEnrichTaskFinished(self):
self.setEnabled(True)
self.setBlocking(False)
try:
pathways, org, unique_genes, unique_ref_genes = \
self._enrichTask.result()
except Exception:
raise
self.progressBarFinished()
self.org = org
self.genes = unique_genes.keys()
self.uniqueGenesDict = unique_genes
self.revUniqueGenesDict = dict([(val, key) for key, val in
self.uniqueGenesDict.items()])
self.referenceGenes = unique_ref_genes.keys()
self.pathways = pathways
if not self.pathways:
self.warning(0, "No enriched pathways found.")
else:
self.warning(0)
count = len(set(self.queryGenes))
self.infoLabel.setText(
"%i unique gene names on input\n"
"%i (%.1f%%) genes names matched" %
(count, len(unique_genes),
100.0 * len(unique_genes) / count if count else 0.0)
)
self.UpdateListView()
@Slot(float)
def setProgress(self, value):
if self.__in_setProgress:
return
self.__in_setProgress = True
self.progressBarSet(value)
self.__in_setProgress = False
def GeneNamesFromData(self, data):
"""
Extract and return gene names from `data`.
"""
if self.useAttrNames:
genes = [str(v.name).strip() for v in data.domain.attributes]
elif self.geneAttrCandidates:
index = min(self.geneAttrIndex, len(self.geneAttrCandidates) - 1)
geneAttr = self.geneAttrCandidates[index]
genes = [str(e[geneAttr]) for e in data
if not numpy.isnan(e[geneAttr])]
else:
raise ValueError("No gene names in data.")
return genes
def SelectedOrganismCode(self):
"""
Return the selected organism code.
"""
return self.organismCodes[min(self.organismIndex,
len(self.organismCodes) - 1)]
def selectAll(self):
"""
Select all items in the pathway view.
"""
changed = False
scene = self.pathwayView.scene()
with disconnected(scene.selectionChanged, self._onSelectionChanged):
for item in scene.items():
if item.flags() & QGraphicsItem.ItemIsSelectable and \
not item.isSelected():
item.setSelected(True)
changed = True
if changed:
self._onSelectionChanged()
def _onSelectionChanged(self):
# Item selection in the pathwayView/scene has changed
self.commit()
def commit(self):
if self.data:
selectedItems = self.pathwayView.scene().selectedItems()
selectedGenes = reduce(set.union, [item.marked_objects
for item in selectedItems],
set())
if self.useAttrNames:
selected = [self.data.domain[self.uniqueGenesDict[gene]]
for gene in selectedGenes]
# newDomain = Orange.data.Domain(selectedVars, 0)
data = self.data[:, selected]
# data = Orange.data.Table(newDomain, self.data)
self.send("Selected Examples", data)
elif self.geneAttrCandidates:
geneAttr = self.geneAttrCandidates[min(self.geneAttrIndex,
len(self.geneAttrCandidates) - 1)]
selectedIndices = []
otherIndices = []
for i, ex in enumerate(self.data):
names = [self.revUniqueGenesDict.get(name, None)
for name in split_and_strip(str(ex[geneAttr]), ",")]
if any(name and name in selectedGenes for name in names):
selectedIndices.append(i)
else:
otherIndices.append(i)
if selectedIndices:
selected = self.data[selectedIndices]
else:
selected = None
if otherIndices:
other = self.data[otherIndices]
else:
other = None
self.send("Selected Examples", selected)
self.send("Unselected Examples", other)
else:
self.send("Selected Examples", None)
self.send("Unselected Examples", None)
def ClearCache(self):
kegg.caching.clear_cache()
def onDeleteWidget(self):
"""
Called before the widget is removed from the canvas.
"""
super().onDeleteWidget()
self.org = None
self._executor.shutdown(wait=False)
gc.collect() # Force collection (WHY?)
def sizeHint(self):
return QSize(1024, 720)
class OWDatabasesUpdate(OWWidget):
name = "Databases Update"
description = "Update local systems biology databases."
icon = "../widgets/icons/Databases.svg"
priority = 10
inputs = []
outputs = []
want_main_area = False
def __init__(self, parent=None, signalManager=None,
name="Databases update", domains=None):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
self.accessCode = ""
self.domains = domains or DOMAINS
self.serverFiles = serverfiles.ServerFiles()
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
gui.lineEdit(box, self, "accessCode", "Access Code",
orientation="horizontal",
callback=self.RetrieveFilesList)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def RetrieveFilesList(self):
self.retryButton.hide()
self.warning(0)
self.progress.setRange(0, 3)
self.serverFiles = serverfiles.ServerFiles(access_code=self.accessCode)
task = Task(function=partial(retrieveFilesList, self.serverFiles,
self.domains,
methodinvoke(self.progress, "advance")))
task.resultReady.connect(self.SetFilesList)
task.exceptionReady.connect(self.HandleError)
self.executor.submit(task)
self.setEnabled(False)
def SetFilesList(self, serverInfo):
"""
Set the files to show.
"""
self.setEnabled(True)
domains = serverInfo.keys()
if not domains:
if self.domains:
domains = self.domains
else:
domains = serverfiles.listdomains()
localInfo = dict([(dom, serverfiles.allinfo(dom)) for dom in domains])
all_tags = set()
self.filesView.clear()
self.updateItems = []
for item in join_info_dict(localInfo, serverInfo):
tree_item = UpdateTreeWidgetItem(item)
options_widget = UpdateOptionsWidget(item.state)
options_widget.item = item
options_widget.installClicked.connect(
partial(self.SubmitDownloadTask, item.domain, item.filename)
)
options_widget.removeClicked.connect(
partial(self.SubmitRemoveTask, item.domain, item.filename)
)
self.updateItems.append((item, tree_item, options_widget))
all_tags.update(item.tags)
self.filesView.addTopLevelItems(
[tree_item for _, tree_item, _ in self.updateItems]
)
for item, tree_item, options_widget in self.updateItems:
self.filesView.setItemWidget(tree_item, 0, options_widget)
# Add an update button if the file is updateable
if item.state == OUTDATED:
button = QToolButton(
None, text="Update",
maximumWidth=120,
minimumHeight=20,
maximumHeight=20
)
if sys.platform == "darwin":
button.setAttribute(Qt.WA_MacSmallSize)
button.clicked.connect(
partial(self.SubmitDownloadTask, item.domain,
item.filename)
)
self.filesView.setItemWidget(tree_item, 2, button)
self.progress.advance()
self.filesView.setColumnWidth(0, self.filesView.sizeHintForColumn(0))
for column in range(1, 4):
contents_hint = self.filesView.sizeHintForColumn(column)
header_hint = self.filesView.header().sectionSizeHint(column)
width = max(min(contents_hint, 400), header_hint)
self.filesView.setColumnWidth(column, width)
hints = [hint for hint in sorted(all_tags) if not hint.startswith("#")]
self.completer.setTokenList(hints)
self.SearchUpdate()
self.UpdateInfoLabel()
self.toggleButtons()
self.cancelButton.setEnabled(False)
self.progress.setRange(0, 0)
def buttonCheck(self, selected_items, state, button):
for item in selected_items:
if item.state != state:
button.setEnabled(False)
else:
button.setEnabled(True)
break
def toggleButtons(self):
selected_items = [item for item, tree_item, _ in self.updateItems if not tree_item.isHidden()]
self.buttonCheck(selected_items, OUTDATED, self.updateButton)
self.buttonCheck(selected_items, AVAILABLE, self.downloadButton)
def HandleError(self, exception):
if isinstance(exception, ConnectionError):
self.warning(0,
"Could not connect to server! Check your connection "
"and try to reconnect.")
self.SetFilesList({})
self.retryButton.show()
else:
sys.excepthook(type(exception), exception.args, None)
self.progress.setRange(0, 0)
self.setEnabled(True)
def UpdateInfoLabel(self):
local = [item for item, tree_item, _ in self.updateItems
if item.state != AVAILABLE and not tree_item.isHidden()]
size = sum(float(item.size) for item in local)
onServer = [item for item, tree_item, _ in self.updateItems if not tree_item.isHidden()]
sizeOnServer = sum(float(item.size) for item in onServer)
text = ("%i items, %s (on server: %i items, %s)" %
(len(local),
sizeof_fmt(size),
len(onServer),
sizeof_fmt(sizeOnServer)))
self.infoLabel.setText(text)
def UpdateAll(self):
self.warning(0)
for item, tree_item, _ in self.updateItems:
if item.state == OUTDATED and not tree_item.isHidden():
self.SubmitDownloadTask(item.domain, item.filename)
def DownloadFiltered(self):
# TODO: submit items in the order shown.
for item, tree_item, _ in self.updateItems:
if not tree_item.isHidden() and item.state in \
[AVAILABLE, OUTDATED]:
self.SubmitDownloadTask(item.domain, item.filename)
def SearchUpdate(self, searchString=None):
strings = str(self.lineEditFilter.text()).split()
for item, tree_item, _ in self.updateItems:
hide = not all(UpdateItem_match(item, string)
for string in strings)
tree_item.setHidden(hide)
self.UpdateInfoLabel()
self.toggleButtons()
def SubmitDownloadTask(self, domain, filename):
"""
Submit the (domain, filename) to be downloaded/updated.
"""
self.cancelButton.setEnabled(True)
index = self.updateItemIndex(domain, filename)
_, tree_item, opt_widget = self.updateItems[index]
if self.accessCode:
sf = serverfiles.ServerFiles(access_code=self.accessCode)
else:
sf = serverfiles.ServerFiles()
task = DownloadTask(domain, filename, sf)
self.progress.adjustRange(0, 100)
pb = ItemProgressBar(self.filesView)
pb.setRange(0, 100)
pb.setTextVisible(False)
task.advanced.connect(pb.advance)
task.advanced.connect(self.progress.advance)
task.finished.connect(pb.hide)
task.finished.connect(self.onDownloadFinished, Qt.QueuedConnection)
task.exception.connect(self.onDownloadError, Qt.QueuedConnection)
self.filesView.setItemWidget(tree_item, 2, pb)
# Clear the text so it does not show behind the progress bar.
tree_item.setData(2, Qt.DisplayRole, "")
pb.show()
# Disable the options widget
opt_widget.setEnabled(False)
self._tasks.append(task)
self.executor.submit(task)
def EndDownloadTask(self, task):
future = task.future()
index = self.updateItemIndex(task.domain, task.filename)
item, tree_item, opt_widget = self.updateItems[index]
self.filesView.removeItemWidget(tree_item, 2)
opt_widget.setEnabled(True)
if future.cancelled():
# Restore the previous state
tree_item.setUpdateItem(item)
opt_widget.setState(item.state)
elif future.exception():
tree_item.setUpdateItem(item)
opt_widget.setState(item.state)
# Show the exception string in the size column.
self.warning(0, "Error while downloading. Check your connection "
"and retry.")
# recreate button for download
button = QToolButton(
None, text="Retry",
maximumWidth=120,
minimumHeight=20,
maximumHeight=20
)
if sys.platform == "darwin":
button.setAttribute(Qt.WA_MacSmallSize)
button.clicked.connect(
partial(self.SubmitDownloadTask, item.domain,
item.filename)
)
self.filesView.setItemWidget(tree_item, 2, button)
else:
# get the new updated info dict and replace the the old item
self.warning(0)
info = serverfiles.info(item.domain, item.filename)
new_item = update_item_from_info(item.domain, item.filename,
info, info)
self.updateItems[index] = (new_item, tree_item, opt_widget)
tree_item.setUpdateItem(new_item)
opt_widget.setState(new_item.state)
self.UpdateInfoLabel()
def SubmitRemoveTask(self, domain, filename):
serverfiles.remove(domain, filename)
index = self.updateItemIndex(domain, filename)
item, tree_item, opt_widget = self.updateItems[index]
if item.info_server:
new_item = item._replace(state=AVAILABLE, local=None,
info_local=None)
else:
new_item = item._replace(local=None, info_local=None)
# Disable the options widget. No more actions can be performed
# for the item.
opt_widget.setEnabled(False)
tree_item.setUpdateItem(new_item)
opt_widget.setState(new_item.state)
self.updateItems[index] = (new_item, tree_item, opt_widget)
self.UpdateInfoLabel()
def Cancel(self):
"""
Cancel all pending update/download tasks (that have not yet started).
"""
for task in self._tasks:
task.future().cancel()
def onDeleteWidget(self):
self.Cancel()
self.executor.shutdown(wait=False)
OWWidget.onDeleteWidget(self)
def onDownloadFinished(self):
# on download completed/canceled/error
assert QThread.currentThread() is self.thread()
for task in list(self._tasks):
future = task.future()
if future.done():
self.EndDownloadTask(task)
self._tasks.remove(task)
if not self._tasks:
# Clear/reset the overall progress
self.progress.setRange(0, 0)
self.cancelButton.setEnabled(False)
def onDownloadError(self, exc_info):
sys.excepthook(*exc_info)
self.warning(0, "Error while downloading. Check your connection and "
"retry.")
def updateItemIndex(self, domain, filename):
for i, (item, _, _) in enumerate(self.updateItems):
if item.domain == domain and item.filename == filename:
return i
raise ValueError("%r, %r not in update list" % (domain, filename))
def _updateProgress(self, *args):
rmin, rmax = self.progress.range()
if rmin != rmax:
if not self._haveProgress:
self._haveProgress = True
self.progressBarInit()
self.progressBarSet(self.progress.ratioCompleted() * 100,
processEvents=None)
if rmin == rmax:
self._haveProgress = False
self.progressBarFinished()
class RecentProjectsViewer( QWidget ):
" Recent projects viewer implementation "
def __init__( self, parent = None ):
QWidget.__init__( self, parent )
self.__projectContextItem = None
self.__fileContextItem = None
self.upper = self.__createRecentFilesLayout()
self.lower = self.__createRecentProjectsLayout()
self.__createProjectPopupMenu()
self.__createFilePopupMenu()
layout = QVBoxLayout()
layout.setContentsMargins( 1, 1, 1, 1 )
splitter = QSplitter( Qt.Vertical )
splitter.addWidget( self.upper )
splitter.addWidget( self.lower )
splitter.setCollapsible( 0, False )
splitter.setCollapsible( 1, False )
layout.addWidget( splitter )
self.setLayout( layout )
self.__populateProjects()
self.__populateFiles()
self.__updateProjectToolbarButtons()
self.__updateFileToolbarButtons()
# Debugging mode support
self.__debugMode = False
parent.debugModeChanged.connect( self.__onDebugMode )
return
def setTooltips( self, switchOn ):
" Switches the tooltips mode "
for index in xrange( 0, self.recentFilesView.topLevelItemCount() ):
self.recentFilesView.topLevelItem( index ).updateIconAndTooltip()
for index in xrange( 0, self.projectsView.topLevelItemCount() ):
self.projectsView.topLevelItem( index ).updateTooltip()
return
def __createFilePopupMenu( self ):
" create the recent files popup menu "
self.__fileMenu = QMenu( self.recentFilesView )
self.__openMenuItem = self.__fileMenu.addAction( \
PixmapCache().getIcon( 'openitem.png' ),
'Open', self.__openFile )
self.__copyPathFileMenuItem = self.__fileMenu.addAction( \
PixmapCache().getIcon( 'copytoclipboard.png' ),
'Copy path to clipboard', self.__filePathToClipboard )
self.__fileMenu.addSeparator()
self.__delFileMenuItem = self.__fileMenu.addAction( \
PixmapCache().getIcon( 'trash.png' ),
'Delete from recent',
self.__deleteFile )
self.recentFilesView.setContextMenuPolicy( Qt.CustomContextMenu )
self.connect( self.recentFilesView,
SIGNAL( "customContextMenuRequested(const QPoint &)" ),
self.__handleShowFileContextMenu )
self.connect( GlobalData().project, SIGNAL( 'recentFilesChanged' ),
self.__populateFiles )
return
def __createProjectPopupMenu( self ):
" Creates the recent project popup menu "
self.__projectMenu = QMenu( self.projectsView )
self.__prjLoadMenuItem = self.__projectMenu.addAction( \
PixmapCache().getIcon( 'load.png' ),
'Load',
self.__loadProject )
self.__projectMenu.addSeparator()
self.__propsMenuItem = self.__projectMenu.addAction( \
PixmapCache().getIcon( 'smalli.png' ),
'Properties',
self.__viewProperties )
self.__prjCopyPathMenuItem = self.__projectMenu.addAction( \
PixmapCache().getIcon( 'copytoclipboard.png' ),
'Copy path to clipboard',
self.__prjPathToClipboard )
self.__projectMenu.addSeparator()
self.__delPrjMenuItem = self.__projectMenu.addAction( \
PixmapCache().getIcon( 'trash.png' ),
'Delete from recent',
self.__deleteProject )
self.projectsView.setContextMenuPolicy( Qt.CustomContextMenu )
self.connect( self.projectsView,
SIGNAL( "customContextMenuRequested(const QPoint &)" ),
self.__handleShowPrjContextMenu )
self.connect( Settings().iInstance, SIGNAL( 'recentListChanged' ),
self.__populateProjects )
GlobalData().project.projectChanged.connect( self.__projectChanged )
return
def __createRecentFilesLayout( self ):
" Creates the upper part - recent files "
headerFrame = QFrame()
headerFrame.setFrameStyle( QFrame.StyledPanel )
headerFrame.setAutoFillBackground( True )
headerPalette = headerFrame.palette()
headerBackground = headerPalette.color( QPalette.Background )
headerBackground.setRgb( min( headerBackground.red() + 30, 255 ),
min( headerBackground.green() + 30, 255 ),
min( headerBackground.blue() + 30, 255 ) )
headerPalette.setColor( QPalette.Background, headerBackground )
headerFrame.setPalette( headerPalette )
headerFrame.setFixedHeight( 24 )
recentFilesLabel = QLabel()
recentFilesLabel.setText( "Recent files" )
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins( 3, 0, 0, 0 )
headerLayout.addWidget( recentFilesLabel )
headerFrame.setLayout( headerLayout )
self.recentFilesView = QTreeWidget()
self.recentFilesView.setAlternatingRowColors( True )
self.recentFilesView.setRootIsDecorated( False )
self.recentFilesView.setItemsExpandable( False )
self.recentFilesView.setSortingEnabled( True )
self.recentFilesView.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.recentFilesView.setUniformRowHeights( True )
self.__filesHeaderItem = QTreeWidgetItem( [ "", "File",
"Absolute path" ] )
self.recentFilesView.setHeaderItem( self.__filesHeaderItem )
self.recentFilesView.header().setSortIndicator( 1, Qt.AscendingOrder )
self.connect( self.recentFilesView,
SIGNAL( "itemSelectionChanged()" ),
self.__fileSelectionChanged )
self.connect( self.recentFilesView,
SIGNAL( "itemActivated(QTreeWidgetItem *, int)" ),
self.__fileActivated )
# Toolbar part - buttons
self.openFileButton = QAction( PixmapCache().getIcon( 'openitem.png' ),
'Open the highlighted file', self )
self.connect( self.openFileButton, SIGNAL( "triggered()" ),
self.__openFile )
self.copyFilePathButton = QAction( \
PixmapCache().getIcon( 'copytoclipboard.png' ),
'Copy path to clipboard', self )
self.connect( self.copyFilePathButton, SIGNAL( "triggered()" ),
self.__filePathToClipboard )
spacer = QWidget()
spacer.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Expanding )
self.trashFileButton = QAction( PixmapCache().getIcon( 'delitem.png' ),
'Remove selected (not from the disk)',
self )
self.connect( self.trashFileButton, SIGNAL( "triggered()" ),
self.__deleteFile )
self.upperToolbar = QToolBar()
self.upperToolbar.setMovable( False )
self.upperToolbar.setAllowedAreas( Qt.TopToolBarArea )
self.upperToolbar.setIconSize( QSize( 16, 16 ) )
self.upperToolbar.setFixedHeight( 28 )
self.upperToolbar.setContentsMargins( 0, 0, 0, 0 )
self.upperToolbar.addAction( self.openFileButton )
self.upperToolbar.addAction( self.copyFilePathButton )
self.upperToolbar.addWidget( spacer )
self.upperToolbar.addAction( self.trashFileButton )
recentFilesLayout = QVBoxLayout()
recentFilesLayout.setContentsMargins( 0, 0, 0, 0 )
recentFilesLayout.setSpacing( 0 )
recentFilesLayout.addWidget( headerFrame )
recentFilesLayout.addWidget( self.upperToolbar )
recentFilesLayout.addWidget( self.recentFilesView )
upperContainer = QWidget()
upperContainer.setContentsMargins( 0, 0, 0, 0 )
upperContainer.setLayout( recentFilesLayout )
return upperContainer
def getRecentFilesToolbar( self ):
" Provides a reference to the recent files toolbar "
return self.upperToolbar
def __createRecentProjectsLayout( self ):
" Creates the bottom layout "
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle( QFrame.StyledPanel )
self.headerFrame.setAutoFillBackground( True )
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color( QPalette.Background )
headerBackground.setRgb( min( headerBackground.red() + 30, 255 ),
min( headerBackground.green() + 30, 255 ),
min( headerBackground.blue() + 30, 255 ) )
headerPalette.setColor( QPalette.Background, headerBackground )
self.headerFrame.setPalette( headerPalette )
self.headerFrame.setFixedHeight( 24 )
recentProjectsLabel = QLabel()
recentProjectsLabel.setText( "Recent projects" )
expandingSpacer = QSpacerItem( 10, 10, QSizePolicy.Expanding )
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setFixedSize( 20, 20 )
self.__showHideButton.setToolTip( "Hide recent projects list" )
self.__showHideButton.setFocusPolicy( Qt.NoFocus )
self.connect( self.__showHideButton, SIGNAL( 'clicked()' ),
self.__onShowHide )
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins( 3, 0, 0, 0 )
headerLayout.addWidget( recentProjectsLabel )
headerLayout.addSpacerItem( expandingSpacer )
headerLayout.addWidget( self.__showHideButton )
self.headerFrame.setLayout( headerLayout )
# Toolbar part - buttons
self.loadButton = QAction( PixmapCache().getIcon( 'load.png' ),
'Load the highlighted project', self )
self.connect( self.loadButton, SIGNAL( "triggered()" ),
self.__loadProject )
self.propertiesButton = QAction( PixmapCache().getIcon( 'smalli.png' ),
'Show the highlighted project ' \
'properties', self )
self.connect( self.propertiesButton, SIGNAL( "triggered()" ),
self.__viewProperties )
self.copyPrjPathButton = QAction( \
PixmapCache().getIcon( 'copytoclipboard.png' ),
'Copy path to clipboard', self )
self.connect( self.copyPrjPathButton, SIGNAL( "triggered()" ),
self.__prjPathToClipboard )
spacer = QWidget()
spacer.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Expanding )
self.trashButton = QAction( PixmapCache().getIcon( 'delitem.png' ),
'Remove selected (not from the disk)',
self )
self.connect( self.trashButton, SIGNAL( "triggered()" ),
self.__deleteProject )
self.lowerToolbar = QToolBar()
self.lowerToolbar.setMovable( False )
self.lowerToolbar.setAllowedAreas( Qt.TopToolBarArea )
self.lowerToolbar.setIconSize( QSize( 16, 16 ) )
self.lowerToolbar.setFixedHeight( 28 )
self.lowerToolbar.setContentsMargins( 0, 0, 0, 0 )
self.lowerToolbar.addAction( self.loadButton )
self.lowerToolbar.addAction( self.propertiesButton )
self.lowerToolbar.addAction( self.copyPrjPathButton )
self.lowerToolbar.addWidget( spacer )
self.lowerToolbar.addAction( self.trashButton )
self.projectsView = QTreeWidget()
self.projectsView.setAlternatingRowColors( True )
self.projectsView.setRootIsDecorated( False )
self.projectsView.setItemsExpandable( False )
self.projectsView.setSortingEnabled( True )
self.projectsView.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.projectsView.setUniformRowHeights( True )
self.__projectsHeaderItem = QTreeWidgetItem( [ "", "Project",
"Absolute path" ] )
self.projectsView.setHeaderItem( self.__projectsHeaderItem )
self.projectsView.header().setSortIndicator( 1, Qt.AscendingOrder )
self.connect( self.projectsView,
SIGNAL( "itemActivated(QTreeWidgetItem *, int)" ),
self.__projectActivated )
self.connect( self.projectsView,
SIGNAL( "itemSelectionChanged()" ),
self.__projectSelectionChanged )
recentProjectsLayout = QVBoxLayout()
recentProjectsLayout.setContentsMargins( 0, 0, 0, 0 )
recentProjectsLayout.setSpacing( 0 )
recentProjectsLayout.addWidget( self.headerFrame )
recentProjectsLayout.addWidget( self.lowerToolbar )
recentProjectsLayout.addWidget( self.projectsView )
lowerContainer = QWidget()
lowerContainer.setContentsMargins( 0, 0, 0, 0 )
lowerContainer.setLayout( recentProjectsLayout )
return lowerContainer
def getRecentProjectsToolbar( self ):
" Provides a reference to the projects toolbar "
return self.lowerToolbar
def __projectSelectionChanged( self ):
" Handles the projects changed selection "
selected = list( self.projectsView.selectedItems() )
if selected:
self.__projectContextItem = selected[ 0 ]
else:
self.__projectContextItem = None
self.__updateProjectToolbarButtons()
return
def __fileSelectionChanged( self ):
" Handles the files changed selection "
selected = list( self.recentFilesView.selectedItems() )
if selected:
self.__fileContextItem = selected[ 0 ]
else:
self.__fileContextItem = None
self.__updateFileToolbarButtons()
return
def __updateProjectToolbarButtons( self ):
" Updates the toolbar buttons depending on the __projectContextItem "
if self.__projectContextItem is None:
self.loadButton.setEnabled( False )
self.propertiesButton.setEnabled( False )
self.copyPrjPathButton.setEnabled( False )
self.trashButton.setEnabled( False )
else:
enabled = self.__projectContextItem.isValid()
isCurrentProject = self.__projectContextItem.isCurrent()
self.propertiesButton.setEnabled( enabled )
self.copyPrjPathButton.setEnabled( True )
self.loadButton.setEnabled( enabled and
not isCurrentProject and
not self.__debugMode )
self.trashButton.setEnabled( not isCurrentProject )
return
def __updateFileToolbarButtons( self ):
" Updates the toolbar buttons depending on the __fileContextItem "
enabled = self.__fileContextItem is not None
self.openFileButton.setEnabled( enabled )
self.copyFilePathButton.setEnabled( enabled )
self.trashFileButton.setEnabled( enabled )
return
def __handleShowPrjContextMenu( self, coord ):
" Show the project item context menu "
self.__projectContextItem = self.projectsView.itemAt( coord )
if self.__projectContextItem is None:
return
enabled = self.__projectContextItem.isValid()
isCurrentProject = self.__projectContextItem.isCurrent()
self.__propsMenuItem.setEnabled( enabled )
self.__delPrjMenuItem.setEnabled( not isCurrentProject )
# fName = self.__projectContextItem.getFilename()
self.__prjLoadMenuItem.setEnabled( enabled and \
not isCurrentProject and \
not self.__debugMode )
self.__projectMenu.popup( QCursor.pos() )
return
def __sortProjects( self ):
" Sort the project items "
self.projectsView.sortItems( \
self.projectsView.sortColumn(),
self.projectsView.header().sortIndicatorOrder() )
return
def __sortFiles( self ):
" Sort the file items "
self.recentFilesView.sortItems( \
self.recentFilesView.sortColumn(),
self.recentFilesView.header().sortIndicatorOrder() )
return
def __resizeProjectColumns( self ):
""" Resize the projects list columns """
self.projectsView.header().setStretchLastSection( True )
self.projectsView.header().resizeSections( \
QHeaderView.ResizeToContents )
self.projectsView.header().resizeSection( 0, 22 )
self.projectsView.header().setResizeMode( 0, QHeaderView.Fixed )
return
def __resizeFileColumns( self ):
" Resize the files list columns "
self.recentFilesView.header().setStretchLastSection( True )
self.recentFilesView.header().resizeSections( \
QHeaderView.ResizeToContents )
self.recentFilesView.header().resizeSection( 0, 22 )
self.recentFilesView.header().setResizeMode( 0, QHeaderView.Fixed )
return
def __projectActivated( self, item, column ):
" Handles the double click (or Enter) on the item "
self.__projectContextItem = item
self.__loadProject()
return
def __fileActivated( self, item, column ):
" Handles the double click (or Enter) on a file item "
self.__fileContextItem = item
self.__openFile()
return
def __viewProperties( self ):
" Handles the 'view properties' context menu item "
if self.__projectContextItem is None:
return
if not self.__projectContextItem.isValid():
return
if self.__projectContextItem.isCurrent():
# This is the current project - it can be edited
project = GlobalData().project
dialog = ProjectPropertiesDialog( project )
if dialog.exec_() == QDialog.Accepted:
importDirs = []
for index in xrange( dialog.importDirList.count() ):
importDirs.append( dialog.importDirList.item( index ).text() )
scriptName = dialog.scriptEdit.text().strip()
relativePath = relpath( scriptName, project.getProjectDir() )
if not relativePath.startswith( '..' ):
scriptName = relativePath
project.updateProperties(
scriptName, importDirs,
dialog.creationDateEdit.text().strip(),
dialog.authorEdit.text().strip(),
dialog.licenseEdit.text().strip(),
dialog.copyrightEdit.text().strip(),
dialog.versionEdit.text().strip(),
dialog.emailEdit.text().strip(),
dialog.descriptionEdit.toPlainText().strip() )
else:
# This is not the current project - it can be viewed
fName = self.__projectContextItem.getFilename()
dialog = ProjectPropertiesDialog( fName )
dialog.exec_()
return
def __deleteProject( self ):
" Handles the 'delete from recent' context menu item "
if self.__projectContextItem is None:
return
# Removal from the visible list is done via a signal which comes back
# from settings
fName = self.__projectContextItem.getFilename()
Settings().deleteRecentProject( fName )
return
def __loadProject( self ):
" handles 'Load' context menu item "
if self.__projectContextItem is None:
return
if not self.__projectContextItem.isValid():
return
if self.__debugMode:
return
projectFileName = self.__projectContextItem.getFilename()
if self.__projectContextItem.isCurrent():
GlobalData().mainWindow.openFile( projectFileName, -1 )
return # This is the current project, open for text editing
QApplication.processEvents()
QApplication.setOverrideCursor( QCursor( Qt.WaitCursor ) )
if os.path.exists( projectFileName ):
mainWin = GlobalData().mainWindow
editorsManager = mainWin.editorsManagerWidget.editorsManager
if editorsManager.closeRequest():
prj = GlobalData().project
prj.setTabsStatus( editorsManager.getTabsStatus() )
editorsManager.closeAll()
prj.loadProject( projectFileName )
mainWin.activateProjectTab()
else:
logging.error( "The project " + \
os.path.basename( projectFileName ) + \
" disappeared from the file system." )
self.__populateProjects()
QApplication.restoreOverrideCursor()
return
def __populateProjects( self ):
" Populates the recent projects "
self.projectsView.clear()
for item in Settings().recentProjects:
self.projectsView.addTopLevelItem( RecentProjectViewItem( item ) )
self.__sortProjects()
self.__resizeProjectColumns()
self.__updateProjectToolbarButtons()
return
def __populateFiles( self ):
" Populates the recent files "
self.recentFilesView.clear()
for path in GlobalData().project.recentFiles:
self.recentFilesView.addTopLevelItem( RecentFileViewItem( path ) )
self.__sortFiles()
self.__resizeFileColumns()
self.__updateFileToolbarButtons()
return
def __projectChanged( self, what ):
" Triggered when the current project is changed "
if what == CodimensionProject.CompleteProject:
self.__populateProjects()
self.__populateFiles()
return
if what == CodimensionProject.Properties:
# Update the corresponding tooltip
items = self.projectsView.findItems( GlobalData().project.fileName,
Qt.MatchExactly, 2 )
if len( items ) != 1:
logging.error( "Unexpected number of matched projects: " + \
str( len( items ) ) )
return
items[ 0 ].updateTooltip()
return
def __openFile( self ):
" Handles 'open' file menu item "
self.__fileContextItem.updateIconAndTooltip()
fName = self.__fileContextItem.getFilename()
if not self.__fileContextItem.isValid():
logging.warning( "Cannot open " + fName )
return
fileType = detectFileType( fName )
if fileType == PixmapFileType:
GlobalData().mainWindow.openPixmapFile( fName )
return
GlobalData().mainWindow.openFile( fName, -1 )
return
def __deleteFile( self ):
" Handles 'delete from recent' file menu item "
self.removeRecentFile( self.__fileContextItem.getFilename() )
return
def __handleShowFileContextMenu( self, coord ):
" File context menu "
self.__fileContextItem = self.recentFilesView.itemAt( coord )
if self.__fileContextItem is not None:
self.__fileMenu.popup( QCursor.pos() )
return
def __filePathToClipboard( self ):
" Copies the file item path to the clipboard "
if self.__fileContextItem is not None:
QApplication.clipboard().setText( \
self.__fileContextItem.getFilename() )
return
def __prjPathToClipboard( self ):
" Copies the project item path to the clipboard "
if self.__projectContextItem is not None:
QApplication.clipboard().setText( \
self.__projectContextItem.getFilename() )
return
def onFileUpdated( self, fileName, uuid ):
" Triggered when the file is updated: python or project "
realPath = os.path.realpath( fileName )
count = self.recentFilesView.topLevelItemCount()
for index in xrange( 0, count ):
item = self.recentFilesView.topLevelItem( index )
itemRealPath = os.path.realpath( item.getFilename() )
if realPath == itemRealPath:
item.updateIconAndTooltip()
break
for index in xrange( 0, self.projectsView.topLevelItemCount() ):
item = self.projectsView.topLevelItem( index )
itemRealPath = os.path.realpath( item.getFilename() )
if realPath == itemRealPath:
item.updateTooltip()
break
return
def __onShowHide( self ):
" Triggered when show/hide button is clicked "
if self.projectsView.isVisible():
self.projectsView.setVisible( False )
self.lowerToolbar.setVisible( False )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'more.png' ) )
self.__showHideButton.setToolTip( "Show recent projects list" )
self.__minH = self.lower.minimumHeight()
self.__maxH = self.lower.maximumHeight()
self.lower.setMinimumHeight( self.headerFrame.height() )
self.lower.setMaximumHeight( self.headerFrame.height() )
else:
self.projectsView.setVisible( True )
self.lowerToolbar.setVisible( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setToolTip( "Hide recent projects list" )
self.lower.setMinimumHeight( self.__minH )
self.lower.setMaximumHeight( self.__maxH )
return
def __onDebugMode( self, newState ):
" Triggered when debug mode has changed "
self.__debugMode = newState
# Disable the load project button
self.__updateProjectToolbarButtons()
return
def removeRecentFile( self, fName ):
" Removes a single file from the recent files list "
GlobalData().project.removeRecentFile( fName )
for index in xrange( self.recentFilesView.topLevelItemCount() ):
candidate = self.recentFilesView.topLevelItem( index )
if candidate.getFilename() == fName:
self.recentFilesView.takeTopLevelItem( index )
return
return
class MemUsageDialog(QDialog):
def __init__(self, parent=None, update=True):
QDialog.__init__(self, parent=parent)
layout = QVBoxLayout()
self.tree = QTreeWidget()
self.tree.setHeaderLabels(["cache", "memory", "roi", "dtype", "type"])
layout.addWidget(self.tree)
self.setLayout(layout)
self.memMgr = ArrayCacheMemoryMgr.instance
self.timer = QTimer(self)
if update:
self.timer.timeout.connect(self._updateReport)
self._updateReport()
def _updateReport(self):
reports = []
for c in self.memMgr.namedCaches:
r = MemInfoNode()
try:
c.generateReport(r)
reports.append(r)
except NotImplementedError:
warnings.warn('cache operator {} does not implement generateReport()'.format(c))
self._showReports(reports)
'''
import pickle
f = open("/tmp/reports.pickle",'w')
pickle.dump(reports, f)
f.close()
print "... saved MEM reports to file ..."
'''
def _showReports(self, reports):
self.tree.clear()
root = self.tree.invisibleRootItem()
for r in reports:
self._showReportsImpl(r, root, 0)
def _makeTreeWidgetItem(self, node):
l = []
l.append("%r" % node.name)
l.append("%1.1f MB" % (node.usedMemory/1024**2.0))
if node.roi is not None:
l.append("%r\n%r" % (list(node.roi[0]), list(node.roi[1])))
else:
l.append("")
if node.dtype is not None:
if node.dtype == numpy.float32:
l.append("float32")
elif node.dtype == numpy.uint8:
l.append("uint8")
elif node.dtype == numpy.uint32:
l.append("uint32")
elif node.dtype == numpy.float64:
l.append("float64")
else:
l.append(str(node.dtype))
else:
l.append("")
t = str(node.type)
t = t[len("<type '")+1:-len("'>")]
t = t.split(".")[-1]
l.append(t)
return QTreeWidgetItem(l)
def _showReportsImpl(self, node, itm, level):
#print " "*level,
#print "node", node.name
root = self._makeTreeWidgetItem(node)
itm.addChild(root)
root.setExpanded(True)
for c in node.children:
self._showReportsImpl(c, root, level+1)
def hideEvent(self, event):
self.timer.stop()
def showEvent(self, show):
self.timer.start(5*1000) #update every 5 sec.
class OWPIPAx(widget.OWWidget):
name = "PIPAx"
description = "Access data from PIPA RNA-Seq database."
icon = "../widgets/icons/PIPA.svg"
priority = 35
inputs = []
outputs = [("Data", Orange.data.Table)]
username = settings.Setting("")
password = settings.Setting("")
log2 = settings.Setting(False)
rtypei = settings.Setting(5) # hardcoded rpkm mapability polya
excludeconstant = settings.Setting(False)
joinreplicates = settings.Setting(False)
#: The stored current selection (in experiments view)
#: SelectionByKey | None
currentSelection = settings.Setting(None)
#: Stored selections (presets)
#: list of SelectionByKey
storedSelections = settings.Setting([])
#: Stored column sort keys (from Sort view)
#: list of strings
storedSortingOrder = settings.Setting(
["Strain", "Experiment", "Genotype", "Timepoint"])
experimentsHeaderState = settings.Setting(
{name: False for _, name in HEADER[:ID_INDEX + 1]}
)
def __init__(self, parent=None, signalManager=None, name="PIPAx"):
super().__init__(parent)
self.selectedExperiments = []
self.buffer = dicty.CacheSQLite(bufferfile)
self.searchString = ""
self.result_types = []
self.mappings = {}
self.controlArea.setMaximumWidth(250)
self.controlArea.setMinimumWidth(250)
gui.button(self.controlArea, self, "Reload",
callback=self.Reload)
gui.button(self.controlArea, self, "Clear cache",
callback=self.clear_cache)
b = gui.widgetBox(self.controlArea, "Experiment Sets")
self.selectionSetsWidget = SelectionSetsWidget(self)
self.selectionSetsWidget.setSizePolicy(
QSizePolicy.Preferred, QSizePolicy.Maximum)
def store_selections(modified):
if not modified:
self.storedSelections = self.selectionSetsWidget.selections
self.selectionSetsWidget.selectionModified.connect(store_selections)
b.layout().addWidget(self.selectionSetsWidget)
gui.separator(self.controlArea)
b = gui.widgetBox(self.controlArea, "Sort output columns")
self.columnsSortingWidget = SortedListWidget(self)
self.columnsSortingWidget.setSizePolicy(
QSizePolicy.Preferred, QSizePolicy.Maximum)
def store_sort_order():
self.storedSortingOrder = self.columnsSortingWidget.sortingOrder
self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order)
b.layout().addWidget(self.columnsSortingWidget)
sorting_model = QStringListModel(SORTING_MODEL_LIST)
self.columnsSortingWidget.setModel(sorting_model)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Expression Type')
self.expressionTypesCB = gui.comboBox(
box, self, "rtypei", items=[], callback=self.UpdateResultsList)
gui.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
gui.checkBox(self.controlArea, self, "joinreplicates",
"Average replicates (use median)")
gui.checkBox(self.controlArea, self, "log2",
"Logarithmic (base 2) transformation")
self.commit_button = gui.button(self.controlArea, self, "&Commit",
callback=self.Commit)
self.commit_button.setDisabled(True)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Authentication")
gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"searchString", "Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.headerLabels = [t[1] for t in HEADER]
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.experimentsWidget, self.experimentsWidget
)
self.experimentsWidget.header().installEventFilter(contextEventFilter)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.setAlternatingRowColors(True)
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.selectionSetsWidget.setSelectionModel(
self.experimentsWidget.selectionModel()
)
self.mainArea.layout().addWidget(self.experimentsWidget)
# Restore the selection states from the stored settings
self.selectionSetsWidget.selections = self.storedSelections
self.columnsSortingWidget.sortingOrder = self.storedSortingOrder
self.restoreHeaderState()
self.experimentsWidget.header().geometriesChanged.connect(
self.saveHeaderState)
self.dbc = None
self.AuthSet()
QTimer.singleShot(100, self.UpdateExperiments)
def sizeHint(self):
return QSize(800, 600)
def AuthSet(self):
if len(self.username):
self.passf.setDisabled(False)
else:
self.passf.setDisabled(True)
def AuthChanged(self):
self.AuthSet()
self.ConnectAndUpdate()
def ConnectAndUpdate(self):
self.Connect()
self.UpdateExperiments(reload=True)
def Connect(self):
self.error(1)
self.warning(1)
def en(x):
return x if len(x) else None
self.dbc = dicty.PIPAx(cache=self.buffer,
username=en(self.username),
password=self.password)
# check password
if en(self.username) != None:
try:
self.dbc.mappings(reload=True)
except dicty.AuthenticationError:
self.error(1, "Wrong username or password")
self.dbc = None
except Exception as ex:
print("Error when contacting the PIPA database", ex)
sys.excepthook(*sys.exc_info())
try: # maybe cached?
self.dbc.mappings()
self.warning(1, "Can not access database - using cached data.")
except Exception as ex:
self.dbc = None
self.error(1, "Can not access database.")
def Reload(self):
self.UpdateExperiments(reload=True)
def clear_cache(self):
self.buffer.clear()
self.Reload()
def rtype(self):
"""Return selected result template type """
if self.result_types:
return self.result_types[self.rtypei][0]
else:
return "-1"
def UpdateExperimentTypes(self):
self.expressionTypesCB.clear()
items = [desc for _, desc in self.result_types]
self.expressionTypesCB.addItems(items)
self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1))
def UpdateExperiments(self, reload=False):
self.experimentsWidget.clear()
self.items = []
self.progressBarInit()
if not self.dbc:
self.Connect()
mappings = {}
result_types = []
sucind = False # success indicator for database index
try:
mappings = self.dbc.mappings(reload=reload)
result_types = self.dbc.result_types(reload=reload)
sucind = True
except Exception as ex:
try:
mappings = self.dbc.mappings()
result_types = self.dbc.result_types()
self.warning(0, "Can not access database - using cached data.")
sucind = True
except Exception as ex:
self.error(0, "Can not access database.")
if sucind:
self.warning(0)
self.error(0)
self.mappings = mappings
self.result_types = result_types
self.UpdateExperimentTypes()
self.UpdateResultsList(reload=reload)
self.progressBarFinished()
if self.currentSelection:
self.currentSelection.select(
self.experimentsWidget.selectionModel())
self.handle_commit_button()
def UpdateResultsList(self, reload=False):
results_list = {}
try:
results_list = self.dbc.results_list(self.rtype(), reload=reload)
except Exception as ex:
try:
results_list = self.dbc.results_list(self.rtype())
except Exception as ex:
self.error(0, "Can not access database.")
self.results_list = results_list
mappings_key_dict = dict(((m["data_id"], m["id"]), key) \
for key, m in self.mappings.items())
def mapping_unique_id(annot):
"""Map annotations dict from results_list to unique
`mappings` ids.
"""
data_id, mappings_id = annot["data_id"], annot["mappings_id"]
return mappings_key_dict[data_id, mappings_id]
elements = []
# softly change the view so that the selection stays the same
items_shown = {}
for i, item in enumerate(self.items):
c = str(item.text(10))
items_shown[c] = i
items_to_show = dict((mapping_unique_id(annot), annot)
for annot in self.results_list.values())
add_items = set(items_to_show) - set(items_shown)
delete_items = set(items_shown) - set(items_to_show)
i = 0
while i < self.experimentsWidget.topLevelItemCount():
it = self.experimentsWidget.topLevelItem(i)
if str(it.text(10)) in delete_items:
self.experimentsWidget.takeTopLevelItem(i)
else:
i += 1
delete_ind = set([items_shown[i] for i in delete_items])
self.items = [it for i, it in enumerate(self.items) if i not in delete_ind]
for r_annot in [items_to_show[i] for i in add_items]:
d = defaultdict(lambda: "?", r_annot)
row_items = [""] + [d.get(key, "?") for key, _ in HEADER[1:]]
try:
time_dict = literal_eval(row_items[DATE_INDEX])
date_rna = date(time_dict["fullYearUTC"],
time_dict["monthUTC"] + 1, # Why is month 0 based?
time_dict["dateUTC"])
row_items[DATE_INDEX] = date_rna.strftime("%x")
except Exception:
row_items[DATE_INDEX] = ''
row_items[ID_INDEX] = mapping_unique_id(r_annot)
elements.append(row_items)
ci = MyTreeWidgetItem(self.experimentsWidget, row_items)
self.items.append(ci)
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
# which is the ok buffer version
# FIXME: what attribute to use for version?
self.wantbufver = \
lambda x, ad=self.results_list: \
defaultdict(lambda: "?", ad[x])["date"]
self.wantbufver = lambda x: "0"
self.UpdateCached()
def UpdateCached(self):
if self.wantbufver and self.dbc:
fn = self.dbc.download_key_function()
result_id_key = dict(((m["data_id"], m["mappings_id"]), key) \
for key, m in self.results_list.items())
for item in self.items:
c = str(item.text(10))
mapping = self.mappings[c]
data_id, mappings_id = mapping["data_id"], mapping["id"]
r_id = result_id_key[data_id, mappings_id]
# Get the buffered version
buffered = self.dbc.inBuffer(fn(r_id))
value = " " if buffered == self.wantbufver(r_id) else ""
item.setData(0, Qt.DisplayRole, value)
def SearchUpdate(self, string=""):
for item in self.items:
item.setHidden(not all(s in item \
for s in self.searchString.split())
)
def Commit(self):
if not self.dbc:
self.Connect()
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(10))
annots = self.mappings[unique_id]
ids.append((annots["data_id"], annots["id"]))
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = dict((name, key) for key, name in HEADER)
hview = self.experimentsWidget.header()
shownHeaders = [label for i, label in \
list(enumerate(self.headerLabels))[1:] \
if not hview.isSectionHidden(i)
]
allowed_labels = [reverse_header_dict.get(label, label) \
for label in shownHeaders]
if self.joinreplicates and "id" not in allowed_labels:
# need 'id' labels in join_replicates for attribute names
allowed_labels.append("id")
if len(ids):
table = self.dbc.get_data(ids=ids, result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
# bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=["replicate", "data_id", "mappings_id",
"data_name", "id", "unique_id"],
namefn=None,
avg=dicty.median
)
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name) \
for name in sortOrder])
attributes = sorted(table.domain.attributes,
key=sorting_key)
domain = Orange.data.Domain(
attributes, table.domain.class_var, table.domain.metas)
table = table.from_table(domain, table)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def onSelectionChanged(self, selected, deselected):
self.handle_commit_button()
def handle_commit_button(self):
self.currentSelection = \
SelectionByKey(self.experimentsWidget.selectionModel().selection(),
key=(1, 2, 3, 10))
self.commit_button.setDisabled(not len(self.currentSelection))
def saveHeaderState(self):
hview = self.experimentsWidget.header()
for i, label in enumerate(self.headerLabels):
self.experimentsHeaderState[label] = hview.isSectionHidden(i)
def restoreHeaderState(self):
hview = self.experimentsWidget.header()
state = self.experimentsHeaderState
for i, label in enumerate(self.headerLabels):
hview.setSectionHidden(i, state.get(label, True))
self.experimentsWidget.resizeColumnToContents(i)
class BookmarksWindow(QDialog):
"""
A simple UI for showing bookmarks and navigating to them.
FIXME: For now, this window is tied to a particular lane.
If your project has more than one lane, then each one
will have it's own bookmark window, which is kinda dumb.
"""
def __init__(self, parent, topLevelOperatorView):
super(BookmarksWindow, self).__init__(parent)
self.setWindowTitle("Bookmarks")
self.topLevelOperatorView = topLevelOperatorView
self.bookmark_tree = QTreeWidget(self)
self.bookmark_tree.setHeaderLabels(["Location", "Notes"])
self.bookmark_tree.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Preferred)
self.bookmark_tree.setColumnWidth(0, 200)
self.bookmark_tree.setColumnWidth(1, 300)
self.note_edit = QLineEdit(self)
self.add_bookmark_button = QPushButton("Add Bookmark",
self,
clicked=self.add_bookmark)
geometry = self.geometry()
geometry.setSize(QSize(520, 520))
self.setGeometry(geometry)
layout = QVBoxLayout()
layout.addWidget(self.bookmark_tree)
layout.addWidget(self.note_edit)
layout.addWidget(self.add_bookmark_button)
self.setLayout(layout)
self._load_bookmarks()
self.bookmark_tree.setContextMenuPolicy(Qt.CustomContextMenu)
self.bookmark_tree.customContextMenuRequested.connect(
self.showContextMenu)
self.bookmark_tree.itemDoubleClicked.connect(self._handle_doubleclick)
def _handle_doubleclick(self, item, col):
"""
Navigate to the bookmark
"""
data = item.data(0, Qt.UserRole).toPyObject()
if data is None:
return
(coord, notes) = data
axes = self.topLevelOperatorView.InputImages.meta.getAxisKeys()
axes = axes[:-1] # drop channel
axes = sorted(axes)
assert len(axes) == len(coord)
tagged_coord = dict(zip(axes, coord))
tagged_location = OrderedDict(zip('txyzc', (0, 0, 0, 0, 0)))
tagged_location.update(tagged_coord)
t = tagged_location.values()[0]
coord3d = tagged_location.values()[1:4]
self.parent().editor.posModel.time = t
self.parent().editor.navCtrl.panSlicingViews(coord3d, [0, 1, 2])
self.parent().editor.posModel.slicingPos = coord3d
def showContextMenu(self, pos):
item = self.bookmark_tree.itemAt(pos)
data = item.data(0, Qt.UserRole).toPyObject()
if data is None:
return
def delete_bookmark():
(coord, notes) = data
bookmarks = list(self.topLevelOperatorView.Bookmarks.value)
i = bookmarks.index((coord, notes))
bookmarks.pop(i)
self.topLevelOperatorView.Bookmarks.setValue(bookmarks)
self._load_bookmarks()
menu = QMenu(parent=self)
menu.addAction(QAction("Delete", menu, triggered=delete_bookmark))
globalPos = self.bookmark_tree.viewport().mapToGlobal(pos)
menu.exec_(globalPos)
#selection = menu.exec_( globalPos )
#if selection is removeLanesAction:
# self.removeLanesRequested.emit( self._selectedLanes )
def add_bookmark(self):
coord_txyzc = self.parent().editor.posModel.slicingPos5D
tagged_coord_txyzc = dict(zip('txyzc', coord_txyzc))
axes = self.topLevelOperatorView.InputImages.meta.getAxisKeys()
axes = axes[:-1] # drop channel
axes = sorted(axes)
coord = tuple(tagged_coord_txyzc[c] for c in axes)
notes = str(self.note_edit.text())
bookmarks = list(self.topLevelOperatorView.Bookmarks.value)
bookmarks.append((coord, notes))
self.topLevelOperatorView.Bookmarks.setValue(bookmarks)
self._load_bookmarks()
def _load_bookmarks(self):
self.bookmark_tree.clear()
lane_index = self.topLevelOperatorView.current_view_index()
lane_nickname = self.topLevelOperatorView.InputImages.meta.nickname or "Lane {}".format(
lane_index)
bookmarks = self.topLevelOperatorView.Bookmarks.value
group_item = QTreeWidgetItem(self.bookmark_tree,
QStringList(lane_nickname))
for coord, notes in bookmarks:
item = QTreeWidgetItem(group_item, QStringList())
item.setText(0, str(coord))
item.setData(0, Qt.UserRole, (coord, notes))
item.setText(1, notes)
self.bookmark_tree.expandAll()
class OWPIPAx(widget.OWWidget):
name = "PIPAx"
description = "Access data from PIPA RNA-Seq database."
icon = "../widgets/icons/PIPA.svg"
priority = 35
inputs = []
outputs = [("Data", Orange.data.Table)]
username = settings.Setting("")
password = settings.Setting("")
log2 = settings.Setting(False)
rtypei = settings.Setting(5) # hardcoded rpkm mapability polya
excludeconstant = settings.Setting(False)
joinreplicates = settings.Setting(False)
#: The stored current selection (in experiments view)
#: SelectionByKey | None
currentSelection = settings.Setting(None)
#: Stored selections (presets)
#: list of SelectionByKey
storedSelections = settings.Setting([])
#: Stored column sort keys (from Sort view)
#: list of strings
storedSortingOrder = settings.Setting(
["Strain", "Experiment", "Genotype", "Timepoint"])
experimentsHeaderState = settings.Setting(
{name: False
for _, name in HEADER[:ID_INDEX + 1]})
def __init__(self, parent=None, signalManager=None, name="PIPAx"):
super().__init__(parent)
self.selectedExperiments = []
self.buffer = dicty.CacheSQLite(bufferfile)
self.searchString = ""
self.result_types = []
self.mappings = {}
self.controlArea.setMaximumWidth(250)
self.controlArea.setMinimumWidth(250)
gui.button(self.controlArea, self, "Reload", callback=self.Reload)
gui.button(self.controlArea,
self,
"Clear cache",
callback=self.clear_cache)
b = gui.widgetBox(self.controlArea, "Experiment Sets")
self.selectionSetsWidget = SelectionSetsWidget(self)
self.selectionSetsWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
def store_selections(modified):
if not modified:
self.storedSelections = self.selectionSetsWidget.selections
self.selectionSetsWidget.selectionModified.connect(store_selections)
b.layout().addWidget(self.selectionSetsWidget)
gui.separator(self.controlArea)
b = gui.widgetBox(self.controlArea, "Sort output columns")
self.columnsSortingWidget = SortedListWidget(self)
self.columnsSortingWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
def store_sort_order():
self.storedSortingOrder = self.columnsSortingWidget.sortingOrder
self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order)
b.layout().addWidget(self.columnsSortingWidget)
sorting_model = QStringListModel(SORTING_MODEL_LIST)
self.columnsSortingWidget.setModel(sorting_model)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Expression Type')
self.expressionTypesCB = gui.comboBox(box,
self,
"rtypei",
items=[],
callback=self.UpdateResultsList)
gui.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
gui.checkBox(self.controlArea, self, "joinreplicates",
"Average replicates (use median)")
gui.checkBox(self.controlArea, self, "log2",
"Logarithmic (base 2) transformation")
self.commit_button = gui.button(self.controlArea,
self,
"&Commit",
callback=self.Commit)
self.commit_button.setDisabled(True)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, "Authentication")
gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"searchString",
"Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.headerLabels = [t[1] for t in HEADER]
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.experimentsWidget, self.experimentsWidget)
self.experimentsWidget.header().installEventFilter(contextEventFilter)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.setAlternatingRowColors(True)
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.selectionSetsWidget.setSelectionModel(
self.experimentsWidget.selectionModel())
self.mainArea.layout().addWidget(self.experimentsWidget)
# Restore the selection states from the stored settings
self.selectionSetsWidget.selections = self.storedSelections
self.columnsSortingWidget.sortingOrder = self.storedSortingOrder
self.restoreHeaderState()
self.experimentsWidget.header().geometriesChanged.connect(
self.saveHeaderState)
self.dbc = None
self.AuthSet()
QTimer.singleShot(100, self.UpdateExperiments)
def sizeHint(self):
return QSize(800, 600)
def AuthSet(self):
if len(self.username):
self.passf.setDisabled(False)
else:
self.passf.setDisabled(True)
def AuthChanged(self):
self.AuthSet()
self.ConnectAndUpdate()
def ConnectAndUpdate(self):
self.Connect()
self.UpdateExperiments(reload=True)
def Connect(self):
self.error(1)
self.warning(1)
def en(x):
return x if len(x) else None
self.dbc = dicty.PIPAx(cache=self.buffer,
username=en(self.username),
password=self.password)
# check password
if en(self.username) != None:
try:
self.dbc.mappings(reload=True)
except dicty.AuthenticationError:
self.error(1, "Wrong username or password")
self.dbc = None
except Exception as ex:
print("Error when contacting the PIPA database", ex)
sys.excepthook(*sys.exc_info())
try: # maybe cached?
self.dbc.mappings()
self.warning(
1, "Can not access database - using cached data.")
except Exception as ex:
self.dbc = None
self.error(1, "Can not access database.")
def Reload(self):
self.UpdateExperiments(reload=True)
def clear_cache(self):
self.buffer.clear()
self.Reload()
def rtype(self):
"""Return selected result template type """
if self.result_types:
return self.result_types[self.rtypei][0]
else:
return "-1"
def UpdateExperimentTypes(self):
self.expressionTypesCB.clear()
items = [desc for _, desc in self.result_types]
self.expressionTypesCB.addItems(items)
self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1))
def UpdateExperiments(self, reload=False):
self.experimentsWidget.clear()
self.items = []
self.progressBarInit()
if not self.dbc:
self.Connect()
mappings = {}
result_types = []
sucind = False # success indicator for database index
try:
mappings = self.dbc.mappings(reload=reload)
result_types = self.dbc.result_types(reload=reload)
sucind = True
except Exception as ex:
try:
mappings = self.dbc.mappings()
result_types = self.dbc.result_types()
self.warning(0, "Can not access database - using cached data.")
sucind = True
except Exception as ex:
self.error(0, "Can not access database.")
if sucind:
self.warning(0)
self.error(0)
self.mappings = mappings
self.result_types = result_types
self.UpdateExperimentTypes()
self.UpdateResultsList(reload=reload)
self.progressBarFinished()
if self.currentSelection:
self.currentSelection.select(
self.experimentsWidget.selectionModel())
self.handle_commit_button()
def UpdateResultsList(self, reload=False):
results_list = {}
try:
results_list = self.dbc.results_list(self.rtype(), reload=reload)
except Exception as ex:
try:
results_list = self.dbc.results_list(self.rtype())
except Exception as ex:
self.error(0, "Can not access database.")
self.results_list = results_list
mappings_key_dict = dict(((m["data_id"], m["id"]), key) \
for key, m in self.mappings.items())
def mapping_unique_id(annot):
"""Map annotations dict from results_list to unique
`mappings` ids.
"""
data_id, mappings_id = annot["data_id"], annot["mappings_id"]
return mappings_key_dict[data_id, mappings_id]
elements = []
# softly change the view so that the selection stays the same
items_shown = {}
for i, item in enumerate(self.items):
c = str(item.text(10))
items_shown[c] = i
items_to_show = dict((mapping_unique_id(annot), annot)
for annot in self.results_list.values())
add_items = set(items_to_show) - set(items_shown)
delete_items = set(items_shown) - set(items_to_show)
i = 0
while i < self.experimentsWidget.topLevelItemCount():
it = self.experimentsWidget.topLevelItem(i)
if str(it.text(10)) in delete_items:
self.experimentsWidget.takeTopLevelItem(i)
else:
i += 1
delete_ind = set([items_shown[i] for i in delete_items])
self.items = [
it for i, it in enumerate(self.items) if i not in delete_ind
]
for r_annot in [items_to_show[i] for i in add_items]:
d = defaultdict(lambda: "?", r_annot)
row_items = [""] + [d.get(key, "?") for key, _ in HEADER[1:]]
try:
time_dict = literal_eval(row_items[DATE_INDEX])
date_rna = date(
time_dict["fullYearUTC"],
time_dict["monthUTC"] + 1, # Why is month 0 based?
time_dict["dateUTC"])
row_items[DATE_INDEX] = date_rna.strftime("%x")
except Exception:
row_items[DATE_INDEX] = ''
row_items[ID_INDEX] = mapping_unique_id(r_annot)
elements.append(row_items)
ci = MyTreeWidgetItem(self.experimentsWidget, row_items)
self.items.append(ci)
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
# which is the ok buffer version
# FIXME: what attribute to use for version?
self.wantbufver = \
lambda x, ad=self.results_list: \
defaultdict(lambda: "?", ad[x])["date"]
self.wantbufver = lambda x: "0"
self.UpdateCached()
def UpdateCached(self):
if self.wantbufver and self.dbc:
fn = self.dbc.download_key_function()
result_id_key = dict(((m["data_id"], m["mappings_id"]), key) \
for key, m in self.results_list.items())
for item in self.items:
c = str(item.text(10))
mapping = self.mappings[c]
data_id, mappings_id = mapping["data_id"], mapping["id"]
r_id = result_id_key[data_id, mappings_id]
# Get the buffered version
buffered = self.dbc.inBuffer(fn(r_id))
value = " " if buffered == self.wantbufver(r_id) else ""
item.setData(0, Qt.DisplayRole, value)
def SearchUpdate(self, string=""):
for item in self.items:
item.setHidden(not all(s in item \
for s in self.searchString.split())
)
def Commit(self):
if not self.dbc:
self.Connect()
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(10))
annots = self.mappings[unique_id]
ids.append((annots["data_id"], annots["id"]))
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = dict((name, key) for key, name in HEADER)
hview = self.experimentsWidget.header()
shownHeaders = [label for i, label in \
list(enumerate(self.headerLabels))[1:] \
if not hview.isSectionHidden(i)
]
allowed_labels = [reverse_header_dict.get(label, label) \
for label in shownHeaders]
if self.joinreplicates and "id" not in allowed_labels:
# need 'id' labels in join_replicates for attribute names
allowed_labels.append("id")
if len(ids):
table = self.dbc.get_data(
ids=ids,
result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
# bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=[
"replicate", "data_id",
"mappings_id", "data_name",
"id", "unique_id"
],
namefn=None,
avg=dicty.median)
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(
atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name) \
for name in sortOrder])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(attributes, table.domain.class_var,
table.domain.metas)
table = table.from_table(domain, table)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def onSelectionChanged(self, selected, deselected):
self.handle_commit_button()
def handle_commit_button(self):
self.currentSelection = \
SelectionByKey(self.experimentsWidget.selectionModel().selection(),
key=(1, 2, 3, 10))
self.commit_button.setDisabled(not len(self.currentSelection))
def saveHeaderState(self):
hview = self.experimentsWidget.header()
for i, label in enumerate(self.headerLabels):
self.experimentsHeaderState[label] = hview.isSectionHidden(i)
def restoreHeaderState(self):
hview = self.experimentsWidget.header()
state = self.experimentsHeaderState
for i, label in enumerate(self.headerLabels):
hview.setSectionHidden(i, state.get(label, True))
self.experimentsWidget.resizeColumnToContents(i)
class PluginsDialog( QDialog ):
" Codimension plugins dialog "
def __init__( self, pluginManager, parent = None ):
QDialog.__init__( self, parent )
self.setWindowTitle( "Plugin Manager" )
self.__pluginManager = pluginManager
self.__configFuncs = {} # int -> callable
self.__createLayout()
self.__populate()
self.__pluginsView.setFocus()
self.__inItemChange = False
return
def __createLayout( self ):
" Creates the dialog layout "
self.resize( 640, 480 )
self.setSizeGripEnabled( True )
layout = QVBoxLayout()
# Plugins list
self.__pluginsView = QTreeWidget()
self.__pluginsView.setAlternatingRowColors( True )
self.__pluginsView.setRootIsDecorated( False )
self.__pluginsView.setItemsExpandable( False )
self.__pluginsView.setSortingEnabled( True )
self.__pluginsView.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.__pluginsView.setUniformRowHeights( True )
# Alert | system/user | Enable | Name | Version
self.__pluginsHeader = QTreeWidgetItem( [ "", "", "", "Name", "Version", "" ] )
self.__pluginsView.setHeaderItem( self.__pluginsHeader )
self.__pluginsView.header().setSortIndicator( NAME_COL, Qt.AscendingOrder )
self.connect( self.__pluginsView,
SIGNAL( "itemSelectionChanged()" ),
self.__pluginSelectionChanged )
self.connect( self.__pluginsView,
SIGNAL( "itemChanged(QTreeWidgetItem*,int)" ),
self.__onItemChanged )
layout.addWidget( self.__pluginsView )
# Detailed information
detailsLabel = QLabel( "Detailed information" )
layout.addWidget( detailsLabel )
self.__details = QTreeWidget()
self.__details.setAlternatingRowColors( False )
self.__details.setRootIsDecorated( False )
self.__details.setItemsExpandable( False )
self.__details.setSortingEnabled( False )
self.__details.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.__details.setUniformRowHeights( True )
detailsHeader = QTreeWidgetItem( [ "", "" ] )
self.__details.setHeaderItem( detailsHeader )
self.__details.setHeaderHidden( True )
metrics = QFontMetrics( self.__details.font() )
rect = metrics.boundingRect( "X" )
self.__details.setFixedHeight( rect.height() * 6 + 5 )
layout.addWidget( self.__details )
# Errors/warnings
errorsLabel = QLabel( "Errors / warnings" )
layout.addWidget( errorsLabel )
self.__errorsText = QTextEdit()
self.__errorsText.setReadOnly( True )
self.__errorsText.setAcceptRichText( False )
metrics = QFontMetrics( self.__errorsText.font() )
rect = metrics.boundingRect( "X" )
self.__errorsText.setFixedHeight( rect.height() * 4 + 5 )
layout.addWidget( self.__errorsText )
# Buttons box
buttonBox = QDialogButtonBox( self )
buttonBox.setOrientation( Qt.Horizontal )
buttonBox.setStandardButtons( QDialogButtonBox.Ok )
self.__OKButton = buttonBox.button( QDialogButtonBox.Ok )
self.__OKButton.setDefault( True )
self.connect( buttonBox, SIGNAL( "accepted()" ), self.close )
self.connect( buttonBox, SIGNAL( "rejected()" ), self.close )
layout.addWidget( buttonBox )
self.setLayout( layout )
return
def __createConfigButton( self ):
" Creates a configure button for a plugin "
button = SettingsButton()
self.connect( button, SIGNAL( 'CustomClick' ), self.onPluginSettings )
return button
def __populate( self ):
" Populates the list with the plugins "
index = 0
for category in self.__pluginManager.activePlugins:
for cdmPlugin in self.__pluginManager.activePlugins[ category ]:
newItem = PluginItem( self.__pluginManager, cdmPlugin, True, category )
self.__pluginsView.addTopLevelItem( newItem )
settingsButton = self.__createConfigButton()
try:
configFunction = cdmPlugin.getObject().getConfigFunction()
if configFunction is None:
settingsButton.setToolTip( "Plugin does not need configuring" )
settingsButton.setEnabled( False )
else:
settingsButton.setToolTip( "Click to configure" )
settingsButton.setEnabled( True )
self.__configFuncs[ index ] = configFunction
settingsButton.index = index
index += 1
except Exception:
settingsButton.setToolTip( "Bad plugin interface. No "
"configuration function received." )
settingsButton.setEnabled( False )
self.__pluginsView.setItemWidget( newItem, SETTINGS_COL, settingsButton )
for category in self.__pluginManager.inactivePlugins:
for cdmPlugin in self.__pluginManager.inactivePlugins[ category ]:
newItem = PluginItem( self.__pluginManager, cdmPlugin, False, category )
self.__pluginsView.addTopLevelItem( newItem )
settingsButton = self.__createConfigButton()
try:
configFunction = cdmPlugin.getObject().getConfigFunction()
if configFunction is None:
settingsButton.setToolTip( "Plugin does not need configuring" )
settingsButton.setEnabled( False )
else:
settingsButton.setToolTip( "Enable plugin and then click to configure" )
settingsButton.setEnabled( False )
self.__configFuncs[ index ] = configFunction
settingsButton.index = index
index += 1
except:
settingsButton.setToolTip( "Bad plugin interface. No "
"configuration function received." )
settingsButton.setEnabled( False )
self.__pluginsView.setItemWidget( newItem, SETTINGS_COL, settingsButton )
for cdmPlugin in self.__pluginManager.unknownPlugins:
newItem = PluginItem( self.__pluginManager, cdmPlugin, False, None )
self.__pluginsView.addTopLevelItem( newItem )
settingsButton = self.__createConfigButton()
settingsButton.setToolTip( "Unknown plugins are not configurable" )
settingsButton.setEnabled( False )
self.__pluginsView.setItemWidget( newItem, SETTINGS_COL, settingsButton )
self.__sortPlugins()
self.__resizePlugins()
return
def __sortPlugins( self ):
" Sorts the plugins table "
self.__pluginsView.sortItems(
self.__pluginsView.sortColumn(),
self.__pluginsView.header().sortIndicatorOrder() )
return
def __resizePlugins( self ):
" Resizes the plugins table "
self.__pluginsView.header().setStretchLastSection( False )
self.__pluginsView.header().resizeSections(
QHeaderView.ResizeToContents )
self.__pluginsView.header().resizeSection( STATE_COL, 28 )
self.__pluginsView.header().setResizeMode( STATE_COL, QHeaderView.Fixed )
self.__pluginsView.header().resizeSection( CONFLICT_COL, 28 )
self.__pluginsView.header().setResizeMode( CONFLICT_COL, QHeaderView.Fixed )
self.__pluginsView.header().resizeSection( TYPE_COL, 28 )
self.__pluginsView.header().setResizeMode( TYPE_COL, QHeaderView.Fixed )
self.__pluginsView.header().setResizeMode( VERSION_COL, QHeaderView.Stretch )
self.__pluginsView.header().resizeSection( SETTINGS_COL, 24 )
self.__pluginsView.header().setResizeMode( SETTINGS_COL, QHeaderView.Fixed )
return
def __pluginSelectionChanged( self ):
" Triggered when an item is selected "
selected = list( self.__pluginsView.selectedItems() )
if selected:
self.__updateDetails( selected[ 0 ] )
else:
self.__updateDetails( None )
return
def __updateDetails( self, item ):
" Updates the content of the details and the error boxes "
self.__details.clear()
self.__errorsText.setText( "" )
if item is None:
return
self.__details.addTopLevelItem(
QTreeWidgetItem( [ "Author", item.plugin.getAuthor() ] ) )
self.__details.addTopLevelItem(
QTreeWidgetItem( [ "Path", os.path.normpath( item.plugin.getPath() ) ] ) )
self.__details.addTopLevelItem(
QTreeWidgetItem( [ "Description", item.plugin.getDescription() ] ) )
self.__details.addTopLevelItem(
QTreeWidgetItem( [ "Web site", item.plugin.getWebsite() ] ) )
copyright = item.plugin.getCopyright()
if copyright is not None:
if copyright.lower() != "unknown":
self.__details.addTopLevelItem(
QTreeWidgetItem( [ "Copyright", copyright ] ) )
for name in item.plugin.getDetails():
value = item.plugin.getDetails()[ name ]
self.__details.addTopLevelItem( QTreeWidgetItem( [ name, value ] ) )
self.__errorsText.setText( item.plugin.conflictMessage )
return
def __onItemChanged( self, item, column ):
" Triggered when an item is changed "
if self.__inItemChange:
return
if item.active:
self.__inItemChange = True
item.plugin.disable()
item.active = False
settingsButton = self.__pluginsView.itemWidget( item, SETTINGS_COL )
settingsButton.setEnabled( False )
if settingsButton.index != -1:
settingsButton.setToolTip( "Enable plugin and then click to configure" )
if item.category in self.__pluginManager.inactivePlugins:
self.__pluginManager.inactivePlugins[ item.category ].append( item.plugin )
else:
self.__pluginManager.inactivePlugins[ item.category ] = [ item.plugin ]
self.__pluginManager.activePlugins[ item.category ].remove( item.plugin )
self.__pluginManager.saveDisabledPlugins()
self.__inItemChange = False
self.__pluginManager.sendPluginDeactivated( item.plugin )
return
self.__inItemChange = True
message = self.__pluginManager.checkConflict( item.plugin )
if message is not None:
item.setCheckState( STATE_COL, Qt.Unchecked )
self.__errorsText.setText( message )
self.__inItemChange = False
return
try:
item.plugin.enable()
item.active = True
if item.category in self.__pluginManager.activePlugins:
self.__pluginManager.activePlugins[ item.category ].append( item.plugin )
else:
self.__pluginManager.activePlugins[ item.category ] = [ item.plugin ]
self.__pluginManager.inactivePlugins[ item.category ].remove( item.plugin )
self.__pluginManager.saveDisabledPlugins()
self.__errorsText.setText( "" )
item.setIcon( CONFLICT_COL, PixmapCache().getIcon( 'empty.png' ) )
item.setToolTip( CONFLICT_COL, "" )
settingsButton = self.__pluginsView.itemWidget( item, SETTINGS_COL )
if settingsButton.index != -1:
settingsButton.setToolTip( "Click to configure" )
settingsButton.setEnabled( True )
self.__pluginManager.sendPluginActivated( item.plugin )
except:
item.setCheckState( STATE_COL, Qt.Unchecked )
self.__errorsText.setText( "Error activating the plugin - exception is generated" )
self.__inItemChange = False
return
def onPluginSettings( self, index ):
" Triggered when a configuring function is called "
if index not in self.__configFuncs:
return
try:
self.__configFuncs[ index ]()
except Exception, exc:
logging.error( "Error calling the plugin configuration function. "
"Message: " + str( exc ) )
return
class DBDatabasesWidget(QWidget):
"""Displays a list of Databases"""
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.debug = False
self.db = None
self.setWindowTitle("Databases")
#s#elf.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
self.mainLayout = QVBoxLayout()
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(0)
self.setLayout(self.mainLayout)
#=============================================
## Top Toolbar
topBar = QToolBar()
topBar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.mainLayout.addWidget(topBar)
## Add the action buttons
topBar.addAction(Ico.icon(Ico.ServerAdd), "Add", self.on_server_add)
self.actionServerEdit = topBar.addAction(Ico.icon(Ico.ServerEdit), "Edit", self.on_server_edit)
self.actionServerDelete = topBar.addAction(Ico.icon(Ico.ServerDelete), "Delete", self.on_server_delete)
#=============================================
## Tree
self.tree = QTreeWidget()
self.mainLayout.addWidget(self.tree)
self.tree.setHeaderLabels(["Server", "User", ""])
self.tree.setUniformRowHeights(True)
self.tree.setRootIsDecorated(False)
self.tree.setColumnWidth(C.widget, 20)
self.connect( self.tree, SIGNAL( 'itemSelectionChanged()' ), self.on_tree_selection_changed )
self.connect( self.tree, SIGNAL( 'itemDoubleClicked (QTreeWidgetItem *,int)' ), self.on_tree_double_clicked )
self.buttGroup = QButtonGroup(self)
self.connect(self.buttGroup, SIGNAL("buttonClicked(QAbstractButton*)"), self.on_open_server)
self.on_tree_selection_changed()
self.load_servers()
#=======================================
##== Tree Events
def on_tree_selection_changed(self):
disabled = self.tree.selectionModel().hasSelection() == False
self.actionServerEdit.setDisabled(disabled)
self.actionServerDelete.setDisabled(disabled)
def on_tree_double_clicked(self):
self.actionServerEdit.trigger()
#=======================================
## Server Actions
def on_server_add(self):
self.show_server_dialog(None)
def on_server_edit(self):
item = self.tree.currentItem()
if item == None:
return
server = str(item.text(C.server))
self.show_server_dialog(server)
def show_server_dialog(self, server=None):
d = DBServerDialog.DBServerDialog(self, server)
if d.exec_():
self.load_servers()
def on_open_server(self, butt):
self.emit(SIGNAL("open_server"), butt.property("server").toString())
def load_servers(self):
"""Load servers from :py:meth:`pyqtdb.XSettings.XSettings.get_servers` """
self.tree.clear()
for butt in self.buttGroup.buttons():
self.buttGroup.removeButton(butt)
for srv in G.settings.get_servers_list():
item = QTreeWidgetItem()
item.setText(C.server, srv['server'])
item.setText(C.user, srv['user'])
self.tree.addTopLevelItem(item)
butt = QToolButton()
butt.setIcon(Ico.icon(Ico.Connect))
butt.setProperty("server", srv['server'])
self.tree.setItemWidget(item, C.widget, butt)
self.buttGroup.addButton(butt)
def on_server_delete(self):
item = self.tree.currentItem()
if item == None:
return
srv = str(item.text(C.server))
G.settings.delete_server(srv)
self.load_servers()
class OWGenExpress(widget.OWWidget):
name = "GenExpress"
description = "Expression data from GenExpress."
icon = "../widgets/icons/GenCloud.svg"
priority = 36
inputs = []
outputs = [("Data", Orange.data.Table)]
username = settings.Setting("anonymous")
password = settings.Setting("")
log2 = settings.Setting(False)
transpose = settings.Setting(False)
rtypei = settings.Setting(0)
projecti = settings.Setting(0)
serveri = settings.Setting(0)
exnamei = settings.Setting(6)
excludeconstant = settings.Setting(False)
joinreplicates = settings.Setting(False)
currentSelection = settings.Setting(None)
experimentsHeaderState = settings.Setting({
name: False for _, name in HEADER[:ID_INDEX + 1]}
)
storedSortOrder = settings.Setting([])
storedSelections = settings.Setting([])
def __init__(self, parent=None):
super().__init__(parent)
self.servers = [
('https://dictyexpress.research.bcm.edu/', 'dictyExpress'),
('https://cloud.genialis.com/', 'Genialis'),
]
self.selectedExperiments = []
self.buffer = dicty.CacheSQLite(bufferfile)
self.searchString = ""
self.items = []
self.result_types = []
self.controlArea.setMaximumWidth(250)
self.controlArea.setMinimumWidth(250)
box = gui.widgetBox(self.controlArea, 'Project')
self.projectCB = gui.comboBox(
box, self, "projecti", items=[], callback=self.ProjectChosen)
self.projects = []
b = gui.widgetBox(self.controlArea, "Selection bookmarks")
self.selectionSetsWidget = SelectionSetsWidget(self)
self.selectionSetsWidget.setSizePolicy(
QSizePolicy.Preferred, QSizePolicy.Maximum)
def store_selections(modified):
if not modified:
self.storedSelections = self.selectionSetsWidget.selections
self.selectionSetsWidget.selectionModified.connect(store_selections)
b.layout().addWidget(self.selectionSetsWidget)
gui.separator(self.controlArea)
b = gui.widgetBox(self.controlArea, "Sort output columns")
self.columnsSortingWidget = SortedListWidget(self)
self.columnsSortingWidget.setSizePolicy(
QSizePolicy.Preferred, QSizePolicy.Maximum)
box = gui.widgetBox(self.controlArea, 'Experiment name')
self.experimentNameCB = gui.comboBox(
box, self, "exnamei", items=SORTING_MODEL_LIST)
b.layout().addWidget(self.columnsSortingWidget)
sorting_model = QStringListModel(SORTING_MODEL_LIST)
self.columnsSortingWidget.setModel(sorting_model)
self.columnsSortingWidget.sortingOrder = self.storedSortOrder
def store_sort_order():
self.storedSortOrder = self.columnsSortingWidget.sortingOrder
self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Expression Type')
self.expressionTypesCB = gui.comboBox(
box, self, "rtypei", items=[], callback=self.UpdateResultsList)
gui.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
gui.checkBox(self.controlArea, self, "joinreplicates",
"Average replicates (use median)")
gui.checkBox(self.controlArea, self, "log2",
"Logarithmic (base 2) transformation")
gui.checkBox(self.controlArea, self, "transpose",
"Genes as attributes")
self.commit_button = gui.button(self.controlArea, self, "&Commit",
callback=self.Commit)
self.commit_button.setDisabled(True)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Server')
gui.comboBox(box, self, "serveri",
items=[title for url, title in self.servers],
callback=self.ServerChosen)
gui.lineEdit(box, self, "username", "Username:"******"password", "Password:"******"Clear cache",
callback=self.clear_cache)
gui.lineEdit(self.mainArea, self, "searchString", "Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.headerLabels = [t[1] for t in HEADER]
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.experimentsWidget, self.experimentsWidget)
self.experimentsWidget.header().installEventFilter(contextEventFilter)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.setAlternatingRowColors(True)
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.selectionSetsWidget.setSelectionModel(
self.experimentsWidget.selectionModel())
self.selectionSetsWidget.setSelections(self.storedSelections)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.restoreHeaderState()
self.experimentsWidget.header().geometriesChanged.connect(
self.saveHeaderState)
self.dbc = None
self.AuthSet()
QTimer.singleShot(100, self.ConnectAndUpdate)
def sizeHint(self):
return QSize(800, 600)
def AuthSet(self):
if len(self.username):
self.passf.setDisabled(False)
else:
self.passf.setDisabled(True)
def AuthChanged(self):
self.AuthSet()
self.ConnectAndUpdate()
def ConnectAndUpdate(self):
self.Connect()
if self.dbc:
def get_data_count(project_id):
# XXX: is there a better way?
# Note: limit 0 would return all objects
return self.dbc.gen.api.data.get(case_ids__contains=project_id,
type__startswith='data:expression:',
limit=1)['meta']['total_count']
self.projects = sorted([p for p in self.dbc.projects().items() if
get_data_count(p[0]) > 0], key=lambda x: x[1])
self.UpdateProjects()
self.ProjectChosen()
self.UpdateExperimentTypes()
def Connect(self):
self.error(1)
self.warning(1)
username = '******'
password = '******'
url = self.servers[self.serveri][0]
if self.username:
username = self.username
password = self.password
if username.lower() in ['*****@*****.**', 'anonymous']:
username = '******'
password = '******'
self.dbc = None
self.projects = []
self.result_types = []
try:
self.dbc = Genesis(
address=url, username=username, password=password,
cache=self.buffer)
except requests.exceptions.ConnectionError:
self.dbc = Genesis(
address=url, username=username, password=password,
connect=False, cache=self.buffer)
self.warning(1, "Could not connect to server, working from cache.")
except Exception:
self.error(1, "Wrong username or password.")
self.UpdateProjects()
self.UpdateExperimentTypes() # clear lists
def Reload(self):
self.UpdateExperiments(reload=True)
def clear_cache(self):
self.buffer.clear()
self.Reload()
def rtype(self):
"""Return selected result template type """
if self.result_types:
return self.result_types[self.rtypei]
else:
return None
def UpdateExperimentTypes(self):
self.expressionTypesCB.clear()
items = [self.result_types_labels[desc] for desc in self.result_types]
self.expressionTypesCB.addItems(items)
#do not update anything if the list is empty
if len(self.result_types):
self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1))
def UpdateProjects(self):
self.projectCB.clear()
items = [desc for pid, desc in self.projects]
self.projectCB.addItems(items)
#do not update anything if the list if empty
if len(self.projects) > 0:
self.projecti = max(0, min(self.projecti, len(self.projects) - 1))
def UpdateExperiments(self, reload=False):
self.experimentsWidget.clear()
if not self.dbc or not self.dbc.projectid: # the connection did not succeed
return
self.items = []
self.progressBarInit()
result_types = []
result_types_labels = []
sucind = False # success indicator for database index
try:
result_types, result_types_labels = self.dbc.result_types(reload=reload)
sucind = True
except Exception:
try:
result_types, result_types_labels = self.dbc.result_types()
self.warning(0, "Can not access database - using cached data.")
sucind = True
except Exception:
self.error(0, "Can not access database.")
if sucind:
self.warning(0)
self.error(0)
self.result_types = result_types
self.result_types_labels = result_types_labels
self.UpdateExperimentTypes()
self.UpdateResultsList(reload=reload)
self.progressBarFinished()
if self.currentSelection:
self.currentSelection.select(self.experimentsWidget.selectionModel())
self.handle_commit_button()
def ProjectChosen(self, reload=False):
if self.projects:
self.dbc.projectid = self.projects[self.projecti][0]
else:
self.dbc.projectid = None
self.UpdateExperiments(reload=reload)
def ServerChosen(self):
self.ConnectAndUpdate()
def UpdateResultsList(self, reload=False):
results_list = self.dbc.results_list(self.rtype(), reload=reload)
try:
results_list = self.dbc.results_list(self.rtype(), reload=reload)
except Exception:
try:
results_list = self.dbc.results_list(self.rtype())
except Exception:
self.error(0, "Can not access database.")
self.results_list = results_list
#softly change the view so that the selection stays the same
items_shown = {}
for i, item in enumerate(self.items):
c = str(item.text(ID_INDEX))
items_shown[c] = i
items_to_show = set(id_ for id_ in self.results_list)
add_items = set(items_to_show) - set(items_shown)
delete_items = set(items_shown) - set(items_to_show)
i = 0
while i < self.experimentsWidget.topLevelItemCount():
it = self.experimentsWidget.topLevelItem(i)
if str(it.text(ID_INDEX)) in delete_items:
self.experimentsWidget.takeTopLevelItem(i)
else:
i += 1
delete_ind = set([items_shown[i] for i in delete_items])
self.items = [it for i, it in enumerate(self.items)
if i not in delete_ind]
for r_annot in add_items:
d = defaultdict(lambda: "?", self.results_list[r_annot])
row_items = [""] + [to_text(d.get(key, "?"))
for key, _ in HEADER[1:]]
row_items[ID_INDEX] = r_annot
ci = MyTreeWidgetItem(self.experimentsWidget, row_items)
self.items.append(ci)
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
self.wantbufver = lambda x: self.results_list[x]["date_modified"]
self.UpdateCached()
def UpdateCached(self):
if self.wantbufver and self.dbc:
for item in self.items:
id = str(item.text(ID_INDEX))
version = self.dbc._in_buffer(id + "|||" + self.rtype())
value = " " if version == self.wantbufver(id) else ""
item.setData(0, Qt.DisplayRole, value)
def SearchUpdate(self, string=""):
for item in self.items:
item.setHidden(
not all(s in item for s in self.searchString.split()))
def Commit(self):
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(ID_INDEX))
ids.append(unique_id)
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = {name: name for key, name in HEADER}
reverse_header_dict["ID"] = "id"
allowed_labels = None
def namefn(a):
name = SORTING_MODEL_LIST[self.exnamei]
name = reverse_header_dict.get(name, "id")
return dict(a)[name]
if len(ids):
table = self.dbc.get_data(
ids=ids, result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels,
namefn=namefn)
if self.joinreplicates:
table = dicty.join_replicates(table,
ignorenames=self.dbc.IGNORE_REPLICATE,
namefn="name",
avg=dicty.median,
fnshow=lambda x: " | ".join(map(str, x)))
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except ValueError:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([optfloat(atts.get(reverse_header_dict[name], ""), name)
for name in sortOrder])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(
attributes, table.domain.class_vars, table.domain.metas)
table = Orange.data.Table.from_table(domain, table)
table = Orange.data.Table(domain, table)
if self.transpose:
experiments = [at for at in table.domain.variables]
attr = [compat.ContinuousVariable.make(ex['DDB'].value) for ex in table]
metavars = sorted(table.domain.variables[0].attributes.keys())
metavars = [compat.StringVariable.make(name) for name in metavars]
domain = compat.create_domain(attr, None, metavars)
metavars = compat.get_metas(domain)
metas = [[exp.attributes[var.name] for var in metavars] for exp in experiments]
table = compat.create_table(domain, table.X.transpose(), None, metas)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def onSelectionChanged(self, selected, deselected):
self.handle_commit_button()
def handle_commit_button(self):
self.currentSelection = \
SelectionByKey(self.experimentsWidget.selectionModel().selection(),
key=(ID_INDEX,))
self.commit_button.setDisabled(not len(self.currentSelection))
def saveHeaderState(self):
hview = self.experimentsWidget.header()
for i, label in enumerate(self.headerLabels):
self.experimentsHeaderState[label] = hview.isSectionHidden(i)
def restoreHeaderState(self):
hview = self.experimentsWidget.header()
state = self.experimentsHeaderState
for i, label in enumerate(self.headerLabels):
hview.setSectionHidden(i, state.get(label, True))
self.experimentsWidget.resizeColumnToContents(i)
class yarascanTreeView():
def __init__(self, data):
self.treeWidget = QTreeWidget()
self.data = data
self.detections = DetectionContainer()
self.initialLoad()
def initialLoad(self):
for detection in self.generateDetections():
self.detections.addDetection(detection)
self.populateTree()
def populateTree(self, selectedDetection=None):
selected = None
self.treeWidget.clear()
self.treeWidget.setColumnCount(3)
self.treeWidget.setHeaderLabels(["Rule/Process", "Pid", "Text"])
self.treeWidget.setItemsExpandable(True)
parentRule = {}
parentRuleProcess = {}
for detection in self.detections:
ancestor = parentRule.get(detection.rule_name)
if ancestor is None:
ancestor = QTreeWidgetItem(self.treeWidget, [detection.rule_name])
parentRule[detection.rule_name] = ancestor
process = detection.process
parent = parentRuleProcess.get(process)
if parent is None:
parent = QTreeWidgetItem(ancestor, [process, QString("%L1").arg(detection.pid)])
parentRuleProcess[process] = parent
item = QTreeWidgetItem(parent, ['','', detection.text])
item.setTextAlignment(3, Qt.AlignRight|Qt.AlignVCenter)
if selectedDetection is not None and selectedDetection == id(detection):
selected = item
#self.treeWidget.expandItem(parent)
self.treeWidget.expandItem(ancestor)
self.treeWidget.resizeColumnToContents(0)
self.treeWidget.resizeColumnToContents(1)
if selected is not None:
selected.setSelected(True)
self.treeWidget.setCurrentItem(selected)
def generateDetections(self):
for x in range(len(self.data)):
line = self.data["Owner"][x]
matchObj = re.match(r'(.*):\s{1,}\(pid\s(\d{1,})', line, re.I)
#if matchObj:
# print "matchObj.group() :", matchObj.group()
process = matchObj.group(1)
pid = matchObj.group(2)
bindata = self.data["Data"][x]
textB = ''
for i in range(0, len(bindata), 2):
if not i%32:
textB+="\n"
else:
textB+=chr(int(bindata[i:i+2], 16))
yield Detection(self.data["Rule"][x], process, pid, textB)
class RecentProjectsViewer(QWidget):
" Recent projects viewer implementation "
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.__projectContextItem = None
self.__fileContextItem = None
self.upper = self.__createRecentFilesLayout()
self.lower = self.__createRecentProjectsLayout()
self.__createProjectPopupMenu()
self.__createFilePopupMenu()
layout = QVBoxLayout()
layout.setContentsMargins(1, 1, 1, 1)
splitter = QSplitter(Qt.Vertical)
splitter.addWidget(self.upper)
splitter.addWidget(self.lower)
splitter.setCollapsible(0, False)
splitter.setCollapsible(1, False)
layout.addWidget(splitter)
self.setLayout(layout)
self.__populateProjects()
self.__populateFiles()
self.__updateProjectToolbarButtons()
self.__updateFileToolbarButtons()
# Debugging mode support
self.__debugMode = False
parent.debugModeChanged.connect(self.__onDebugMode)
return
def setTooltips(self, switchOn):
" Switches the tooltips mode "
for index in xrange(0, self.recentFilesView.topLevelItemCount()):
self.recentFilesView.topLevelItem(index).updateIconAndTooltip()
for index in xrange(0, self.projectsView.topLevelItemCount()):
self.projectsView.topLevelItem(index).updateTooltip()
return
def __createFilePopupMenu(self):
" create the recent files popup menu "
self.__fileMenu = QMenu(self.recentFilesView)
self.__openMenuItem = self.__fileMenu.addAction(
getIcon('openitem.png'), 'Open', self.__openFile)
self.__copyPathFileMenuItem = self.__fileMenu.addAction(
getIcon('copytoclipboard.png'), 'Copy path to clipboard',
self.__filePathToClipboard)
self.__fileMenu.addSeparator()
self.__delFileMenuItem = self.__fileMenu.addAction(
getIcon('trash.png'), 'Delete from recent', self.__deleteFile)
self.recentFilesView.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self.recentFilesView,
SIGNAL("customContextMenuRequested(const QPoint &)"),
self.__handleShowFileContextMenu)
self.connect(GlobalData().project, SIGNAL('recentFilesChanged'),
self.__populateFiles)
return
def __createProjectPopupMenu(self):
" Creates the recent project popup menu "
self.__projectMenu = QMenu(self.projectsView)
self.__prjLoadMenuItem = self.__projectMenu.addAction(
getIcon('load.png'), 'Load', self.__loadProject)
self.__projectMenu.addSeparator()
self.__propsMenuItem = self.__projectMenu.addAction(
getIcon('smalli.png'), 'Properties', self.__viewProperties)
self.__prjCopyPathMenuItem = self.__projectMenu.addAction(
getIcon('copytoclipboard.png'), 'Copy path to clipboard',
self.__prjPathToClipboard)
self.__projectMenu.addSeparator()
self.__delPrjMenuItem = self.__projectMenu.addAction(
getIcon('trash.png'), 'Delete from recent', self.__deleteProject)
self.projectsView.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self.projectsView,
SIGNAL("customContextMenuRequested(const QPoint &)"),
self.__handleShowPrjContextMenu)
Settings().recentListChanged.connect(self.__populateProjects)
GlobalData().project.projectChanged.connect(self.__projectChanged)
return
def __createRecentFilesLayout(self):
" Creates the upper part - recent files "
headerFrame = QFrame()
headerFrame.setFrameStyle(QFrame.StyledPanel)
headerFrame.setAutoFillBackground(True)
headerPalette = headerFrame.palette()
headerBackground = headerPalette.color(QPalette.Background)
headerBackground.setRgb(min(headerBackground.red() + 30, 255),
min(headerBackground.green() + 30, 255),
min(headerBackground.blue() + 30, 255))
headerPalette.setColor(QPalette.Background, headerBackground)
headerFrame.setPalette(headerPalette)
headerFrame.setFixedHeight(24)
recentFilesLabel = QLabel()
recentFilesLabel.setText("Recent files")
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins(3, 0, 0, 0)
headerLayout.addWidget(recentFilesLabel)
headerFrame.setLayout(headerLayout)
self.recentFilesView = QTreeWidget()
self.recentFilesView.setAlternatingRowColors(True)
self.recentFilesView.setRootIsDecorated(False)
self.recentFilesView.setItemsExpandable(False)
self.recentFilesView.setSortingEnabled(True)
self.recentFilesView.setItemDelegate(NoOutlineHeightDelegate(4))
self.recentFilesView.setUniformRowHeights(True)
self.__filesHeaderItem = QTreeWidgetItem(["", "File", "Absolute path"])
self.recentFilesView.setHeaderItem(self.__filesHeaderItem)
self.recentFilesView.header().setSortIndicator(1, Qt.AscendingOrder)
self.connect(self.recentFilesView, SIGNAL("itemSelectionChanged()"),
self.__fileSelectionChanged)
self.connect(self.recentFilesView,
SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self.__fileActivated)
# Toolbar part - buttons
self.openFileButton = QAction(getIcon('openitem.png'),
'Open the highlighted file', self)
self.connect(self.openFileButton, SIGNAL("triggered()"),
self.__openFile)
self.copyFilePathButton = QAction(getIcon('copytoclipboard.png'),
'Copy path to clipboard', self)
self.connect(self.copyFilePathButton, SIGNAL("triggered()"),
self.__filePathToClipboard)
spacer = QWidget()
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.trashFileButton = QAction(getIcon('delitem.png'),
'Remove selected (not from the disk)',
self)
self.connect(self.trashFileButton, SIGNAL("triggered()"),
self.__deleteFile)
self.upperToolbar = QToolBar()
self.upperToolbar.setMovable(False)
self.upperToolbar.setAllowedAreas(Qt.TopToolBarArea)
self.upperToolbar.setIconSize(QSize(16, 16))
self.upperToolbar.setFixedHeight(28)
self.upperToolbar.setContentsMargins(0, 0, 0, 0)
self.upperToolbar.addAction(self.openFileButton)
self.upperToolbar.addAction(self.copyFilePathButton)
self.upperToolbar.addWidget(spacer)
self.upperToolbar.addAction(self.trashFileButton)
recentFilesLayout = QVBoxLayout()
recentFilesLayout.setContentsMargins(0, 0, 0, 0)
recentFilesLayout.setSpacing(0)
recentFilesLayout.addWidget(headerFrame)
recentFilesLayout.addWidget(self.upperToolbar)
recentFilesLayout.addWidget(self.recentFilesView)
upperContainer = QWidget()
upperContainer.setContentsMargins(0, 0, 0, 0)
upperContainer.setLayout(recentFilesLayout)
return upperContainer
def getRecentFilesToolbar(self):
" Provides a reference to the recent files toolbar "
return self.upperToolbar
def __createRecentProjectsLayout(self):
" Creates the bottom layout "
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle(QFrame.StyledPanel)
self.headerFrame.setAutoFillBackground(True)
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color(QPalette.Background)
headerBackground.setRgb(min(headerBackground.red() + 30, 255),
min(headerBackground.green() + 30, 255),
min(headerBackground.blue() + 30, 255))
headerPalette.setColor(QPalette.Background, headerBackground)
self.headerFrame.setPalette(headerPalette)
self.headerFrame.setFixedHeight(24)
recentProjectsLabel = QLabel()
recentProjectsLabel.setText("Recent projects")
expandingSpacer = QSpacerItem(10, 10, QSizePolicy.Expanding)
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise(True)
self.__showHideButton.setIcon(getIcon('less.png'))
self.__showHideButton.setFixedSize(20, 20)
self.__showHideButton.setToolTip("Hide recent projects list")
self.__showHideButton.setFocusPolicy(Qt.NoFocus)
self.connect(self.__showHideButton, SIGNAL('clicked()'),
self.__onShowHide)
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins(3, 0, 0, 0)
headerLayout.addWidget(recentProjectsLabel)
headerLayout.addSpacerItem(expandingSpacer)
headerLayout.addWidget(self.__showHideButton)
self.headerFrame.setLayout(headerLayout)
# Toolbar part - buttons
self.loadButton = QAction(getIcon('load.png'),
'Load the highlighted project', self)
self.connect(self.loadButton, SIGNAL("triggered()"),
self.__loadProject)
self.propertiesButton = QAction(
getIcon('smalli.png'), 'Show the highlighted project '
'properties', self)
self.connect(self.propertiesButton, SIGNAL("triggered()"),
self.__viewProperties)
self.copyPrjPathButton = QAction(getIcon('copytoclipboard.png'),
'Copy path to clipboard', self)
self.connect(self.copyPrjPathButton, SIGNAL("triggered()"),
self.__prjPathToClipboard)
spacer = QWidget()
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.trashButton = QAction(getIcon('delitem.png'),
'Remove selected (not from the disk)', self)
self.connect(self.trashButton, SIGNAL("triggered()"),
self.__deleteProject)
self.lowerToolbar = QToolBar()
self.lowerToolbar.setMovable(False)
self.lowerToolbar.setAllowedAreas(Qt.TopToolBarArea)
self.lowerToolbar.setIconSize(QSize(16, 16))
self.lowerToolbar.setFixedHeight(28)
self.lowerToolbar.setContentsMargins(0, 0, 0, 0)
self.lowerToolbar.addAction(self.loadButton)
self.lowerToolbar.addAction(self.propertiesButton)
self.lowerToolbar.addAction(self.copyPrjPathButton)
self.lowerToolbar.addWidget(spacer)
self.lowerToolbar.addAction(self.trashButton)
self.projectsView = QTreeWidget()
self.projectsView.setAlternatingRowColors(True)
self.projectsView.setRootIsDecorated(False)
self.projectsView.setItemsExpandable(False)
self.projectsView.setSortingEnabled(True)
self.projectsView.setItemDelegate(NoOutlineHeightDelegate(4))
self.projectsView.setUniformRowHeights(True)
self.__projectsHeaderItem = QTreeWidgetItem(
["", "Project", "Absolute path"])
self.projectsView.setHeaderItem(self.__projectsHeaderItem)
self.projectsView.header().setSortIndicator(1, Qt.AscendingOrder)
self.connect(self.projectsView,
SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self.__projectActivated)
self.connect(self.projectsView, SIGNAL("itemSelectionChanged()"),
self.__projectSelectionChanged)
recentProjectsLayout = QVBoxLayout()
recentProjectsLayout.setContentsMargins(0, 0, 0, 0)
recentProjectsLayout.setSpacing(0)
recentProjectsLayout.addWidget(self.headerFrame)
recentProjectsLayout.addWidget(self.lowerToolbar)
recentProjectsLayout.addWidget(self.projectsView)
lowerContainer = QWidget()
lowerContainer.setContentsMargins(0, 0, 0, 0)
lowerContainer.setLayout(recentProjectsLayout)
return lowerContainer
def getRecentProjectsToolbar(self):
" Provides a reference to the projects toolbar "
return self.lowerToolbar
def __projectSelectionChanged(self):
" Handles the projects changed selection "
selected = list(self.projectsView.selectedItems())
if selected:
self.__projectContextItem = selected[0]
else:
self.__projectContextItem = None
self.__updateProjectToolbarButtons()
return
def __fileSelectionChanged(self):
" Handles the files changed selection "
selected = list(self.recentFilesView.selectedItems())
if selected:
self.__fileContextItem = selected[0]
else:
self.__fileContextItem = None
self.__updateFileToolbarButtons()
return
def __updateProjectToolbarButtons(self):
" Updates the toolbar buttons depending on the __projectContextItem "
if self.__projectContextItem is None:
self.loadButton.setEnabled(False)
self.propertiesButton.setEnabled(False)
self.copyPrjPathButton.setEnabled(False)
self.trashButton.setEnabled(False)
else:
enabled = self.__projectContextItem.isValid()
isCurrentProject = self.__projectContextItem.isCurrent()
self.propertiesButton.setEnabled(enabled)
self.copyPrjPathButton.setEnabled(True)
self.loadButton.setEnabled(enabled and not isCurrentProject
and not self.__debugMode)
self.trashButton.setEnabled(not isCurrentProject)
return
def __updateFileToolbarButtons(self):
" Updates the toolbar buttons depending on the __fileContextItem "
enabled = self.__fileContextItem is not None
self.openFileButton.setEnabled(enabled)
self.copyFilePathButton.setEnabled(enabled)
self.trashFileButton.setEnabled(enabled)
return
def __handleShowPrjContextMenu(self, coord):
" Show the project item context menu "
self.__projectContextItem = self.projectsView.itemAt(coord)
if self.__projectContextItem is None:
return
enabled = self.__projectContextItem.isValid()
isCurrentProject = self.__projectContextItem.isCurrent()
self.__propsMenuItem.setEnabled(enabled)
self.__delPrjMenuItem.setEnabled(not isCurrentProject)
# fName = self.__projectContextItem.getFilename()
self.__prjLoadMenuItem.setEnabled(enabled and not isCurrentProject
and not self.__debugMode)
self.__projectMenu.popup(QCursor.pos())
return
def __sortProjects(self):
" Sort the project items "
self.projectsView.sortItems( \
self.projectsView.sortColumn(),
self.projectsView.header().sortIndicatorOrder() )
return
def __sortFiles(self):
" Sort the file items "
self.recentFilesView.sortItems(
self.recentFilesView.sortColumn(),
self.recentFilesView.header().sortIndicatorOrder())
return
def __resizeProjectColumns(self):
""" Resize the projects list columns """
self.projectsView.header().setStretchLastSection(True)
self.projectsView.header().resizeSections(QHeaderView.ResizeToContents)
self.projectsView.header().resizeSection(0, 22)
self.projectsView.header().setResizeMode(0, QHeaderView.Fixed)
return
def __resizeFileColumns(self):
" Resize the files list columns "
self.recentFilesView.header().setStretchLastSection(True)
self.recentFilesView.header().resizeSections(
QHeaderView.ResizeToContents)
self.recentFilesView.header().resizeSection(0, 22)
self.recentFilesView.header().setResizeMode(0, QHeaderView.Fixed)
return
def __projectActivated(self, item, column):
" Handles the double click (or Enter) on the item "
self.__projectContextItem = item
self.__loadProject()
return
def __fileActivated(self, item, column):
" Handles the double click (or Enter) on a file item "
self.__fileContextItem = item
self.__openFile()
return
def __viewProperties(self):
" Handles the 'view properties' context menu item "
if self.__projectContextItem is None:
return
if not self.__projectContextItem.isValid():
return
if self.__projectContextItem.isCurrent():
# This is the current project - it can be edited
project = GlobalData().project
dialog = ProjectPropertiesDialog(project, self)
if dialog.exec_() == QDialog.Accepted:
importDirs = []
for index in xrange(dialog.importDirList.count()):
importDirs.append(dialog.importDirList.item(index).text())
scriptName = dialog.scriptEdit.text().strip()
relativePath = relpath(scriptName, project.getProjectDir())
if not relativePath.startswith('..'):
scriptName = relativePath
project.updateProperties(
scriptName, importDirs,
dialog.creationDateEdit.text().strip(),
dialog.authorEdit.text().strip(),
dialog.licenseEdit.text().strip(),
dialog.copyrightEdit.text().strip(),
dialog.versionEdit.text().strip(),
dialog.emailEdit.text().strip(),
dialog.descriptionEdit.toPlainText().strip())
else:
# This is not the current project - it can be viewed
fName = self.__projectContextItem.getFilename()
dialog = ProjectPropertiesDialog(fName, self)
dialog.exec_()
return
def __deleteProject(self):
" Handles the 'delete from recent' context menu item "
if self.__projectContextItem is None:
return
# Removal from the visible list is done via a signal which comes back
# from settings
fName = self.__projectContextItem.getFilename()
Settings().deleteRecentProject(fName)
return
def __loadProject(self):
" handles 'Load' context menu item "
if self.__projectContextItem is None:
return
if not self.__projectContextItem.isValid():
return
if self.__debugMode:
return
projectFileName = self.__projectContextItem.getFilename()
if self.__projectContextItem.isCurrent():
GlobalData().mainWindow.openFile(projectFileName, -1)
return # This is the current project, open for text editing
QApplication.processEvents()
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
if os.path.exists(projectFileName):
mainWin = GlobalData().mainWindow
editorsManager = mainWin.editorsManagerWidget.editorsManager
if editorsManager.closeRequest():
prj = GlobalData().project
prj.setTabsStatus(editorsManager.getTabsStatus())
editorsManager.closeAll()
prj.loadProject(projectFileName)
mainWin.activateProjectTab()
else:
logging.error("The project " + os.path.basename(projectFileName) +
" disappeared from the file system.")
self.__populateProjects()
QApplication.restoreOverrideCursor()
return
def __populateProjects(self):
" Populates the recent projects "
self.projectsView.clear()
for item in Settings().recentProjects:
self.projectsView.addTopLevelItem(RecentProjectViewItem(item))
self.__sortProjects()
self.__resizeProjectColumns()
self.__updateProjectToolbarButtons()
return
def __populateFiles(self):
" Populates the recent files "
self.recentFilesView.clear()
for path in GlobalData().project.recentFiles:
self.recentFilesView.addTopLevelItem(RecentFileViewItem(path))
self.__sortFiles()
self.__resizeFileColumns()
self.__updateFileToolbarButtons()
return
def __projectChanged(self, what):
" Triggered when the current project is changed "
if what == CodimensionProject.CompleteProject:
self.__populateProjects()
self.__populateFiles()
return
if what == CodimensionProject.Properties:
# Update the corresponding tooltip
items = self.projectsView.findItems(GlobalData().project.fileName,
Qt.MatchExactly, 2)
if len(items) != 1:
logging.error("Unexpected number of matched projects: " +
str(len(items)))
return
items[0].updateTooltip()
return
def __openFile(self):
" Handles 'open' file menu item "
self.__fileContextItem.updateIconAndTooltip()
fName = self.__fileContextItem.getFilename()
if not self.__fileContextItem.isValid():
logging.warning("Cannot open " + fName)
return
fileType = detectFileType(fName)
if fileType == PixmapFileType:
GlobalData().mainWindow.openPixmapFile(fName)
return
GlobalData().mainWindow.openFile(fName, -1)
return
def __deleteFile(self):
" Handles 'delete from recent' file menu item "
self.removeRecentFile(self.__fileContextItem.getFilename())
return
def __handleShowFileContextMenu(self, coord):
" File context menu "
self.__fileContextItem = self.recentFilesView.itemAt(coord)
if self.__fileContextItem is not None:
self.__fileMenu.popup(QCursor.pos())
return
def __filePathToClipboard(self):
" Copies the file item path to the clipboard "
if self.__fileContextItem is not None:
QApplication.clipboard().setText(
self.__fileContextItem.getFilename())
return
def __prjPathToClipboard(self):
" Copies the project item path to the clipboard "
if self.__projectContextItem is not None:
QApplication.clipboard().setText(
self.__projectContextItem.getFilename())
return
def onFileUpdated(self, fileName, uuid):
" Triggered when the file is updated: python or project "
realPath = os.path.realpath(fileName)
count = self.recentFilesView.topLevelItemCount()
for index in xrange(0, count):
item = self.recentFilesView.topLevelItem(index)
itemRealPath = os.path.realpath(item.getFilename())
if realPath == itemRealPath:
item.updateIconAndTooltip()
break
for index in xrange(0, self.projectsView.topLevelItemCount()):
item = self.projectsView.topLevelItem(index)
itemRealPath = os.path.realpath(item.getFilename())
if realPath == itemRealPath:
item.updateTooltip()
break
return
def __onShowHide(self):
" Triggered when show/hide button is clicked "
if self.projectsView.isVisible():
self.projectsView.setVisible(False)
self.lowerToolbar.setVisible(False)
self.__showHideButton.setIcon(getIcon('more.png'))
self.__showHideButton.setToolTip("Show recent projects list")
self.__minH = self.lower.minimumHeight()
self.__maxH = self.lower.maximumHeight()
self.lower.setMinimumHeight(self.headerFrame.height())
self.lower.setMaximumHeight(self.headerFrame.height())
else:
self.projectsView.setVisible(True)
self.lowerToolbar.setVisible(True)
self.__showHideButton.setIcon(getIcon('less.png'))
self.__showHideButton.setToolTip("Hide recent projects list")
self.lower.setMinimumHeight(self.__minH)
self.lower.setMaximumHeight(self.__maxH)
return
def __onDebugMode(self, newState):
" Triggered when debug mode has changed "
self.__debugMode = newState
# Disable the load project button
self.__updateProjectToolbarButtons()
return
def removeRecentFile(self, fName):
" Removes a single file from the recent files list "
GlobalData().project.removeRecentFile(fName)
for index in xrange(self.recentFilesView.topLevelItemCount()):
candidate = self.recentFilesView.topLevelItem(index)
if candidate.getFilename() == fName:
self.recentFilesView.takeTopLevelItem(index)
return
return
class Main(plugin.Plugin):
" Main Class "
def initialize(self, *args, **kwargs):
" Init Main Class "
super(Main, self).initialize(*args, **kwargs)
self.scriptPath, self.scriptArgs = "", []
self.profilerPath, self.tempPath = profilerPath, tempPath
self.output = " ERROR: FAIL: No output ! "
self.process = QProcess()
self.process.finished.connect(self.on_process_finished)
self.process.error.connect(self.on_process_error)
self.tabWidget, self.stat = QTabWidget(), QWidget()
self.tabWidget.tabCloseRequested.connect(
lambda: self.tabWidget.setTabPosition(1) if self.tabWidget.
tabPosition() == 0 else self.tabWidget.setTabPosition(0))
self.tabWidget.setStyleSheet('QTabBar{font-weight:bold;}')
self.tabWidget.setMovable(True)
self.tabWidget.setTabsClosable(True)
self.vboxlayout1 = QVBoxLayout(self.stat)
self.hboxlayout1 = QHBoxLayout()
self.filterTableLabel = QLabel("<b>Type to Search : </b>", self.stat)
self.hboxlayout1.addWidget(self.filterTableLabel)
self.filterTableLineEdit = QLineEdit(self.stat)
self.filterTableLineEdit.setPlaceholderText(' Type to Search . . . ')
self.hboxlayout1.addWidget(self.filterTableLineEdit)
self.filterHintTableLabel = QLabel(" ? ", self.stat)
self.hboxlayout1.addWidget(self.filterHintTableLabel)
self.vboxlayout1.addLayout(self.hboxlayout1)
self.tableWidget = QTableWidget(self.stat)
self.tableWidget.setAlternatingRowColors(True)
self.tableWidget.setColumnCount(8)
self.tableWidget.setRowCount(2)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(0, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(1, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(2, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(3, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(4, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(5, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(6, item)
item = QTableWidgetItem()
self.tableWidget.setHorizontalHeaderItem(7, item)
self.tableWidget.itemDoubleClicked.connect(
self.on_tableWidget_itemDoubleClicked)
self.vboxlayout1.addWidget(self.tableWidget)
self.tabWidget.addTab(self.stat, " ? ")
self.source = QWidget()
self.gridlayout = QGridLayout(self.source)
self.scintillaWarningLabel = QLabel(
"QScintilla is not installed!. Falling back to basic text edit!.",
self.source)
self.gridlayout.addWidget(self.scintillaWarningLabel, 1, 0, 1, 2)
self.sourceTreeWidget = QTreeWidget(self.source)
self.sourceTreeWidget.setAlternatingRowColors(True)
self.sourceTreeWidget.itemActivated.connect(
self.on_sourceTreeWidget_itemActivated)
self.sourceTreeWidget.itemClicked.connect(
self.on_sourceTreeWidget_itemClicked)
self.sourceTreeWidget.itemDoubleClicked.connect(
self.on_sourceTreeWidget_itemClicked)
self.gridlayout.addWidget(self.sourceTreeWidget, 0, 0, 1, 1)
self.sourceTextEdit = QTextEdit(self.source)
self.sourceTextEdit.setReadOnly(True)
self.gridlayout.addWidget(self.sourceTextEdit, 0, 1, 1, 1)
self.tabWidget.addTab(self.source, " ? ")
self.result = QWidget()
self.vlayout = QVBoxLayout(self.result)
self.globalStatGroupBox = QGroupBox(self.result)
self.hboxlayout = QHBoxLayout(self.globalStatGroupBox)
self.totalTimeLcdNumber = QLCDNumber(self.globalStatGroupBox)
self.totalTimeLcdNumber.setSegmentStyle(QLCDNumber.Filled)
self.totalTimeLcdNumber.setNumDigits(7)
self.totalTimeLcdNumber.display(1000000)
self.totalTimeLcdNumber.setFrameShape(QFrame.StyledPanel)
self.totalTimeLcdNumber.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.hboxlayout.addWidget(self.totalTimeLcdNumber)
self.tTimeLabel = QLabel("<b>Total Time (Sec)</b>",
self.globalStatGroupBox)
self.tTimeLabel.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.hboxlayout.addWidget(self.tTimeLabel)
self.numCallLcdNumber = QLCDNumber(self.globalStatGroupBox)
self.numCallLcdNumber.setNumDigits(7)
self.numCallLcdNumber.display(1000000)
self.numCallLcdNumber.setSegmentStyle(QLCDNumber.Filled)
self.numCallLcdNumber.setFrameShape(QFrame.StyledPanel)
self.numCallLcdNumber.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.hboxlayout.addWidget(self.numCallLcdNumber)
self.numCallLabel = QLabel("<b>Number of calls</b>",
self.globalStatGroupBox)
self.numCallLabel.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Minimum)
self.hboxlayout.addWidget(self.numCallLabel)
self.primCallLcdNumber = QLCDNumber(self.globalStatGroupBox)
self.primCallLcdNumber.setSegmentStyle(QLCDNumber.Filled)
self.primCallLcdNumber.setFrameShape(QFrame.StyledPanel)
self.primCallLcdNumber.setNumDigits(7)
self.primCallLcdNumber.display(1000000)
self.primCallLcdNumber.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.hboxlayout.addWidget(self.primCallLcdNumber)
self.primCallLabel = QLabel("<b>Primitive calls (%)</b>",
self.globalStatGroupBox)
self.primCallLabel.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Minimum)
self.hboxlayout.addWidget(self.primCallLabel)
self.vlayout.addWidget(self.globalStatGroupBox)
try:
from PyKDE4.kdeui import KRatingWidget
self.rating = KRatingWidget(self.globalStatGroupBox)
self.rating.setToolTip('Profiling Performance Rating')
except ImportError:
pass
self.tabWidget.addTab(self.result, " Get Results ! ")
self.resgraph = QWidget()
self.vlayout2 = QVBoxLayout(self.result)
self.graphz = QGroupBox(self.resgraph)
self.hboxlayout2 = QHBoxLayout(self.graphz)
try:
from PyKDE4.kdeui import KLed
KLed(self.graphz)
except ImportError:
pass
self.hboxlayout2.addWidget(
QLabel('''
Work in Progress :) Not Ready Yet'''))
self.vlayout2.addWidget(self.graphz)
self.tabWidget.addTab(self.resgraph, " Graphs and Charts ")
self.pathz = QWidget()
self.vlayout3 = QVBoxLayout(self.pathz)
self.patz = QGroupBox(self.pathz)
self.hboxlayout3 = QVBoxLayout(self.patz)
self.profilepath = QLineEdit(profilerPath)
self.getprofile = QPushButton(QIcon.fromTheme("document-open"), 'Open')
self.getprofile.setToolTip(
'Dont touch if you dont know what are doing')
self.getprofile.clicked.connect(lambda: self.profilepath.setText(
str(
QFileDialog.getOpenFileName(
self.patz, ' Open the profile.py file ',
path.expanduser("~"), ';;(profile.py)'))))
self.hboxlayout3.addWidget(
QLabel(
'<center><b>Profile.py Python Library Full Path:</b></center>')
)
self.hboxlayout3.addWidget(self.profilepath)
self.hboxlayout3.addWidget(self.getprofile)
self.argGroupBox = QGroupBox(self.pathz)
self.hbxlayout = QHBoxLayout(self.argGroupBox)
self.argLineEdit = QLineEdit(self.argGroupBox)
self.argLineEdit.setToolTip(
'Not touch if you dont know what are doing')
self.argLineEdit.setPlaceholderText(
'Dont touch if you dont know what are doing')
self.hbxlayout.addWidget(
QLabel('<b>Additional Profile Arguments:</b>'))
self.hbxlayout.addWidget(self.argLineEdit)
self.hboxlayout3.addWidget(self.argGroupBox)
self.vlayout3.addWidget(self.patz)
self.tabWidget.addTab(self.pathz, " Paths and Configs ")
self.outp = QWidget()
self.vlayout4 = QVBoxLayout(self.outp)
self.outgro = QGroupBox(self.outp)
self.outgro.setTitle(" MultiProcessing Output Logs ")
self.hboxlayout4 = QVBoxLayout(self.outgro)
self.outputlog = QTextEdit()
self.outputlog.setText('''
I do not fear computers, I fear the lack of them. -Isaac Asimov ''')
self.hboxlayout4.addWidget(self.outputlog)
self.vlayout4.addWidget(self.outgro)
self.tabWidget.addTab(self.outp, " Logs ")
self.actionNew_profiling = QAction(QIcon.fromTheme("document-new"),
'New Profiling', self)
self.actionLoad_profile = QAction(QIcon.fromTheme("document-open"),
'Open Profiling', self)
self.actionClean = QAction(QIcon.fromTheme("edit-clear"), 'Clean',
self)
self.actionClean.triggered.connect(lambda: self.clearContent)
self.actionAbout = QAction(QIcon.fromTheme("help-about"), 'About',
self)
self.actionAbout.triggered.connect(lambda: QMessageBox.about(
self.dock, __doc__, ', '.join(
(__doc__, __license__, __author__, __email__))))
self.actionSave_profile = QAction(QIcon.fromTheme("document-save"),
'Save Profiling', self)
self.actionManual = QAction(QIcon.fromTheme("help-contents"), 'Help',
self)
self.actionManual.triggered.connect(lambda: open_new_tab(
'http://docs.python.org/library/profile.html'))
self.tabWidget.setCurrentIndex(2)
self.globalStatGroupBox.setTitle("Global Statistics")
item = self.tableWidget.horizontalHeaderItem(0)
item.setText("Number of Calls")
item = self.tableWidget.horizontalHeaderItem(1)
item.setText("Total Time")
item = self.tableWidget.horizontalHeaderItem(2)
item.setText("Per Call")
item = self.tableWidget.horizontalHeaderItem(3)
item.setText("Cumulative Time")
item = self.tableWidget.horizontalHeaderItem(4)
item.setText("Per Call")
item = self.tableWidget.horizontalHeaderItem(5)
item.setText("Filename")
item = self.tableWidget.horizontalHeaderItem(6)
item.setText("Line")
item = self.tableWidget.horizontalHeaderItem(7)
item.setText("Function")
self.tabWidget.setTabText(self.tabWidget.indexOf(self.stat),
"Statistics per Function")
self.sourceTreeWidget.headerItem().setText(0, "Source files")
self.tabWidget.setTabText(self.tabWidget.indexOf(self.source),
"Sources Navigator")
#######################################################################
self.scrollable, self.dock = QScrollArea(), QDockWidget()
self.scrollable.setWidgetResizable(True)
self.scrollable.setWidget(self.tabWidget)
self.dock.setWindowTitle(__doc__)
self.dock.setStyleSheet('QDockWidget::title{text-align: center;}')
self.dock.setWidget(self.scrollable)
QToolBar(self.dock).addActions(
(self.actionNew_profiling, self.actionClean,
self.actionSave_profile, self.actionLoad_profile,
self.actionManual, self.actionAbout))
self.actionNew_profiling.triggered.connect(
self.on_actionNew_profiling_triggered)
self.actionLoad_profile.triggered.connect(
self.on_actionLoad_profile_triggered)
self.actionSave_profile.triggered.connect(
self.on_actionSave_profile_triggered)
self.locator.get_service('misc').add_widget(
self.dock, QIcon.fromTheme("document-open-recent"), __doc__)
if QSCI:
# Scintilla source editor management
self.scintillaWarningLabel.setText(' QScintilla is Ready ! ')
layout = self.source.layout()
layout.removeWidget(self.sourceTextEdit)
self.sourceTextEdit = Qsci.QsciScintilla(self.source)
layout.addWidget(self.sourceTextEdit, 0, 1)
doc = self.sourceTextEdit
doc.setLexer(Qsci.QsciLexerPython(self.sourceTextEdit))
doc.setReadOnly(True)
doc.setEdgeMode(Qsci.QsciScintilla.EdgeLine)
doc.setEdgeColumn(80)
doc.setEdgeColor(QColor("#FF0000"))
doc.setFolding(Qsci.QsciScintilla.BoxedTreeFoldStyle)
doc.setBraceMatching(Qsci.QsciScintilla.SloppyBraceMatch)
doc.setCaretLineVisible(True)
doc.setMarginLineNumbers(1, True)
doc.setMarginWidth(1, 25)
doc.setTabWidth(4)
doc.setEolMode(Qsci.QsciScintilla.EolUnix)
self.marker = {}
for color in COLORS:
mnr = doc.markerDefine(Qsci.QsciScintilla.Background)
doc.setMarkerBackgroundColor(color, mnr)
self.marker[color] = mnr
self.currentSourcePath = None
# Connect table and tree filter edit signal to unique slot
self.filterTableLineEdit.textEdited.connect(
self.on_filterLineEdit_textEdited)
# Timer to display filter hint message
self.filterHintTimer = QTimer(self)
self.filterHintTimer.setSingleShot(True)
self.filterHintTimer.timeout.connect(self.on_filterHintTimer_timeout)
# Timer to start search
self.filterSearchTimer = QTimer(self)
self.filterSearchTimer.setSingleShot(True)
self.filterSearchTimer.timeout.connect(
self.on_filterSearchTimer_timeout)
self.tabLoaded = {}
for i in range(10):
self.tabLoaded[i] = False
self.backgroundTreeMatchedItems = {}
self.resizeWidgetToContent(self.tableWidget)
def on_actionNew_profiling_triggered(self):
self.clearContent()
self.scriptPath = str(
QFileDialog.getOpenFileName(self.dock,
"Choose your script to profile",
path.expanduser("~"),
"Python (*.py *.pyw)"))
commandLine = [
self.profilerPath, "-o", self.tempPath, self.scriptPath
] + self.scriptArgs
commandLine = " ".join(commandLine)
##if self.termCheckBox.checkState() == Qt.Checked:
#termList = ["xterm", "aterm"]
#for term in termList:
#termPath = which(term)
#if termPath:
#break
#commandLine = """%s -e "%s ; echo 'Press ENTER Exit' ; read" """ \
#% (termPath, commandLine)
self.process.start(commandLine)
if not self.process.waitForStarted():
print((" ERROR: {} failed!".format(commandLine)))
return
def on_process_finished(self, exitStatus):
' whan the process end '
print((" INFO: OK: QProcess is %s" % self.process.exitCode()))
self.output = self.process.readAll().data()
if not self.output:
self.output = " ERROR: FAIL: No output ! "
self.outputlog.setText(self.output + str(self.process.exitCode()))
if path.exists(self.tempPath):
self.setStat(self.tempPath)
remove(self.tempPath)
else:
self.outputlog.setText(" ERROR: QProcess FAIL: Profiling failed.")
self.tabWidget.setCurrentIndex(2)
def on_process_error(self, error):
' when the process fail, I hope you never see this '
print(" ERROR: QProcess FAIL: Profiler Dead, wheres your God now ? ")
if error == QProcess.FailedToStart:
self.outputlog.setText(" ERROR: FAIL: Profiler execution failed ")
elif error == QProcess.Crashed:
self.outputlog.setText(" ERROR: FAIL: Profiler execution crashed ")
else:
self.outputlog.setText(" ERROR: FAIL: Profiler unknown error ")
def on_actionLoad_profile_triggered(self):
"""Load a previous profile sessions"""
statPath = str(
QFileDialog.getOpenFileName(self.dock, "Open profile dump",
path.expanduser("~"),
"Profile file (*)"))
if statPath:
self.clearContent()
print(' INFO: OK: Loading profiling from ' + statPath)
self.setStat(statPath)
def on_actionSave_profile_triggered(self):
"""Save a profile sessions"""
statPath = str(
QFileDialog.getSaveFileName(self.dock, "Save profile dump",
path.expanduser("~"),
"Profile file (*)"))
if statPath:
#TODO: handle error case and give feelback to user
print(' INFO: OK: Saving profiling to ' + statPath)
self.stat.save(statPath)
#=======================================================================#
# Common parts #
#=======================================================================#
def on_tabWidget_currentChanged(self, index):
"""slot for tab change"""
# Kill search and hint timer if running to avoid cross effect
for timer in (self.filterHintTimer, self.filterSearchTimer):
if timer.isActive():
timer.stop()
if not self.stat:
#No stat loaded, nothing to do
return
self.populateTable()
self.populateSource()
def on_filterLineEdit_textEdited(self, text):
"""slot for filter change (table or tree"""
if self.filterSearchTimer.isActive():
# Already runnning, stop it
self.filterSearchTimer.stop()
# Start timer
self.filterSearchTimer.start(300)
def on_filterHintTimer_timeout(self):
"""Timeout to warn user about text length"""
print("timeout")
tab = self.tabWidget.currentIndex()
if tab == TAB_FUNCTIONSTAT:
label = self.filterHintTableLabel
label.setText("Type > 2 characters to search")
def on_filterSearchTimer_timeout(self):
"""timeout to start search"""
tab = self.tabWidget.currentIndex()
if tab == TAB_FUNCTIONSTAT:
text = self.filterTableLineEdit.text()
label = self.filterHintTableLabel
edit = self.filterTableLineEdit
widget = self.tableWidget
else:
print("Unknow tab for filterSearch timeout !")
print(("do search for %s" % text))
if not len(text):
# Empty keyword, just clean all
if self.filterHintTimer.isActive():
self.filterHintTimer.stop()
label.setText(" ? ")
self.warnUSer(True, edit)
self.clearSearch()
return
if len(text) < 2:
# Don't filter if text is too short and tell it to user
self.filterHintTimer.start(600)
return
else:
if self.filterHintTimer.isActive():
self.filterHintTimer.stop()
label.setText(" ? ")
# Search
self.clearSearch()
matchedItems = []
if tab == TAB_FUNCTIONSTAT:
# Find items
matchedItems = widget.findItems(text, Qt.MatchContains)
widget.setSortingEnabled(False)
matchedRows = [item.row() for item in matchedItems]
# Hide matched items
header = widget.verticalHeader()
for row in range(widget.rowCount()):
if row not in matchedRows:
header.hideSection(row)
widget.setSortingEnabled(True)
else:
print(" Unknow tab for filterSearch timeout ! ")
print(("got %s members" % len(matchedItems)))
self.warnUSer(matchedItems, edit)
self.resizeWidgetToContent(widget)
def resizeWidgetToContent(self, widget):
"""Resize all columns according to content"""
for i in range(widget.columnCount()):
widget.resizeColumnToContents(i)
def clearSearch(self):
"""Clean search result
For table, show all items
For tree, remove colored items"""
tab = self.tabWidget.currentIndex()
if tab == TAB_FUNCTIONSTAT:
header = self.tableWidget.verticalHeader()
if header.hiddenSectionCount():
for i in range(header.count()):
if header.isSectionHidden(i):
header.showSection(i)
def clearContent(self):
# Clear tabs
self.tableWidget.clearContents()
self.sourceTreeWidget.clear()
# Reset LCD numbers
for lcdNumber in (self.totalTimeLcdNumber, self.numCallLcdNumber,
self.primCallLcdNumber):
lcdNumber.display(1000000)
# Reset stat
self.pstat = None
# Disable save as menu
self.actionSave_profile.setEnabled(False)
# Mark all tabs as unloaded
for i in range(10):
self.tabLoaded[i] = False
def warnUSer(self, result, inputWidget):
palette = inputWidget.palette()
if result:
palette.setColor(QPalette.Normal, QPalette.Base,
QColor(255, 255, 255))
else:
palette.setColor(QPalette.Normal, QPalette.Base,
QColor(255, 136, 138))
inputWidget.setPalette(palette)
inputWidget.update()
def setStat(self, statPath):
self.stat = Stat(path=statPath)
# Global stat update
self.totalTimeLcdNumber.display(self.stat.getTotalTime())
self.numCallLcdNumber.display(self.stat.getCallNumber())
self.primCallLcdNumber.display(self.stat.getPrimitiveCallRatio())
# Refresh current tab
self.on_tabWidget_currentChanged(self.tabWidget.currentIndex())
# Activate save as menu
self.actionSave_profile.setEnabled(True)
try:
self.rating.setMaxRating(10)
self.rating.setRating(
int(self.stat.getPrimitiveCallRatio()) / 10 - 1)
except:
pass
#========================================================================#
# Statistics table #
#=======================================================================#
def populateTable(self):
row = 0
rowCount = self.stat.getStatNumber()
progress = QProgressDialog("Populating statistics table...", "Abort",
0, 2 * rowCount)
self.tableWidget.setSortingEnabled(False)
self.tableWidget.setRowCount(rowCount)
progress.setWindowModality(Qt.WindowModal)
for (key, value) in self.stat.getStatItems():
#ncalls
item = StatTableWidgetItem(str(value[0]))
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_NCALLS, item)
colorTableItem(item, self.stat.getCallNumber(), value[0])
#total time
item = StatTableWidgetItem(str(value[2]))
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_TTIME, item)
colorTableItem(item, self.stat.getTotalTime(), value[2])
#per call (total time)
if value[0] != 0:
tPerCall = str(value[2] / value[0])
cPerCall = str(value[3] / value[0])
else:
tPerCall = ""
cPerCall = ""
item = StatTableWidgetItem(tPerCall)
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_TPERCALL, item)
colorTableItem(
item,
100.0 * self.stat.getTotalTime() / self.stat.getCallNumber(),
tPerCall)
#per call (cumulative time)
item = StatTableWidgetItem(cPerCall)
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_CPERCALL, item)
colorTableItem(
item,
100.0 * self.stat.getTotalTime() / self.stat.getCallNumber(),
cPerCall)
#cumulative time
item = StatTableWidgetItem(str(value[3]))
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_CTIME, item)
colorTableItem(item, self.stat.getTotalTime(), value[3])
#Filename
self.tableWidget.setItem(row, STAT_FILENAME,
StatTableWidgetItem(str(key[0])))
#Line
item = StatTableWidgetItem(str(key[1]))
item.setTextAlignment(Qt.AlignRight)
self.tableWidget.setItem(row, STAT_LINE, item)
#Function name
self.tableWidget.setItem(row, STAT_FUNCTION,
StatTableWidgetItem(str(key[2])))
row += 1
# Store it in stat hash array
self.stat.setStatLink(item, key, TAB_FUNCTIONSTAT)
progress.setValue(row)
if progress.wasCanceled():
return
for i in range(self.tableWidget.rowCount()):
progress.setValue(row + i)
for j in range(self.tableWidget.columnCount()):
item = self.tableWidget.item(i, j)
if item:
item.setFlags(Qt.ItemIsEnabled)
self.tableWidget.setSortingEnabled(True)
self.resizeWidgetToContent(self.tableWidget)
progress.setValue(2 * rowCount)
def on_tableWidget_itemDoubleClicked(self, item):
matchedItems = []
filename = str(self.tableWidget.item(item.row(), STAT_FILENAME).text())
if not filename or filename.startswith("<"):
# No source code associated, return immediatly
return
function = self.tableWidget.item(item.row(), STAT_FUNCTION).text()
line = self.tableWidget.item(item.row(), STAT_LINE).text()
self.on_tabWidget_currentChanged(TAB_SOURCE) # load source tab
function = "%s (%s)" % (function, line)
fathers = self.sourceTreeWidget.findItems(filename, Qt.MatchContains,
SOURCE_FILENAME)
print(("find %s father" % len(fathers)))
for father in fathers:
findItems(father, function, SOURCE_FILENAME, matchedItems)
print(("find %s items" % len(matchedItems)))
if matchedItems:
self.tabWidget.setCurrentIndex(TAB_SOURCE)
self.sourceTreeWidget.scrollToItem(matchedItems[0])
self.on_sourceTreeWidget_itemClicked(matchedItems[0],
SOURCE_FILENAME)
matchedItems[0].setSelected(True)
else:
print("oups, item found but cannot scroll to it !")
#=======================================================================#
# Source explorer #
#=====================================================================#
def populateSource(self):
items = {}
for stat in self.stat.getStatKeys():
source = stat[0]
function = "%s (%s)" % (stat[2], stat[1])
if source in ("", "profile") or source.startswith("<"):
continue
# Create the function child
child = QTreeWidgetItem([function])
# Store it in stat hash array
self.stat.setStatLink(child, stat, TAB_SOURCE)
if source in items:
father = items[source]
else:
# Create the father
father = QTreeWidgetItem([source])
items[source] = father
father.addChild(child)
self.sourceTreeWidget.setSortingEnabled(False)
for value in list(items.values()):
self.sourceTreeWidget.addTopLevelItem(value)
self.sourceTreeWidget.setSortingEnabled(True)
def on_sourceTreeWidget_itemActivated(self, item, column):
self.on_sourceTreeWidget_itemClicked(item, column)
def on_sourceTreeWidget_itemClicked(self, item, column):
line = 0
parent = item.parent()
if QSCI:
doc = self.sourceTextEdit
if parent:
pathz = parent.text(column)
result = match("(.*) \(([0-9]+)\)", item.text(column))
if result:
try:
function = str(result.group(1))
line = int(result.group(2))
except ValueError:
# We got garbage... falling back to line 0
pass
else:
pathz = item.text(column)
pathz = path.abspath(str(pathz))
if self.currentSourcePath != pathz:
# Need to load source
self.currentSourcePath == pathz
try:
if QSCI:
doc.clear()
doc.insert(file(pathz).read())
else:
self.sourceTextEdit.setPlainText(file(pathz).read())
except IOError:
QMessageBox.warning(self, "Error",
"Source file could not be found",
QMessageBox.Ok)
return
if QSCI:
for function, line in [(i[2], i[1])
for i in self.stat.getStatKeys()
if i[0] == pathz]:
# expr, regexp, case sensitive, whole word, wrap, forward
doc.findFirst("def", False, True, True, False, True, line,
0, True)
end, foo = doc.getCursorPosition()
time = self.stat.getStatTotalTime((pathz, line, function))
colorSource(doc, self.stat.getTotalTime(), time, line, end,
self.marker)
if QSCI:
doc.ensureLineVisible(line)
class explorador(QDialog):
def __init__(self):
self.a = 0
super(explorador, self).__init__(None)
self.setWindowTitle("Explorador de archivos y carpetas")
self.resize(610, 450)
self.back_history = []
self.forward_history = []
self.back = QPushButton('<-', self)
self.back.clicked.connect(self.back_click)
self.back.setGeometry(10, 10, 30, 20)
self.back.setEnabled(False)
self.forward = QPushButton('->', self)
self.forward.clicked.connect(self.forward_click)
self.forward.setGeometry(50, 10, 30, 20)
self.forward.setEnabled(False)
self.up = QPushButton('^', self)
self.up.clicked.connect(self.up_button_click)
self.up.setGeometry(90, 10, 30, 20)
self.address = QLineEdit(self)
self.address.setGeometry(130, 10, 420, 20)
self.refresh = QPushButton('@', self)
self.refresh.clicked.connect(self.refresh_click)
self.refresh.setGeometry(560, 10, 30, 20)
self.items = QTreeWidget(self)
self.items.setRootIsDecorated(False)
self.items.setHeaderLabels(
("Nombre", u"Fecha de modificación", u"Tamaño"))
self.items.itemDoubleClicked.connect(self.item_double_clicked)
self.items.setGeometry(5, 40, 600, 400)
# Iniciar en el directorio actual.
self.load_path(getcwd())
def back_click(self, checked):
if self.back_history and len(self.back_history) > 1:
# Obtener el último elemento.
path = self.back_history[-2]
self.forward_history.append(self.back_history[-1])
# Remover el directorio actual.
del self.back_history[-1]
self.load_path(path, False)
def forward_click(self, checked):
if self.forward_history:
path = self.forward_history[-1]
self.back_history.append(path)
del self.forward_history[-1]
self.load_path(path, False)
def item_double_clicked(self, item, column):
filepath = join(self.current_path, unicode(item.text(0)))
if isdir(filepath):
self.load_path(filepath)
else:
# Iniciar archivo con el programa predeterminado.
#startfile(filepath)
a = filepath
#print a
e = entrar()
e.ponfoto(a)
#parcial.ponfoto(a)
#print self.a
def up_button_click(self, checked):
parent = dirname(self.current_path)
if parent != self.current_path:
self.load_path(parent)
def load_path(self, path, use_history=True):
# Obtener archivos y carpetas.
items = listdir(unicode(path))
# Eliminar el contenido anterior.
self.items.clear()
for i in items:
# Omitir archivos ocultos.
if i.startswith("."):
continue
filepath = join(path, i)
# Obtener informacion del archivo.
stats = stat(filepath)
# Crear el control ítem.
item_widget = QTreeWidgetItem(
(i, strftime("%c", localtime(stats.st_mtime)).decode("utf-8"),
size(stats.st_size) if isfile(filepath) else ""))
# Establecer el ícono correspondiente.
item_widget.setIcon(
0,
QIcon("images/%s.png" %
("file" if isfile(filepath) else "folder")))
# Añadir elemento.
self.items.addTopLevelItem(item_widget)
# Ajustar el tamaño de las columnas.
for i in range(3):
self.items.resizeColumnToContents(i)
self.current_path = path
self.address.setText(self.current_path)
# Añadir al historial.
if use_history:
self.back_history.append(self.current_path)
# Habilitar / dehabilitar botones del historial.
if self.back_history and len(self.back_history) > 1:
if not self.back.isEnabled():
self.back.setEnabled(True)
else:
if self.back.isEnabled():
self.forward_history = []
self.back.setEnabled(False)
if self.forward_history:
if not self.forward.isEnabled():
self.forward.setEnabled(True)
else:
if self.forward.isEnabled():
self.forward.setEnabled(False)
def refresh_click(self, checked):
self.load_path(self.current_path)
class OWItemsets(widget.OWWidget):
name = 'Frequent Itemsets'
description = 'Explore sets of items that frequently appear together.'
icon = 'icons/FrequentItemsets.svg'
priority = 10
inputs = [("Data", Table, 'set_data')]
outputs = [(Output.DATA, Table)]
minSupport = settings.Setting(30)
maxItemsets = settings.Setting(10000)
filterSearch = settings.Setting(True)
autoFind = settings.Setting(False)
autoSend = settings.Setting(True)
filterKeywords = settings.Setting('')
filterMinItems = settings.Setting(1)
filterMaxItems = settings.Setting(10000)
UserAdviceMessages = [
widget.Message(
'Itemset are listed in item-sorted order, i.e. '
'an itemset containing A and B is only listed once, as '
'A > B (and not also B > A).', 'itemsets-order',
widget.Message.Warning),
widget.Message(
'To select all the itemsets that are descendants of '
'(include) some item X (i.e. the whole subtree), you '
'can fold the subtree at that item and then select it.',
'itemsets-order', widget.Message.Information)
]
def __init__(self):
self._is_running = False
self.isRegexMatch = lambda x: True
self.tree = QTreeWidget(self.mainArea,
columnCount=2,
allColumnsShowFocus=True,
alternatingRowColors=True,
selectionMode=QTreeWidget.ExtendedSelection,
uniformRowHeights=True)
self.tree.setHeaderLabels(["Itemsets", "Support", "%"])
self.tree.header().setStretchLastSection(True)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.mainArea.layout().addWidget(self.tree)
box = gui.widgetBox(self.controlArea, "Info")
self.nItemsets = self.nSelectedExamples = self.nSelectedItemsets = ''
gui.label(box, self, "Number of itemsets: %(nItemsets)s")
gui.label(box, self, "Selected itemsets: %(nSelectedItemsets)s")
gui.label(box, self, "Selected examples: %(nSelectedExamples)s")
hbox = gui.widgetBox(box, orientation='horizontal')
gui.button(hbox, self, "Expand all", callback=self.tree.expandAll)
gui.button(hbox, self, "Collapse all", callback=self.tree.collapseAll)
box = gui.widgetBox(self.controlArea, 'Find itemsets')
gui.valueSlider(box,
self,
'minSupport',
values=[.0001, .0005, .001, .005, .01, .05, .1, .5] +
list(range(1, 101)),
label='Minimal support:',
labelFormat="%g%%",
callback=lambda: self.find_itemsets())
gui.hSlider(box,
self,
'maxItemsets',
minValue=10000,
maxValue=100000,
step=10000,
label='Max. number of itemsets:',
labelFormat="%d",
callback=lambda: self.find_itemsets())
self.button = gui.auto_commit(box,
self,
'autoFind',
'Find itemsets',
commit=self.find_itemsets)
box = gui.widgetBox(self.controlArea, 'Filter itemsets')
gui.lineEdit(box,
self,
'filterKeywords',
'Contains:',
callback=self.filter_change,
orientation='horizontal',
tooltip='A comma or space-separated list of regular '
'expressions.')
hbox = gui.widgetBox(box, orientation='horizontal')
gui.spin(hbox,
self,
'filterMinItems',
1,
998,
label='Min. items:',
callback=self.filter_change)
gui.spin(hbox,
self,
'filterMaxItems',
2,
999,
label='Max. items:',
callback=self.filter_change)
gui.checkBox(box,
self,
'filterSearch',
label='Apply these filters in search',
tooltip='If checked, the itemsets are filtered according '
'to these filter conditions already in the search '
'phase. \nIf unchecked, the only filters applied '
'during search are the ones above, '
'and the itemsets are \nfiltered afterwards only for '
'display, i.e. only the matching itemsets are shown.')
gui.rubber(hbox)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, 'autoSend', 'Send selection')
self.filter_change()
ITEM_DATA_ROLE = Qt.UserRole + 1
def selectionChanged(self):
X = self.X
mapping = self.onehot_mapping
instances = set()
where = np.where
def whole_subtree(node):
yield node
for i in range(node.childCount()):
yield from whole_subtree(node.child(i))
def itemset(node):
while node:
yield node.data(0, self.ITEM_DATA_ROLE)
node = node.parent()
def selection_ranges(node):
n_children = node.childCount()
if n_children:
yield (self.tree.indexFromItem(node.child(0)),
self.tree.indexFromItem(node.child(n_children - 1)))
for i in range(n_children):
yield from selection_ranges(node.child(i))
nSelectedItemsets = 0
item_selection = QItemSelection()
for node in self.tree.selectedItems():
nodes = (node, ) if node.isExpanded() else whole_subtree(node)
if not node.isExpanded():
for srange in selection_ranges(node):
item_selection.select(*srange)
for node in nodes:
nSelectedItemsets += 1
cols, vals = zip(*(mapping[i] for i in itemset(node)))
if issparse(X):
rows = (len(cols) == np.bincount(
(X[:, cols] != 0).indices,
minlength=X.shape[0])).nonzero()[0]
else:
rows = where((X[:, cols] == vals).all(axis=1))[0]
instances.update(rows)
self.tree.itemSelectionChanged.disconnect(self.selectionChanged)
self.tree.selectionModel().select(
item_selection,
QItemSelectionModel.Select | QItemSelectionModel.Rows)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.nSelectedExamples = len(instances)
self.nSelectedItemsets = nSelectedItemsets
self.output = self.data[sorted(instances)] or None
self.commit()
def commit(self):
self.send(Output.DATA, self.output)
def filter_change(self):
self.warning(9)
try:
isRegexMatch = self.isRegexMatch = re.compile(
'|'.join(
i.strip()
for i in re.split('(,|\s)+', self.filterKeywords.strip())
if i.strip()), re.IGNORECASE).search
except Exception as e:
self.warning(9,
'Error in regular expression: {}'.format(e.args[0]))
isRegexMatch = self.isRegexMatch = lambda x: True
def hide(node, depth, has_kw):
if not has_kw:
has_kw = isRegexMatch(node.text(0))
hidden = (
sum(
hide(node.child(i), depth + 1, has_kw)
for i in range(node.childCount())) == node.childCount()
if node.childCount() else
(not has_kw
or not self.filterMinItems <= depth <= self.filterMaxItems))
node.setHidden(hidden)
return hidden
hide(self.tree.invisibleRootItem(), 0, False)
class TreeWidgetItem(QTreeWidgetItem):
def data(self, column, role):
"""Construct lazy tooltips"""
if role != Qt.ToolTipRole:
return super().data(column, role)
tooltip = []
while self:
tooltip.append(self.text(0))
self = self.parent()
return ' '.join(reversed(tooltip))
def find_itemsets(self):
if self.data is None:
return
if self._is_running:
return
self._is_running = True
data = self.data
self.tree.clear()
self.tree.setUpdatesEnabled(False)
self.tree.blockSignals(True)
class ItemDict(dict):
def __init__(self, item):
self.item = item
top = ItemDict(self.tree.invisibleRootItem())
X, mapping = OneHot.encode(data)
self.onehot_mapping = mapping
ITEM_FMT = '{}' if issparse(data.X) else '{}={}'
names = {
item: ITEM_FMT.format(var.name, val)
for item, var, val in OneHot.decode(mapping.keys(), data, mapping)
}
nItemsets = 0
filterSearch = self.filterSearch
filterMinItems, filterMaxItems = self.filterMinItems, self.filterMaxItems
isRegexMatch = self.isRegexMatch
# Find itemsets and populate the TreeView
with self.progressBar(self.maxItemsets + 1) as progress:
for itemset, support in frequent_itemsets(X,
self.minSupport / 100):
if filterSearch and not filterMinItems <= len(
itemset) <= filterMaxItems:
continue
parent = top
first_new_item = None
itemset_matches_filter = False
for item in sorted(itemset):
name = names[item]
if filterSearch and not itemset_matches_filter:
itemset_matches_filter = isRegexMatch(name)
child = parent.get(name)
if child is None:
try:
wi = self.TreeWidgetItem(parent.item, [
name,
str(support), '{:.4g}'.format(
100 * support / len(data))
])
except RuntimeError:
# FIXME: When autoFind was in effect and the support
# slider was moved, this line excepted with:
# RuntimeError: wrapped C/C++ object of type
# TreeWidgetItem has been deleted
return
wi.setData(0, self.ITEM_DATA_ROLE, item)
child = parent[name] = ItemDict(wi)
if first_new_item is None:
first_new_item = (parent, name)
parent = child
if filterSearch and not itemset_matches_filter:
parent, name = first_new_item
parent.item.removeChild(parent[name].item)
del parent[name].item
del parent[name]
else:
nItemsets += 1
progress.advance()
if nItemsets >= self.maxItemsets:
break
if not filterSearch:
self.filter_change()
self.nItemsets = nItemsets
self.nSelectedItemsets = 0
self.nSelectedExamples = 0
self.tree.expandAll()
for i in range(self.tree.columnCount()):
self.tree.resizeColumnToContents(i)
self.tree.setUpdatesEnabled(True)
self.tree.blockSignals(False)
self._is_running = False
def set_data(self, data):
self.data = data
is_error = False
if data is not None:
self.warning(0)
self.error(1)
self.button.setDisabled(False)
self.X = data.X
if issparse(data.X):
self.X = data.X.tocsc()
else:
if not data.domain.has_discrete_attributes():
self.error(
1, 'Discrete features required but data has none.')
is_error = True
self.button.setDisabled(True)
elif data.domain.has_continuous_attributes():
self.warning(
0,
'Data has continuous attributes which will be skipped.'
)
else:
self.output = None
self.commit()
if self.autoFind and not is_error:
self.find_itemsets()
class Info(QDockWidget):
def __init__(self, mainWindow):
super(Info, self).__init__()
self.__mainWindow = mainWindow
self.loader = loader.loader()
self.env = env.env()
self.tm = TaskManager()
self.addAction()
self.configure()
self.g_display()
self.initCallback()
self.Load()
def configure(self):
self.setAllowedAreas(Qt.AllDockWidgetAreas)
self.setObjectName("dockWidgetBrowser")
self.setWindowTitle(
QApplication.translate("Info", "Info", None,
QApplication.UnicodeUTF8))
def addAction(self):
self.__action = QAction(self)
self.__action.setCheckable(True)
self.__action.setChecked(True)
self.__action.setObjectName("actionCoreInformations")
self.__action.setText(
QApplication.translate("MainWindow", "Info", None,
QApplication.UnicodeUTF8))
self.__mainWindow.menuWindow.addAction(self.__action)
self.connect(self.__action, SIGNAL("triggered()"),
self.changeVisibleInformations)
def changeVisibleInformations(self):
if not self.isVisible():
self.setVisible(True)
self.__action.setChecked(True)
else:
self.setVisible(False)
self.__action.setChecked(False)
def g_display(self):
self.Info = QWidget(self)
self.layout = QHBoxLayout(self.Info)
self.Info.setLayout(self.layout)
self.tabWidget = QTabWidget(self)
self.tabWidget.setElideMode(Qt.ElideRight)
self.initTreeProcess()
self.initTreeModule()
self.initTreeEnv()
self.layout.addWidget(self.tabWidget)
self.setWidget(self.Info)
def initCallback(self):
self.connect(self, SIGNAL("visibilityChanged(bool)"),
self.visibilityChanged)
self.timer = QTimer(self)
self.connect(self.timer, SIGNAL("timeout()"), self.refresh)
self.timer.start(2000)
def visibilityChanged(self, bool):
if not self.isVisible():
self.__action.setChecked(False)
else:
self.__action.setChecked(True)
def Load(self):
self.LoadInfoProcess()
self.LoadInfoModules()
self.LoadInfoEnv()
pass
def refresh(self):
self.LoadInfoProcess()
self.LoadInfoModules()
self.LoadInfoEnv()
pass
def deleteInfos(self):
self.deleteInfoProcess()
self.deleteInfoModule()
self.deleteInfoEnv()
#MODULES
def initTreeModule(self):
self.treeModule = QTreeWidget(self)
self.treeModule.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "Name", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Key", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Value", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Info", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Type", None,
QApplication.UnicodeUTF8)
]
self.treeModule.setHeaderLabels(headerLabel)
self.treeModule.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeModule, "Modules")
self.itemModuleDic = dict()
self.itemListArgDic = dict()
self.itemArgDic = dict()
self.itemListResDic = dict()
self.itemResDic = dict()
def LoadInfoModules(self):
modules = self.loader.modules
for mod in modules:
try:
itemModule = self.itemModuleDic[mod]
except KeyError:
itemModule = QTreeWidgetItem(self.treeModule)
self.itemModuleDic[mod] = itemModule
itemModule.setText(0, str(mod))
itemConfig = QTreeWidgetItem(itemModule)
itemConfig.setText(0, "Config")
cdesc = modules[mod].conf.descr_l
for key in cdesc:
itemConfKey = QTreeWidgetItem(itemConfig)
itemConfKey.setText(0, "var")
itemConfKey.setText(1, key.name)
itemConfKey.setText(4, key.type)
if len(key.description):
itemConfKey.setText(3, key.description)
for type, name, val, _from in self.env.get_val_list(
modules[mod].conf.val_l):
itemConfKey = QTreeWidgetItem(itemConfig)
itemConfKey.setText(0, "const")
itemConfKey.setText(1, name)
itemConfKey.setText(2, val)
itemConfKey.setText(4, type)
for proc in self.tm.lprocessus:
if proc.mod.name == mod:
try:
itemListArg = self.itemListArgDic[mod]
except KeyError:
itemListArg = QTreeWidgetItem(itemModule)
self.itemListArgDic[mod] = itemListArg
itemListArg.setText(0, "Arg")
for type, name, val in self.env.get_val_map(
proc.args.val_m):
try:
itemArgKey = self.itemArgDic[(type, name, val)]
except KeyError:
itemArgKey = QTreeWidgetItem(itemListArg)
self.itemArgDic[(type, name, val)] = itemArgKey
itemArgKey.setText(1, name)
itemArgKey.setText(2, val)
itemArgKey.setText(4, type)
try:
itemListRes = self.itemListResDic[mod]
except KeyError:
itemListRes = QTreeWidgetItem(itemModule)
self.itemListResDic[mod] = itemListRes
itemListRes.setText(0, "Results")
if proc.res:
for type, name, val in self.env.get_val_map(
proc.res.val_m):
try:
itemResKey = self.itemResDic[(type, name, val)]
except KeyError:
itemResKey = QTreeWidgetItem(itemListRes)
self.itemResDic[(type, name, val)] = itemResKey
itemResKey.setText(1, name)
itemResKey.setText(2, val)
itemResKey.setText(4, type)
def deleteInfoModule(self):
self.treeModule.clear()
#ENV
def initTreeEnv(self):
self.treeEnv = QTreeWidget(self)
self.treeEnv.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "Key", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Type", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Value", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "From", None,
QApplication.UnicodeUTF8)
]
self.treeEnv.setHeaderLabels(headerLabel)
self.treeEnv.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeEnv, "Environment")
self.envItemDic = dict()
self.envConfKeyDic = dict()
self.envValKeyDic = dict()
def LoadInfoEnv(self):
db = self.env.vars_db
for key in db:
try:
(itemEnv, itemVar, itemValues) = self.envItemDic[key]
except KeyError:
itemEnv = QTreeWidgetItem(self.treeEnv)
itemEnv.setText(0, key)
itemVar = QTreeWidgetItem(itemEnv)
itemVar.setText(0, "var")
itemValues = QTreeWidgetItem(itemEnv)
self.envItemDic[key] = (itemEnv, itemVar, itemValues)
cdesc = db[key].descr_l
for vk in cdesc:
try:
itemConfKey = self.envConfKeyDic[(vk.type, vk._from)]
except KeyError:
itemConfKey = QTreeWidgetItem(itemVar)
self.envConfKeyDic[(vk.type, vk._from)] = itemConfKey
itemConfKey.setText(1, vk.type)
itemConfKey.setText(3, vk._from)
itemValues.setText(0, "values")
for type, name, val, _from in self.env.get_val_list(db[key].val_l):
try:
itemValKey = self.envValKeyDic[(type, _from, val)]
except:
itemValKey = QTreeWidgetItem(itemValues)
self.envValKeyDic[(type, _from, val)] = itemValKey
itemValKey.setText(1, type)
itemValKey.setText(2, val)
itemValKey.setText(3, _from)
def deleteInfoEnv(self):
self.treeEnv.clear()
#PROCESSUS
def initTreeProcess(self):
self.treeProcess = QTreeWidget(self)
self.treeProcess.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "PID", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Name", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "State", None,
QApplication.UnicodeUTF8),
QApplication.translate("Info", "Info", None,
QApplication.UnicodeUTF8)
]
self.treeProcess.setHeaderLabels(headerLabel)
self.treeProcess.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeProcess, "Task Manager")
self.connect(self.treeProcess,
SIGNAL("itemDoubleClicked(QTreeWidgetItem*,int)"),
self.procClicked)
self.procItemDic = dict()
self.procChildItemDic = dict()
def procClicked(self, item, column):
dial = procMB(self, item.text(0))
dial.exec_()
def LoadInfoProcess(self):
lproc = self.tm.lprocessus
for proc in lproc:
try:
item = self.procItemDic[proc]
except KeyError:
item = QTreeWidgetItem(self.treeProcess)
self.procItemDic[proc] = item
item.setText(0, str(proc.pid))
item.setText(1, str(proc.name))
if item.text(2) != str(proc.state):
item.setText(2, str(proc.state))
if item.text(3) != str(proc.stateinfo):
item.setText(3, str(proc.stateinfo))
def deleteInfoProcess(self):
self.treeProcess.clear()
class IgnoredExceptionsViewer(QWidget):
" Implements the client exceptions viewer for a debugger "
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.__createPopupMenu()
self.__createLayout()
self.__ignored = []
self.__currentItem = None
GlobalData().project.projectChanged.connect(self.__onProjectChanged)
if Settings().showIgnoredExcViewer == False:
self.__onShowHide(True)
return
def __createPopupMenu(self):
" Creates the popup menu "
self.__excptMenu = QMenu()
self.__removeMenuItem = self.__excptMenu.addAction(
PixmapCache().getIcon('ignexcptdel.png'),
"Remove from ignore list", self.__onRemoveFromIgnore)
return
def __createLayout(self):
" Creates the widget layout "
verticalLayout = QVBoxLayout(self)
verticalLayout.setContentsMargins(0, 0, 0, 0)
verticalLayout.setSpacing(0)
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle(QFrame.StyledPanel)
self.headerFrame.setAutoFillBackground(True)
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color(QPalette.Background)
headerBackground.setRgb(min(headerBackground.red() + 30, 255),
min(headerBackground.green() + 30, 255),
min(headerBackground.blue() + 30, 255))
headerPalette.setColor(QPalette.Background, headerBackground)
self.headerFrame.setPalette(headerPalette)
self.headerFrame.setFixedHeight(24)
self.__excptLabel = QLabel("Ignored exception types")
expandingSpacer = QSpacerItem(10, 10, QSizePolicy.Expanding)
fixedSpacer = QSpacerItem(3, 3)
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise(True)
self.__showHideButton.setIcon(PixmapCache().getIcon('less.png'))
self.__showHideButton.setFixedSize(20, 20)
self.__showHideButton.setToolTip("Hide ignored exceptions list")
self.__showHideButton.setFocusPolicy(Qt.NoFocus)
self.__showHideButton.clicked.connect(self.__onShowHide)
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins(1, 1, 1, 1)
headerLayout.addSpacerItem(fixedSpacer)
headerLayout.addWidget(self.__excptLabel)
headerLayout.addSpacerItem(expandingSpacer)
headerLayout.addWidget(self.__showHideButton)
self.headerFrame.setLayout(headerLayout)
self.exceptionsList = QTreeWidget(self)
self.exceptionsList.setSortingEnabled(False)
self.exceptionsList.setAlternatingRowColors(True)
self.exceptionsList.setRootIsDecorated(False)
self.exceptionsList.setItemsExpandable(True)
self.exceptionsList.setUniformRowHeights(True)
self.exceptionsList.setSelectionMode(QAbstractItemView.SingleSelection)
self.exceptionsList.setSelectionBehavior(QAbstractItemView.SelectRows)
self.exceptionsList.setItemDelegate(NoOutlineHeightDelegate(4))
self.exceptionsList.setContextMenuPolicy(Qt.CustomContextMenu)
self.exceptionsList.customContextMenuRequested.connect(
self.__showContextMenu)
self.exceptionsList.itemSelectionChanged.connect(
self.__onSelectionChanged)
self.exceptionsList.setHeaderLabels(["Exception type"])
self.__excTypeEdit = QLineEdit()
self.__excTypeEdit.setFixedHeight(26)
self.__excTypeEdit.textChanged.connect(self.__onNewFilterChanged)
self.__excTypeEdit.returnPressed.connect(self.__onAddExceptionFilter)
self.__addButton = QPushButton("Add")
# self.__addButton.setFocusPolicy( Qt.NoFocus )
self.__addButton.setEnabled(False)
self.__addButton.clicked.connect(self.__onAddExceptionFilter)
expandingSpacer2 = QWidget()
expandingSpacer2.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.__removeButton = QAction(PixmapCache().getIcon('delitem.png'),
"Remove selected exception type", self)
self.__removeButton.triggered.connect(self.__onRemoveFromIgnore)
self.__removeButton.setEnabled(False)
fixedSpacer1 = QWidget()
fixedSpacer1.setFixedWidth(5)
self.__removeAllButton = QAction(
PixmapCache().getIcon('ignexcptdelall.png'),
"Remove all the exception types", self)
self.__removeAllButton.triggered.connect(self.__onRemoveAllFromIgnore)
self.__removeAllButton.setEnabled(False)
self.toolbar = QToolBar()
self.toolbar.setOrientation(Qt.Horizontal)
self.toolbar.setMovable(False)
self.toolbar.setAllowedAreas(Qt.TopToolBarArea)
self.toolbar.setIconSize(QSize(16, 16))
self.toolbar.setFixedHeight(28)
self.toolbar.setContentsMargins(0, 0, 0, 0)
self.toolbar.addWidget(expandingSpacer2)
self.toolbar.addAction(self.__removeButton)
self.toolbar.addWidget(fixedSpacer1)
self.toolbar.addAction(self.__removeAllButton)
addLayout = QHBoxLayout()
addLayout.setContentsMargins(1, 1, 1, 1)
addLayout.setSpacing(1)
addLayout.addWidget(self.__excTypeEdit)
addLayout.addWidget(self.__addButton)
verticalLayout.addWidget(self.headerFrame)
verticalLayout.addWidget(self.toolbar)
verticalLayout.addWidget(self.exceptionsList)
verticalLayout.addLayout(addLayout)
return
def clear(self):
" Clears the content "
self.exceptionsList.clear()
self.__excTypeEdit.clear()
self.__addButton.setEnabled(False)
self.__ignored = []
self.__currentItem = None
self.__updateTitle()
return
def __onShowHide(self, startup=False):
" Triggered when show/hide button is clicked "
if startup or self.exceptionsList.isVisible():
self.exceptionsList.setVisible(False)
self.__excTypeEdit.setVisible(False)
self.__addButton.setVisible(False)
self.__removeButton.setVisible(False)
self.__removeAllButton.setVisible(False)
self.__showHideButton.setIcon(PixmapCache().getIcon('more.png'))
self.__showHideButton.setToolTip("Show ignored exceptions list")
self.__minH = self.minimumHeight()
self.__maxH = self.maximumHeight()
self.setMinimumHeight(self.headerFrame.height())
self.setMaximumHeight(self.headerFrame.height())
Settings().showIgnoredExcViewer = False
else:
self.exceptionsList.setVisible(True)
self.__excTypeEdit.setVisible(True)
self.__addButton.setVisible(True)
self.__removeButton.setVisible(True)
self.__removeAllButton.setVisible(True)
self.__showHideButton.setIcon(PixmapCache().getIcon('less.png'))
self.__showHideButton.setToolTip("Hide ignored exceptions list")
self.setMinimumHeight(self.__minH)
self.setMaximumHeight(self.__maxH)
Settings().showIgnoredExcViewer = True
return
def __onSelectionChanged(self):
" Triggered when the current item is changed "
selected = list(self.exceptionsList.selectedItems())
if selected:
self.__currentItem = selected[0]
self.__removeButton.setEnabled(True)
else:
self.__currentItem = None
self.__removeButton.setEnabled(False)
return
def __showContextMenu(self, coord):
" Shows the frames list context menu "
contextItem = self.exceptionsList.itemAt(coord)
if contextItem is not None:
self.__currentItem = contextItem
self.__excptMenu.popup(QCursor.pos())
return
def __updateTitle(self):
" Updates the section title "
count = self.exceptionsList.topLevelItemCount()
if count == 0:
self.__excptLabel.setText("Ignored exception types")
else:
self.__excptLabel.setText("Ignored exception types (total: " +
str(count) + ")")
self.__removeAllButton.setEnabled(count != 0)
return
def __onProjectChanged(self, what):
" Triggered when a project is changed "
if what != CodimensionProject.CompleteProject:
return
self.clear()
project = GlobalData().project
if project.isLoaded():
self.__ignored = list(project.ignoredExcpt)
else:
self.__ignored = list(Settings().ignoredExceptions)
for exceptionType in self.__ignored:
item = QTreeWidgetItem(self.exceptionsList)
item.setText(0, exceptionType)
self.__updateTitle()
return
def __onNewFilterChanged(self, text):
" Triggered when the text is changed "
text = str(text).strip()
if text == "":
self.__addButton.setEnabled(False)
return
if " " in text:
self.__addButton.setEnabled(False)
return
if text in self.__ignored:
self.__addButton.setEnabled(False)
return
self.__addButton.setEnabled(True)
return
def __onAddExceptionFilter(self):
" Adds an item into the ignored exceptions list "
text = self.__excTypeEdit.text().strip()
self.addExceptionFilter(text)
def addExceptionFilter(self, excType):
" Adds a new item into the ignored exceptions list "
if excType == "":
return
if " " in excType:
return
if excType in self.__ignored:
return
item = QTreeWidgetItem(self.exceptionsList)
item.setText(0, excType)
project = GlobalData().project
if project.isLoaded():
project.addExceptionFilter(excType)
else:
Settings().addExceptionFilter(excType)
self.__ignored.append(excType)
self.__updateTitle()
return
def __onRemoveFromIgnore(self):
" Removes an item from the ignored exception types list "
if self.__currentItem is None:
return
text = self.__currentItem.text(0)
# Find the item index and remove it
index = 0
while True:
if self.exceptionsList.topLevelItem(index).text(0) == text:
self.exceptionsList.takeTopLevelItem(index)
break
index += 1
project = GlobalData().project
if project.isLoaded():
project.deleteExceptionFilter(text)
else:
Settings().deleteExceptionFilter(text)
self.__ignored.remove(text)
self.__updateTitle()
return
def __onRemoveAllFromIgnore(self):
" Triggered when all the ignored exceptions should be deleted "
self.clear()
project = GlobalData().project
if project.isLoaded():
project.setExceptionFilters([])
else:
Settings().setExceptionFilters([])
return
def isIgnored(self, exceptionType):
" Returns True if this exception type should be ignored "
return exceptionType in self.__ignored
class NPhotoMainWindow(QMainWindow):
rootAlbum = None
currentPage = 0
def __init__(self, parent=None):
super(NPhotoMainWindow, self).__init__(parent)
self.image = None
self.status = self.statusBar()
self.status.setSizeGripEnabled(False)
fileMenu = self.menuBar().addMenu("&File")
fileEditAction = createAction(self, "&Edit", self.doEdit, "Ctrl-E", "fileedit", "Edit photo details")
fileDeleteAction = createAction(self, "&Delete", self.doDelete, "Ctrl-D", "filedelete", "Delete selected file(s)")
fileImportAction = createAction(self, "&Import", self.doImport, "Ctrl-I", "fileimport", "Import photos into your library")
fileRescanLibraryAction = createAction(self, "&Rescan", self.doRescan, "Ctrl-R", "filerescan", "Rescan library folder and update sidecar files, and thumbnails")
fileBackupAction = createAction(self, "&Backup", self.doBackup, "Ctrl-B", "filebkup", "Backup your library")
fileSettingsAction = createAction(self, "&Settings", self.doSettings, "Ctrl-S", "filesettings", "Settings")
fileQuitAction = createAction(self, "&Quit", self.close, "Ctrl+Q", "filequit", "Close the application")
helpMenu = self.menuBar().addMenu("&Help")
helpAboutAction = createAction(self, "&About", self.doAbout, None, "helpabout", "About nPhoto")
addActions(fileMenu, (fileEditAction, fileDeleteAction, None, fileImportAction, fileRescanLibraryAction,
fileBackupAction, fileSettingsAction, None, fileQuitAction))
addActions(helpMenu, (helpAboutAction,))
size = getSettingQVar("MainWindow/Size", QSize(600,500)).toSize()
self.resize(size)
position = getSettingQVar("MainWindow/Position", QPoint(0,0)).toPoint()
self.move(position)
self.restoreState(getSettingQVar("MainWindow/State").toByteArray())
self.setWindowTitle("nPhoto")
self.controlFrame = QFrame()
self.controlLayout = QBoxLayout(QBoxLayout.TopToBottom)
#TODO Make this a combo box that populates the tree by date or by folder
self.viewByCombo = QLabel("PLACEHOLDER")
self.tree = QTreeWidget()
self.tree.setColumnCount(1)
self.tree.setHeaderLabels(["Album"])
self.tree.setItemsExpandable(True)
self.connect(self.tree, SIGNAL("itemSelectionChanged()"), self.treeSelection)
self.controlLayout.addWidget(self.viewByCombo)
self.controlLayout.addWidget(self.tree)
self.controlFrame.setLayout(self.controlLayout)
self.browserFrame = QFrame()
self.browserGrid = QGridLayout()
self.imageLabels = []
for row in range(0,BROWSER_GRID_HEIGHT):
self.imageLabels.append([])
for col in range(0,BROWSER_GRID_WIDTH):
self.imageLabels[row].append(QLabel())
self.imageLabels[row][col].setBackgroundRole(QPalette.Base)
self.imageLabels[row][col].setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Ignored)
self.imageLabels[row][col].setScaledContents = True
self.imageLabels[row][col].setAlignment(Qt.AlignCenter)
self.imageLabels[row][col].setStyleSheet("border:2px solid #000")
dbl = functools.partial(self.imgDoubleClick, row, col)
click = functools.partial(self.imgMouseRelease, row, col)
self.imageLabels[row][col].mouseDoubleClickEvent = dbl
self.imageLabels[row][col].mouseReleaseEvent = click
self.browserGrid.addWidget(self.imageLabels[row][col],row,col)
self.prevPage = QPushButton("Prev")
self.pageInfoLabel = QLabel("Page 0 of 0")
self.pageInfoLabel.setAlignment(Qt.AlignCenter)
self.nextPage = QPushButton("Next")
self.prevPage.clicked.connect(self.goPreviousPage)
self.nextPage.clicked.connect(self.goNextPage)
self.browserGrid.addWidget(self.prevPage, row+1, 0)
self.browserGrid.addWidget(self.pageInfoLabel, row+1, 1)
self.browserGrid.addWidget(self.nextPage, row+1, 2)
self.browserFrame.setLayout(self.browserGrid)
self.mainSplitter = QSplitter(Qt.Horizontal)
self.mainSplitter.addWidget(self.controlFrame)
self.mainSplitter.addWidget(self.browserFrame)
self.mainSplitter.setStretchFactor(1,4)
self.setCentralWidget(self.mainSplitter)
self.mainSplitter.restoreState(getSettingQVar("MainWindow/Splitter").toByteArray())
if getSettingStr("Paths/Library") not in (None, ''):
QTimer.singleShot(0, self.loadLibrary)
else:
self.status.showMessage("No Library Path in settings", 10000)
def getPhotoByBrowserLocation(self, row, col):
idx = ((self.currentPage - 1) * BROWSER_THUMBS_PER_PAGE) + (row * BROWSER_GRID_WIDTH) + col
if idx < len(self.currentAlbum.photos):
return self.currentAlbum.photos[idx]
else:
return None
def imgDoubleClick(self, row, col, event):
if event.button() == Qt.LeftButton:
if event.modifiers() & Qt.ControlModifier or event.modifiers() & Qt.AltModifier \
or event.modifiers() & Qt.ShiftModifier:
pass
else:
curr = self.getPhotoByBrowserLocation(row,col)
if curr:
self.currentSelection = [curr,]
self.highlightSelected()
self.doEdit()
def imgMouseRelease(self, row, col, event):
if event.button() == Qt.LeftButton:
if event.modifiers() & Qt.ControlModifier or event.modifiers() & Qt.AltModifier \
or event.modifiers() & Qt.ShiftModifier:
pass
else:
curr = self.getPhotoByBrowserLocation(row,col)
if curr:
if not hasattr(self, "currentSelection"):
self.currentSelection = []
if curr in self.currentSelection:
self.currentSelection.remove(curr)
else:
self.currentSelection.append(curr)
self.highlightSelected()
def highlightSelected(self):
if hasattr(self, "currentSelection"):
for x in range(0, BROWSER_GRID_HEIGHT):
for y in range(0, BROWSER_GRID_WIDTH):
ph = self.getPhotoByBrowserLocation(x,y)
if ph:
if ph in self.currentSelection:
self.imageLabels[x][y].setStyleSheet("border:2px solid #FFF")
else:
self.imageLabels[x][y].setStyleSheet("border:2px solid #000")
def regenAlbumThumbnails(self, album):
for al in album.albums:
self.regenAlbumThumbnails(al)
for ph in album.photos:
createThumbnail(ph.path, True)
def doRescan(self):
#TODO Rebuild sidecar files!
self.regenAlbumThumbnails(self.rootAlbum)
self.reloadLibrary()
def treeSelection(self):
curr = self.tree.currentItem()
path = curr.data(0,0).toString()
tmp = curr
while tmp.parent() is not None:
tmp = tmp.parent()
path = tmp.data(0,0).toString() + "." + path
album = self.getAlbum(path)
if hasattr(self, 'currentAlbum'):
if self.currentAlbum != album:
self.currentAlbum = album
else:
self.currentAlbum = album
self.changeAlbums()
def changeAlbums(self):
if len(self.currentAlbum.photos) == 0:
self.currentPage = 0
else:
self.currentPage = 1
for row in range(0, BROWSER_GRID_HEIGHT):
for col in range(0, BROWSER_GRID_WIDTH):
if len(self.currentAlbum.photos)<= (row*BROWSER_GRID_WIDTH + col):
self.imageLabels[row][col].setPixmap(QPixmap())
else:
self.imageLabels[row][col].setPixmap(loadQPixMap(self.image, self.currentAlbum.photos[
(BROWSER_THUMBS_PER_PAGE * (self.currentPage - 1)) + row*BROWSER_GRID_WIDTH+col]
.path, self.imageLabels[0][0].width(), self.imageLabels[0][0].height(), True))
self.imageLabels[row][col].adjustSize()
self.updatePageInfo()
def loadPageThumbs(self):
for row in range(0, BROWSER_GRID_HEIGHT):
for col in range(0, BROWSER_GRID_WIDTH):
if len(self.currentAlbum.photos)<= (
(BROWSER_THUMBS_PER_PAGE * (self.currentPage - 1)) + row*BROWSER_GRID_WIDTH + col):
self.imageLabels[row][col].setPixmap(QPixmap())
else:
self.imageLabels[row][col].setPixmap(loadQPixMap(self.image, self.currentAlbum.photos[
(BROWSER_THUMBS_PER_PAGE * (self.currentPage - 1)) + row*BROWSER_GRID_WIDTH+col]
.path, self.imageLabels[0][0].width(), self.imageLabels[0][0].height(), True))
self.imageLabels[row][col].adjustSize()
def goPreviousPage(self):
if self.currentPage > 1:
self.currentPage -= 1
self.loadPageThumbs()
self.updatePageInfo()
def goNextPage(self):
if self.currentPage < self.getMaxPage():
self.currentPage += 1
self.loadPageThumbs()
self.updatePageInfo()
def getMaxPage(self):
totalPages = len(self.currentAlbum.photos) / BROWSER_THUMBS_PER_PAGE
if (len(self.currentAlbum.photos) % BROWSER_THUMBS_PER_PAGE) != 0:
totalPages += 1
return totalPages
def updatePageInfo(self):
if self.currentPage == 0:
self.pageInfoLabel.setText("Page 0 of 0")
else:
self.pageInfoLabel.setText("Page %d of %d" % (self.currentPage, self.getMaxPage()))
def getAlbum(self, path):
nodes = path.split(".")
if nodes[0] != 'Library':
print "WTF?!?!?!"
else:
album = self.rootAlbum
for albumName in nodes[1:]:
album = album.albums[unicode(albumName)]
return album
def doBackup(self):
libDir = getSettingStr("Paths/Library")
bkupPaths = getSettingStr("Paths/Backup")
if libDir in (None, ''):
QMessageBox.warning(self, "Backup Failed", "You need to specify a library directory in your settings")
return
if not os.path.exists(libDir) or os.path.isfile(libDir):
QMessageBox.warning(self, "Backup Failed", "The library directory in your settings either doesn't exist, or its not a directory")
return
if bkupPaths in (None, ''):
QMessageBox.warning(self, "Backup Failed", "You need to specify at least one backup directory in your settings")
return
dt = datetime.date.today()
bkupDirName = str(dt.year) + str(dt.month) + str(dt.day)
for path in bkupPaths.split(","):
if not os.path.exists(path.strip()) or os.path.isfile(path.strip()):
QMessageBox.warning(self, "Backup Failed", "The backup directory <%s> in your settings either doesn't exist, or its not a directory" % (path))
return
if os.path.exists(path.strip() + os.sep + bkupDirName):
QMessageBox.warning(self, "Backup Failed", "There is already a backup for today in a backup directory <%s>" % (path.strip()))
return
for path in bkupPaths.split(","):
shutil.copytree(libDir, path.strip() + os.sep + bkupDirName)
QMessageBox.information(self, "Backup", "Backup completed!")
def doDelete(self):
if hasattr(self, "currentSelection"):
if len(self.currentSelection) > 0:
msg = "Are you sure you want to delete the selected image?"
if len(self.currentSelection) > 1:
msg = "Are you sure you want to delete the %s selected images?" % len(self.currentSelection)
if QMessageBox.warning(self, "Delete Image(s)", msg,
QMessageBox.Yes|QMessageBox.No) == QMessageBox.Yes:
for ph in self.currentSelection:
msg = ph.delete()
if msg not in (None, ''):
QMessageBox.warning(self, "Error while deleting", msg)
break
self.reloadLibrary()
def reloadLibrary(self):
self.currentSelection = []
self.highlightSelected()
currPage = self.currentPage
self.loadLibrary()
if currPage > self.getMaxPage():
#Assumes you can't delete more than one page worth of photos at a time
currPage = self.getMaxPage()
self.currentPage = currPage
self.loadPageThumbs()
self.updatePageInfo()
def doEdit(self):
if hasattr(self, "currentSelection"):
if len(self.currentSelection) == 1:
ph = self.currentSelection[0]
comment = ph.comment
keywords = (" ".join(ph.keywords)).strip()
dialog = EditPhotoDialog(self, ph.path, comment, keywords)
if dialog.exec_():
ph.comment = unicode(dialog.commentEdit.text()).strip()
ph.keywords = unicode(dialog.keywordEdit.text()).strip().split(" ")
ph.save(ph.path)
def doSettings(self):
libPath = getSettingStr("Paths/Library", "")
backupPaths = getSettingStr("Paths/Backup", "")
fileExt = getSettingStr("FileExtensions", "jpg, CR2")
fileExtOther = getSettingStr("FileExtensionsOther", "mov, avi")
dialog = SettingsDialog(self, libPath, backupPaths, fileExt, fileExtOther)
if dialog.exec_():
saveSetting("Paths/Library", dialog.libPathEdit.text())
saveSetting("Paths/Backup", dialog.backupPathsEdit.text())
saveSetting("FileExtensions", dialog.fileExtensionEdit.text())
saveSetting("FileExtensionsOther", dialog.fileExtensionOtherEdit.text())
self.status.showMessage("Settings updated", 5000)
def buildTree(self, parentNode, parentAlbum):
for name in parentAlbum.albums:
childNode = QTreeWidgetItem(parentNode, [name])
childAlbum = parentAlbum.albums[name]
if childAlbum.albums != None and len(childAlbum.albums) > 0:
self.buildTree(childNode, childAlbum)
def loadLibrary(self):
self.status.showMessage("Loading Photo Library")
self.rootAlbum = self.loadAlbum(getSettingStr("Paths/Library"), "Library")
if self.rootAlbum == None:
self.rootAlbum = Album(name="Library")
self.refreshTree()
self.status.showMessage("Library successfully loaded", 5000)
def refreshTree(self):
self.tree.clear()
node = QTreeWidgetItem(self.tree, ["Library"])
self.buildTree(node, self.rootAlbum)
self.tree.setCurrentItem(node)
def loadAlbum(self, path, title = None):
album = Album()
if title not in (None, ''):
album.name = title
else:
album.name = path[path.rfind(os.sep)+1:]
album.albums = {}
album.photos = []
album.path = path
files = os.listdir(path)
files.sort()
tmpPhotos = []
for fl in files:
if not os.path.isfile(path + os.sep + fl):
album.albums[fl] = self.loadAlbum(path + os.sep + fl)
else:
if self.isImageFile(path + os.sep + fl):
ph = None
if os.path.exists(path + os.sep + fl + ".sidecar"):
ph = Photo.load(path + os.sep + fl + ".sidecar")
else:
ph = Photo()
ph.comment = ""
ph.keywords = {}
ph.srcPath = None
ph.path = path + os.sep + fl
exif = loadExif(path + os.sep + fl, EXIF_TAGS)
ph.setExif(exif)
ph.save(path + os.sep + fl)
ph.path = path + os.sep + fl
tmpPhotos.append(ph)
album.photos = sorted(tmpPhotos, key = lambda photo: photo.date)
return album
def doImport(self):
libPath = getSettingStr("Paths/Library")
fileExt = getSettingStr("FileExtensions")
if libPath in (None, ''):
QMessageBox.warning(self, "Import Failed", "You need to specify a library directory in your settings")
return
if not os.path.exists(libPath) or os.path.isfile(libPath):
QMessageBox.warning(self, "Import Failed", "The library directory in your settings either doesn't exist, or its not a directory")
return
if not fileExt or fileExt in (None, ''):
QMessageBox.warning(self, "Import Failed", "You need to specify file extensions to manage in your settings")
return
lastImport = getSettingStr("Paths/LastImport")
importFrom = QFileDialog.getExistingDirectory(self, "Choose a Path to Import From", lastImport)
if importFrom in (None, ''):
return
if not os.path.exists(importFrom) or os.path.isfile(importFrom):
QMessageBox.warning(self, "Import Failed", "The import directory either doesn't exist, or is not a directory")
return
if importFrom == libPath:
QMessageBox.warning(self, "Import Failed", "Your import directory and library directory can not be the same")
return
imd = ImportMetadataDialog(self)
if imd.exec_():
album = imd.albumEdit.text()
comments = imd.commentsEdit.text()
keywords = imd.keywordsEdit.text()
if album and album not in (None, ''):
albumpath = album + os.sep
else:
album = None
albumpath = ""
if not keywords or keywords in (None, ''):
keywords = ""
if not comments or comments in (None, ''):
comments = ""
paths = self.buildFileList(importFrom)
numTotal = len(paths)
nonDupes = self.removeDuplicates(paths, importFrom, albumpath)
numDuplicates = numTotal - len(nonDupes)
if QMessageBox.question(self, "Import", "Out of %d files found, %d look to be duplicates. Continue with import?"
% (numTotal, numDuplicates), QMessageBox.Yes|QMessageBox.No) == QMessageBox.Yes:
saveSetting("Paths/LastImport", importFrom)
for path in nonDupes:
dest = self.buildLibPath(importFrom, path, albumpath)
copyFileIncludingDirectories(path, dest)
# TODO Handle copy failure exceptions!
if not os.path.exists(dest):
QMessageBox.warming(self, "Import Failed", "The file <%s> was not imported properly, aborting import" % (path))
return
if self.isImageFile(path):
exif = loadExif(unicode(path), EXIF_TAGS)
ph = Photo()
ph.path = dest
ph.srcPath = path
ph.comment = comments
ph.keywords = keywords
ph.setExif(exif)
ph.save(dest)
#Create Thumbnail
createThumbnail(unicode(ph.path))
QMessageBox.information(self, "Import", "Import completed")
self.loadLibrary()
def buildLibPath(self, importFrom, path, albumpath):
relPath = path[len(importFrom):]
libPath = getSettingStr("Paths/Library") + os.sep + albumpath + relPath
return libPath
def isImageFile(self, filepath):
extensionList = unicode(getSettingStr("FileExtensions")).split(",")
for extension in extensionList:
if unicode(filepath).upper().endswith(unicode(extension).upper()):
return True
return False
def isOtherManagedFile(self, filepath):
#TODO Implement list of other files to import into lib folders and to backup
extensionList = unicode(getSettingStr("FileExtensionsOther")).split(",")
for extension in extensionList:
if unicode(filepath).upper().endswith(unicode(extension).upper()):
return True
return False
def removeDuplicates(self, paths, importFrom, albumpath):
nonDupes = []
for path in paths:
libPath = self.buildLibPath(importFrom, path, albumpath)
if not os.path.exists(libPath):
nonDupes.append(path)
return nonDupes
def buildFileList(self, importFrom):
#TODO Can probably be done with Glob or whatever it is?
paths = []
for f in os.listdir(importFrom):
fullpath = importFrom + os.sep + f
if not os.path.isfile(fullpath):
paths.extend(self.buildFileList(fullpath))
else:
if self.isImageFile(fullpath):
paths.append(fullpath)
elif self.isOtherManagedFile(fullpath):
paths.append(fullpath)
return paths
def closeEvent(self, event):
saveSetting("MainWindow/Size", self.size())
saveSetting("MainWindow/Position", self.pos())
saveSetting("MainWindow/State", self.saveState())
saveSetting("MainWindow/Splitter", self.mainSplitter.saveState())
def doAbout(self):
QMessageBox.about(self, "About nPhoto",
"<p>nPhoto allows simple reviewing, commenting, and keywording of images, useful for running"
" on a netbook while travelling, to then import into programs such as Lightroom"
" on return from your holiday</p>")
class DBBrowser(QMainWindow):
def __init__(self, parent, server):
QMainWindow.__init__(self, parent)
self.debug = False
self.server = server
self.db = None
self.setWindowTitle("Database Browser")
#s#elf.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
topBar = QToolBar()
self.addToolBar(Qt.TopToolBarArea, topBar)
self.cenWid = QWidget()
self.setCentralWidget(self.cenWid)
self.mainLayout = QHBoxLayout()
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(0)
self.cenWid.setLayout( self.mainLayout )
self.treeTables = QTreeWidget()
self.mainLayout.addWidget(self.treeTables, 1)
self.treeTables.setHeaderLabels(["Table"])
self.treeTables.setSelectionBehavior( QAbstractItemView.SelectRows )
self.treeTables.setSelectionMode( QTreeView.SingleSelection )
self.connect( self.treeTables, SIGNAL( 'itemSelectionChanged()' ), self.on_table )
self.treeColumns = QTreeWidget()
self.mainLayout.addWidget(self.treeColumns, 4)
self.treeColumns.setHeaderLabels(["Column", "Type", "Nullable"])
self.db_connect()
#self.fetch()
def on_table(self):
item = self.treeTables.currentItem()
if item == None:
return
self.fetch( table = str(item.text(0)) )
def db_connect(self):
#print "db_connect", self.server
self.db = QSqlDatabase.addDatabase("QMYSQL")
self.db.setHostName(self.server['server'])
self.db.setUserName(self.server['user'])
self.db.setPassword(self.server['passwd'])
ok = self.db.open()
print "open", ok
#self.db.setHostName(self.server['server'])
def load_data(self, data):
if "tables" in data:
self.treeTables.clear()
for t in data['tables']:
item = QTreeWidgetItem()
item.setText(0, t['table'])
self.treeTables.addTopLevelItem(item)
else:
self.treeColumns.clear()
for t in data['columns']:
item = QTreeWidgetItem()
item.setText(0, t['column'])
item.setText(1, t['type'])
item.setText(2, "Yes" if t['nullable'] else "-")
self.treeColumns.addTopLevelItem(item)
class ArbolDeSimbolos(custom_dock.CustomDock):
_ir_a_linea = pyqtSignal(int, name='irALinea')
iconos = {
'clase': paths.ICONOS['class'],
'funcion': paths.ICONOS['funcion'],
'struct': paths.ICONOS['struct'],
'miembro': paths.ICONOS['miembro'],
'global': paths.ICONOS['variable'],
'enumerator': paths.ICONOS['enumerator'],
'enums': paths.ICONOS['enums']
}
def __init__(self):
custom_dock.CustomDock.__init__(self)
self.tree = QTreeWidget()
self.setWidget(self.tree)
self.tree.setObjectName("simbolos")
self.tree.header().setHidden(True)
self.tree.setSelectionMode(self.tree.SingleSelection)
self.tree.setAnimated(True)
self.tree.header().setStretchLastSection(False)
self.tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
# Conexión
self.tree.itemClicked[QTreeWidgetItem, int].connect(self.ir_a_linea)
self.tree.itemActivated[QTreeWidgetItem, int].connect(self.ir_a_linea)
EDIS.cargar_lateral("simbolos", self)
def actualizar_simbolos(self, archivo):
#FIXME: mover esto
self.ctags = ectags.Ctags()
tag = self.ctags.run_ctags(archivo)
simbolos = self.ctags.parser(tag)
self._actualizar_simbolos(simbolos)
def _actualizar_simbolos(self, simbolos):
#FIXME:
# Limpiar
self.tree.clear()
if simbolos is None:
no_ctags = Item(self.tree, [self.tr('Ctags no está instalado.')])
no_ctags.clickeable = False
return
if 'variable' in simbolos:
variables = Item(self.tree, [self.tr('Variables')])
variables.clickeable = False
for v in simbolos['variable']:
variable = Item(variables, [v.get('nombre')])
linea = v['linea']
variable.linea = linea
variable.setIcon(0, QIcon(self.iconos['global']))
variables.setExpanded(True)
if 'function' in simbolos:
funciones = Item(self.tree, [self.tr('Funciones')])
funciones.clickeable = False
for f in simbolos['function']:
funcion = Item(funciones, [f.get('nombre')])
linea = f['linea']
funcion.linea = linea
funcion.setIcon(0, QIcon(self.iconos['funcion']))
funciones.setExpanded(True)
if 'struct' in simbolos:
structs = Item(self.tree, [self.tr('Estructuras')])
structs.clickeable = False
for s in simbolos['struct']:
struct = Item(structs, [s.get('nombre')])
linea = s['linea']
struct.linea = linea
struct.setIcon(0, QIcon(self.iconos['struct']))
structs.setExpanded(True)
if 'member' in simbolos:
miembros = Item(self.tree, [self.tr('Miembros')])
miembros.clickeable = False
for m in simbolos['member']:
nombre = m['nombre'] + ' [' + m['padre'] + ']'
miembro = Item(miembros, [nombre])
miembro.setIcon(0, QIcon(self.iconos['miembro']))
linea = m['linea']
miembro.linea = linea
miembros.setExpanded(True)
def ir_a_linea(self, item):
if item.clickeable:
self._ir_a_linea.emit(int(item.linea) - 1)
class Info(QDockWidget):
def __init__(self, mainWindow):
super(Info, self).__init__()
self.__mainWindow = mainWindow
self.loader = loader.loader()
self.env = env.env()
self.tm = TaskManager()
self.addAction()
self.configure()
self.g_display()
self.initCallback()
self.Load()
def configure(self):
self.setAllowedAreas(Qt.AllDockWidgetAreas)
self.setObjectName("dockWidgetBrowser")
self.setWindowTitle(QApplication.translate("Info", "Info", None, QApplication.UnicodeUTF8))
def addAction(self):
self.__action = QAction(self)
self.__action.setCheckable(True)
self.__action.setChecked(True)
self.__action.setObjectName("actionCoreInformations")
self.__action.setText(QApplication.translate("MainWindow", "Info", None, QApplication.UnicodeUTF8))
self.__mainWindow.menuWindow.addAction(self.__action)
self.connect(self.__action, SIGNAL("triggered()"), self.changeVisibleInformations)
def changeVisibleInformations(self):
if not self.isVisible():
self.setVisible(True)
self.__action.setChecked(True)
else:
self.setVisible(False)
self.__action.setChecked(False)
def g_display(self):
self.Info = QWidget(self)
self.layout = QHBoxLayout(self.Info)
self.Info.setLayout(self.layout)
self.tabWidget = QTabWidget(self)
self.tabWidget.setElideMode(Qt.ElideRight)
self.initTreeProcess()
self.initTreeModule()
self.initTreeEnv()
self.layout.addWidget(self.tabWidget)
self.setWidget(self.Info)
def initCallback(self):
self.connect(self, SIGNAL("visibilityChanged(bool)"), self.visibilityChanged)
self.timer = QTimer(self)
self.connect(self.timer, SIGNAL("timeout()"), self.refresh)
self.timer.start(2000)
def visibilityChanged(self, bool):
if not self.isVisible():
self.__action.setChecked(False)
else:
self.__action.setChecked(True)
def Load(self):
self.LoadInfoProcess()
self.LoadInfoModules()
self.LoadInfoEnv()
pass
def refresh(self):
self.LoadInfoProcess()
self.LoadInfoModules()
self.LoadInfoEnv()
pass
def deleteInfos(self):
self.deleteInfoProcess()
self.deleteInfoModule()
self.deleteInfoEnv()
# MODULES
def initTreeModule(self):
self.treeModule = QTreeWidget(self)
self.treeModule.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "Name", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Key", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Value", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Info", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Type", None, QApplication.UnicodeUTF8),
]
self.treeModule.setHeaderLabels(headerLabel)
self.treeModule.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeModule, "Modules")
self.itemModuleDic = dict()
self.itemListArgDic = dict()
self.itemArgDic = dict()
self.itemListResDic = dict()
self.itemResDic = dict()
def LoadInfoModules(self):
modules = self.loader.modules
for mod in modules:
try:
itemModule = self.itemModuleDic[mod]
except KeyError:
itemModule = QTreeWidgetItem(self.treeModule)
self.itemModuleDic[mod] = itemModule
itemModule.setText(0, str(mod))
itemConfig = QTreeWidgetItem(itemModule)
itemConfig.setText(0, "Config")
cdesc = modules[mod].conf.descr_l
for key in cdesc:
itemConfKey = QTreeWidgetItem(itemConfig)
itemConfKey.setText(0, "var")
itemConfKey.setText(1, key.name)
itemConfKey.setText(4, key.type)
if len(key.description):
itemConfKey.setText(3, key.description)
for type, name, val, _from in self.env.get_val_list(modules[mod].conf.val_l):
itemConfKey = QTreeWidgetItem(itemConfig)
itemConfKey.setText(0, "const")
itemConfKey.setText(1, name)
itemConfKey.setText(2, val)
itemConfKey.setText(4, type)
for proc in self.tm.lprocessus:
if proc.mod.name == mod:
try:
itemListArg = self.itemListArgDic[mod]
except KeyError:
itemListArg = QTreeWidgetItem(itemModule)
self.itemListArgDic[mod] = itemListArg
itemListArg.setText(0, "Arg")
for type, name, val in self.env.get_val_map(proc.args.val_m):
try:
itemArgKey = self.itemArgDic[(type, name, val)]
except KeyError:
itemArgKey = QTreeWidgetItem(itemListArg)
self.itemArgDic[(type, name, val)] = itemArgKey
itemArgKey.setText(1, name)
itemArgKey.setText(2, val)
itemArgKey.setText(4, type)
try:
itemListRes = self.itemListResDic[mod]
except KeyError:
itemListRes = QTreeWidgetItem(itemModule)
self.itemListResDic[mod] = itemListRes
itemListRes.setText(0, "Results")
if proc.res:
for type, name, val in self.env.get_val_map(proc.res.val_m):
try:
itemResKey = self.itemResDic[(type, name, val)]
except KeyError:
itemResKey = QTreeWidgetItem(itemListRes)
self.itemResDic[(type, name, val)] = itemResKey
itemResKey.setText(1, name)
itemResKey.setText(2, val)
itemResKey.setText(4, type)
def deleteInfoModule(self):
self.treeModule.clear()
# ENV
def initTreeEnv(self):
self.treeEnv = QTreeWidget(self)
self.treeEnv.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "Key", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Type", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Value", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "From", None, QApplication.UnicodeUTF8),
]
self.treeEnv.setHeaderLabels(headerLabel)
self.treeEnv.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeEnv, "Environment")
self.envItemDic = dict()
self.envConfKeyDic = dict()
self.envValKeyDic = dict()
def LoadInfoEnv(self):
db = self.env.vars_db
for key in db:
try:
(itemEnv, itemVar, itemValues) = self.envItemDic[key]
except KeyError:
itemEnv = QTreeWidgetItem(self.treeEnv)
itemEnv.setText(0, key)
itemVar = QTreeWidgetItem(itemEnv)
itemVar.setText(0, "var")
itemValues = QTreeWidgetItem(itemEnv)
self.envItemDic[key] = (itemEnv, itemVar, itemValues)
cdesc = db[key].descr_l
for vk in cdesc:
try:
itemConfKey = self.envConfKeyDic[(vk.type, vk._from)]
except KeyError:
itemConfKey = QTreeWidgetItem(itemVar)
self.envConfKeyDic[(vk.type, vk._from)] = itemConfKey
itemConfKey.setText(1, vk.type)
itemConfKey.setText(3, vk._from)
itemValues.setText(0, "values")
for type, name, val, _from in self.env.get_val_list(db[key].val_l):
try:
itemValKey = self.envValKeyDic[(type, _from, val)]
except:
itemValKey = QTreeWidgetItem(itemValues)
self.envValKeyDic[(type, _from, val)] = itemValKey
itemValKey.setText(1, type)
itemValKey.setText(2, val)
itemValKey.setText(3, _from)
def deleteInfoEnv(self):
self.treeEnv.clear()
# PROCESSUS
def initTreeProcess(self):
self.treeProcess = QTreeWidget(self)
self.treeProcess.setColumnCount(3)
headerLabel = [
QApplication.translate("Info", "PID", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Name", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "State", None, QApplication.UnicodeUTF8),
QApplication.translate("Info", "Info", None, QApplication.UnicodeUTF8),
]
self.treeProcess.setHeaderLabels(headerLabel)
self.treeProcess.setAlternatingRowColors(True)
self.tabWidget.addTab(self.treeProcess, "Task Manager")
self.connect(self.treeProcess, SIGNAL("itemDoubleClicked(QTreeWidgetItem*,int)"), self.procClicked)
self.procItemDic = dict()
self.procChildItemDic = dict()
def procClicked(self, item, column):
dial = procMB(self, item.text(0))
dial.exec_()
def LoadInfoProcess(self):
lproc = self.tm.lprocessus
for proc in lproc:
try:
item = self.procItemDic[proc]
except KeyError:
item = QTreeWidgetItem(self.treeProcess)
self.procItemDic[proc] = item
item.setText(0, str(proc.pid))
item.setText(1, str(proc.name))
if item.text(2) != str(proc.state):
item.setText(2, str(proc.state))
if item.text(3) != str(proc.stateinfo):
item.setText(3, str(proc.stateinfo))
def deleteInfoProcess(self):
self.treeProcess.clear()
class ThreadsViewer(QWidget):
" Implements the threads viewer for a debugger "
def __init__(self, debugger, parent=None):
QWidget.__init__(self, parent)
self.__debugger = debugger
self.__createLayout()
if Settings().showThreadViewer == False:
self.__onShowHide(True)
return
def __createLayout(self):
" Creates the widget layout "
verticalLayout = QVBoxLayout(self)
verticalLayout.setContentsMargins(0, 0, 0, 0)
verticalLayout.setSpacing(0)
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle(QFrame.StyledPanel)
self.headerFrame.setAutoFillBackground(True)
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color(QPalette.Background)
headerBackground.setRgb(min(headerBackground.red() + 30, 255),
min(headerBackground.green() + 30, 255),
min(headerBackground.blue() + 30, 255))
headerPalette.setColor(QPalette.Background, headerBackground)
self.headerFrame.setPalette(headerPalette)
self.headerFrame.setFixedHeight(24)
self.__threadsLabel = QLabel("Threads")
expandingSpacer = QSpacerItem(10, 10, QSizePolicy.Expanding)
fixedSpacer = QSpacerItem(3, 3)
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise(True)
self.__showHideButton.setIcon(PixmapCache().getIcon('less.png'))
self.__showHideButton.setFixedSize(20, 20)
self.__showHideButton.setToolTip("Hide threads list")
self.__showHideButton.setFocusPolicy(Qt.NoFocus)
self.__showHideButton.clicked.connect(self.__onShowHide)
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins(0, 0, 0, 0)
headerLayout.addSpacerItem(fixedSpacer)
headerLayout.addWidget(self.__threadsLabel)
headerLayout.addSpacerItem(expandingSpacer)
headerLayout.addWidget(self.__showHideButton)
self.headerFrame.setLayout(headerLayout)
self.__threadsList = QTreeWidget()
self.__threadsList.setSortingEnabled(False)
# I might not need that because of two reasons:
# - the window has no focus
# - the window has custom current indicator
# self.__threadsList.setAlternatingRowColors( True )
self.__threadsList.setRootIsDecorated(False)
self.__threadsList.setItemsExpandable(False)
self.__threadsList.setUniformRowHeights(True)
self.__threadsList.setSelectionMode(QAbstractItemView.NoSelection)
self.__threadsList.setSelectionBehavior(QAbstractItemView.SelectRows)
self.__threadsList.setItemDelegate(NoOutlineHeightDelegate(4))
self.__threadsList.setFocusPolicy(Qt.NoFocus)
self.__threadsList.itemClicked.connect(self.__onThreadClicked)
self.__threadsList.setHeaderLabels(["", "Name", "State", "TID"])
verticalLayout.addWidget(self.headerFrame)
verticalLayout.addWidget(self.__threadsList)
return
def __onShowHide(self, startup=False):
" Triggered when show/hide button is clicked "
if startup or self.__threadsList.isVisible():
self.__threadsList.setVisible(False)
self.__showHideButton.setIcon(PixmapCache().getIcon('more.png'))
self.__showHideButton.setToolTip("Show threads list")
self.__minH = self.minimumHeight()
self.__maxH = self.maximumHeight()
self.setMinimumHeight(self.headerFrame.height())
self.setMaximumHeight(self.headerFrame.height())
Settings().showThreadViewer = False
else:
self.__threadsList.setVisible(True)
self.__showHideButton.setIcon(PixmapCache().getIcon('less.png'))
self.__showHideButton.setToolTip("Hide threads list")
self.setMinimumHeight(self.__minH)
self.setMaximumHeight(self.__maxH)
Settings().showThreadViewer = True
return
def __resizeColumns(self):
" Resize the files list columns "
self.__threadsList.header().setStretchLastSection(True)
self.__threadsList.header().resizeSections(
QHeaderView.ResizeToContents)
self.__threadsList.header().resizeSection(0, 22)
self.__threadsList.header().setResizeMode(0, QHeaderView.Fixed)
return
def clear(self):
" Clears the content "
self.__threadsList.clear()
self.__threadsLabel.setText("Threads")
return
def populate(self, currentThreadID, threadList):
" Populates the thread list from the client "
self.clear()
for thread in threadList:
if thread['broken']:
state = "Waiting at breakpoint"
else:
state = "Running"
item = ThreadItem(thread['id'], thread['name'], state)
if thread['id'] == currentThreadID:
item.setCurrent(True)
self.__threadsList.addTopLevelItem(item)
self.__resizeColumns()
self.__threadsLabel.setText("Threads (total: " + str(len(threadList)) +
")")
return
def switchControl(self, isInIDE):
" Switches the UI depending where the control flow is "
self.__threadsList.setEnabled(isInIDE)
return
def __onThreadClicked(self, item, column):
" Triggered when a thread is clicked "
if item.isCurrent():
return
for index in xrange(self.__threadsList.topLevelItemCount()):
listItem = self.__threadsList.topLevelItem(index)
if listItem.isCurrent():
listItem.setCurrent(False)
break
item.setCurrent(True)
self.__debugger.remoteSetThread(item.getTID())
return
def clear(self):
self._client.stopPoller()
self._items.clear()
QTreeWidget.clear(self)
class ChooseSectionsPage(QIWizardPage):
"""
page to choose the sections that should be compared in the table
"""
def __init__(self, parent=None):
super(ChooseSectionsPage, self).__init__(parent)
self.selected_sections = [] # sections in the right tree
self.sections = [] # all sections without the selected
self.filtered_sections = [] # filtered sections without the selected
self.initUI()
def initUI(self):
mainlayout = QVBoxLayout()
# layout containing the treewidgets
sectionlistlayout = QHBoxLayout()
# layout for filter form
filterbox = QGroupBox("Filter")
self.LEsecname = QLineEdit()
self.LEsectype = QLineEdit()
self.LEpropname = QLineEdit()
filterlayout = QGridLayout()
filterlayout.addWidget(QLabel("Section Name"), 1, 0)
filterlayout.addWidget(QLabel("Section Type"), 2, 0)
filterlayout.addWidget(QLabel("Property Name"), 3, 0)
filterlayout.addWidget(self.LEsecname, 1, 1)
filterlayout.addWidget(self.LEsectype, 2, 1)
filterlayout.addWidget(self.LEpropname, 3, 1)
filterbox.setLayout(filterlayout)
self.LEsecname.textChanged.connect(self.filterSections)
self.LEsectype.textChanged.connect(self.filterSections)
self.LEpropname.textChanged.connect(self.filterSections)
# define layout for the trre-widgets containing the sections
self.section_tree = QTreeWidget()
self.section_tree.setColumnCount(2)
self.section_tree.setHeaderLabels(["Name", "Path"])
self.section_tree.itemDoubleClicked.connect(self.toright)
self.selection_tree = QTreeWidget()
self.selection_tree.setColumnCount(2)
self.selection_tree.setHeaderLabels(["Name", "Path"])
self.selection_tree.itemDoubleClicked.connect(self.toleft)
self.selection_tree.setSelectionMode(3)
self.section_tree.setSelectionMode(3)
self.settings.register("selected_secs", self.selected_sections)
# buttons to move items of the tree-widgets
movebuttonlayout = QVBoxLayout()
btn_right = QToolButton()
btn_right.setArrowType(Qt.RightArrow)
btn_right.clicked.connect(self.toright)
btn_left = QToolButton()
btn_left.setArrowType(Qt.LeftArrow)
btn_left.clicked.connect(self.toleft)
movebuttonlayout.addStretch(1)
movebuttonlayout.addWidget(btn_right)
movebuttonlayout.addSpacing(1)
movebuttonlayout.addWidget(btn_left)
movebuttonlayout.addStretch(1)
sectionlistlayout.addWidget(self.section_tree)
sectionlistlayout.addSpacing(1)
sectionlistlayout.addLayout(movebuttonlayout)
sectionlistlayout.addSpacing(1)
sectionlistlayout.addWidget(self.selection_tree)
mainlayout.addLayout(sectionlistlayout)
self.selectallcb = QCheckBox('select all (Ctrl+A)')
self.selectallcb.stateChanged.connect(self.selectall)
mainlayout.addWidget(self.selectallcb)
mainlayout.addWidget(filterbox)
self.setTitle("Select Sections")
self.setLayout(mainlayout)
self.adjustSize()
def initializePage(self):
# load sections and properties from the selected file
odmldoc = odml.tools.xmlparser.load(self.settings.get_object(
"inputfilename"))
for section in odmldoc.itersections():
self.sections.append([section.name,
section.get_path(),
[p.name for p in section.properties],
section.type])
# fill tree widget with sections and properties
for line in self.sections:
parent = QTreeWidgetItem([line[0], line[1]])
for p in line[2]:
QTreeWidgetItem(parent, [str(p)])
self.section_tree.addTopLevelItem(parent)
self.filtered_sections = list(self.sections)
self.setTitle("Choose Sections")
self.setSubTitle("Choose the sections you want to compare")
def _get_selected_rows(self, tree):
"""
function to determine the selected rows in a specified QTreeWidget
"""
rows = []
for index in tree.selectedIndexes():
if index.parent().row() is -1:
rows.append(index.row())
else:
# if a property is selected, the whole section containing this
# property shall be moved
rows.append(index.parent().row())
# sort rownumbers in descending order to prevent shifting when moving
# the items
return sorted(list(set(rows)), reverse=True)
def toright(self):
"""
function to shift items from the left TreeWidget to the right
"""
rows = self._get_selected_rows(self.section_tree)
for row in rows:
self.selection_tree.addTopLevelItem(
self.section_tree.takeTopLevelItem(row))
self.selected_sections.append(self.sections.pop(
self.sections.index(self.filtered_sections[row])))
self.filtered_sections.pop(row)
def toleft(self):
"""
function to shift items from the right TreeWidget to the left
"""
rows = self._get_selected_rows(self.selection_tree)
for row in rows:
self.section_tree.addTopLevelItem(
self.selection_tree.takeTopLevelItem(row))
item = self.selected_sections.pop(row)
self.sections.append(item)
self.filtered_sections.append(item)
def filterSections(self):
# find sections that match the filter
self.filtered_sections = [s for s in self.sections
if str(self.LEsecname.text()) in s[0]
and str(self.LEsectype.text()) in s[3]
and any([str(self.LEpropname.text())
in p for p in s[2]])]
# clear left treewidget
self.section_tree.clear()
# fill left treewidget with the filtered sections
for line in self.filtered_sections:
parent = QTreeWidgetItem([line[0], line[1]])
for p in line[2]:
QTreeWidgetItem(parent, [p])
self.section_tree.addTopLevelItem(parent)
def selectall(self):
if self.selectallcb.isChecked():
self.section_tree.selectAll()
else:
self.section_tree.clearSelection()
def validatePage(self):
if not self.settings.get_object("selected_secs"):
QMessageBox.warning(self, 'No sections chosen',
'You should choose at least two sections to be '
'compared in the table.')
return 0
return 1
class WProbes(QWidget, Logger.ClassLogger):
"""
Widget for probes
"""
def __init__(self, parent):
"""
Constructs WProbes widget
@param parent:
@type parent:
"""
QWidget.__init__(self, parent)
self.parent = parent
self.name = self.tr("Probes")
self.itemCurrentRunning = None
self.itemCurrentInstalled = None
self.itemCurrentDefault = None
self.probes = {}
self.nbPrbs = 0
# self.prbsInstalled = None
self.createWidgets()
self.createConnections()
self.createActions()
self.createToolbar()
self.deactivate()
def createWidgets (self):
"""
QtWidgets creation
QTreeWidget (Name, Running on address, Type, Sched at, Version, Description)
_______________
| |
|---------------|
| |
| |
|_______________|
"""
layout = QHBoxLayout()
self.deployBox = QGroupBox("Default probes")
self.probesAvailable = QTreeWidget(self)
self.probesAvailable.setIndentation(10)
self.labelsAvail = [ self.tr("Installed") ]
self.probesAvailable.setHeaderLabels(self.labelsAvail)
self.runningBox = QGroupBox("Running")
self.probesRegistered = QTreeWidget(self)
self.probesRegistered.setIndentation(10)
self.runningDockToolbar = QToolBar(self)
self.runningDockToolbar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.availDockToolbar = QToolBar(self)
self.availDockToolbar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.labels = [ self.tr("Name"), self.tr("Running on address"), self.tr("Started at"),
self.tr("Type"), self.tr("Auto Startup"), self.tr("Description") ]
self.probesRegistered.setHeaderLabels(self.labels)
self.probesRegistered.setColumnWidth(0, 180)
self.probesRegistered.setColumnWidth(1, 120)
self.probesRegistered.setColumnWidth(2, 150)
self.probesRegistered.setColumnWidth(3, 70)
self.probesRegistered.setContextMenuPolicy(Qt.CustomContextMenu)
self.probesDefault = QTreeWidget(self)
self.probesDefault.setIndentation(10)
self.labelsDefault = [ self.tr("Enabled"), self.tr("Name"), self.tr("Type"), self.tr("Description") ]
self.probesDefault.setHeaderLabels(self.labelsDefault)
self.probesDefault.setContextMenuPolicy(Qt.CustomContextMenu)
self.probesDefault.setColumnWidth(1, 180)
layoutRunning = QVBoxLayout()
layoutRunning.addWidget(self.runningDockToolbar)
layoutRunning.addWidget(self.probesRegistered)
self.runningBox.setLayout(layoutRunning)
self.probeNameEdit = QLineEdit('')
self.probeNameEdit.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Fixed )
self.probeDescEdit = QLineEdit('')
self.probeDescEdit.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Fixed )
self.probeTypeEdit = QLineEdit('')
self.probeTypeEdit.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Fixed )
self.probeTypeEdit.setEnabled(False)
self.probeDescrInstalledEdit = QTextEdit('')
self.probeDescrInstalledEdit.setEnabled(False)
self.checkAutoStartOption = QCheckBox()
self.checkStartNowOption = QCheckBox()
paramLayout = QGridLayout()
paramLayout.addWidget(QLabel("Type:"), 0, 0, Qt.AlignRight)
paramLayout.addWidget(self.probeTypeEdit, 0, 1)
paramLayout.addWidget(QLabel("Name:"), 1, 0, Qt.AlignRight)
paramLayout.addWidget(self.probeNameEdit, 1, 1)
paramLayout.addWidget(QLabel("Description:"), 2, 0, Qt.AlignRight)
paramLayout.addWidget(self.probeDescEdit, 2, 1)
paramLayout.addWidget(QLabel("Startup on boot:"), 3, 0, Qt.AlignRight)
paramLayout.addWidget(self.checkAutoStartOption, 3, 1)
paramLayout.addWidget(QLabel("Start now:"), 4, 0, Qt.AlignRight)
paramLayout.addWidget(self.checkStartNowOption, 4, 1)
layoutLeft = QVBoxLayout()
layoutAvail = QHBoxLayout()
layoutAvail.addWidget(self.probesAvailable)
layoutAvail.addWidget(self.probeDescrInstalledEdit)
layoutLeft.addLayout(layoutAvail)
layoutLeft.addWidget(self.runningBox)
layoutDeploy = QVBoxLayout()
layoutDeploy.addWidget(self.availDockToolbar)
layoutDeploy.addLayout(paramLayout)
layoutDeploy.addWidget(self.probesDefault)
self.deployBox.setLayout(layoutDeploy)
layoutRight = QVBoxLayout()
layoutRight.addWidget(self.deployBox)
layout.addLayout(layoutLeft)
layout.addLayout(layoutRight)
self.setLayout(layout)
def createConnections (self):
"""
Create Qt Connections
"""
self.probesRegistered.customContextMenuRequested.connect(self.onPopupMenu)
self.probesRegistered.currentItemChanged.connect(self.currentItemChanged)
self.probesRegistered.itemClicked.connect(self.itemClicked)
self.probesAvailable.currentItemChanged.connect(self.currentItemChanged)
self.probesDefault.currentItemChanged.connect(self.currentItemChanged)
self.probesDefault.customContextMenuRequested.connect(self.onPopupMenuDefault)
def createActions (self):
"""
Actions defined:
* stop probe
* start probe
* delete one probe
* clear fields
* refresh running probes
* refresh default probes
"""
self.stopAction = QtHelper.createAction(self, "&Stop", self.stopProbe, tip = 'Stop probe',
icon = QIcon(":/act-stop.png"))
self.startAction = QtHelper.createAction(self, "&Add / Start", self.startProbe, tip = 'Add default probe',
icon = QIcon(":/probe-add.png"))
self.delProbeAction = QtHelper.createAction(self, "&Delete", self.delProbe, tip = 'Delete default probe',
icon = QIcon(":/probe-del.png"))
self.cancelAction = QtHelper.createAction(self, "&Clear", self.resetProbe, tip = 'Clear fields',
icon = QIcon(":/clear.png") )
self.refreshRunningAction = QtHelper.createAction(self, "&Refresh",
self.refreshRunningProbe, tip = 'Refresh running probes',
icon = QIcon(":/act-refresh.png") )
self.refreshDefaultAction = QtHelper.createAction(self, "&Refresh",
self.refreshDefaultProbe, tip = 'Refresh default probes',
icon = QIcon(":/act-refresh.png") )
def createToolbar(self):
"""
Toolbar creation
||-------||
|| Empty ||
||-------||
"""
self.runningDockToolbar.setObjectName("Registered Probe toolbar")
self.runningDockToolbar.addAction(self.refreshRunningAction)
self.runningDockToolbar.addSeparator()
self.runningDockToolbar.addAction(self.stopAction)
self.runningDockToolbar.addSeparator()
self.runningDockToolbar.setIconSize(QSize(16, 16))
self.availDockToolbar.setObjectName("Installed Probe toolbar")
self.availDockToolbar.addAction(self.refreshDefaultAction)
self.availDockToolbar.addSeparator()
self.availDockToolbar.addAction(self.startAction)
self.availDockToolbar.addAction(self.delProbeAction)
self.availDockToolbar.addSeparator()
self.availDockToolbar.addAction(self.cancelAction)
self.availDockToolbar.addSeparator()
self.availDockToolbar.setIconSize(QSize(16, 16))
def itemClicked(self, currentItem):
"""
On item clicked
@param currentItem:
@type currentItem:
"""
if currentItem is not None:
if isinstance( currentItem, ProbeItem ):
self.itemCurrentRunning = currentItem
self.stopAction.setEnabled(True)
def currentItemChanged(self, currentItem, previousItem):
"""
On current item changed
@param currentItem:
@type currentItem:
@param previousItem:
@type previousItem:
"""
if currentItem is not None:
if isinstance( currentItem, ProbeInstalledItem ):
self.itemCurrentInstalled = currentItem
if 'description' in currentItem.dataProbe:
self.probeDescrInstalledEdit.setText( currentItem.dataProbe['description'] )
self.probeTypeEdit.setText( currentItem.dataProbe['type'] )
else:
self.probeDescrInstalledEdit.setText( '' )
elif isinstance( currentItem, ProbeItem ):
self.itemCurrentRunning = currentItem
self.stopAction.setEnabled(True)
elif isinstance( currentItem, ProbeDefaultItem ):
self.itemCurrentDefault = currentItem
self.delProbeAction.setEnabled(True)
else:
self.stopAction.setEnabled(False)
self.delProbeAction.setEnabled(False)
self.probeDescrInstalledEdit.setText( '' )
def onPopupMenu(self, pos):
"""
Display menu on right click
@param pos:
@type pos:
"""
self.menu = QMenu()
item = self.probesRegistered.itemAt(pos)
if item:
self.itemCurrentRunning = item
self.menu.addAction( "Stop...", self.stopProbe)
self.menu.popup(self.probesRegistered.mapToGlobal(pos))
def onPopupMenuDefault(self, pos):
"""
Display menu on right click
@param pos:
@type pos:
"""
self.menu = QMenu()
item = self.probesDefault.itemAt(pos)
if item:
self.itemCurrentDefault = item
self.menu.addAction( "Delete...", self.delProbe)
self.menu.popup(self.probesDefault.mapToGlobal(pos))
def refreshDefaultProbe(self):
"""
Refresh the default list of probes
"""
RCI.instance().defaultProbes()
def refreshRunningProbe(self):
"""
Refresh the running list of probes
"""
RCI.instance().runningProbes()
def delProbe(self):
"""
Delete probe
"""
if self.itemCurrentDefault is not None:
reply = QMessageBox.question(self, "Stop probe", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
probeName = self.itemCurrentDefault.dataProbe['name']
self.delProbeAction.setEnabled(False)
# rest call
RCI.instance().removeProbe(probeName=probeName)
def stopProbe(self):
"""
Stop the selected probe
"""
if self.itemCurrentRunning is not None:
reply = QMessageBox.question(self, "Stop probe", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
probeName = self.itemCurrentRunning.dataProbe['id']
self.itemCurrentRunning = None
self.stopAction.setEnabled(False)
# rest call
RCI.instance().disconnectProbe(probeName=probeName)
def startProbe(self):
"""
Start a new probe
"""
# some checks before
if self.probeTypeEdit.text() == '':
QMessageBox.information(self, "Add Default Probe" , "Please select the probe type.")
return
if self.probeNameEdit.text() == '':
QMessageBox.information(self, "Add Default Probe" , "Probe name is mandatory.")
return
if not self.checkAutoStartOption.isChecked() and not self.checkStartNowOption.isChecked():
QMessageBox.information(self, "Add Default Probe" , "Select startup option.")
return
# call web services
probeType = str( self.probeTypeEdit.text() )
probeName = str( self.probeNameEdit.text() )
probeDescription = str( self.probeDescEdit.text() )
probeAutoStart = self.checkAutoStartOption.isChecked()
if not self.checkStartNowOption.isChecked():
RCI.instance().addProbe(probeName=probeName, probeType=probeType,
probeDescription=probeDescription)
else:
RCI.instance().connectProbe(probeName=probeName, probeType=probeType,
probeDescription=probeDescription,
probeBoot=probeAutoStart)
def resetProbe(self):
"""
Clear probe field
"""
self.probeDescrInstalledEdit.setText( '' )
self.probeDescEdit.setText( '' )
self.probeNameEdit.setText( '' )
self.probeTypeEdit.setText( '' )
# clear selection
itms = self.probesAvailable.selectedItems()
for i in itms:
if i.isSelected():
i.setSelected(False)
self.itemCurrentInstalled = None
def active (self):
"""
Enables QTreeWidget
"""
self.probesRegistered.setEnabled(True)
self.probesAvailable.setEnabled(True)
self.deployBox.setEnabled(True)
self.runningBox.setEnabled(True)
self.refreshRunningAction.setEnabled(True)
def deactivate (self):
"""
Clears QTreeWidget and disables it
"""
self.checkAutoStartOption.setCheckState(Qt.Unchecked)
self.checkStartNowOption.setCheckState(Qt.Unchecked)
self.probesAvailable.clear()
self.probeDescrInstalledEdit.setText('')
self.probesRegistered.clear()
self.probesDefault.clear()
self.probes = {}
self.probesRegistered.setEnabled(False)
self.probesAvailable.setEnabled(False)
self.deployBox.setEnabled(False)
self.runningBox.setEnabled(False)
# actions
self.stopAction.setEnabled(False)
self.delProbeAction.setEnabled(False)
self.itemCurrentRunning = None
self.itemCurrentInstalled = None
self.probeDescEdit.setText( '' )
self.probeTypeEdit.setText( '' )
self.probeNameEdit.setText( '' )
self.resetNbProbes()
self.refreshRunningAction.setEnabled(False)
def getRunningProbes(self):
"""
Get running probes
"""
if sys.version_info > (3,): # python3 support
return list(self.probes.keys())
else:
return self.probes.keys()
def getProbeTypeByName(self, name):
"""
Get probe type by name
@param name:
@type name:
"""
if name in self.probes:
return self.probes[name].getProbeType()
else:
return ''
def loadDefault (self, data):
"""
Loads default probes
@param data:
@type data: dict
"""
self.probesDefault.clear()
for defProbe in data:
defProbeItem = ProbeDefaultItem( probe = defProbe, parent= self.probesDefault)
def loadData (self, data, dataInstalled=None):
"""
Loads probes
@param data:
@type data: dict
@param dataInstalled:
@type dataInstalled:
"""
if isinstance(data, dict):
data = [ data ]
self.probesRegistered.clear()
for probe in data:
probeItem = ProbeItem( probe = probe, parent= self.probesRegistered)
self.probes[probe['id']] = probeItem
# load tests stats
if dataInstalled is not None:
if len(dataInstalled) == 0:
self.deployBox.setEnabled(False)
self.probesAvailable.setEnabled(False)
def resetNbProbes(self, data=None):
"""
Reset the number of probes
"""
pass
def refreshData (self, data, action):
"""
Refresh probes
@param data:
@type data: dict
@param action: expected values in 'del' and 'add'
@type action: string
"""
if action == 'del':
self.probesRegistered.clear()
self.probes = {}
self.resetNbProbes(data=data)
self.loadData( data = data )
elif action == 'add':
self.resetNbProbes(data=data)
self.loadData( data = data )
else:
self.error( 'action unknown: %s' % str(action) )
def refreshDataDefault(self, data, action):
"""
Refresh probes
@param data:
@type data: dict
@param action: expected values in 'del' and 'add'
@type action: string
"""
if action == 'del':
self.probesDefault.clear()
self.loadDefault( data = data )
elif action == 'add':
self.probesDefault.clear()
self.loadDefault( data = data )
else:
self.error( 'action unknown: %s' % str(action) )
class StackViewer( QWidget ):
" Implements the stack viewer for a debugger "
def __init__( self, debugger, parent = None ):
QWidget.__init__( self, parent )
self.__debugger = debugger
self.currentStack = None
self.currentFrame = 0
self.__createPopupMenu()
self.__createLayout()
if Settings().showStackViewer == False:
self.__onShowHide( True )
return
def __createPopupMenu( self ):
" Creates the popup menu "
self.__framesMenu = QMenu()
self.__setCurrentMenuItem = self.__framesMenu.addAction(
"Set current (single click)", self.__onSetCurrent )
self.__jumpMenuItem = self.__framesMenu.addAction(
"Set current and jump to the source (double click)",
self.__onSetCurrentAndJump )
return
def __createLayout( self ):
" Creates the widget layout "
verticalLayout = QVBoxLayout( self )
verticalLayout.setContentsMargins( 0, 0, 0, 0 )
verticalLayout.setSpacing( 0 )
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle( QFrame.StyledPanel )
self.headerFrame.setAutoFillBackground( True )
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color( QPalette.Background )
headerBackground.setRgb( min( headerBackground.red() + 30, 255 ),
min( headerBackground.green() + 30, 255 ),
min( headerBackground.blue() + 30, 255 ) )
headerPalette.setColor( QPalette.Background, headerBackground )
self.headerFrame.setPalette( headerPalette )
self.headerFrame.setFixedHeight( 24 )
self.__stackLabel = QLabel( "Stack" )
expandingSpacer = QSpacerItem( 10, 10, QSizePolicy.Expanding )
fixedSpacer = QSpacerItem( 3, 3 )
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setFixedSize( 20, 20 )
self.__showHideButton.setToolTip( "Hide frames list" )
self.__showHideButton.setFocusPolicy( Qt.NoFocus )
self.__showHideButton.clicked.connect( self.__onShowHide )
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins( 0, 0, 0, 0 )
headerLayout.addSpacerItem( fixedSpacer )
headerLayout.addWidget( self.__stackLabel )
headerLayout.addSpacerItem( expandingSpacer )
headerLayout.addWidget( self.__showHideButton )
self.headerFrame.setLayout( headerLayout )
self.__framesList = QTreeWidget( self )
self.__framesList.setSortingEnabled( False )
# I might not need that because of two reasons:
# - the window has no focus
# - the window has custom current indicator
# self.__framesList.setAlternatingRowColors( True )
self.__framesList.setRootIsDecorated( False )
self.__framesList.setItemsExpandable( False )
self.__framesList.setUniformRowHeights( True )
self.__framesList.setSelectionMode( QAbstractItemView.NoSelection )
self.__framesList.setSelectionBehavior( QAbstractItemView.SelectRows )
self.__framesList.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.__framesList.setFocusPolicy( Qt.NoFocus )
self.__framesList.setContextMenuPolicy( Qt.CustomContextMenu )
self.__framesList.itemClicked.connect( self.__onFrameClicked )
self.__framesList.itemDoubleClicked.connect( self.__onFrameDoubleClicked )
self.__framesList.customContextMenuRequested.connect( self.__showContextMenu )
self.__framesList.setHeaderLabels( [ "", "File:line", "Function",
"Full path" ] )
verticalLayout.addWidget( self.headerFrame )
verticalLayout.addWidget( self.__framesList )
return
def __onShowHide( self, startup = False ):
" Triggered when show/hide button is clicked "
if startup or self.__framesList.isVisible():
self.__framesList.setVisible( False )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'more.png' ) )
self.__showHideButton.setToolTip( "Show frames list" )
self.__minH = self.minimumHeight()
self.__maxH = self.maximumHeight()
self.setMinimumHeight( self.headerFrame.height() )
self.setMaximumHeight( self.headerFrame.height() )
Settings().showStackViewer = False
else:
self.__framesList.setVisible( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setToolTip( "Hide frames list" )
self.setMinimumHeight( self.__minH )
self.setMaximumHeight( self.__maxH )
Settings().showStackViewer = True
return
def clear( self ):
" Clears the content "
self.__framesList.clear()
self.currentStack = None
self.__stackLabel.setText( "Stack" )
return
def __resizeColumns( self ):
" Resize the files list columns "
self.__framesList.header().setStretchLastSection( True )
self.__framesList.header().resizeSections(
QHeaderView.ResizeToContents )
self.__framesList.header().resizeSection( 0, 22 )
self.__framesList.header().setResizeMode( 0, QHeaderView.Fixed )
return
def populate( self, stack ):
" Sets the new call stack and selects the first item in it "
self.clear()
self.currentStack = stack
self.currentFrame = 0
frameNumber = 0
for s in stack:
if len( s ) == 2:
# This is when an exception comes
funcName = ""
else:
funcName = s[ 2 ]
item = StackFrameItem( s[ 0 ], s[ 1 ], funcName, frameNumber )
self.__framesList.addTopLevelItem( item )
frameNumber += 1
self.__resizeColumns()
self.__framesList.topLevelItem( 0 ).setCurrent( True )
self.__stackLabel.setText( "Stack (total: " +
str( len( stack ) ) + ")" )
return
def getFrameNumber( self ):
" Provides the current frame number "
return self.currentFrame
def __onFrameClicked( self, item, column ):
" Triggered when a frame is clicked "
if item.isCurrent():
return
# Hide the current indicator
self.__framesList.topLevelItem( self.currentFrame ).setCurrent( False )
# Show the new indicator
self.currentFrame = item.getFrameNumber()
for index in xrange( self.__framesList.topLevelItemCount() ):
item = self.__framesList.topLevelItem( index )
if item.getFrameNumber() == self.currentFrame:
item.setCurrent( True )
self.__debugger.remoteClientVariables( 1, self.currentFrame ) # globals
self.__debugger.remoteClientVariables( 0, self.currentFrame ) # locals
return
def __onFrameDoubleClicked( self, item, column ):
" Triggered when a frame is double clicked "
# The frame has been switched already because the double click
# signal always comes after the single click one
fileName = item.getFilename()
lineNumber = item.getLineNumber()
editorsManager = GlobalData().mainWindow.editorsManager()
editorsManager.openFile( fileName, lineNumber )
editor = editorsManager.currentWidget().getEditor()
editor.gotoLine( lineNumber )
editorsManager.currentWidget().setFocus()
return
def __showContextMenu( self, coord ):
" Shows the frames list context menu "
self.__contextItem = self.__framesList.itemAt( coord )
if self.__contextItem is not None:
self.__setCurrentMenuItem.setEnabled(
not self.__contextItem.isCurrent() )
self.__framesMenu.popup( QCursor.pos() )
return
def __onSetCurrent( self ):
" Context menu item handler "
self.__onFrameClicked( self.__contextItem, 0 )
return
def __onSetCurrentAndJump( self ):
" Context menu item handler "
self.__onFrameClicked( self.__contextItem, 0 )
self.__onFrameDoubleClicked( self.__contextItem, 0 )
return
def switchControl( self, isInIDE ):
" Switches the UI depending where the control flow is "
self.__framesList.setEnabled( isInIDE )
return
class PymetricsViewer(QWidget):
" Pymetrics tab widget "
# Limits to colorize the McCabe score
LittleRiskLimit = 10
ModerateRiskLimit = 20
HighRiskLimit = 50
# Options of providing a report
SingleFile = 0
DirectoryFiles = 1
ProjectFiles = 2
SingleBuffer = 3
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.__reportUUID = ""
self.__reportFileName = ""
self.__reportOption = -1
self.__reportShown = False
self.__report = None
# Prepare members for reuse
self.__noneLabel = QLabel("\nNo results available")
self.__noneLabel.setFrameShape(QFrame.StyledPanel)
self.__noneLabel.setAlignment(Qt.AlignHCenter)
self.__headerFont = self.__noneLabel.font()
self.__headerFont.setPointSize(self.__headerFont.pointSize() + 4)
self.__noneLabel.setFont(self.__headerFont)
self.__noneLabel.setAutoFillBackground(True)
noneLabelPalette = self.__noneLabel.palette()
noneLabelPalette.setColor(QPalette.Background,
GlobalData().skin.nolexerPaper)
self.__noneLabel.setPalette(noneLabelPalette)
self.__createLayout(parent)
self.__updateButtonsStatus()
return
def __createLayout(self, parent):
" Creates the toolbar and layout "
# Buttons
self.__mcCabeButton = QAction(PixmapCache().getIcon('tableview.png'),
'Switch to McCabe only table view', self)
self.__mcCabeButton.setCheckable(True)
self.connect(self.__mcCabeButton, SIGNAL('toggled(bool)'),
self.__onMcCabe)
self.printButton = QAction(PixmapCache().getIcon('printer.png'),
'Print', self)
#printButton.setShortcut( 'Ctrl+' )
self.connect(self.printButton, SIGNAL('triggered()'), self.__onPrint)
self.printButton.setVisible(False)
self.printPreviewButton = QAction(
PixmapCache().getIcon('printpreview.png'), 'Print preview', self)
#printPreviewButton.setShortcut( 'Ctrl+' )
self.connect(self.printPreviewButton, SIGNAL('triggered()'),
self.__onPrintPreview)
self.printPreviewButton.setVisible(False)
spacer = QWidget()
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.clearButton = QAction(PixmapCache().getIcon('trash.png'), 'Clear',
self)
self.connect(self.clearButton, SIGNAL('triggered()'), self.__clear)
# The toolbar
self.toolbar = QToolBar(self)
self.toolbar.setOrientation(Qt.Vertical)
self.toolbar.setMovable(False)
self.toolbar.setAllowedAreas(Qt.RightToolBarArea)
self.toolbar.setIconSize(QSize(16, 16))
self.toolbar.setFixedWidth(28)
self.toolbar.setContentsMargins(0, 0, 0, 0)
self.toolbar.addAction(self.__mcCabeButton)
self.toolbar.addAction(self.printPreviewButton)
self.toolbar.addAction(self.printButton)
self.toolbar.addWidget(spacer)
self.toolbar.addAction(self.clearButton)
self.__totalResultsTree = QTreeWidget()
self.__totalResultsTree.setAlternatingRowColors(True)
self.__totalResultsTree.setRootIsDecorated(True)
self.__totalResultsTree.setItemsExpandable(True)
self.__totalResultsTree.setUniformRowHeights(True)
self.__totalResultsTree.setItemDelegate(NoOutlineHeightDelegate(4))
headerLabels = ["Path / name", "Value", ""]
self.__totalResultsTree.setHeaderLabels(headerLabels)
self.connect(self.__totalResultsTree,
SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self.__allItemActivated)
self.connect(self.__totalResultsTree,
SIGNAL("itemExpanded(QTreeWidgetItem *)"),
self.__onResultsExpanded)
self.__totalResultsTree.setColumnHidden(2, True)
self.__totalResultsTree.hide()
self.__mcCabeTable = QTreeWidget()
self.__mcCabeTable.setAlternatingRowColors(True)
self.__mcCabeTable.setRootIsDecorated(False)
self.__mcCabeTable.setItemsExpandable(False)
self.__mcCabeTable.setSortingEnabled(True)
self.__mcCabeTable.setItemDelegate(NoOutlineHeightDelegate(4))
self.__mcCabeTable.setUniformRowHeights(True)
headerLabels = ["", "File name", "Object", "McCabe Complexity"]
self.__mcCabeTable.setHeaderLabels(headerLabels)
self.connect(self.__mcCabeTable,
SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self.__mcCabeActivated)
self.__mcCabeTable.hide()
self.__hLayout = QHBoxLayout()
self.__hLayout.setContentsMargins(0, 0, 0, 0)
self.__hLayout.setSpacing(0)
self.__hLayout.addWidget(self.toolbar)
self.__hLayout.addWidget(self.__noneLabel)
self.__hLayout.addWidget(self.__totalResultsTree)
self.__hLayout.addWidget(self.__mcCabeTable)
self.setLayout(self.__hLayout)
return
def getTotalResultsWidget(self):
" Provides a reference to the total results widget "
return self.__totalResultsTree
def getMcCabeResultsWidget(self):
" Provides a reference to the McCabe results widget "
return self.__mcCabeTable
def __updateButtonsStatus(self):
" Updates the buttons status "
self.__mcCabeButton.setEnabled(self.__reportShown)
self.printButton.setEnabled(self.__reportShown)
self.printPreviewButton.setEnabled(self.__reportShown)
self.clearButton.setEnabled(self.__reportShown)
return
def __onResultsExpanded(self, item):
" An item has been expanded, so the column width should be adjusted "
self.__totalResultsTree.header().resizeSections(
QHeaderView.ResizeToContents)
return
def __onPrint(self):
" Triggered when the print button is pressed "
pass
def __onPrintPreview(self):
" triggered when the print preview button is pressed "
pass
def __onMcCabe(self, state):
" Triggered when the metrics view is switched "
if not self.__reportShown:
return
if state:
self.__totalResultsTree.hide()
self.__mcCabeTable.show()
self.__mcCabeButton.setIcon(PixmapCache().getIcon('treeview.png'))
self.__mcCabeButton.setToolTip("Switch to complete "
"results tree view")
else:
self.__mcCabeTable.hide()
self.__totalResultsTree.show()
self.__mcCabeButton.setIcon(PixmapCache().getIcon('tableview.png'))
self.__mcCabeButton.setToolTip("Switch to McCabe only table view")
return
def setFocus(self):
" Overridden setFocus "
self.__hLayout.setFocus()
return
def __clear(self):
" Clears the content of the vertical layout "
if not self.__reportShown:
return
self.__totalResultsTree.clear()
self.__totalResultsTree.hide()
self.__mcCabeTable.clear()
self.__mcCabeTable.hide()
self.__noneLabel.show()
self.__report = None
self.__reportShown = False
self.__updateButtonsStatus()
# self.resizeEvent()
self.__mcCabeButton.setIcon(PixmapCache().getIcon('tableview.png'))
self.__mcCabeButton.setToolTip("Switch to McCabe only table view")
self.__mcCabeButton.setChecked(False)
self.__updateTooltip()
return
def __updateTooltip(self):
" Generates a signal with appropriate string message "
if not self.__reportShown:
tooltip = "No metrics available"
elif self.__reportOption == self.DirectoryFiles:
tooltip = "Metrics generated for directory: " + \
self.__reportFileName
elif self.__reportOption == self.ProjectFiles:
tooltip = "Metrics generated for the whole project"
elif self.__reportOption == self.SingleFile:
tooltip = "Metrics generated for file: " + self.__reportFileName
elif self.__reportOption == self.SingleBuffer:
tooltip = "Metrics generated for unsaved file: " + \
self.__reportFileName
else:
tooltip = ""
self.emit(SIGNAL('updatePymetricsTooltip'), tooltip)
return
@staticmethod
def __shouldShowFileName(table, column):
" Checks if the file name is the same "
size = table.topLevelItemCount()
if size == 0:
return False
index = size - 1
firstName = table.topLevelItem(index).text(column)
index -= 1
while index >= 0:
if table.topLevelItem(index).text(column) != firstName:
return True
index -= 1
return False
def showReport(self, metrics, reportOption, fileName, uuid):
" Shows the pymetrics results "
self.__clear()
self.__noneLabel.hide()
self.__report = metrics
self.__reportUUID = uuid
self.__reportFileName = fileName
self.__reportOption = reportOption
if len(metrics.report) > 1:
accumulatedBasic = self.__accumulateBasicMetrics()
accItem = QTreeWidgetItem(["Cumulative basic metrics"])
self.__totalResultsTree.addTopLevelItem(accItem)
for key in accumulatedBasic:
bmItem = [
BasicMetrics.metricsOfInterest[key],
splitThousands(str(accumulatedBasic[key]))
]
basicMetric = QTreeWidgetItem(bmItem)
accItem.addChild(basicMetric)
# Add the complete information
for fileName in metrics.report:
if reportOption == self.SingleBuffer:
fileItem = QTreeWidgetItem(["Editor buffer"])
else:
fileItem = QTreeWidgetItem([fileName])
info = GlobalData().briefModinfoCache.get(fileName)
if info.docstring is not None:
fileItem.setToolTip(0, info.docstring.text)
else:
fileItem.setToolTip(0, "")
self.__totalResultsTree.addTopLevelItem(fileItem)
# Messages part
messages = metrics.report[fileName].messages
if len(messages) > 0:
messagesItem = QTreeWidgetItem(["Messages"])
fileItem.addChild(messagesItem)
for message in messages:
mItem = [message, "", "E"]
messagesItem.addChild(QTreeWidgetItem(mItem))
# Basic metrics part
basicItem = QTreeWidgetItem(["Basic metrics"])
fileItem.addChild(basicItem)
basic = metrics.report[fileName].basicMetrics
for key in basic.metrics:
bmItem = [
BasicMetrics.metricsOfInterest[key],
str(basic.metrics[key])
]
basicMetric = QTreeWidgetItem(bmItem)
basicItem.addChild(basicMetric)
# McCabe part
mccabeItem = QTreeWidgetItem(["McCabe metrics"])
fileItem.addChild(mccabeItem)
mccabe = metrics.report[fileName].mcCabeMetrics.metrics
for objName in mccabe:
objItem = [objName, str(mccabe[objName]), "M"]
mccabeMetric = QTreeWidgetItem(objItem)
mccabeItem.addChild(mccabeMetric)
# COCOMO 2 part
cocomo = [
"COCOMO 2",
str(metrics.report[fileName].cocomo2Metrics.value)
]
cocomoItem = QTreeWidgetItem(cocomo)
fileItem.addChild(cocomoItem)
# Resizing the table
self.__totalResultsTree.header().resizeSections(
QHeaderView.ResizeToContents)
# Add McCabe complexity information
for fileName in metrics.report:
mccabe = metrics.report[fileName].mcCabeMetrics.metrics
for objName in mccabe:
values = ["", fileName, objName, str(mccabe[objName])]
self.__mcCabeTable.addTopLevelItem(McCabeTableItem(values))
if not self.__shouldShowFileName(self.__mcCabeTable, 1):
self.__mcCabeTable.setColumnHidden(1, True)
# Resizing and sorting the table
self.__mcCabeTable.header().setSortIndicator(3, Qt.DescendingOrder)
self.__mcCabeTable.sortItems(
3,
self.__mcCabeTable.header().sortIndicatorOrder())
self.__mcCabeTable.header().resizeSections(
QHeaderView.ResizeToContents)
# Show the complete information
self.__mcCabeTable.hide()
self.__totalResultsTree.show()
self.__reportShown = True
self.__updateButtonsStatus()
self.__updateTooltip()
# It helps, but why do I have flickering?
QApplication.processEvents()
return
def __accumulateBasicMetrics(self):
" Accumulates basic metrics for all the processed files "
basic = {}
for fileName in self.__report.report:
singleBasic = self.__report.report[fileName].basicMetrics.metrics
for key in singleBasic:
if not key.startswith('num'):
continue
if key in basic:
basic[key] += int(singleBasic[key])
else:
basic[key] = int(singleBasic[key])
return basic
def __mcCabeActivated(self, item, column):
" Handles the double click (or Enter) on the mccabe table item "
objName = str(item.text(2))
if self.__reportOption == self.SingleBuffer:
if os.path.isabs(self.__reportFileName):
fileName = self.__reportFileName
else:
fileName = ""
else:
fileName = str(item.text(1))
self.__onMcCabeObject(objName, fileName)
return
def __allItemActivated(self, item, column):
" Handles the double click (or Enter) in the total results tree "
# We process only the error messages and McCabe items
hiddenColumnText = str(item.text(2))
if not hiddenColumnText in ["M", "E"]:
return
fileName = self.__getTreeItemFileName(item)
lineNumber = 0
if hiddenColumnText == "M":
# This is McCabe item
objName = str(item.text(0))
self.__onMcCabeObject(objName, fileName)
return
elif hiddenColumnText == "E":
# This is an error message
message = str(item.text(0))
pos = message.find("at line")
if pos == -1:
logging.error("Unknown format of the message. "
"Please inform the developers.")
return
parts = message[pos:].split()
try:
lineNumber = int(parts[2].replace(',', ''))
except:
logging.error("Unknown format of the message. "
"Please inform the developers.")
return
if fileName == "":
# This is an unsaved buffer, try to find the editor by UUID
mainWindow = GlobalData().mainWindow
widget = mainWindow.getWidgetByUUID(self.__reportUUID)
if widget is None:
logging.error("The unsaved buffer has been closed")
return
# The widget was found, so jump to the required
editor = widget.getEditor()
editor.gotoLine(lineNumber)
editor.setFocus()
return
GlobalData().mainWindow.openFile(fileName, lineNumber)
return
def __getTreeItemFileName(self, item):
" Identifies the tree view item file name "
if self.__reportOption == self.SingleBuffer:
if os.path.isabs(self.__reportFileName):
return self.__reportFileName
return ""
# The file name is always two levels up
fileItem = item.parent().parent()
return str(fileItem.text(0))
def __onMcCabeObject(self, objName, fileName):
" Called when the user activated McCabe item "
info = None
mainWindow = GlobalData().mainWindow
widget = mainWindow.getWidgetByUUID(self.__reportUUID)
if widget is None:
if fileName == "":
logging.error("The unsaved buffer has been closed")
return
# No widget, but we know the file name
info = getBriefModuleInfoFromFile(fileName)
else:
# The widget was found
editor = widget.getEditor()
# The editor content has been modified, so re-parse the buffer
info = getBriefModuleInfoFromMemory(editor.text())
parts = objName.split('.')
currentIndex = 0
functionsContainer = info.functions
classesContainer = info.classes
line = -1
if objName == "__main__" and len(parts) == 1:
# Special case - global file scope
line = 1
currentIndex = 1
while currentIndex < len(parts):
found = False
for func in functionsContainer:
if func.name == parts[currentIndex]:
if currentIndex == len(parts) - 1:
# Found, jump to the line
line = func.line
break
functionsContainer = func.functions
classesContainer = func.classes
found = True
break
if line != -1:
break
if found:
currentIndex += 1
continue
for klass in classesContainer:
if klass.name == parts[currentIndex]:
if currentIndex == len(parts) - 1:
# Found, jump to the line
line = klass.line
break
functionsContainer = klass.functions
classesContainer = klass.classes
found = True
if line != -1:
break
if found:
currentIndex += 1
continue
# Not found
logging.error("Cannot find the " + objName)
return
# Here we have the line number
if widget is None:
GlobalData().mainWindow.openFile(fileName, line)
else:
editor = widget.getEditor()
editor.gotoLine(line)
editor.setFocus()
return
def onFileUpdated(self, fileName, uuid):
" Called when a buffer is saved or saved as "
if not self.__reportShown:
return
if self.__reportUUID != uuid:
return
# Currently shown report is for the saved buffer
# File name is expected being absolute
self.__reportFileName = fileName
self.emit(SIGNAL('updatePymetricsTooltip'),
"Metrics generated for buffer saved as " + fileName)
return
class MembersWidget(QWidget):
def __init__(self, parent, logger):
super(MembersWidget, self).__init__(parent)
self.logger = logger
layout = QVBoxLayout(self)
layout.setSpacing(0)
self.dropdown_members_dict = {}
self.dropdown_members_model = DropdownModel(get_peers(), self.logger)
self.dropdown_members = QComboBox(self)
self.dropdown_members.setModel(self.dropdown_members_model)
topLayout = QHBoxLayout()
topLayout.setSpacing(10)
topLayout.addWidget(self.dropdown_members, 1)
self.requestLogsButton = QPushButton("Request Logfiles", self)
topLayout.addWidget(self.requestLogsButton)
layout.addLayout(topLayout)
layout.addWidget(QLabel("Member Information:", self))
self.memberInformationTable = QTreeWidget(self)
self.memberInformationTable.setMaximumHeight(65)
self.memberInformationTable.setSelectionMode(QTreeWidget.NoSelection)
layout.addWidget(self.memberInformationTable, 0)
layout.addWidget(QLabel("Send Message:", self))
sendMessageLayout = QHBoxLayout()
sendMessageLayout.setSpacing(10)
messageInput = HistoryLineEdit(self, "Enter a message")
self.sendMessageButton = QPushButton("Send", self)
sendMessageLayout.addWidget(messageInput, 1)
sendMessageLayout.addWidget(self.sendMessageButton)
layout.addLayout(sendMessageLayout)
layout.addWidget(QLabel("Log files:", self))
logSplitter = QSplitter(Qt.Horizontal, self)
logListWidget = QWidget(self)
logListLayout = QVBoxLayout(logListWidget)
logListLayout.setContentsMargins(0, 0, 0, 0)
self.log_tree_view = QTreeWidget(logSplitter)
self.log_tree_view.setAlternatingRowColors(True)
self.log_tree_view.setColumnCount(1)
self.log_tree_view.setHeaderHidden(True)
self.log_tree_view.setItemsExpandable(False)
self.log_tree_view.setIndentation(0)
logListLayout.addWidget(self.log_tree_view, 1)
logListBottomLayout = QHBoxLayout()
self.logSizeLabel = QLabel(logListWidget)
logListBottomLayout.addWidget(self.logSizeLabel, 1)
self.clearLogsButton = QPushButton("Clear", logListWidget)
self.clearLogsButton.setEnabled(False)
self.clearLogsButton.clicked.connect(self.clearLogs)
logListBottomLayout.addWidget(self.clearLogsButton, 0)
logListLayout.addLayout(logListBottomLayout)
logSplitter.addWidget(logListWidget)
self.log_area = QTextEdit(logListWidget)
self.log_area.setLineWrapMode(QTextEdit.WidgetWidth)
self.log_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.log_area.setReadOnly(True)
logSplitter.addWidget(self.log_area)
logSplitter.setStretchFactor(0, 0)
logSplitter.setStretchFactor(1, 1)
layout.addWidget(logSplitter, 1)
self.memberSelectionChanged()
self.log_tree_view.selectionModel().selectionChanged.connect(self.displaySelectedLogfile)
self.dropdown_members.currentIndexChanged.connect(self.memberSelectionChanged)
self.requestLogsButton.clicked.connect(self.requestLogClicked)
self.sendMessageButton.clicked.connect(partial(self.sendMessageToMember, messageInput))
messageInput.returnPressed.connect(partial(self.sendMessageToMember, messageInput))
get_notification_center().connectPeerAppended(self.dropdown_members_model.externalRowAppended)
get_notification_center().connectPeerUpdated(self.dropdown_members_model.externalRowUpdated)
get_notification_center().connectPeerRemoved(self.dropdown_members_model.externalRowRemoved)
get_notification_center().connectPeerUpdated(self.updateMemberInformation)
def destroy_widget(self):
get_notification_center().disconnectPeerAppended(self.dropdown_members_model.externalRowAppended)
get_notification_center().disconnectPeerUpdated(self.dropdown_members_model.externalRowUpdated)
get_notification_center().disconnectPeerRemoved(self.dropdown_members_model.externalRowRemoved)
get_notification_center().disconnectPeerUpdated(self.updateMemberInformation)
def listLogfiles(self, basePath, sort=None):
if sort is None:
sort = lambda aFile: -self.getLogNumber(aFile)
logList = [
os.path.join(basePath, aFile)
for aFile in os.listdir(basePath)
if aFile.endswith(".log") and not os.path.isdir(os.path.join(basePath, aFile))
]
return sorted(logList, key=sort)
def getNumLogsToKeep(self, oldLogFiles, newLogFiles, logOffset):
oldestNew = None
for aLogFile in newLogFiles:
oldestNew, _ = self.getLogDates(aLogFile)
if oldestNew != None:
break
if oldestNew == None:
# new new log file contains timestamps (they are probably all empty)
return len(oldLogFiles)
numToKeep = 0
while numToKeep < len(oldLogFiles) - logOffset:
curTime, _ = self.getLogDates(oldLogFiles[numToKeep])
if curTime == None or curTime < oldestNew:
# keep empty log files
numToKeep = numToKeep + 1
else:
break
return numToKeep
def getLogDates(self, aLogFile):
with codecs.open(aLogFile, "rb", "utf-8") as logContent:
logLines = logContent.readlines()
firstDate = None
for aLine in logLines:
firstDate = getLogLineTime(aLine)
if firstDate != None:
break
lastDate = None
for aLine in reversed(logLines):
lastDate = getLogLineTime(aLine)
if lastDate != None:
break
return firstDate, lastDate
def getLogNumber(self, aLogFile):
aLogFile = os.path.basename(aLogFile)
try:
return int(aLogFile[: aLogFile.rfind(".")])
except:
return -1
def shiftLogFiles(self, oldLogFiles, numToKeep, shift, logOffset):
renamedLogfiles = []
for index, aFile in enumerate(oldLogFiles):
logNum = self.getLogNumber(aFile)
if logNum < logOffset:
# don't touch up-to-date logs
break
if index < numToKeep:
newName = os.path.join(os.path.dirname(aFile), "%d.log" % (logNum + shift))
renamedLogfiles.append((len(oldLogFiles) - index - 1, aFile, newName))
os.rename(aFile, newName)
else:
os.remove(aFile)
return renamedLogfiles
def handleNewLogFiles(self, basePath, tmpPath, logOffset=0):
oldLogFiles = self.listLogfiles(basePath)
newLogFiles = self.listLogfiles(tmpPath)
# check how many log files are actually new
numToKeep = self.getNumLogsToKeep(oldLogFiles, newLogFiles, logOffset)
# rename / remove old log files to make room for the new ones
numNew = len(newLogFiles) - (len(oldLogFiles) - logOffset - numToKeep)
renamedLogfiles = self.shiftLogFiles(oldLogFiles, numToKeep, numNew, logOffset)
# move new log files
addedLogfiles = []
for index, aLogFile in enumerate(reversed(newLogFiles)):
shutil.move(aLogFile, basePath)
if index < numNew:
addedLogfiles.append((index + logOffset, os.path.join(basePath, os.path.basename(aLogFile))))
shutil.rmtree(tmpPath, True)
return numNew, addedLogfiles, renamedLogfiles
def requestFinished(self):
self.requestLogsButton.setEnabled(True)
self.dropdown_members.setEnabled(True)
@loggingSlot(QThread, object)
def cb_log_transfer_success(self, thread, path):
path = convert_string(path)
basePath = os.path.dirname(path)
tmpPath = os.path.join(basePath, "tmp")
if not os.path.exists(tmpPath):
os.makedirs(tmpPath)
logsAdded = []
if path.endswith(".tgz"):
# extract received log files
with contextlib.closing(tarfile.open(path, "r:gz")) as tarContent:
tarContent.extractall(tmpPath)
_, logsAdded, logsRenamed = self.handleNewLogFiles(basePath, tmpPath)
self.requestFinished()
else:
# log comes from old version
logNum = 0
if thread.sender in self.logRequests:
logNum, requestTime = self.logRequests[thread.sender]
now = datetime.now()
td = now - requestTime
tdSeconds = (td.microseconds + (td.seconds + td.days * 24 * 3600) * 10 ** 6) / 10 ** 6
if tdSeconds > self.LOG_REQUEST_TIMEOUT:
# request timed out or was finished already
logNum = 0
shutil.move(path, os.path.join(tmpPath, "%d.log" % logNum))
numNew, logsAdded, logsRenamed = self.handleNewLogFiles(basePath, tmpPath, logNum)
if numNew > 0 and logNum < 9:
# there might be more new ones
self.logRequests[thread.sender] = (logNum + 1, datetime.now())
self.logger.debug("log seems to be new, another!!!")
logsAdded.append((logNum + 1, None))
self.request_log(thread.sender, logNum + 1)
elif thread.sender in self.logRequests:
# request finished
del self.logRequests[thread.sender]
self.requestFinished()
else:
self.requestFinished()
if len(logsAdded) > 0 or len(logsRenamed) > 0:
self.updateLogList(logsAdded, logsRenamed)
@loggingSlot(QThread, object)
def cb_log_transfer_error(self, _thread, message):
if not self.isVisible():
return False
self.log_area.setText("Error while getting log (%s)" % message)
self.requestFinished()
def get_selected_log_member(self):
member = convert_string(self.dropdown_members.currentText())
if not member:
return None
if "(" in member:
# member contains name, extract ID
member = member[member.rfind("(") + 1 : member.rfind(")")]
return member
def request_log(self, member=None, logNum=0):
if member == None:
member = self.get_selected_log_member()
if member != None:
self.logger.debug("Requesting log %d from %s", logNum, member)
get_server().call(
"HELO_REQUEST_LOGFILE %s %d" % (DataReceiverThread.getOpenPort(category="log%s" % member), logNum),
set([member]),
)
else:
self.log_area.setText("No Member selected!")
@loggingSlot()
def requestLogClicked(self):
self.requestLogsButton.setEnabled(False)
self.dropdown_members.setEnabled(False)
self.updateLogList([(0, None)])
self.request_log()
def listLogFilesForMember(self, member):
if member is None:
return []
logDir = os.path.join(get_settings().get_main_config_dir(), "logs", member)
if not os.path.exists(logDir):
return []
return self.listLogfiles(logDir)
def numLogFilesForMember(self, member):
return len(self.listLogFilesForMember(member))
def requestTimedOut(self, item):
if not sip.isdeleted(item) and item != None and item.data(0, Qt.UserRole) == None:
self.log_tree_view.takeTopLevelItem(self.log_tree_view.indexFromItem(item).row())
self.requestFinished()
def formatFileSize(self, num):
for x in ["Bytes", "KB", "MB", "GB", "TB"]:
if num < 1024.0:
return "%3.1f %s" % (num, x)
num /= 1024.0
def initializeLogItem(self, item, logFile):
firstDate, lastDate = self.getLogDates(logFile)
text = None
tooltip = None
if firstDate != None:
text = firstDate.strftime("%Y-%m-%d %H:%M:%S")
tooltip = u"File: %s\nFirst entry: %s\nLast entry: %s" % (
logFile,
firstDate.strftime("%Y-%m-%d %H:%M:%S"),
lastDate.strftime("%Y-%m-%d %H:%M:%S"),
)
else:
timestamp = datetime.fromtimestamp(os.path.getmtime(logFile)).strftime("%Y-%m-%d %H:%M:%S")
text = u"%s" % os.path.basename(logFile)
tooltip = u"File:%s\nModification Date: %s" % (logFile, timestamp)
text = text + "\n%s" % self.formatFileSize(os.path.getsize(logFile))
if tooltip != None:
item.setData(0, Qt.ToolTipRole, QVariant(tooltip))
item.setData(0, Qt.UserRole, logFile)
item.setData(0, Qt.DisplayRole, QVariant(text))
@loggingSlot()
def clearLogs(self):
for aLogFile in self.listLogFilesForMember(self.get_selected_log_member()):
os.remove(aLogFile)
self.updateLogList()
def updateLogList(self, logsAdded=None, logsRenamed=None):
selectedMember = self.get_selected_log_member()
if logsAdded == None:
self.log_tree_view.clear()
logsAdded = []
for index, logFile in enumerate(reversed(self.listLogFilesForMember(selectedMember))):
logsAdded.append((index, logFile))
if len(logsAdded) == 0:
self.log_tree_view.clear()
self.log_tree_view.addTopLevelItem(
QTreeWidgetItem(self.log_tree_view, QStringList("No logs available."))
)
self.log_tree_view.setSelectionMode(QTreeWidget.NoSelection)
self.logSizeLabel.setText("No logs")
self.clearLogsButton.setEnabled(False)
return
if logsRenamed != None:
for index, oldName, newName in logsRenamed:
# index + 1 because of the "requesting" item
item = self.log_tree_view.topLevelItem(index + 1)
if item != None:
itemLogFile = convert_string(item.data(0, Qt.UserRole).toString())
if itemLogFile != oldName:
self.logger.warning(
"index does not correspond to item in list:\n\t%s\n\t%s", itemLogFile, oldName
)
self.initializeLogItem(item, newName)
if len(logsAdded) == 0:
self.log_tree_view.takeTopLevelItem(0)
else:
for index, logFile in logsAdded:
oldItem = self.log_tree_view.topLevelItem(index)
item = None
if oldItem != None and oldItem.data(0, Qt.UserRole) == None:
# requested item has been received
item = oldItem
else:
item = QTreeWidgetItem()
oldItem = None
if logFile == None:
item.setData(0, Qt.DisplayRole, QVariant("Requesting..."))
QTimer.singleShot(6000, partial(self.requestTimedOut, item))
else:
self.initializeLogItem(item, logFile)
if oldItem == None:
# else, the old item is being modified
self.log_tree_view.insertTopLevelItem(index, item)
self.log_tree_view.setSelectionMode(QTreeWidget.SingleSelection)
totalSize = 0
for aLogFile in self.listLogFilesForMember(selectedMember):
totalSize += os.path.getsize(aLogFile)
self.logSizeLabel.setText("%s consumed" % self.formatFileSize(totalSize))
self.clearLogsButton.setEnabled(True)
# self.displaySelectedLogfile()
def getSelectedLogContent(self):
member = self.get_selected_log_member()
if member == None:
return "No Log selected."
selection = self.log_tree_view.selectedIndexes()
if len(selection) is 0:
return "No Log selected."
logPath = convert_string(selection[0].data(Qt.UserRole).toString())
if logPath == None:
return "ERROR: path is None"
if not os.path.exists(logPath):
return "File not found: " + logPath
fcontent = ""
try:
with codecs.open(logPath, "r", "utf8") as fhandler:
fcontent = fhandler.read()
except Exception as e:
self.logger.exception("Error reading file")
fcontent = "Error reading file: %s" % str(e)
return fcontent
@loggingSlot(QItemSelection, QItemSelection)
def displaySelectedLogfile(self, _new, _old):
self.log_area.setText(self.getSelectedLogContent())
@loggingSlot(int)
def memberSelectionChanged(self, _new=None):
self.updateLogList()
isMemberSelected = self.get_selected_log_member() != None
self.sendMessageButton.setEnabled(isMemberSelected)
self.requestLogsButton.setEnabled(isMemberSelected)
self.updateMemberInformation()
@loggingSlot(object)
def sendMessageToMember(self, lineEdit):
selectedMember = self.get_selected_log_member()
if selectedMember != None:
get_server().call(convert_string(lineEdit.text()), set([selectedMember]))
lineEdit.clear()
@loggingSlot(object, object)
def updateMemberInformation(self, peerID=None, peerInfo=None):
if peerID != None and peerID != self.get_selected_log_member():
# only update if selected member updated
return
self.memberInformationTable.clear()
if self.get_selected_log_member() == None:
self.memberInformationTable.setColumnCount(0)
self.memberInformationTable.setHeaderLabel("No member selected.")
return
if peerInfo == None:
peerInfo = get_peers().getPeerInfo(pID=self.get_selected_log_member())
if peerInfo == None:
self.memberInformationTable.setColumnCount(0)
self.memberInformationTable.setHeaderLabel("No member information available.")
return
self.memberInformationTable.setColumnCount(len(peerInfo))
headers = sorted(peerInfo.keys(), key=lambda s: s.lower())
self.memberInformationTable.setHeaderLabels(QStringList(headers))
item = QTreeWidgetItem(self.memberInformationTable)
for col, header in enumerate(headers):
item.setData(col, Qt.DisplayRole, QVariant(peerInfo[header]))
for col in range(self.memberInformationTable.columnCount()):
self.memberInformationTable.resizeColumnToContents(col)
class WServerReleaseNote(QWidget, Logger.ClassLogger):
"""
Widget for display all release notes
"""
def __init__(self, parent = None):
"""
Constructs WServerReleaseNote widget
@param parent:
@type parent:
"""
QWidget.__init__(self, parent)
self.parent = parent
self.name = self.tr("Release Notes")
self.createWidgets()
self.deactivate()
def createWidgets(self):
"""
QtWidgets creation
"""
self.mainTab = QTabWidget()
mainLayout = QVBoxLayout()
self.toRead = QLabel( "%s" % "Release notes are specific to each version of the server, SUT adapters, libraries and toolbox. More details on each HISTORY files." )
mainLayout.addWidget(self.toRead)
mainLayout.addWidget(self.mainTab)
palette = QPalette()
brush = QBrush(QColor(240, 240, 240))
brush.setStyle(Qt.SolidPattern)
palette.setBrush(QPalette.Active, QPalette.Base, brush)
# treewidget for server rn
self.rn = QTreeWidget(self)
self.rn.setHeaderHidden(True)
self.rn.setFrameShape(QFrame.NoFrame)
self.rn.setSelectionMode(QAbstractItemView.NoSelection)
self.rn.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
self.rn.setRootIsDecorated(False)
self.rn.setPalette(palette)
# treewidget for adapter rn
self.rnAdp = QTreeWidget(self)
self.rnAdp.setHeaderHidden(True)
self.rnAdp.setFrameShape(QFrame.NoFrame)
self.rnAdp.setSelectionMode(QAbstractItemView.NoSelection)
self.rnAdp.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
self.rnAdp.setRootIsDecorated(False)
self.rnAdp.setPalette(palette)
# treewidget for library rn
self.rnLibAdp = QTreeWidget(self)
self.rnLibAdp.setHeaderHidden(True)
self.rnLibAdp.setFrameShape(QFrame.NoFrame)
self.rnLibAdp.setSelectionMode(QAbstractItemView.NoSelection)
self.rnLibAdp.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
self.rnLibAdp.setRootIsDecorated(False)
self.rnLibAdp.setPalette(palette)
# treewidget for agent rn
self.rnToolbox = QTreeWidget(self)
self.rnToolbox.setHeaderHidden(True)
self.rnToolbox.setFrameShape(QFrame.NoFrame)
self.rnToolbox.setSelectionMode(QAbstractItemView.NoSelection)
self.rnToolbox.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
self.rnToolbox.setRootIsDecorated(False)
self.rnToolbox.setPalette(palette)
self.mainTab.addTab( self.rn, Settings.instance().readValue( key = 'Common/acronym-server' ) )
self.mainTab.addTab( self.rnAdp, "Sut Adapters" )
self.mainTab.addTab( self.rnLibAdp, "Sut Librairies" )
self.mainTab.addTab( self.rnToolbox, "Toolbox" )
self.setLayout(mainLayout)
def active (self):
"""
Enables QTreeWidget
Active all qwidget
"""
self.rn.setEnabled(True)
self.rnAdp.setEnabled(True)
self.rnLibAdp.setEnabled(True)
self.rnToolbox.setEnabled(True)
def deactivate (self):
"""
Clears QTreeWidget and disables it
"""
self.rn.clear()
self.rn.setEnabled(False)
self.rnAdp.clear()
self.rnAdp.setEnabled(False)
self.rnLibAdp.clear()
self.rnLibAdp.setEnabled(False)
self.rnToolbox.clear()
self.rnToolbox.setEnabled(False)
def loadData (self, data, dataAdp, dataLibAdp, dataToolbox):
"""
Dispatch data between tas tab and adapter tab
@param data:
@type data:
@param dataAdp:
@type dataAdp:
@param dataProbes:
@type dataProbes:
"""
# load server rn
self.constructItem(parent=self.rn, data= data )
# load adapters rn
if not len(dataAdp): # dataAdp is false then adapters are not installed on the server
emptyItem = KeyItem( key = b"", parent = self.rnAdp, type = 0)
notInstalledItem = KeyItem( key = b" Package adapters not installed on server",
parent = self.rnAdp, type = 1)
else:
try:
self.constructItem(parent=self.rnAdp, data=dataAdp )
except Exception as e:
self.error( e )
# load libraries rn
if not len(dataLibAdp): # dataLibAdp is false then libraries are not installed on the server
emptyItem = KeyItem( key = b"", parent = self.rnLibAdp, type = 0)
notInstalledItem = KeyItem( key = b" Package libraries not installed on server",
parent = self.rnLibAdp, type = 1)
else:
try:
self.constructItem(parent=self.rnLibAdp, data=dataLibAdp )
except Exception as e:
self.error( e )
# load toolbox rn
if not len(dataToolbox): # dataToolbox is false then toolbox are not installed on the server
emptyItem = KeyItem( key = b"", parent = self.rnToolbox, type = 0)
notInstalledItem = KeyItem( key = b" Package toolbox not installed on server",
parent = self.rnToolbox, type = 1)
else:
try:
self.constructItem(parent=self.rnToolbox, data=dataToolbox )
except Exception as e:
self.error( e )
def constructItem (self, parent, data):
"""
Add items to tree widget
@param data:
@type data:
@param parent:
@type parent:
"""
rootItem = None
subItem = None
for line in data.splitlines():
if sys.version_info > (3,):
line = bytes(line, 'utf8')
if not line.startswith(b'\t'): # wrap to bytes for python 3 support
rootItem = KeyItem( key = line, parent = parent, type = 0)
rootItem.setExpanded(True)
elif line.startswith(b'\t\t'): # wrap to bytes for python 3 support
KeyItem( key = line[2:], parent = subItem, type = 2)
elif line.startswith(b'\t'): # wrap to bytes for python 3 support
subItem = KeyItem( key = line[1:], parent = rootItem, type = 1)
subItem.setExpanded(True)
class OWItemsets(widget.OWWidget):
name = "Frequent Itemsets"
description = "Explore sets of items that frequently appear together."
icon = "icons/FrequentItemsets.svg"
priority = 10
inputs = [("Data", Table, "set_data")]
outputs = [(Output.DATA, Table)]
minSupport = settings.Setting(30)
maxItemsets = settings.Setting(10000)
filterSearch = settings.Setting(True)
autoFind = settings.Setting(False)
autoSend = settings.Setting(True)
filterKeywords = settings.Setting("")
filterMinItems = settings.Setting(1)
filterMaxItems = settings.Setting(10000)
UserAdviceMessages = [
widget.Message(
"Itemset are listed in item-sorted order, i.e. "
"an itemset containing A and B is only listed once, as "
"A > B (and not also B > A).",
"itemsets-order",
widget.Message.Warning,
),
widget.Message(
"To select all the itemsets that are descendants of "
"(include) some item X (i.e. the whole subtree), you "
"can fold the subtree at that item and then select it.",
"itemsets-order",
widget.Message.Information,
),
]
def __init__(self):
self._is_running = False
self.isRegexMatch = lambda x: True
self.tree = QTreeWidget(
self.mainArea,
columnCount=2,
allColumnsShowFocus=True,
alternatingRowColors=True,
selectionMode=QTreeWidget.ExtendedSelection,
uniformRowHeights=True,
)
self.tree.setHeaderLabels(["Itemsets", "Support", "%"])
self.tree.header().setStretchLastSection(True)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.mainArea.layout().addWidget(self.tree)
box = gui.widgetBox(self.controlArea, "Info")
self.nItemsets = self.nSelectedExamples = self.nSelectedItemsets = ""
gui.label(box, self, "Number of itemsets: %(nItemsets)s")
gui.label(box, self, "Selected itemsets: %(nSelectedItemsets)s")
gui.label(box, self, "Selected examples: %(nSelectedExamples)s")
hbox = gui.widgetBox(box, orientation="horizontal")
gui.button(hbox, self, "Expand all", callback=self.tree.expandAll)
gui.button(hbox, self, "Collapse all", callback=self.tree.collapseAll)
box = gui.widgetBox(self.controlArea, "Find itemsets")
gui.valueSlider(
box,
self,
"minSupport",
values=[0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1, 0.5] + list(range(1, 101)),
label="Minimal support:",
labelFormat="%g%%",
callback=lambda: self.find_itemsets(),
)
gui.hSlider(
box,
self,
"maxItemsets",
minValue=10000,
maxValue=100000,
step=10000,
label="Max. number of itemsets:",
labelFormat="%d",
callback=lambda: self.find_itemsets(),
)
self.button = gui.auto_commit(box, self, "autoFind", "Find itemsets", commit=self.find_itemsets)
box = gui.widgetBox(self.controlArea, "Filter itemsets")
gui.lineEdit(
box,
self,
"filterKeywords",
"Contains:",
callback=self.filter_change,
orientation="horizontal",
tooltip="A comma or space-separated list of regular " "expressions.",
)
hbox = gui.widgetBox(box, orientation="horizontal")
gui.spin(hbox, self, "filterMinItems", 1, 998, label="Min. items:", callback=self.filter_change)
gui.spin(hbox, self, "filterMaxItems", 2, 999, label="Max. items:", callback=self.filter_change)
gui.checkBox(
box,
self,
"filterSearch",
label="Apply these filters in search",
tooltip="If checked, the itemsets are filtered according "
"to these filter conditions already in the search "
"phase. \nIf unchecked, the only filters applied "
"during search are the ones above, "
"and the itemsets are \nfiltered afterwards only for "
"display, i.e. only the matching itemsets are shown.",
)
gui.rubber(hbox)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, "autoSend", "Send selection")
self.filter_change()
ITEM_DATA_ROLE = Qt.UserRole + 1
def selectionChanged(self):
X = self.X
mapping = self.onehot_mapping
instances = set()
where = np.where
def whole_subtree(node):
yield node
for i in range(node.childCount()):
yield from whole_subtree(node.child(i))
def itemset(node):
while node:
yield node.data(0, self.ITEM_DATA_ROLE)
node = node.parent()
def selection_ranges(node):
n_children = node.childCount()
if n_children:
yield (self.tree.indexFromItem(node.child(0)), self.tree.indexFromItem(node.child(n_children - 1)))
for i in range(n_children):
yield from selection_ranges(node.child(i))
nSelectedItemsets = 0
item_selection = QItemSelection()
for node in self.tree.selectedItems():
nodes = (node,) if node.isExpanded() else whole_subtree(node)
if not node.isExpanded():
for srange in selection_ranges(node):
item_selection.select(*srange)
for node in nodes:
nSelectedItemsets += 1
cols, vals = zip(*(mapping[i] for i in itemset(node)))
if issparse(X):
rows = (len(cols) == np.bincount((X[:, cols] != 0).indices, minlength=X.shape[0])).nonzero()[0]
else:
rows = where((X[:, cols] == vals).all(axis=1))[0]
instances.update(rows)
self.tree.itemSelectionChanged.disconnect(self.selectionChanged)
self.tree.selectionModel().select(item_selection, QItemSelectionModel.Select | QItemSelectionModel.Rows)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.nSelectedExamples = len(instances)
self.nSelectedItemsets = nSelectedItemsets
self.output = self.data[sorted(instances)] or None
self.commit()
def commit(self):
self.send(Output.DATA, self.output)
def filter_change(self):
self.warning(9)
try:
isRegexMatch = self.isRegexMatch = re.compile(
"|".join(i.strip() for i in re.split("(,|\s)+", self.filterKeywords.strip()) if i.strip()),
re.IGNORECASE,
).search
except Exception as e:
self.warning(9, "Error in regular expression: {}".format(e.args[0]))
isRegexMatch = self.isRegexMatch = lambda x: True
def hide(node, depth, has_kw):
if not has_kw:
has_kw = isRegexMatch(node.text(0))
hidden = (
sum(hide(node.child(i), depth + 1, has_kw) for i in range(node.childCount())) == node.childCount()
if node.childCount()
else (not has_kw or not self.filterMinItems <= depth <= self.filterMaxItems)
)
node.setHidden(hidden)
return hidden
hide(self.tree.invisibleRootItem(), 0, False)
class TreeWidgetItem(QTreeWidgetItem):
def data(self, column, role):
"""Construct lazy tooltips"""
if role != Qt.ToolTipRole:
return super().data(column, role)
tooltip = []
while self:
tooltip.append(self.text(0))
self = self.parent()
return " ".join(reversed(tooltip))
def find_itemsets(self):
if self.data is None:
return
if self._is_running:
return
self._is_running = True
data = self.data
self.tree.clear()
self.tree.setUpdatesEnabled(False)
self.tree.blockSignals(True)
class ItemDict(dict):
def __init__(self, item):
self.item = item
top = ItemDict(self.tree.invisibleRootItem())
X, mapping = OneHot.encode(data)
self.onehot_mapping = mapping
ITEM_FMT = "{}" if issparse(data.X) else "{}={}"
names = {
item: ITEM_FMT.format(var.name, val) for item, var, val in OneHot.decode(mapping.keys(), data, mapping)
}
nItemsets = 0
filterSearch = self.filterSearch
filterMinItems, filterMaxItems = self.filterMinItems, self.filterMaxItems
isRegexMatch = self.isRegexMatch
# Find itemsets and populate the TreeView
with self.progressBar(self.maxItemsets + 1) as progress:
for itemset, support in frequent_itemsets(X, self.minSupport / 100):
if filterSearch and not filterMinItems <= len(itemset) <= filterMaxItems:
continue
parent = top
first_new_item = None
itemset_matches_filter = False
for item in sorted(itemset):
name = names[item]
if filterSearch and not itemset_matches_filter:
itemset_matches_filter = isRegexMatch(name)
child = parent.get(name)
if child is None:
try:
wi = self.TreeWidgetItem(
parent.item, [name, str(support), "{:.4g}".format(100 * support / len(data))]
)
except RuntimeError:
# FIXME: When autoFind was in effect and the support
# slider was moved, this line excepted with:
# RuntimeError: wrapped C/C++ object of type
# TreeWidgetItem has been deleted
return
wi.setData(0, self.ITEM_DATA_ROLE, item)
child = parent[name] = ItemDict(wi)
if first_new_item is None:
first_new_item = (parent, name)
parent = child
if filterSearch and not itemset_matches_filter:
parent, name = first_new_item
parent.item.removeChild(parent[name].item)
del parent[name].item
del parent[name]
else:
nItemsets += 1
progress.advance()
if nItemsets >= self.maxItemsets:
break
if not filterSearch:
self.filter_change()
self.nItemsets = nItemsets
self.nSelectedItemsets = 0
self.nSelectedExamples = 0
self.tree.expandAll()
for i in range(self.tree.columnCount()):
self.tree.resizeColumnToContents(i)
self.tree.setUpdatesEnabled(True)
self.tree.blockSignals(False)
self._is_running = False
def set_data(self, data):
self.data = data
is_error = False
if data is not None:
self.warning(0)
self.error(1)
self.button.setDisabled(False)
self.X = data.X
if issparse(data.X):
self.X = data.X.tocsc()
else:
if not data.domain.has_discrete_attributes():
self.error(1, "Discrete features required but data has none.")
is_error = True
self.button.setDisabled(True)
elif data.domain.has_continuous_attributes():
self.warning(0, "Data has continuous attributes which will be skipped.")
else:
self.output = None
self.commit()
if self.autoFind and not is_error:
self.find_itemsets()
class RumorSettings(KDialog):
"""
Dialog with more Rumor settings.
"""
def __init__(self, mainwin):
KDialog.__init__(self, mainwin)
self.setAttribute(Qt.WA_DeleteOnClose)
self.setCaption(i18n("Rumor Settings"))
self.setButtons(KDialog.ButtonCode(
KDialog.Ok | KDialog.Cancel | KDialog.Help))
self.setHelp("rumor")
layout = QGridLayout(self.mainWidget())
# MIDI input and output.
# Get the list of available OSS and ALSA devices
oslist = [('oss:{0}'.format(i), i18n("OSS device %1", i))
for i in range(getOSSnrMIDIs())]
i = oslist + parseAconnect('i') + [("keyboard", i18n("Keyboard"))]
o = oslist + parseAconnect('o')
self.ilist, ititles = map(list, zip(*i))
self.olist, otitles = map(list, zip(*o))
# input
l = QLabel(i18n("MIDI input:"))
layout.addWidget(l, 1, 0)
self.ibut = QComboBox()
self.ibut.addItems(ititles)
self.ibut.setToolTip(i18n("MIDI input to use. Choose 'Keyboard' if "
"you want to play on the keyboard of your computer."))
layout.addWidget(self.ibut, 1, 1)
l.setBuddy(self.ibut)
# output
l = QLabel(i18n("MIDI output:"))
layout.addWidget(l, 2, 0)
self.obut = QComboBox()
self.obut.addItems(otitles)
self.obut.setToolTip(i18n("MIDI output to use."))
layout.addWidget(self.obut, 2, 1)
l.setBuddy(self.obut)
# Language
l = QLabel(i18n("Language:"))
layout.addWidget(l, 3, 0)
self.lang = QComboBox()
self.lang.addItems((
AUTO(), 'ne', 'en', 'en-short', 'de', 'no', 'sv', 'it', 'ca', 'es'))
self.lang.setToolTip(i18n("The LilyPond language you want Rumor to "
"output the pitches in."))
layout.addWidget(self.lang, 3, 1)
l.setBuddy(self.lang)
hb = QHBoxLayout()
layout.addLayout(hb, 4, 0, 1, 2)
# explicit durations
self.explDur = QCheckBox(i18n("Explicit durations"))
self.explDur.setToolTip(i18n(
"Add a duration after every note, even if it is the same as the "
"preceding note."))
hb.addWidget(self.explDur)
# absolute pitches
self.absPitches = QCheckBox(i18n("Absolute pitch"))
self.absPitches.setToolTip(i18n(
"Use absolute pitches instead of relative."))
hb.addWidget(self.absPitches)
hb = QHBoxLayout()
layout.addLayout(hb, 5, 0, 1, 2)
# No Barlines
self.noBar = QCheckBox(i18n("No barlines"))
self.noBar.setToolTip(i18n(
"Filter the barlines out of Rumor's output."))
hb.addWidget(self.noBar)
# No dots
self.noDots = QCheckBox(i18n("No dots"))
self.noDots.setToolTip(i18n(
"Do not use dotted notes, but ties instead."))
hb.addWidget(self.noDots)
# Legato
self.legato = QCheckBox(i18n("Legato"))
self.legato.setToolTip(i18n("Do not use rests, but give all notes "
"the maximum length."))
hb.addWidget(self.legato)
# Strip rests
self.stripRests = QCheckBox(i18n("Strip rests"))
self.stripRests.setToolTip(i18n(
"Strip leading and trialing rests from output."))
hb.addWidget(self.stripRests)
layout.addWidget(QLabel(i18n(
"Guile scripts to load:")), 6, 0, 1, 2)
# Guile scripts listview
self.scripts = QTreeWidget()
self.scripts.setRootIsDecorated(False)
self.scripts.setHeaderLabels((i18n("Name"), i18n("Description")))
self.scripts.setToolTip(i18n(
"Here you can select which Guile scripts you want Rumor to load. "
"Check \"What's this\" for more information."))
localRumorDir = "~/.kde/share/apps/frescobaldi/rumor/"
self.scripts.setWhatsThis(i18n(
"Here you can select which Guile scripts you want Rumor to load. "
"You can add your own scripts by putting them in %1. "
"If the first line of your script starts with a semicolon (;) "
"that line will be shown as description.", localRumorDir))
layout.addWidget(self.scripts, 7, 0, 1, 2)
self.loadSettings()
def done(self, result):
if result:
self.saveSettings()
KDialog.done(self, result)
def loadSettings(self):
""" Load the settings """
conf = config("rumor")
if 'oss:1' in self.ilist:
idefault = odefault = 'oss:1'
else:
idefault = 'kbd'
odefault = self.olist and self.olist[-1] or ""
i = conf.readEntry("midi in", idefault)
o = conf.readEntry("midi out", odefault)
if i in self.ilist:
self.ibut.setCurrentIndex(self.ilist.index(i))
if o in self.olist:
self.obut.setCurrentIndex(self.olist.index(o))
setComboBox(self.lang, unautofy(conf.readEntry("language", "auto")))
self.absPitches.setChecked(conf.readEntry("absolute pitches", False))
self.explDur.setChecked(conf.readEntry("explicit durations", False))
self.noBar.setChecked(conf.readEntry("no barlines", False))
self.noDots.setChecked(conf.readEntry("no dots", False))
self.legato.setChecked(conf.readEntry("legato", False))
self.stripRests.setChecked(conf.readEntry("strip rests", False))
# Guile scripts
self.scripts.clear()
scripts = conf.readEntry("scripts", [])
for path in rumorScripts():
name = os.path.basename(path)
try:
desc = open(path).readline().strip()
item = QTreeWidgetItem(self.scripts)
item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
item.setCheckState(0, (name in scripts) and Qt.Checked or Qt.Unchecked)
item.setText(0, name)
if desc.startswith(';'):
item.setText(1, desc.strip(";"))
except IOError:
pass
for col in 0, 1:
self.scripts.resizeColumnToContents(col)
def saveSettings(self):
""" Save the settings """
conf = config("rumor")
conf.writeEntry("midi in", self.ilist[self.ibut.currentIndex()])
conf.writeEntry("midi out", self.olist[self.obut.currentIndex()])
conf.writeEntry("language", autofy(self.lang.currentText()))
conf.writeEntry("absolute pitches", self.absPitches.isChecked())
conf.writeEntry("explicit durations", self.explDur.isChecked())
conf.writeEntry("no barlines", self.noBar.isChecked())
conf.writeEntry("no dots", self.noDots.isChecked())
conf.writeEntry("legato", self.legato.isChecked())
conf.writeEntry("strip rests", self.stripRests.isChecked())
# Read script treeview
names = []
for row in range(self.scripts.topLevelItemCount()):
item = self.scripts.topLevelItem(row)
if item.checkState(0) == Qt.Checked:
names.append(item.text(0))
conf.writeEntry("scripts", names)
class MemUsageDialog(QDialog):
def __init__(self, parent=None, update=True):
QDialog.__init__(self, parent=parent)
layout = QVBoxLayout()
self.tree = QTreeWidget()
self.tree.setHeaderLabels(["cache", "memory", "roi", "dtype", "type"])
layout.addWidget(self.tree)
self.setLayout(layout)
self.memMgr = ArrayCacheMemoryMgr.instance
self.timer = QTimer(self)
if update:
self.timer.timeout.connect(self._updateReport)
self._updateReport()
def _updateReport(self):
reports = []
for c in self.memMgr.namedCaches:
r = MemInfoNode()
try:
c.generateReport(r)
reports.append(r)
except NotImplementedError:
warnings.warn("cache operator {} does not implement generateReport()".format(c))
self._showReports(reports)
"""
import pickle
f = open("/tmp/reports.pickle",'w')
pickle.dump(reports, f)
f.close()
print "... saved MEM reports to file ..."
"""
def _showReports(self, reports):
self.tree.clear()
root = self.tree.invisibleRootItem()
for r in reports:
self._showReportsImpl(r, root, 0)
def _makeTreeWidgetItem(self, node):
l = []
l.append("%r" % node.name)
l.append("%1.1f MB" % (node.usedMemory / 1024 ** 2.0))
if node.roi is not None:
l.append("%r\n%r" % (list(node.roi[0]), list(node.roi[1])))
else:
l.append("")
if node.dtype is not None:
if node.dtype == numpy.float32:
l.append("float32")
elif node.dtype == numpy.uint8:
l.append("uint8")
elif node.dtype == numpy.uint32:
l.append("uint32")
elif node.dtype == numpy.float64:
l.append("float64")
else:
l.append(str(node.dtype))
else:
l.append("")
t = str(node.type)
t = t[len("<type '") + 1 : -len("'>")]
t = t.split(".")[-1]
l.append(t)
return QTreeWidgetItem(l)
def _showReportsImpl(self, node, itm, level):
# print " "*level,
# print "node", node.name
root = self._makeTreeWidgetItem(node)
itm.addChild(root)
root.setExpanded(True)
for c in node.children:
self._showReportsImpl(c, root, level + 1)
def hideEvent(self, event):
self.timer.stop()
def showEvent(self, show):
self.timer.start(5 * 1000) # update every 5 sec.
class OWGEODatasets(OWWidget):
name = "GEO Data Sets"
description = DESCRIPTION
icon = "../widgets/icons/GEODataSets.svg"
priority = PRIORITY
inputs = []
outputs = [("Expression Data", Orange.data.Table)]
settingsList = ["outputRows", "mergeSpots", "gdsSelectionStates",
"splitterSettings", "currentGds", "autoCommit",
"datasetNames"]
outputRows = Setting(False)
mergeSpots = Setting(True)
gdsSelectionStates = Setting({})
currentGds = Setting(None)
datasetNames = Setting({})
splitterSettings = Setting(
(b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02',
b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01')
)
autoCommit = Setting(True)
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.selectionChanged = False
self.filterString = ""
self.datasetName = ""
## GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "Initializing\n\n")
box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
gui.radioButtonsInBox(box, self, "outputRows",
["Genes or spots", "Samples"], "Rows",
callback=self.commitIf)
gui.checkBox(box, self, "mergeSpots", "Merge spots of same gene",
callback=self.commitIf)
gui.separator(box)
self.nameEdit = gui.lineEdit(
box, self, "datasetName", "Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited
)
self.nameEdit.setPlaceholderText("")
if sys.version_info < (3, ):
box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = gui.button(
box, self, "Commit", callback=self.commit)
cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
gui.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
else:
gui.auto_commit(self.controlArea, self, "autoCommit", "Commit",
box="Commit")
gui.rubber(self.controlArea)
# self.filterLineEdit = OWGUIEx.lineEditHint(
# self.mainArea, self, "filterString", "Filter",
# caseSensitive=False, matchAnywhere=True,
# callback=self.filter, delimiters=" ")
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(
textChanged=self.filter
)
self.completer = QCompleter(
caseSensitivity=Qt.CaseInsensitive
)
self.completer.setModel(QStringListModel(self))
self.filterLineEdit.setCompleter(self.completer)
self.mainArea.layout().addWidget(self.filterLineEdit)
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self.treeWidget,
role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection
)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = gui.widgetBox(splitterH, "Description")
self.infoGDS = gui.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
gui.rubber(box)
box = gui.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"]
)
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged
)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = ["dataset_id", "title", "platform_organism",
"description"]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float,)))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
@Slot(float)
def _setProgress(self, value):
self.progressBarValue = value
def _initializemodel(self):
assert self.thread() is QThread.currentThread()
model, self.gds_info, self.gds = self._inittask.result()
model.setParent(self)
proxy = self.treeWidget.model()
proxy.setFilterKeyColumn(0)
proxy.setFilterRole(TextFilterRole)
proxy.setFilterCaseSensitivity(False)
proxy.setFilterFixedString(self.filterString)
proxy.setSourceModel(model)
proxy.sort(0, Qt.DescendingOrder)
self.progressBarFinished()
self.setBlocking(False)
self.setEnabled(True)
filter_items = " ".join(
gds[key] for gds in self.gds for key in self.searchKeys
)
tr_chars = ",.:;!?(){}[]_-+\\|/%#@$^&*<>~`"
tr_table = str.maketrans(tr_chars, " " * len(tr_chars))
filter_items = filter_items.translate(tr_table)
filter_items = sorted(set(filter_items.split(" ")))
filter_items = [item for item in filter_items if len(item) > 3]
self.completer.model().setStringList(filter_items)
# self.filterLineEdit.setItems(filter_items)
if self.currentGds:
current_id = self.currentGds["dataset_id"]
gdss = [(i, qunpack(proxy.data(proxy.index(i, 1), Qt.DisplayRole)))
for i in range(proxy.rowCount())]
current = [i for i, data in gdss if data and data == current_id]
if current:
current_index = proxy.index(current[0], 0)
self.treeWidget.selectionModel().select(
current_index,
QItemSelectionModel.Select | QItemSelectionModel.Rows
)
self.treeWidget.scrollTo(
current_index, QTreeView.PositionAtCenter)
for i in range(8):
self.treeWidget.resizeColumnToContents(i)
self.treeWidget.setColumnWidth(
1, min(self.treeWidget.columnWidth(1), 300))
self.treeWidget.setColumnWidth(
2, min(self.treeWidget.columnWidth(2), 200))
self.updateInfo()
def updateInfo(self):
gds_info = self.gds_info
text = ("%i datasets\n%i datasets cached\n" %
(len(gds_info),
len(glob.glob(serverfiles.localpath("GEO") + "/GDS*"))))
filtered = self.treeWidget.model().rowCount()
if len(self.gds) != filtered:
text += ("%i after filtering") % filtered
self.infoBox.setText(text)
def updateSelection(self, *args):
current = self.treeWidget.selectedIndexes()
mapToSource = self.treeWidget.model().mapToSource
current = [mapToSource(index).row() for index in current]
if current:
self.currentGds = self.gds[current[0]]
self.setAnnotations(self.currentGds)
self.infoGDS.setText(self.currentGds.get("description", ""))
self.nameEdit.setPlaceholderText(self.currentGds["title"])
self.datasetName = \
self.datasetNames.get(self.currentGds["dataset_id"], "")
else:
self.currentGds = None
self.nameEdit.setPlaceholderText("")
self.datasetName = ""
self.commitIf()
def setAnnotations(self, gds):
self._annotationsUpdating = True
self.annotationsTree.clear()
annotations = defaultdict(set)
subsetscount = {}
for desc in gds["subsets"]:
annotations[desc["type"]].add(desc["description"])
subsetscount[desc["description"]] = str(len(desc["sample_id"]))
for type, subsets in annotations.items():
key = (gds["dataset_id"], type)
subsetItem = QTreeWidgetItem(self.annotationsTree, [type])
subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable |
Qt.ItemIsTristate)
subsetItem.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked)
)
subsetItem.key = key
for subset in subsets:
key = (gds["dataset_id"], type, subset)
item = QTreeWidgetItem(
subsetItem, [subset, subsetscount.get(subset, "")]
)
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked)
)
item.key = key
self._annotationsUpdating = False
self.annotationsTree.expandAll()
for i in range(self.annotationsTree.columnCount()):
self.annotationsTree.resizeColumnToContents(i)
def annotationSelectionChanged(self, item, column):
if self._annotationsUpdating:
return
for i in range(self.annotationsTree.topLevelItemCount()):
item = self.annotationsTree.topLevelItem(i)
self.gdsSelectionStates[item.key] = item.checkState(0)
for j in range(item.childCount()):
child = item.child(j)
self.gdsSelectionStates[child.key] = child.checkState(0)
def filter(self):
filter_string = unicode(self.filterLineEdit.text())
proxyModel = self.treeWidget.model()
if proxyModel:
strings = filter_string.lower().strip().split()
proxyModel.setFilterFixedStrings(strings)
self.updateInfo()
def selectedSamples(self):
"""
Return the currently selected sample annotations.
The return value is a list of selected (sample type, sample value)
tuples.
.. note:: if some Sample annotation type has no selected values.
this method will return all values for it.
"""
samples = []
unused_types = []
used_types = []
for stype in childiter(self.annotationsTree.invisibleRootItem()):
selected_values = []
all_values = []
for sval in childiter(stype):
value = (str(stype.text(0)), str(sval.text(0)))
if self.gdsSelectionStates.get(sval.key, True):
selected_values.append(value)
all_values.append(value)
if selected_values:
samples.extend(selected_values)
used_types.append(str(stype.text(0)))
else:
# If no sample of sample type is selected we don't filter
# on it.
samples.extend(all_values)
unused_types.append(str(stype.text(0)))
return samples, used_types
def commitIf(self):
if self.autoCommit:
self.commit()
else:
self.selectionChanged = True
def commit(self):
if self.currentGds:
self.error(0)
sample_type = None
self.progressBarInit()
self.progressBarSet(10)
_, groups = self.selectedSamples()
if len(groups) == 1 and self.outputRows:
sample_type = groups[0]
self.setEnabled(False)
self.setBlocking(True)
def get_data(gds_id, report_genes, transpose, sample_type, title):
gds = geo.GDS(gds_id)
data = gds.getdata(
report_genes=report_genes, transpose=transpose,
sample_type=sample_type
)
data.name = title
return data
get_data = partial(
get_data, self.currentGds["dataset_id"],
report_genes=self.mergeSpots,
transpose=self.outputRows,
sample_type=sample_type,
title=self.datasetName or self.currentGds["title"]
)
self._datatask = Task(function=get_data)
self._datatask.finished.connect(self._on_dataready)
self._executor.submit(self._datatask)
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarSet(50)
try:
data = self._datatask.result()
except urlrequest.URLError as error:
self.error(0, "Error while connecting to the NCBI ftp server! %r" %
error)
self._datatask = None
self.progressBarFinished()
return
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for meta in data.domain.metas:
out.append((meta.name, ex[meta].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name,
ex[data.domain.class_var].value))
return out
samples = set(samples)
mask = [samples.issuperset(samplesinst(ex)) for ex in data]
data = data[numpy.array(mask, dtype=bool)]
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = Orange.data.Domain(
[attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())],
data.domain.class_var,
data.domain.metas
)
# domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes
)
data = Orange.data.Table(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
self.progressBarFinished()
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), " ", Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
def splitterMoved(self, *args):
self.splitterSettings = [str(sp.saveState()) for sp in self.splitters]
def onDeleteWidget(self):
if self._inittask:
self._inittask.future().cancel()
self._inittask.finished.disconnect(self._initializemodel)
if self._datatask:
self._datatask.future().cancel()
self._datatask.finished.disconnect(self._on_dataready)
self._executor.shutdown(wait=False)
super(OWGEODatasets, self).onDeleteWidget()
def onNameEdited(self):
if self.currentGds:
gds_id = self.currentGds["dataset_id"]
self.datasetNames[gds_id] = unicode(self.nameEdit.text())
self.commitIf()
class DBServersWidget(QWidget):
"""Displays a list of servers"""
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.debug = False
self.connections = {}
self.setWindowTitle("Servers")
#s#elf.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
self.mainLayout = QVBoxLayout()
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(0)
self.setLayout(self.mainLayout)
#=============================================
## Top Toolbar
topBar = QToolBar()
topBar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.mainLayout.addWidget(topBar)
## Add the action buttons
topBar.addAction(Ico.icon(Ico.ServerAdd), "Add", self.on_server_add)
self.actionServerEdit = topBar.addAction(Ico.icon(Ico.ServerEdit),
"Edit", self.on_server_edit)
self.actionServerDelete = topBar.addAction(Ico.icon(Ico.ServerDelete),
"Delete",
self.on_server_delete)
#=============================================
## Tree
self.tree = QTreeWidget()
self.mainLayout.addWidget(self.tree)
self.tree.setUniformRowHeights(True)
self.tree.setRootIsDecorated(True)
self.tree.setHeaderLabels(["Server",
"Butt"]) # set header, but hide anyway
self.tree.header().hide()
self.tree.header().setResizeMode(C.node, QHeaderView.Stretch)
self.tree.setColumnWidth(C.butt, 20)
self.connect(self.tree, SIGNAL('itemSelectionChanged()'),
self.on_tree_selection_changed)
self.connect(self.tree,
SIGNAL('itemDoubleClicked (QTreeWidgetItem *,int)'),
self.on_tree_double_clicked)
self.buttGroup = QButtonGroup(self)
self.connect(self.buttGroup, SIGNAL("buttonClicked(QAbstractButton*)"),
self.on_open_server)
self.on_tree_selection_changed()
self.load_servers()
#=======================================
##== Tree Events
def on_tree_selection_changed(self):
disabled = self.tree.selectionModel().hasSelection() == False
self.actionServerEdit.setDisabled(disabled)
self.actionServerDelete.setDisabled(disabled)
def on_tree_double_clicked(self):
self.actionServerEdit.trigger()
#=======================================
## Server Actions
def on_server_add(self):
self.show_server_dialog(None)
def on_server_edit(self):
item = self.tree.currentItem()
if item == None:
return
server = str(item.text(C.server))
self.show_server_dialog(server)
def show_server_dialog(self, server=None):
d = DBServerDialog.DBServerDialog(self, server)
if d.exec_():
self.load_servers()
def load_servers(self):
"""Load servers from :py:meth:`pyqtdb.XSettings.XSettings.get_servers` """
self.tree.clear()
for butt in self.buttGroup.buttons():
self.buttGroup.removeButton(butt)
for srv in G.settings.get_servers_list():
item = QTreeWidgetItem()
item.setText(C.node, srv['server'])
#item.setText(C.user, srv['user'])
self.tree.addTopLevelItem(item)
butt = QToolButton()
butt.setIcon(Ico.icon(Ico.Connect))
butt.setProperty("server", srv['server'])
self.tree.setItemWidget(item, C.butt, butt)
self.buttGroup.addButton(butt)
def on_server_delete(self):
item = self.tree.currentItem()
if item == None:
return
srv = str(item.text(C.server))
G.settings.delete_server(srv)
self.load_servers()
def on_open_server(self, butt):
# self.emit(SIGNAL("open_server"), butt.property("server").toString())
srv_ki = str(butt.property("server").toString())
server = G.settings.get_server(srv_ki)
db = QSqlDatabase.addDatabase("QMYSQL", srv_ki)
db.setHostName(server['server'])
db.setUserName(server['user'])
db.setPassword(server['passwd'])
ok = db.open()
if ok:
#self.connections[srv_ki] =
self.load_databases(srv_ki)
print "open", ok
def load_databases(self, srv_ki):
"""Load databases into tree node for server; executes 'show databases;' or aslike """
sql = "show databases;"
query = QSqlQuery(QSqlDatabase.database(srv_ki))
ok = query.exec_(sql)
print ok, sql, query.result()
# Get the parent node, ie the server node
pItem = self.tree.findItems(srv_ki, Qt.MatchExactly, C.node)[0]
## Assumed value(0) is the table.. we need the defs (ie mysql case)
while query.next():
table_name = query.value(0).toString()
nuItem = QTreeWidgetItem(pItem)
nuItem.setText(C.node, table_name)
#print table_name
self.tree.setItemExpanded(pItem, True)
class WServerInformation(QWidget, Logger.ClassLogger):
"""
Widget for the global server information
"""
def __init__(self, parent=None):
"""
Constructs WServerInformation widget
@param parent:
@type parent:
"""
QWidget.__init__(self, parent)
self.parent = parent
self.name = self.tr("Miscellaneous")
self.createWidgets()
self.createActions()
self.createToolbar()
self.deactivate()
def createWidgets(self):
"""
QtWidgets creation
"""
self.dockToolbar = QToolBar(self)
self.dockToolbar.setStyleSheet(
"QToolBar { border: 0px }") # remove 3D border
self.dockToolbar.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.dockToolbarReset = QToolBar(self)
self.dockToolbarReset.setStyleSheet(
"QToolBar { border: 0px }") # remove 3D border
self.dockToolbarReset.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.dockToolbarGen = QToolBar(self)
self.dockToolbarGen.setStyleSheet(
"QToolBar { border: 0px }") # remove 3D border
self.dockToolbarGen.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
self.refreshBox = QGroupBox("Refresh")
self.refreshBox.setStyleSheet("""
QGroupBox { font: normal; border: 1px solid silver; border-radius: 2px; }
QGroupBox { padding-bottom: 10px; background-color: #FAFAFA; }
QGroupBox::title { subcontrol-position: bottom center;}
""")
layoutRefreshBox = QHBoxLayout()
layoutRefreshBox.addWidget(self.dockToolbar)
layoutRefreshBox.setContentsMargins(0, 0, 0, 0)
self.refreshBox.setLayout(layoutRefreshBox)
self.resetBox = QGroupBox("Reset")
self.resetBox.setStyleSheet("""
QGroupBox { font: normal; border: 1px solid silver; border-radius: 2px; }
QGroupBox { padding-bottom: 10px; background-color: #FAFAFA; }
QGroupBox::title { subcontrol-position: bottom center;}
""")
layoutResetBox = QHBoxLayout()
layoutResetBox.addWidget(self.dockToolbarReset)
layoutResetBox.setContentsMargins(0, 0, 0, 0)
self.resetBox.setLayout(layoutResetBox)
self.genBox = QGroupBox("Prepare")
self.genBox.setStyleSheet("""
QGroupBox { font: normal; border: 1px solid silver; border-radius: 2px; }
QGroupBox { padding-bottom: 10px; background-color: #FAFAFA; }
QGroupBox::title { subcontrol-position: bottom center;}
""")
layoutGenBox = QHBoxLayout()
layoutGenBox.addWidget(self.dockToolbarGen)
layoutGenBox.setContentsMargins(0, 0, 0, 0)
self.genBox.setLayout(layoutGenBox)
layoutToolbars = QHBoxLayout()
layoutToolbars.addWidget(self.refreshBox)
layoutToolbars.addWidget(self.genBox)
layoutToolbars.addWidget(self.resetBox)
layoutToolbars.addStretch(1)
layoutFinal = QHBoxLayout()
layoutLeft = QVBoxLayout()
layoutRight = QVBoxLayout()
layoutRight.addLayout(layoutToolbars)
self.diskUsageBox = QGroupBox("Disk Usage")
self.nbSizeLogsOnDiskLabel = QLabel("0")
self.nbSizeTmpOnDiskLabel = QLabel("0")
self.nbSizeArchivesOnDiskLabel = QLabel("0")
self.nbSizeAdpOnDiskLabel = QLabel("0")
self.nbSizeLibOnDiskLabel = QLabel("0")
self.nbSizeBakOnDiskLabel = QLabel("0")
self.nbSizeTestsOnDiskLabel = QLabel("0")
layout2 = QFormLayout()
layout2.addRow(QLabel("Logs"), self.nbSizeLogsOnDiskLabel)
layout2.addRow(QLabel("Tmp"), self.nbSizeTmpOnDiskLabel)
layout2.addRow(QLabel("Archives"), self.nbSizeArchivesOnDiskLabel)
layout2.addRow(QLabel("Tests"), self.nbSizeTestsOnDiskLabel)
layout2.addRow(QLabel("Adapters"), self.nbSizeAdpOnDiskLabel)
layout2.addRow(QLabel("Libraries"), self.nbSizeLibOnDiskLabel)
layout2.addRow(QLabel("Backups"), self.nbSizeBakOnDiskLabel)
self.diskUsageBox.setLayout(layout2)
layoutGrid = QGridLayout()
layoutGrid.addWidget(self.diskUsageBox, 0, 0)
layoutRight.addLayout(layoutGrid)
layoutRight.addStretch(1)
self.informations = QTreeWidget(self)
self.informations.setVerticalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.informations.setIndentation(10)
self.labels = [self.tr("Key"), self.tr("Value")]
self.informations.setHeaderLabels(self.labels)
layoutLeft.addWidget(self.informations)
layoutFinal.addLayout(layoutLeft)
layoutFinal.addLayout(layoutRight)
self.setLayout(layoutFinal)
def createActions(self):
"""
Actions defined:
* generate the cache for the documentation
* generate all packages
* refresh statistics
* refresh the context of the server
* check the syntax of adapters
* reset statistics
"""
self.genCacheHelpAction = QtHelper.createAction(
self,
"&Generate\nDocumentations",
self.genCacheHelp,
tip='Generate the cache for the documentation',
icon=QIcon(":/generate-doc.png"))
self.genTarAdaptersAction = QtHelper.createAction(
self,
"&Package\nAdapters",
self.genPackageAdapters,
tip='Generate adapters packages',
icon=QIcon(":/generate-tar.png"))
self.genTarLibrariesAction = QtHelper.createAction(
self,
"&Package\nLibraries",
self.genPackageLibraries,
tip='Generate libraries packages',
icon=QIcon(":/generate-tar.png"))
self.genTarSamplesAction = QtHelper.createAction(
self,
"&Package\nSamples",
self.genPackageSamples,
tip='Generate samples packages',
icon=QIcon(":/generate-tar.png"))
self.refreshAction = QtHelper.createAction(
self,
"&Usages",
self.refreshUsages,
tip='Refresh Usages',
tooltip='Refresh usages',
icon=QIcon(":/refresh-statistics.png"))
self.refreshCtxAction = QtHelper.createAction(
self,
"&Session",
self.refreshCtx,
tip='Refresh server context',
tooltip='Refresh server context',
icon=QIcon(":/act-refresh.png"))
self.resetAction = QtHelper.createAction(
self,
"&Reset\nStatistics",
self.resetStats,
tip='Reset all statistics',
icon=QIcon(":/reset-counter.png"))
self.unlockAllTestsAction = QtHelper.createAction(
self,
"&Unlock\nTests",
self.unlockTests,
tip='Unlock all files',
icon=QIcon(":/unlock.png"))
self.unlockAllAdaptersAction = QtHelper.createAction(
self,
"&Unlock\nAdapters",
self.unlockAdapters,
tip='Unlock all files',
icon=QIcon(":/unlock.png"))
self.unlockAllLibrariesAction = QtHelper.createAction(
self,
"&Unlock\nLibraries",
self.unlockLibraries,
tip='Unlock all files',
icon=QIcon(":/unlock.png"))
def createToolbar(self):
"""
Toolbar creation
"""
self.dockToolbar.setObjectName("Misc toolbar")
self.dockToolbar.addAction(self.refreshCtxAction)
self.dockToolbar.addAction(self.refreshAction)
self.dockToolbar.setIconSize(QSize(16, 16))
self.dockToolbarGen.setObjectName("Generate toolbar")
self.dockToolbarGen.addAction(self.genCacheHelpAction)
self.dockToolbarGen.addAction(self.genTarAdaptersAction)
self.dockToolbarGen.addAction(self.genTarLibrariesAction)
self.dockToolbarGen.addAction(self.genTarSamplesAction)
self.dockToolbarGen.setIconSize(QSize(16, 16))
self.dockToolbarReset.setObjectName("Reset toolbar")
self.dockToolbarReset.addAction(self.resetAction)
self.dockToolbarReset.addAction(self.unlockAllTestsAction)
self.dockToolbarReset.addAction(self.unlockAllAdaptersAction)
self.dockToolbarReset.addAction(self.unlockAllLibrariesAction)
self.dockToolbarReset.setIconSize(QSize(16, 16))
def unlockTests(self):
"""
Unlock all files
"""
RCI.instance().unlockTests()
def unlockAdapters(self):
"""
Unlock all files
"""
RCI.instance().unlockAdapters()
def unlockLibraries(self):
"""
Unlock all files
"""
RCI.instance().unlockLibraries()
def genPackageAdapters(self):
"""
Generate all tar packages
"""
RCI.instance().buildAdapters()
def genPackageLibraries(self):
"""
Generate all tar packages
"""
RCI.instance().buildLibraries()
def genPackageSamples(self):
"""
Generate all tar packages
"""
RCI.instance().buildSamples()
def resetStats(self):
"""
Reset statistic manually
"""
reply = QMessageBox.question(self, "Reset statistics",
"Are you sure ?",
QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
RCI.instance().resetTestsMetrics()
def refreshCtx(self):
"""
Call the server to refresh context of the server
"""
RCI.instance().sessionContext()
def refreshUsages(self):
"""
Call the server to refresh statistics of the server
"""
RCI.instance().systemUsages()
def genCacheHelp(self):
"""
Call the server to generate the cache documentation
"""
reply = QMessageBox.question(self, "Generate cache", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No)
if reply == QMessageBox.Yes:
RCI.instance().buildDocumentations()
def active(self):
"""
Enables QTreeWidget
"""
self.diskUsageBox.setEnabled(True)
self.informations.setEnabled(True)
self.genCacheHelpAction.setEnabled(True)
self.resetAction.setEnabled(True)
self.unlockAllTestsAction.setEnabled(True)
self.unlockAllAdaptersAction.setEnabled(True)
self.unlockAllLibrariesAction.setEnabled(True)
def deactivate(self):
"""
Clears QTreeWidget and disables it
"""
self.diskUsageBox.setEnabled(False)
self.informations.clear()
self.informations.setEnabled(False)
self.genCacheHelpAction.setEnabled(False)
self.resetAction.setEnabled(False)
self.unlockAllTestsAction.setEnabled(False)
self.unlockAllAdaptersAction.setEnabled(False)
self.unlockAllLibrariesAction.setEnabled(False)
self.nbSizeLogsOnDiskLabel.setText("0")
self.nbSizeTmpOnDiskLabel.setText("0")
self.nbSizeArchivesOnDiskLabel.setText("0")
self.nbSizeAdpOnDiskLabel.setText("0")
self.nbSizeLibOnDiskLabel.setText("0")
self.nbSizeBakOnDiskLabel.setText("0")
self.nbSizeTestsOnDiskLabel.setText("0")
def cleanContext(self):
"""
Clear the context
Removes all items
"""
self.informations.clear()
def loadStats(self, data):
"""
Load statistics
"""
self.nbSizeLogsOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-logs'])))
self.nbSizeTmpOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-tmp'])))
self.nbSizeArchivesOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-testresults'])))
self.nbSizeAdpOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-adapters'])))
self.nbSizeLibOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-libraries'])))
self.nbSizeBakOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-backups'])))
self.nbSizeTestsOnDiskLabel.setText(
str(QtHelper.bytes2human(data['disk-usage-tests'])))
def loadData(self, data):
"""
Load all config keys
@param data:
@type data:
"""
if isinstance(data, dict):
data = [data]
for param in data:
probeItem = ParamItem(param=param, parent=self.informations)
# resize columns
for i in xrange(len(self.labels) - 1):
self.informations.resizeColumnToContents(i)
class ThreadsViewer( QWidget ):
" Implements the threads viewer for a debugger "
def __init__( self, debugger, parent = None ):
QWidget.__init__( self, parent )
self.__debugger = debugger
self.__createLayout()
if Settings().showThreadViewer == False:
self.__onShowHide( True )
return
def __createLayout( self ):
" Creates the widget layout "
verticalLayout = QVBoxLayout( self )
verticalLayout.setContentsMargins( 0, 0, 0, 0 )
verticalLayout.setSpacing( 0 )
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle( QFrame.StyledPanel )
self.headerFrame.setAutoFillBackground( True )
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color( QPalette.Background )
headerBackground.setRgb( min( headerBackground.red() + 30, 255 ),
min( headerBackground.green() + 30, 255 ),
min( headerBackground.blue() + 30, 255 ) )
headerPalette.setColor( QPalette.Background, headerBackground )
self.headerFrame.setPalette( headerPalette )
self.headerFrame.setFixedHeight( 24 )
self.__threadsLabel = QLabel( "Threads" )
expandingSpacer = QSpacerItem( 10, 10, QSizePolicy.Expanding )
fixedSpacer = QSpacerItem( 3, 3 )
self.__showHideButton = QToolButton()
self.__showHideButton.setAutoRaise( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setFixedSize( 20, 20 )
self.__showHideButton.setToolTip( "Hide threads list" )
self.__showHideButton.setFocusPolicy( Qt.NoFocus )
self.__showHideButton.clicked.connect( self.__onShowHide )
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins( 0, 0, 0, 0 )
headerLayout.addSpacerItem( fixedSpacer )
headerLayout.addWidget( self.__threadsLabel )
headerLayout.addSpacerItem( expandingSpacer )
headerLayout.addWidget( self.__showHideButton )
self.headerFrame.setLayout( headerLayout )
self.__threadsList = QTreeWidget()
self.__threadsList.setSortingEnabled( False )
# I might not need that because of two reasons:
# - the window has no focus
# - the window has custom current indicator
# self.__threadsList.setAlternatingRowColors( True )
self.__threadsList.setRootIsDecorated( False )
self.__threadsList.setItemsExpandable( False )
self.__threadsList.setUniformRowHeights( True )
self.__threadsList.setSelectionMode( QAbstractItemView.NoSelection )
self.__threadsList.setSelectionBehavior( QAbstractItemView.SelectRows )
self.__threadsList.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.__threadsList.setFocusPolicy( Qt.NoFocus )
self.__threadsList.itemClicked.connect( self.__onThreadClicked )
self.__threadsList.setHeaderLabels( [ "", "Name", "State", "TID" ] )
verticalLayout.addWidget( self.headerFrame )
verticalLayout.addWidget( self.__threadsList )
return
def __onShowHide( self, startup = False ):
" Triggered when show/hide button is clicked "
if startup or self.__threadsList.isVisible():
self.__threadsList.setVisible( False )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'more.png' ) )
self.__showHideButton.setToolTip( "Show threads list" )
self.__minH = self.minimumHeight()
self.__maxH = self.maximumHeight()
self.setMinimumHeight( self.headerFrame.height() )
self.setMaximumHeight( self.headerFrame.height() )
Settings().showThreadViewer = False
else:
self.__threadsList.setVisible( True )
self.__showHideButton.setIcon( PixmapCache().getIcon( 'less.png' ) )
self.__showHideButton.setToolTip( "Hide threads list" )
self.setMinimumHeight( self.__minH )
self.setMaximumHeight( self.__maxH )
Settings().showThreadViewer = True
return
def __resizeColumns( self ):
" Resize the files list columns "
self.__threadsList.header().setStretchLastSection( True )
self.__threadsList.header().resizeSections(
QHeaderView.ResizeToContents )
self.__threadsList.header().resizeSection( 0, 22 )
self.__threadsList.header().setResizeMode( 0, QHeaderView.Fixed )
return
def clear( self ):
" Clears the content "
self.__threadsList.clear()
self.__threadsLabel.setText( "Threads" )
return
def populate( self, currentThreadID, threadList ):
" Populates the thread list from the client "
self.clear()
for thread in threadList:
if thread[ 'broken' ]:
state = "Waiting at breakpoint"
else:
state = "Running"
item = ThreadItem( thread[ 'id' ], thread[ 'name' ], state )
if thread[ 'id' ] == currentThreadID:
item.setCurrent( True )
self.__threadsList.addTopLevelItem( item )
self.__resizeColumns()
self.__threadsLabel.setText( "Threads (total: " +
str( len( threadList ) ) + ")" )
return
def switchControl( self, isInIDE ):
" Switches the UI depending where the control flow is "
self.__threadsList.setEnabled( isInIDE )
return
def __onThreadClicked( self, item, column ):
" Triggered when a thread is clicked "
if item.isCurrent():
return
for index in xrange( self.__threadsList.topLevelItemCount() ):
listItem = self.__threadsList.topLevelItem( index )
if listItem.isCurrent():
listItem.setCurrent( False )
break
item.setCurrent( True )
self.__debugger.remoteSetThread( item.getTID() )
return
class DBBrowser(QMainWindow):
def __init__(self, parent, server):
QMainWindow.__init__(self, parent)
self.debug = False
self.server = server
self.db = None
self.setWindowTitle("Database Browser")
#s#elf.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
topBar = QToolBar()
self.addToolBar(Qt.TopToolBarArea, topBar)
self.cenWid = QWidget()
self.setCentralWidget(self.cenWid)
self.mainLayout = QHBoxLayout()
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(0)
self.cenWid.setLayout(self.mainLayout)
self.treeTables = QTreeWidget()
self.mainLayout.addWidget(self.treeTables, 1)
self.treeTables.setHeaderLabels(["Table"])
self.treeTables.setSelectionBehavior(QAbstractItemView.SelectRows)
self.treeTables.setSelectionMode(QTreeView.SingleSelection)
self.connect(self.treeTables, SIGNAL('itemSelectionChanged()'),
self.on_table)
self.treeColumns = QTreeWidget()
self.mainLayout.addWidget(self.treeColumns, 4)
self.treeColumns.setHeaderLabels(["Column", "Type", "Nullable"])
self.db_connect()
#self.fetch()
def on_table(self):
item = self.treeTables.currentItem()
if item == None:
return
self.fetch(table=str(item.text(0)))
def db_connect(self):
#print "db_connect", self.server
self.db = QSqlDatabase.addDatabase("QMYSQL")
self.db.setHostName(self.server['server'])
self.db.setUserName(self.server['user'])
self.db.setPassword(self.server['passwd'])
ok = self.db.open()
print "open", ok
#self.db.setHostName(self.server['server'])
def load_data(self, data):
if "tables" in data:
self.treeTables.clear()
for t in data['tables']:
item = QTreeWidgetItem()
item.setText(0, t['table'])
self.treeTables.addTopLevelItem(item)
else:
self.treeColumns.clear()
for t in data['columns']:
item = QTreeWidgetItem()
item.setText(0, t['column'])
item.setText(1, t['type'])
item.setText(2, "Yes" if t['nullable'] else "-")
self.treeColumns.addTopLevelItem(item)
class VersionSelectDialog( QDialog ):
def __init__( self, parent ):
# initialize the super class
super( VersionSelectDialog, self ).__init__( parent )
# create the tree
self.uiVersionsTREE = QTreeWidget(self)
self.uiVersionsTREE.setAlternatingRowColors(True)
self.uiVersionsTREE.setRootIsDecorated(False)
self.uiVersionsTREE.setSelectionMode( self.uiVersionsTREE.NoSelection )
header = self.uiVersionsTREE.header()
header.setVisible(False)
# create the layout
layout = QVBoxLayout()
layout.addWidget(self.uiVersionsTREE)
layout.setContentsMargins(0,0,0,0)
# inherit the highlight palette
palette = self.palette()
palette.setColor(palette.Highlight,parent.palette().color(palette.Highlight))
self.setPalette(palette)
# set dialog information
self.setLayout(layout)
self.setWindowFlags( Qt.Popup )
self.resize(500,250)
# create connections
self.uiVersionsTREE.itemClicked.connect( self.acceptItem )
def closeEvent( self, event ):
# update all the items for this
for i in range( self.uiVersionsTREE.topLevelItemCount() ):
item = self.uiVersionsTREE.topLevelItem(i)
widget = item.versionWidget()
version = widget.version()
# match the active state
version.setActive(widget.isActive())
super(VersionSelectDialog,self).closeEvent(event)
def acceptItem( self, item ):
# handle version change information
widget = item.versionWidget()
widget.toggleActive()
# accept the dialog
self.close()
def popup( self, versions ):
self.uiVersionsTREE.setUpdatesEnabled(False)
self.uiVersionsTREE.blockSignals(True)
self.uiVersionsTREE.clear()
for version in versions:
item = VersionItem(self.uiVersionsTREE, version)
self.uiVersionsTREE.addTopLevelItem( item )
self.uiVersionsTREE.setItemWidget( item, 0, item.versionWidget() )
# reset the scrolling
self.uiVersionsTREE.verticalScrollBar().setValue(0)
self.uiVersionsTREE.setUpdatesEnabled(True)
self.uiVersionsTREE.blockSignals(False)
return self.exec_()
class OWGenExpress(widget.OWWidget):
name = "GenExpress"
description = "Expression data from GenExpress."
icon = "../widgets/icons/GenCloud.svg"
priority = 36
inputs = []
outputs = [("Data", Orange.data.Table)]
username = settings.Setting("anonymous")
password = settings.Setting("")
log2 = settings.Setting(False)
transpose = settings.Setting(False)
rtypei = settings.Setting(0)
projecti = settings.Setting(0)
serveri = settings.Setting(0)
exnamei = settings.Setting(6)
excludeconstant = settings.Setting(False)
joinreplicates = settings.Setting(False)
currentSelection = settings.Setting(None)
experimentsHeaderState = settings.Setting(
{name: False
for _, name in HEADER[:ID_INDEX + 1]})
storedSortOrder = settings.Setting([])
storedSelections = settings.Setting([])
def __init__(self, parent=None):
super().__init__(parent)
self.servers = [
('https://dictyexpress.research.bcm.edu/', 'dictyExpress'),
('https://cloud.genialis.com/', 'Genialis'),
]
self.selectedExperiments = []
self.buffer = dicty.CacheSQLite(bufferfile)
self.searchString = ""
self.items = []
self.result_types = []
self.controlArea.setMaximumWidth(250)
self.controlArea.setMinimumWidth(250)
box = gui.widgetBox(self.controlArea, 'Project')
self.projectCB = gui.comboBox(box,
self,
"projecti",
items=[],
callback=self.ProjectChosen)
self.projects = []
b = gui.widgetBox(self.controlArea, "Selection bookmarks")
self.selectionSetsWidget = SelectionSetsWidget(self)
self.selectionSetsWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
def store_selections(modified):
if not modified:
self.storedSelections = self.selectionSetsWidget.selections
self.selectionSetsWidget.selectionModified.connect(store_selections)
b.layout().addWidget(self.selectionSetsWidget)
gui.separator(self.controlArea)
b = gui.widgetBox(self.controlArea, "Sort output columns")
self.columnsSortingWidget = SortedListWidget(self)
self.columnsSortingWidget.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Maximum)
box = gui.widgetBox(self.controlArea, 'Experiment name')
self.experimentNameCB = gui.comboBox(box,
self,
"exnamei",
items=SORTING_MODEL_LIST)
b.layout().addWidget(self.columnsSortingWidget)
sorting_model = QStringListModel(SORTING_MODEL_LIST)
self.columnsSortingWidget.setModel(sorting_model)
self.columnsSortingWidget.sortingOrder = self.storedSortOrder
def store_sort_order():
self.storedSortOrder = self.columnsSortingWidget.sortingOrder
self.columnsSortingWidget.sortingOrderChanged.connect(store_sort_order)
gui.separator(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Expression Type')
self.expressionTypesCB = gui.comboBox(box,
self,
"rtypei",
items=[],
callback=self.UpdateResultsList)
gui.checkBox(self.controlArea, self, "excludeconstant",
"Exclude labels with constant values")
gui.checkBox(self.controlArea, self, "joinreplicates",
"Average replicates (use median)")
gui.checkBox(self.controlArea, self, "log2",
"Logarithmic (base 2) transformation")
gui.checkBox(self.controlArea, self, "transpose", "Genes as columns")
self.commit_button = gui.button(self.controlArea,
self,
"&Commit",
callback=self.Commit)
self.commit_button.setDisabled(True)
gui.rubber(self.controlArea)
box = gui.widgetBox(self.controlArea, 'Server')
gui.comboBox(box,
self,
"serveri",
items=[title for url, title in self.servers],
callback=self.ServerChosen)
gui.lineEdit(box,
self,
"username",
"Username:"******"password",
"Password:"******"Clear cache",
callback=self.clear_cache)
gui.lineEdit(self.mainArea,
self,
"searchString",
"Search",
callbackOnType=True,
callback=self.SearchUpdate)
self.headerLabels = [t[1] for t in HEADER]
self.experimentsWidget = QTreeWidget()
self.experimentsWidget.setHeaderLabels(self.headerLabels)
self.experimentsWidget.setSelectionMode(QTreeWidget.ExtendedSelection)
self.experimentsWidget.setRootIsDecorated(False)
self.experimentsWidget.setSortingEnabled(True)
contextEventFilter = gui.VisibleHeaderSectionContextEventFilter(
self.experimentsWidget, self.experimentsWidget)
self.experimentsWidget.header().installEventFilter(contextEventFilter)
self.experimentsWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self, role=Qt.DisplayRole))
self.experimentsWidget.setAlternatingRowColors(True)
self.experimentsWidget.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
self.selectionSetsWidget.setSelectionModel(
self.experimentsWidget.selectionModel())
self.selectionSetsWidget.setSelections(self.storedSelections)
self.mainArea.layout().addWidget(self.experimentsWidget)
self.restoreHeaderState()
self.experimentsWidget.header().geometriesChanged.connect(
self.saveHeaderState)
self.dbc = None
self.AuthSet()
QTimer.singleShot(100, self.ConnectAndUpdate)
def sizeHint(self):
return QSize(800, 600)
def AuthSet(self):
if len(self.username):
self.passf.setDisabled(False)
else:
self.passf.setDisabled(True)
def AuthChanged(self):
self.AuthSet()
self.ConnectAndUpdate()
def ConnectAndUpdate(self):
self.Connect()
if self.dbc:
def get_data_count(project_id):
# XXX: is there a better way?
# Note: limit 0 would return all objects
return self.dbc.gen.api.data.get(
case_ids__contains=project_id,
type__startswith='data:expression:',
limit=1)['meta']['total_count']
self.projects = sorted([
p for p in self.dbc.projects().items()
if get_data_count(p[0]) > 0
],
key=lambda x: x[1])
self.UpdateProjects()
self.ProjectChosen()
self.UpdateExperimentTypes()
def Connect(self):
self.error(1)
self.warning(1)
username = '******'
password = '******'
url = self.servers[self.serveri][0]
if self.username:
username = self.username
password = self.password
if username.lower() in ['*****@*****.**', 'anonymous']:
username = '******'
password = '******'
self.dbc = None
self.projects = []
self.result_types = []
try:
self.dbc = Genesis(address=url,
username=username,
password=password,
cache=self.buffer)
except requests.exceptions.ConnectionError:
self.dbc = Genesis(address=url,
username=username,
password=password,
connect=False,
cache=self.buffer)
self.warning(1, "Could not connect to server, working from cache.")
except Exception:
self.error(1, "Wrong username or password.")
self.UpdateProjects()
self.UpdateExperimentTypes() # clear lists
def Reload(self):
self.UpdateExperiments(reload=True)
def clear_cache(self):
self.buffer.clear()
self.Reload()
def rtype(self):
"""Return selected result template type """
if self.result_types:
return self.result_types[self.rtypei]
else:
return None
def UpdateExperimentTypes(self):
self.expressionTypesCB.clear()
items = [self.result_types_labels[desc] for desc in self.result_types]
self.expressionTypesCB.addItems(items)
#do not update anything if the list is empty
if len(self.result_types):
self.rtypei = max(0, min(self.rtypei, len(self.result_types) - 1))
def UpdateProjects(self):
self.projectCB.clear()
items = [desc for pid, desc in self.projects]
self.projectCB.addItems(items)
#do not update anything if the list if empty
if len(self.projects) > 0:
self.projecti = max(0, min(self.projecti, len(self.projects) - 1))
def UpdateExperiments(self, reload=False):
self.experimentsWidget.clear()
if not self.dbc or not self.dbc.projectid: # the connection did not succeed
return
self.items = []
self.progressBarInit()
result_types = []
result_types_labels = []
sucind = False # success indicator for database index
try:
result_types, result_types_labels = self.dbc.result_types(
reload=reload)
sucind = True
except Exception:
try:
result_types, result_types_labels = self.dbc.result_types()
self.warning(0, "Can not access database - using cached data.")
sucind = True
except Exception:
self.error(0, "Can not access database.")
if sucind:
self.warning(0)
self.error(0)
self.result_types = result_types
self.result_types_labels = result_types_labels
self.UpdateExperimentTypes()
self.UpdateResultsList(reload=reload)
self.progressBarFinished()
if self.currentSelection:
self.currentSelection.select(
self.experimentsWidget.selectionModel())
self.handle_commit_button()
def ProjectChosen(self, reload=False):
if self.projects:
self.dbc.projectid = self.projects[self.projecti][0]
else:
self.dbc.projectid = None
self.UpdateExperiments(reload=reload)
def ServerChosen(self):
self.ConnectAndUpdate()
def UpdateResultsList(self, reload=False):
results_list = self.dbc.results_list(self.rtype(), reload=reload)
try:
results_list = self.dbc.results_list(self.rtype(), reload=reload)
except Exception:
try:
results_list = self.dbc.results_list(self.rtype())
except Exception:
self.error(0, "Can not access database.")
self.results_list = results_list
#softly change the view so that the selection stays the same
items_shown = {}
for i, item in enumerate(self.items):
c = str(item.text(ID_INDEX))
items_shown[c] = i
items_to_show = set(id_ for id_ in self.results_list)
add_items = set(items_to_show) - set(items_shown)
delete_items = set(items_shown) - set(items_to_show)
i = 0
while i < self.experimentsWidget.topLevelItemCount():
it = self.experimentsWidget.topLevelItem(i)
if str(it.text(ID_INDEX)) in delete_items:
self.experimentsWidget.takeTopLevelItem(i)
else:
i += 1
delete_ind = set([items_shown[i] for i in delete_items])
self.items = [
it for i, it in enumerate(self.items) if i not in delete_ind
]
for r_annot in add_items:
d = defaultdict(lambda: "?", self.results_list[r_annot])
row_items = [""] + [
to_text(d.get(key, "?")) for key, _ in HEADER[1:]
]
row_items[ID_INDEX] = r_annot
ci = MyTreeWidgetItem(self.experimentsWidget, row_items)
self.items.append(ci)
for i in range(len(self.headerLabels)):
self.experimentsWidget.resizeColumnToContents(i)
self.wantbufver = lambda x: self.results_list[x]["date_modified"]
self.UpdateCached()
def UpdateCached(self):
if self.wantbufver and self.dbc:
for item in self.items:
id = str(item.text(ID_INDEX))
version = self.dbc._in_buffer(id + "|||" + self.rtype())
value = " " if version == self.wantbufver(id) else ""
item.setData(0, Qt.DisplayRole, value)
def SearchUpdate(self, string=""):
for item in self.items:
item.setHidden(not all(s in item
for s in self.searchString.split()))
def Commit(self):
pb = gui.ProgressBar(self, iterations=100)
table = None
ids = []
for item in self.experimentsWidget.selectedItems():
unique_id = str(item.text(ID_INDEX))
ids.append(unique_id)
transfn = None
if self.log2:
transfn = lambda x: math.log(x + 1.0, 2)
reverse_header_dict = {name: name for key, name in HEADER}
reverse_header_dict["ID"] = "id"
allowed_labels = None
def namefn(a):
name = SORTING_MODEL_LIST[self.exnamei]
name = reverse_header_dict.get(name, "id")
return dict(a)[name]
if len(ids):
table = self.dbc.get_data(
ids=ids,
result_type=self.rtype(),
callback=pb.advance,
exclude_constant_labels=self.excludeconstant,
bufver=self.wantbufver,
transform=transfn,
allowed_labels=allowed_labels,
namefn=namefn)
if self.joinreplicates:
table = dicty.join_replicates(
table,
ignorenames=self.dbc.IGNORE_REPLICATE,
namefn="name",
avg=dicty.median,
fnshow=lambda x: " | ".join(map(str, x)))
# Sort attributes
sortOrder = self.columnsSortingWidget.sortingOrder
all_values = defaultdict(set)
for at in table.domain.attributes:
atts = at.attributes
for name in sortOrder:
all_values[name].add(
atts.get(reverse_header_dict[name], ""))
isnum = {}
for at, vals in all_values.items():
vals = filter(None, vals)
try:
for a in vals:
float(a)
isnum[at] = True
except ValueError:
isnum[at] = False
def optfloat(x, at):
if x == "":
return ""
else:
return float(x) if isnum[at] else x
def sorting_key(attr):
atts = attr.attributes
return tuple([
optfloat(atts.get(reverse_header_dict[name], ""), name)
for name in sortOrder
])
attributes = sorted(table.domain.attributes, key=sorting_key)
domain = Orange.data.Domain(attributes, table.domain.class_vars,
table.domain.metas)
table = Orange.data.Table.from_table(domain, table)
table = Orange.data.Table(domain, table)
if self.transpose:
experiments = [at for at in table.domain.variables]
attr = [
compat.ContinuousVariable.make(ex['DDB'].value)
for ex in table
]
metavars = sorted(table.domain.variables[0].attributes.keys())
metavars = [
compat.StringVariable.make(name) for name in metavars
]
domain = compat.create_domain(attr, None, metavars)
metavars = compat.get_metas(domain)
metas = [[exp.attributes[var.name] for var in metavars]
for exp in experiments]
table = compat.create_table(domain, table.X.transpose(), None,
metas)
data_hints.set_hint(table, "taxid", "352472")
data_hints.set_hint(table, "genesinrows", False)
self.send("Data", table)
self.UpdateCached()
pb.finish()
def onSelectionChanged(self, selected, deselected):
self.handle_commit_button()
def handle_commit_button(self):
self.currentSelection = \
SelectionByKey(self.experimentsWidget.selectionModel().selection(),
key=(ID_INDEX,))
self.commit_button.setDisabled(not len(self.currentSelection))
def saveHeaderState(self):
hview = self.experimentsWidget.header()
for i, label in enumerate(self.headerLabels):
self.experimentsHeaderState[label] = hview.isSectionHidden(i)
def restoreHeaderState(self):
hview = self.experimentsWidget.header()
state = self.experimentsHeaderState
for i, label in enumerate(self.headerLabels):
hview.setSectionHidden(i, state.get(label, True))
self.experimentsWidget.resizeColumnToContents(i)
class OWItemsets(widget.OWWidget):
name = 'Frequent Itemsets'
description = 'Explore sets of items that frequently appear together.'
icon = 'icons/FrequentItemsets.svg'
priority = 10
inputs = [("Data", Table, 'set_data')]
outputs = [(Output.DATA, Table)]
minSupport = settings.Setting(30)
maxItemsets = settings.Setting(10000)
filterSearch = settings.Setting(True)
autoFind = settings.Setting(False)
autoSend = settings.Setting(True)
filterKeywords = settings.Setting('')
filterMinItems = settings.Setting(1)
filterMaxItems = settings.Setting(10000)
UserAdviceMessages = [
widget.Message('Itemset are listed in item-sorted order, i.e. '
'an itemset containing A and B is only listed once, as '
'A > B (and not also B > A).',
'itemsets-order', widget.Message.Warning),
widget.Message('To select all the itemsets that are descendants of '
'(include) some item X (i.e. the whole subtree), you '
'can fold the subtree at that item and then select it.',
'itemsets-order', widget.Message.Information)
]
def __init__(self):
self.tree = QTreeWidget(self.mainArea,
columnCount=2,
allColumnsShowFocus=True,
alternatingRowColors=True,
selectionMode=QTreeWidget.ExtendedSelection,
uniformRowHeights=True)
self.tree.setHeaderLabels(["Itemsets", "Support", "%"])
self.tree.header().setStretchLastSection(True)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.mainArea.layout().addWidget(self.tree)
box = gui.widgetBox(self.controlArea, "Info")
self.nItemsets = self.nSelectedExamples = self.nSelectedItemsets = ''
gui.label(box, self, "Number of itemsets: %(nItemsets)s")
gui.label(box, self, "Selected itemsets: %(nSelectedItemsets)s")
gui.label(box, self, "Selected examples: %(nSelectedExamples)s")
hbox = gui.widgetBox(box, orientation='horizontal')
gui.button(hbox, self, "Expand all", callback=self.tree.expandAll)
gui.button(hbox, self, "Collapse all", callback=self.tree.collapseAll)
box = gui.widgetBox(self.controlArea, 'Find itemsets')
gui.hSlider(box, self, 'minSupport', minValue=1, maxValue=100,
label='Minimal support:', labelFormat="%d%%",
callback=lambda: self.find_itemsets())
gui.hSlider(box, self, 'maxItemsets', minValue=10000, maxValue=100000, step=10000,
label='Max. number of itemsets:', labelFormat="%d",
callback=lambda: self.find_itemsets())
gui.checkBox(box, self, 'filterSearch',
label='Apply below filters in search',
tooltip='If checked, the itemsets are filtered according '
'to below filter conditions already in the search '
'phase. \nIf unchecked, the only filters applied '
'during search are the ones above, '
'and the itemsets are \nfiltered afterwards only for '
'display, i.e. only the matching itemsets are shown.')
self.button = gui.auto_commit(
box, self, 'autoFind', 'Find itemsets', commit=self.find_itemsets)
box = gui.widgetBox(self.controlArea, 'Filter itemsets')
gui.lineEdit(box, self, 'filterKeywords', 'Contains:',
callback=self.filter_change, orientation='horizontal',
tooltip='A comma or space-separated list of regular '
'expressions.')
hbox = gui.widgetBox(box, orientation='horizontal')
gui.spin(hbox, self, 'filterMinItems', 1, 998, label='Min. items:',
callback=self.filter_change)
gui.spin(hbox, self, 'filterMaxItems', 2, 999, label='Max. items:',
callback=self.filter_change)
gui.rubber(hbox)
gui.rubber(self.controlArea)
gui.auto_commit(self.controlArea, self, 'autoSend', 'Send selection')
self.filter_change()
def sendReport(self):
self.reportSettings("Itemset statistics",
[("Number of itemsets", self.nItemsets),
("Selected itemsets", self.nSelectedItemsets),
("Covered examples", self.nSelectedExamples),
])
self.reportSection("Itemsets")
self.reportRaw(OWReport.reportTree(self.tree))
ITEM_DATA_ROLE = Qt.UserRole + 1
def selectionChanged(self):
X = self.data.X
mapping = self.onehot_mapping
instances = set()
where = np.where
def whole_subtree(node):
yield node
for i in range(node.childCount()):
yield from whole_subtree(node.child(i))
def itemset(node):
while node:
yield node.data(0, self.ITEM_DATA_ROLE)
node = node.parent()
def selection_ranges(node):
n_children = node.childCount()
if n_children:
yield (self.tree.indexFromItem(node.child(0)),
self.tree.indexFromItem(node.child(n_children - 1)))
for i in range(n_children):
yield from selection_ranges(node.child(i))
nSelectedItemsets = 0
item_selection = QItemSelection()
for node in self.tree.selectedItems():
nodes = (node,) if node.isExpanded() else whole_subtree(node)
if not node.isExpanded():
for srange in selection_ranges(node):
item_selection.select(*srange)
for node in nodes:
nSelectedItemsets += 1
cols, vals = zip(*(mapping[i] for i in itemset(node)))
instances.update(where((X[:, cols] == vals).all(axis=1))[0])
self.tree.itemSelectionChanged.disconnect(self.selectionChanged)
self.tree.selectionModel().select(item_selection,
QItemSelectionModel.Select | QItemSelectionModel.Rows)
self.tree.itemSelectionChanged.connect(self.selectionChanged)
self.nSelectedExamples = len(instances)
self.nSelectedItemsets = nSelectedItemsets
self.output = self.data[sorted(instances)] or None
self.commit()
def commit(self):
self.send(Output.DATA, self.output)
def filter_change(self):
isRegexMatch = self.isRegexMatch = re.compile(
'|'.join(i.strip()
for i in re.split('(,|\s)+', self.filterKeywords.strip())
if i.strip())).search
def hide(node, depth, has_kw):
if not has_kw:
has_kw = isRegexMatch(node.text(0))
hidden = (sum(hide(node.child(i), depth + 1, has_kw)
for i in range(node.childCount())) == node.childCount()
if node.childCount() else
(not has_kw or
not self.filterMinItems <= depth <= self.filterMaxItems))
node.setHidden(hidden)
return hidden
hide(self.tree.invisibleRootItem(), 0, False)
class TreeWidgetItem(QTreeWidgetItem):
def data(self, column, role):
"""Construct lazy tooltips"""
if role != Qt.ToolTipRole:
return super().data(column, role)
tooltip = []
while self:
tooltip.append(self.text(0))
self = self.parent()
return ' '.join(reversed(tooltip))
def find_itemsets(self):
if self.data is None: return
data = self.data
self.tree.clear()
self.tree.setUpdatesEnabled(False)
self.tree.blockSignals(True)
class ItemDict(dict):
def __init__(self, item):
self.item = item
top = ItemDict(self.tree.invisibleRootItem())
X, mapping = OneHot.encode(data)
self.onehot_mapping = mapping
names = {item: '{}={}'.format(var.name, val)
for item, var, val in OneHot.decode(mapping.keys(), data, mapping)}
nItemsets = 0
filterSearch = self.filterSearch
filterMinItems, filterMaxItems = self.filterMinItems, self.filterMaxItems
isRegexMatch = self.isRegexMatch
# Find itemsets and populate the TreeView
progress = gui.ProgressBar(self, self.maxItemsets + 1)
for itemset, support in frequent_itemsets(X, self.minSupport / 100):
if filterSearch and not filterMinItems <= len(itemset) <= filterMaxItems:
continue
parent = top
first_new_item = None
itemset_matches_filter = False
for item in sorted(itemset):
name = names[item]
if filterSearch and not itemset_matches_filter:
itemset_matches_filter = isRegexMatch(name)
child = parent.get(name)
if child is None:
wi = self.TreeWidgetItem(parent.item, [name, str(support), '{:.1f}'.format(100 * support / len(data))])
wi.setData(0, self.ITEM_DATA_ROLE, item)
child = parent[name] = ItemDict(wi)
if first_new_item is None:
first_new_item = (parent, name)
parent = child
if filterSearch and not itemset_matches_filter:
parent, name = first_new_item
parent.item.removeChild(parent[name].item)
del parent[name].item
del parent[name]
else:
nItemsets += 1
progress.advance()
if nItemsets >= self.maxItemsets:
break
if not filterSearch:
self.filter_change()
self.nItemsets = nItemsets
self.nSelectedItemsets = 0
self.nSelectedExamples = 0
self.tree.expandAll()
for i in range(self.tree.columnCount()):
self.tree.resizeColumnToContents(i)
self.tree.setUpdatesEnabled(True)
self.tree.blockSignals(False)
progress.finish()
def set_data(self, data):
self.data = data
if data is not None:
self.warning(0, 'Data has continuous attributes which will be skipped.'
if data.domain.has_continuous_attributes() else None)
self.error(1, 'Discrete features required but data has none.'
if not data.domain.has_discrete_attributes() else None)
self.button.setDisabled(not data.domain.has_discrete_attributes())
if self.autoFind:
self.find_itemsets()
class RunsDialog(QtHelper.EnhancedQDialog):
"""
Runs several dialog
"""
RefreshRepository = pyqtSignal(str)
def __init__(self, dialogName, parent = None, iRepo=None, lRepo=None, rRepo=None):
"""
Constructor
"""
QtHelper.EnhancedQDialog.__init__(self, parent)
self.name = self.tr("Prepare a group of runs")
self.projectReady = False
self.iRepo = iRepo
self.lRepo = lRepo
self.rRepo = rRepo
self.createDialog()
self.createConnections()
def createDialog(self):
"""
Create qt dialog
"""
self.setWindowTitle( self.name )
mainLayout = QHBoxLayout()
layoutTests = QHBoxLayout()
layoutRepoTest = QVBoxLayout()
self.prjCombo = QComboBox(self)
self.prjCombo.setEnabled(False)
self.repoTests = QTreeWidget(self)
self.repoTests.setFrameShape(QFrame.NoFrame)
if USE_PYQT5:
self.repoTests.header().setSectionResizeMode(QHeaderView.Stretch)
else:
self.repoTests.header().setResizeMode(QHeaderView.Stretch)
self.repoTests.setHeaderHidden(True)
self.repoTests.setContextMenuPolicy(Qt.CustomContextMenu)
self.repoTests.setIndentation(10)
layoutRepoTest.addWidget(self.prjCombo)
layoutRepoTest.addWidget(self.repoTests)
self.testsList = QListWidget(self)
layoutTests.addLayout( layoutRepoTest )
layoutTests.addWidget( self.testsList )
mainLayout.addLayout( layoutTests )
buttonLayout = QVBoxLayout()
self.okButton = QPushButton(self.tr("Execute All"), self)
self.okButton.setEnabled(False)
self.cancelButton = QPushButton(self.tr("Cancel"), self)
self.upButton = QPushButton(self.tr("UP"), self)
self.upButton.setEnabled(False)
self.downButton = QPushButton(self.tr("DOWN"), self)
self.downButton.setEnabled(False)
self.clearButton = QPushButton(self.tr("Remove All"), self)
self.delButton = QPushButton(self.tr("Remove"), self)
self.delButton.setEnabled(False)
self.runSimultaneous = QCheckBox(self.tr("Simultaneous Run"))
self.schedImmed = QRadioButton(self.tr("Run Immediately"))
self.schedImmed.setChecked(True)
self.schedAt = QRadioButton(self.tr("Run At:"))
self.schedAtDateTimeEdit = QDateTimeEdit(QDateTime.currentDateTime())
self.schedAtDateTimeEdit.setEnabled(False)
buttonLayout.addWidget(self.okButton)
buttonLayout.addWidget(self.runSimultaneous)
buttonLayout.addWidget(self.schedImmed)
buttonLayout.addWidget(self.schedAt)
buttonLayout.addWidget(self.schedAtDateTimeEdit)
buttonLayout.addWidget( self.upButton )
buttonLayout.addWidget( self.downButton )
buttonLayout.addWidget( self.delButton )
buttonLayout.addWidget( self.clearButton )
buttonLayout.addWidget(self.cancelButton)
mainLayout.addLayout(buttonLayout)
self.setMinimumHeight(400)
self.setMinimumWidth(750)
self.setLayout(mainLayout)
def initProjects(self, projects=[], defaultProject=1):
"""
Initialize projects
"""
# init date and time
self.schedAtDateTimeEdit.setDateTime(QDateTime.currentDateTime())
self.projectReady = False
self.repoTests.clear()
self.prjCombo.clear()
self.testsList.clear()
self.prjCombo.setEnabled(True)
# insert data
pname = ''
for p in projects:
self.prjCombo.addItem ( p['name'] )
if defaultProject == p['project_id']:
pname = p['name']
for i in xrange(self.prjCombo.count()):
item_text = self.prjCombo.itemText(i)
if str(pname) == str(item_text):
self.prjCombo.setCurrentIndex(i)
self.projectReady = True
self.RefreshRepository.emit(pname)
def initializeTests(self, listing):
"""
Initialize tests
"""
self.repoTests.clear()
self.testRoot = self.rRepo.Item(repo = self.iRepo.remote(),
parent = self.repoTests, txt = "Root",
type = QTreeWidgetItem.UserType+10,
isRoot = True )
self.testRoot.setSelected(True)
self.createRepository(listing=listing, parent=self.testRoot,fileincluded=True)
self.repoTests.sortItems(0, Qt.AscendingOrder)
self.hideItems(hideTsx=False, hideTpx=False, hideTcx=True, hideTdx=True, hideTxt=True, hidePy=True,
hideTux=False, hidePng=True, hideTgx=False, hideTax=False)
def createRepository(self, listing, parent, fileincluded=True):
"""
Create repository
@param listing:
@type listing: list
@param parent:
@type parent:
@param fileincluded:
@type fileincluded: boolean
"""
try:
for dct in listing:
if dct["type"] == "folder":
item = self.rRepo.Item(repo = self.iRepo.remote(), parent = parent,
txt = dct["name"], propertiesFile=dct )
self.createRepository( dct["content"] , item, fileincluded )
else:
if fileincluded:
if dct["type"] == "file":
pname = self.iRepo.remote().getProjectName(dct["project"])
# {'modification': 1342259500, 'type': 'file', 'name': '__init__.py', 'size': '562 }
item = self.rRepo.Item(repo = self.iRepo.remote(), parent = parent, txt = dct["name"] ,
propertiesFile=dct, type = QTreeWidgetItem.UserType+0,
projectId=dct["project"], projectName=pname )
except Exception as e:
self.error( "unable to create tree for runs: %s" % e )
def onProjectChanged(self, projectItem):
"""
Called when the project changed on the combo box
"""
if self.projectReady:
item_text = self.prjCombo.itemText(projectItem)
self.RefreshRepository.emit(item_text)
def createConnections (self):
"""
create qt connections
* ok
* cancel
"""
self.prjCombo.currentIndexChanged.connect(self.onProjectChanged)
self.okButton.clicked.connect( self.acceptClicked )
self.cancelButton.clicked.connect( self.reject )
self.upButton.clicked.connect(self.upTest)
self.downButton.clicked.connect(self.downTest)
self.clearButton.clicked.connect(self.clearList)
self.delButton.clicked.connect(self.delTest)
self.testsList.itemClicked.connect(self.onItemSelected)
self.testsList.itemSelectionChanged.connect(self.onItemSelectionChanged)
self.schedAt.toggled.connect(self.onSchedAtActivated)
self.repoTests.itemDoubleClicked.connect( self.onTestDoucleClicked )
def onSchedAtActivated(self, toggled):
"""
On sched at button activated
"""
if toggled:
self.schedAtDateTimeEdit.setEnabled(True)
else:
self.schedAtDateTimeEdit.setEnabled(False)
def onItemSelectionChanged(self):
"""
Called on item selection changed
"""
self.onItemSelected(itm=None)
def onItemSelected(self, itm):
"""
Call on item selected
"""
selectedItems = self.testsList.selectedItems()
if len(selectedItems):
self.delButton.setEnabled(True)
self.upButton.setEnabled(True)
self.downButton.setEnabled(True)
else:
self.delButton.setEnabled(False)
self.upButton.setEnabled(False)
self.downButton.setEnabled(False)
if not self.testsList.count():
self.okButton.setEnabled(False)
def upTest(self):
"""
Up test
"""
currentRow = self.testsList.currentRow()
currentItem = self.testsList.takeItem(currentRow)
self.testsList.insertItem(currentRow - 1, currentItem)
def downTest(self):
"""
Down test
"""
currentRow = self.testsList.currentRow()
currentItem = self.testsList.takeItem(currentRow)
self.testsList.insertItem(currentRow + 1, currentItem)
def delTest(self):
"""
Del test
"""
currentRow = self.testsList.currentRow()
currentItem = self.testsList.takeItem(currentRow)
def clearList(self):
"""
Clear test
"""
self.testsList.clear()
self.delButton.setEnabled(False)
self.upButton.setEnabled(False)
self.downButton.setEnabled(False)
self.okButton.setEnabled(False)
def iterateTree(self, item, hideTsx, hideTpx, hideTcx, hideTdx, hideTxt,
hidePy, hideTux, hidePng, hideTgx, hideTax):
"""
Iterate tree
"""
child_count = item.childCount()
for i in range(child_count):
subitem = item.child(i)
subchild_count = subitem.childCount()
if subchild_count > 0:
self.iterateTree(item=subitem, hideTsx=hideTsx,
hideTpx=hideTpx, hideTcx=hideTcx,
hideTdx=hideTdx, hideTxt=hideTxt,
hidePy=hidePy, hideTux=hideTux,
hidePng=hidePng, hideTgx=hideTgx, hideTax=hideTax)
else:
if hideTux and subitem.getExtension() == self.rRepo.EXTENSION_TUX:
subitem.setHidden (True)
elif hideTpx and subitem.getExtension() == self.rRepo.EXTENSION_TPX:
subitem.setHidden (True)
elif hideTgx and subitem.getExtension() == self.rRepo.EXTENSION_TGX:
subitem.setHidden (True)
elif hideTcx and subitem.getExtension() == self.rRepo.EXTENSION_TCX:
subitem.setHidden (True)
elif hideTsx and subitem.getExtension() == self.rRepo.EXTENSION_TSX:
subitem.setHidden (True)
elif hideTdx and subitem.getExtension() == self.rRepo.EXTENSION_TDX:
subitem.setHidden (True)
elif hideTxt and subitem.getExtension() == self.rRepo.EXTENSION_TXT:
subitem.setHidden (True)
elif hidePy and subitem.getExtension() == self.rRepo.EXTENSION_PY:
subitem.setHidden (True)
elif hidePng and subitem.getExtension() == self.rRepo.EXTENSION_PNG:
subitem.setHidden (True)
elif hideTax and subitem.getExtension() == self.rRepo.EXTENSION_TAx:
subitem.setHidden (True)
else:
subitem.setHidden(False)
def hideItems(self, hideTsx=False, hideTpx=False, hideTcx=False, hideTdx=False, hideTxt=False, hidePy=False,
hideTux=False, hidePng=False, hideTgx=False, hideTax=False):
"""
Hide items
"""
root = self.repoTests.invisibleRootItem()
self.iterateTree(item=root, hideTsx=hideTsx, hideTpx=hideTpx, hideTcx=hideTcx,
hideTdx=hideTdx, hideTxt=hideTxt, hidePy=hidePy,
hideTux=hideTux, hidePng=hidePng, hideTgx=hideTgx, hideTax=hideTax)
def onTestDoucleClicked(self, testItem):
"""
On tests double clicked
"""
if testItem.type() != QTreeWidgetItem.UserType+0:
return
self.okButton.setEnabled(True)
currentProject = self.prjCombo.currentText()
testName = "%s:%s" % (str(currentProject),testItem.getPath(withFileName = True))
testItem = QListWidgetItem(testName )
if testName.endswith(self.rRepo.EXTENSION_TUX):
testItem.setIcon(QIcon(":/tux.png"))
if testName.endswith(self.rRepo.EXTENSION_TSX):
testItem.setIcon(QIcon(":/tsx.png"))
if testName.endswith(self.rRepo.EXTENSION_TPX):
testItem.setIcon(QIcon(":/tpx.png"))
if testName.endswith(self.rRepo.EXTENSION_TGX):
testItem.setIcon(QIcon(":/tgx.png"))
if testName.endswith(self.rRepo.EXTENSION_TAX):
testItem.setIcon(QIcon(":/tax.png"))
self.testsList.addItem( testItem )
def acceptClicked (self):
"""
Called on accept button
"""
self.accept()
def getTests(self):
"""
Returns all tests in the list
"""
tests = []
for i in xrange(self.testsList.count()):
testItem = self.testsList.item(i)
tests.append( str(testItem.text()) )
runSimultaneous = False
if self.runSimultaneous.isChecked(): runSimultaneous = True
if self.schedImmed.isChecked():
runAt = (0,0,0,0,0,0)
return (tests, False, runAt, runSimultaneous)
else:
pydt = self.schedAtDateTimeEdit.dateTime().toPyDateTime()
runAt = (pydt.year, pydt.month, pydt.day, pydt.hour, pydt.minute, pydt.second)
return (tests, True, runAt, runSimultaneous)
class ClientExceptionsViewer( QWidget ):
" Implements the client exceptions viewer for a debugger "
def __init__( self, parent, ignoredExceptionsViewer ):
QWidget.__init__( self, parent )
self.__ignoredExceptionsViewer = ignoredExceptionsViewer
self.__currentItem = None
self.__createPopupMenu()
self.__createLayout()
GlobalData().project.projectChanged.connect( self.__onProjectChanged )
return
def setFocus( self ):
" Sets the widget focus "
self.exceptionsList.setFocus()
return
def __createPopupMenu( self ):
" Creates the popup menu "
self.__excptMenu = QMenu()
self.__addToIgnoreMenuItem = self.__excptMenu.addAction(
"Add to ignore list", self.__onAddToIgnore )
self.__jumpToCodeMenuItem = self.__excptMenu.addAction(
"Jump to code", self.__onJumpToCode )
return
def __createLayout( self ):
" Creates the widget layout "
verticalLayout = QVBoxLayout( self )
verticalLayout.setContentsMargins( 0, 0, 0, 0 )
verticalLayout.setSpacing( 0 )
self.headerFrame = QFrame()
self.headerFrame.setFrameStyle( QFrame.StyledPanel )
self.headerFrame.setAutoFillBackground( True )
headerPalette = self.headerFrame.palette()
headerBackground = headerPalette.color( QPalette.Background )
headerBackground.setRgb( min( headerBackground.red() + 30, 255 ),
min( headerBackground.green() + 30, 255 ),
min( headerBackground.blue() + 30, 255 ) )
headerPalette.setColor( QPalette.Background, headerBackground )
self.headerFrame.setPalette( headerPalette )
self.headerFrame.setFixedHeight( 24 )
self.__excptLabel = QLabel( "Exceptions" )
fixedSpacer = QSpacerItem( 3, 3 )
headerLayout = QHBoxLayout()
headerLayout.setContentsMargins( 0, 0, 0, 0 )
headerLayout.addSpacerItem( fixedSpacer )
headerLayout.addWidget( self.__excptLabel )
self.headerFrame.setLayout( headerLayout )
self.exceptionsList = QTreeWidget( self )
self.exceptionsList.setSortingEnabled( False )
self.exceptionsList.setAlternatingRowColors( True )
self.exceptionsList.setRootIsDecorated( True )
self.exceptionsList.setItemsExpandable( True )
self.exceptionsList.setUniformRowHeights( True )
self.exceptionsList.setSelectionMode( QAbstractItemView.SingleSelection )
self.exceptionsList.setSelectionBehavior( QAbstractItemView.SelectRows )
self.exceptionsList.setItemDelegate( NoOutlineHeightDelegate( 4 ) )
self.exceptionsList.setContextMenuPolicy( Qt.CustomContextMenu )
self.__addToIgnoreButton = QAction(
PixmapCache().getIcon( 'add.png' ),
"Add exception to the list of ignored", self )
self.__addToIgnoreButton.triggered.connect( self.__onAddToIgnore )
self.__addToIgnoreButton.setEnabled( False )
expandingSpacer = QWidget()
expandingSpacer.setSizePolicy( QSizePolicy.Expanding, QSizePolicy.Expanding )
self.__jumpToCodeButton = QAction(
PixmapCache().getIcon( 'gotoline.png' ),
"Jump to the code", self )
self.__jumpToCodeButton.triggered.connect( self.__onJumpToCode )
self.__jumpToCodeButton.setEnabled( False )
self.__delAllButton = QAction(
PixmapCache().getIcon( 'trash.png' ),
"Delete all the client exceptions", self )
self.__delAllButton.triggered.connect( self.__onDelAll )
self.__delAllButton.setEnabled( False )
self.toolbar = QToolBar()
self.toolbar.setOrientation( Qt.Horizontal )
self.toolbar.setMovable( False )
self.toolbar.setAllowedAreas( Qt.TopToolBarArea )
self.toolbar.setIconSize( QSize( 16, 16 ) )
self.toolbar.setFixedHeight( 28 )
self.toolbar.setContentsMargins( 0, 0, 0, 0 )
self.toolbar.addAction( self.__addToIgnoreButton )
self.toolbar.addAction( self.__jumpToCodeButton )
self.toolbar.addWidget( expandingSpacer )
self.toolbar.addAction( self.__delAllButton )
self.exceptionsList.itemDoubleClicked.connect(
self.__onExceptionDoubleClicked )
self.exceptionsList.customContextMenuRequested.connect(
self.__showContextMenu )
self.exceptionsList.itemSelectionChanged.connect(
self.__onSelectionChanged )
self.exceptionsList.setHeaderLabels( [ "Exception" ] )
verticalLayout.addWidget( self.headerFrame )
verticalLayout.addWidget( self.toolbar )
verticalLayout.addWidget( self.exceptionsList )
return
def clear( self ):
" Clears the content "
self.exceptionsList.clear()
self.__updateExceptionsLabel()
self.__addToIgnoreButton.setEnabled( False )
self.__jumpToCodeButton.setEnabled( False )
self.__delAllButton.setEnabled( False )
self.__currentItem = None
self.emit( SIGNAL( 'ClientExceptionsCleared' ) )
return
def __onExceptionDoubleClicked( self, item, column ):
" Triggered when an exception is double clicked "
if self.__currentItem is not None:
if self.__currentItem.getType() == STACK_FRAME_ITEM:
self.__onJumpToCode()
return
# This is an exception item itself.
# Open a separate dialog window with th detailed info.
return
def __showContextMenu( self, coord ):
" Shows the frames list context menu "
self.__contextItem = self.exceptionsList.itemAt( coord )
self.__addToIgnoreMenuItem.setEnabled( self.__addToIgnoreButton.isEnabled() )
self.__jumpToCodeMenuItem.setEnabled( self.__jumpToCodeButton.isEnabled() )
if self.__contextItem is not None:
self.__excptMenu.popup( QCursor.pos() )
return
def __onAddToIgnore( self ):
" Adds an exception into the ignore list "
if self.__currentItem is not None:
self.__ignoredExceptionsViewer.addExceptionFilter(
str( self.__currentItem.getExceptionType() ) )
self.__addToIgnoreButton.setEnabled( False )
return
def __onJumpToCode( self ):
" Jumps to the corresponding source code line "
if self.__currentItem is not None:
if self.__currentItem.getType() == STACK_FRAME_ITEM:
fileName = self.__currentItem.getFileName()
if '<' not in fileName and '>' not in fileName:
lineNumber = self.__currentItem.getLineNumber()
editorsManager = GlobalData().mainWindow.editorsManager()
editorsManager.openFile( fileName, lineNumber )
editor = editorsManager.currentWidget().getEditor()
editor.gotoLine( lineNumber )
editorsManager.currentWidget().setFocus()
return
def __onDelAll( self ):
" Triggered when all the exceptions should be deleted "
self.clear()
return
def addException( self, exceptionType, exceptionMessage,
stackTrace ):
" Adds the exception to the view "
for index in xrange( self.exceptionsList.topLevelItemCount() ):
item = self.exceptionsList.topLevelItem( index )
if item.equal( exceptionType, exceptionMessage, stackTrace ):
item.incrementCounter()
self.exceptionsList.clearSelection()
self.exceptionsList.setCurrentItem( item )
self.__updateExceptionsLabel()
return
item = ExceptionItem( self.exceptionsList, exceptionType,
exceptionMessage, stackTrace )
self.exceptionsList.clearSelection()
self.exceptionsList.setCurrentItem( item )
self.__updateExceptionsLabel()
self.__delAllButton.setEnabled( True )
return
def __updateExceptionsLabel( self ):
" Updates the exceptions header label "
total = self.getTotalCount()
if total > 0:
self.__excptLabel.setText( "Exceptions (total: " +
str( total ) + ")" )
else:
self.__excptLabel.setText( "Exceptions" )
return
def getTotalCount( self ):
" Provides the total number of exceptions "
count = 0
for index in xrange( self.exceptionsList.topLevelItemCount() ):
count += self.exceptionsList.topLevelItem( index ).getCount()
return count
def __onProjectChanged( self, what ):
" Triggered when a project is changed "
if what == CodimensionProject.CompleteProject:
self.clear()
return
def __onSelectionChanged( self ):
" Triggered when the current item is changed "
selected = list( self.exceptionsList.selectedItems() )
if selected:
self.__currentItem = selected[ 0 ]
if self.__currentItem.getType() == STACK_FRAME_ITEM:
fileName = self.__currentItem.getFileName()
if '<' in fileName or '>' in fileName:
self.__jumpToCodeButton.setEnabled( False )
else:
self.__jumpToCodeButton.setEnabled( True )
self.__addToIgnoreButton.setEnabled( False )
else:
self.__jumpToCodeButton.setEnabled( False )
excType = str( self.__currentItem.getExceptionType() )
if self.__ignoredExceptionsViewer.isIgnored( excType ) or \
" " in excType or excType.startswith( "unhandled" ):
self.__addToIgnoreButton.setEnabled( False )
else:
self.__addToIgnoreButton.setEnabled( True )
else:
self.__currentItem = None
self.__addToIgnoreButton.setEnabled( False )
self.__jumpToCodeButton.setEnabled( False )
return
class TreeSymbolsWidget(QDialog):
"""Class of Dialog for Tree Symbols"""
def __init__(self, parent=None):
super(TreeSymbolsWidget, self).__init__(parent,
Qt.WindowStaysOnTopHint)
vbox = QVBoxLayout(self)
vbox.setContentsMargins(0, 0, 0, 0)
vbox.setSpacing(0)
self.tree = QTreeWidget()
vbox.addWidget(self.tree)
self.tree.header().setHidden(True)
self.tree.setSelectionMode(self.tree.SingleSelection)
self.tree.setAnimated(True)
self.tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
self.actualSymbols = ('', {})
self.docstrings = {}
self.collapsedItems = {}
self.connect(self, SIGNAL("itemClicked(QTreeWidgetItem *, int)"),
self._go_to_definition)
self.connect(self, SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self._go_to_definition)
self.tree.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self,
SIGNAL("customContextMenuRequested(const QPoint &)"),
self._menu_context_tree)
self.connect(self, SIGNAL("itemCollapsed(QTreeWidgetItem *)"),
self._item_collapsed)
self.connect(self, SIGNAL("itemExpanded(QTreeWidgetItem *)"),
self._item_expanded)
IDE.register_service('symbols_explorer', self)
ExplorerContainer.register_tab(translations.TR_TAB_SYMBOLS, self)
def install_tab(self):
"""Connect signals for goingdown"""
ide = IDE.get_service('ide')
self.connect(ide, SIGNAL("goingDown()"), self.close)
def _menu_context_tree(self, point):
"""Context menu"""
index = self.tree.indexAt(point)
if not index.isValid():
return
menu = QMenu(self)
f_all = menu.addAction(translations.TR_FOLD_ALL)
u_all = menu.addAction(translations.TR_UNFOLD_ALL)
menu.addSeparator()
u_class = menu.addAction(translations.TR_UNFOLD_CLASSES)
u_class_method = menu.addAction(
translations.TR_UNFOLD_CLASSES_AND_METHODS)
u_class_attr = menu.addAction(
translations.TR_UNFOLD_CLASSES_AND_ATTRIBUTES)
menu.addSeparator()
#save_state = menu.addAction(self.tr("Save State"))
self.connect(f_all, SIGNAL("triggered()"),
lambda: self.tree.collapseAll())
self.connect(u_all, SIGNAL("triggered()"),
lambda: self.tree.expandAll())
self.connect(u_class, SIGNAL("triggered()"), self._unfold_class)
self.connect(u_class_method, SIGNAL("triggered()"),
self._unfold_class_method)
self.connect(u_class_attr, SIGNAL("triggered()"),
self._unfold_class_attribute)
#self.connect(save_state, SIGNAL("triggered()"),
#self._save_symbols_state)
menu.exec_(QCursor.pos())
def _get_classes_root(self):
"""Return the root of classes"""
class_root = None
for i in range(self.tree.topLevelItemCount()):
item = self.tree.topLevelItem(i)
if item.isClass and not item.isClickable:
class_root = item
break
return class_root
def _unfold_class(self):
"""Method to Unfold Classes"""
self.tree.collapseAll()
classes_root = self._get_classes_root()
if not classes_root:
return
classes_root.setExpanded(True)
def _unfold_class_method(self):
"""Method to Unfold Methods"""
self.tree.expandAll()
classes_root = self._get_classes_root()
if not classes_root:
return
#for each class!
for i in range(classes_root.childCount()):
class_item = classes_root.child(i)
#for each attribute or functions
for j in range(class_item.childCount()):
item = class_item.child(j)
#METHODS ROOT!!
if not item.isMethod and not item.isClickable:
item.setExpanded(False)
break
def _unfold_class_attribute(self):
"""Method to Unfold Attributes"""
self.tree.expandAll()
classes_root = self._get_classes_root()
if not classes_root:
return
#for each class!
for i in range(classes_root.childCount()):
class_item = classes_root.child(i)
#for each attribute or functions
for j in range(class_item.childCount()):
item = class_item.child(j)
#ATTRIBUTES ROOT!!
if not item.isAttribute and not item.isClickable:
item.setExpanded(False)
break
def _save_symbols_state(self):
"""Method to Save a persistent Symbols state"""
#filename = self.actualSymbols[0]
#TODO: persist self.collapsedItems[filename] in QSettings
pass
def _get_expand(self, item):
"""
Returns True or False to be used as setExpanded() with the items
It method is based on the click that the user made in the tree
"""
name = self._get_unique_name(item)
filename = self.actualSymbols[0]
collapsed_items = self.collapsedItems.get(filename, [])
can_check = (not item.isClickable) or item.isClass or item.isMethod
if can_check and name in collapsed_items:
return False
return True
@staticmethod
def _get_unique_name(item):
"""
Returns a string used as unique name
"""
# className_Attributes/className_Functions
parent = item.parent()
if parent:
return "%s_%s" % (parent.text(0), item.text(0))
return "_%s" % item.text(0)
def update_symbols_tree(self, symbols, filename='', parent=None):
"""Method to Update the symbols on the Tree"""
if not parent:
if filename == self.actualSymbols[0] and \
self.actualSymbols[1] and not symbols:
return
if symbols == self.actualSymbols[1]:
# Nothing new then return
return
# we have new symbols refresh it
self.tree.clear()
self.actualSymbols = (filename, symbols)
self.docstrings = symbols.get('docstrings', {})
parent = self.tree
if 'attributes' in symbols:
globalAttribute = ItemTree(parent, [translations.TR_ATTRIBUTES])
globalAttribute.isClickable = False
globalAttribute.isAttribute = True
globalAttribute.setExpanded(self._get_expand(globalAttribute))
for glob in sorted(symbols['attributes']):
globItem = ItemTree(globalAttribute, [glob],
lineno=symbols['attributes'][glob])
globItem.isAttribute = True
globItem.setIcon(0, QIcon(":img/attribute"))
globItem.setExpanded(self._get_expand(globItem))
if 'functions' in symbols and symbols['functions']:
functionsItem = ItemTree(parent, [translations.TR_FUNCTIONS])
functionsItem.isClickable = False
functionsItem.isMethod = True
functionsItem.setExpanded(self._get_expand(functionsItem))
for func in sorted(symbols['functions']):
item = ItemTree(functionsItem, [func],
lineno=symbols['functions'][func]['lineno'])
tooltip = self.create_tooltip(
func, symbols['functions'][func]['lineno'])
item.isMethod = True
item.setIcon(0, QIcon(":img/function"))
item.setToolTip(0, tooltip)
item.setExpanded(self._get_expand(item))
self.update_symbols_tree(
symbols['functions'][func]['functions'], parent=item)
if 'classes' in symbols and symbols['classes']:
classItem = ItemTree(parent, [translations.TR_CLASSES])
classItem.isClickable = False
classItem.isClass = True
classItem.setExpanded(self._get_expand(classItem))
for claz in sorted(symbols['classes']):
line_number = symbols['classes'][claz]['lineno']
item = ItemTree(classItem, [claz], lineno=line_number)
item.isClass = True
tooltip = self.create_tooltip(claz, line_number)
item.setToolTip(0, tooltip)
item.setIcon(0, QIcon(":img/class"))
item.setExpanded(self._get_expand(item))
self.update_symbols_tree(symbols['classes'][claz]['members'],
parent=item)
def _go_to_definition(self, item):
"""Takes and item object and goes to definition on the editor"""
main_container = IDE.get_service('main_container')
if item.isClickable and main_container:
main_container.editor_go_to_line(item.lineno - 1)
def create_tooltip(self, name, lineno):
"""Takes a name and line number and returns a tooltip"""
doc = self.docstrings.get(lineno, None)
if doc is None:
doc = ''
else:
doc = '\n' + doc
tooltip = name + doc
return tooltip
def _item_collapsed(self, item):
"""When item collapsed"""
super(TreeSymbolsWidget, self).collapseItem(item)
can_check = (not item.isClickable) or item.isClass or item.isMethod
if can_check:
n = self._get_unique_name(item)
filename = self.actualSymbols[0]
self.collapsedItems.setdefault(filename, [])
if not n in self.collapsedItems[filename]:
self.collapsedItems[filename].append(n)
def _item_expanded(self, item):
"""When item expanded"""
super(TreeSymbolsWidget, self).expandItem(item)
n = self._get_unique_name(item)
filename = self.actualSymbols[0]
if n in self.collapsedItems.get(filename, []):
self.collapsedItems[filename].remove(n)
if not len(self.collapsedItems[filename]):
# no more items, free space
del self.collapsedItems[filename]
def clean(self):
"""
Reset the tree and reset attributes
"""
self.tree.clear()
self.collapsedItems = {}
def reject(self):
if self.parent() is None:
self.emit(SIGNAL("dockWidget(PyQt_PyObject)"), self)
def closeEvent(self, event):
"""On Close event handling"""
self.emit(SIGNAL("dockWidget(PyQt_PyObject)"), self)
event.ignore()
class WTestManager(QWidget, Logger.ClassLogger):
"""
Widget to display all tests in the scheduler
"""
def __init__(self, parent):
"""
Constructs WTestManager widget
@param parent:
@type parent:
"""
QWidget.__init__(self, parent)
self.parent = parent
self.name = self.tr("Task Manager")
self.ascendingOrder = False
self.ascendingOrderHistory = False
self.ascendingOrderWaiting = False
self.itemCurrent = None
self.projects = []
self.createWidgets()
self.createActions()
self.createConnections()
self.createActions()
self.createToolbar()
self.deactivate()
def createWidgets (self):
"""
QtWidgets creation
QTreeWidget (Id, Name, Init at, Sched at, Start at, Stop at, User, Duration)
_______________
| QToolBar |
|---------------|
_______________
| |
|---------------|
| |
| |
|_______________|
"""
#self.mainTab = QTabWidget()
layout = QVBoxLayout()
topLayout = QHBoxLayout()
# waiting tree widget
self.tabWaiting = QTabWidget()
#self.waitingBox = QGroupBox("Waiting")
self.waitingBox = QFrame(self)
self.testWaiting = QTreeWidget(self)
self.testWaiting.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.waitingToolbar = QToolBar(self)
self.labelsWaiting = [ self.tr("No.") , self.tr("Group"), self.tr("Schedulation Type"),
self.tr("Project"), self.tr("Name") , self.tr("Next run"),
self.tr("Repeat"), self.tr("Probes"), self.tr("Notifications") ,
self.tr("Tests result"), self.tr("Author") ]
self.testWaiting.setHeaderLabels(self.labelsWaiting)
self.testWaiting.setIndentation(10)
self.testWaiting.setContextMenuPolicy(Qt.CustomContextMenu)
layoutWaiting = QVBoxLayout()
layoutWaiting.addWidget(self.waitingToolbar)
layoutWaiting.addWidget(self.testWaiting)
self.waitingBox.setLayout(layoutWaiting)
self.tabWaiting.addTab( self.waitingBox, "Scheduled" )
self.enqueuedBox = QFrame(self)
layoutEnqueued = QVBoxLayout()
self.testEnqueued = QTreeWidget(self)
self.labelsEnqueued = [ self.tr("Group of tests") ]
self.testEnqueued.setHeaderLabels(self.labelsEnqueued)
self.testEnqueued.setIndentation(10)
layoutEnqueued.addWidget(self.testEnqueued)
self.enqueuedBox.setLayout(layoutEnqueued)
self.tabWaiting.addTab( self.enqueuedBox, "Waiting" )
# current tree widget
self.currentBox = QGroupBox("Running")
self.testManager = QTreeWidget(self)
self.testManager.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.dockToolbar = QToolBar(self)
self.labels = [ self.tr("No."), self.tr("Project"), self.tr("Name"), self.tr("Started at"),
self.tr("Author"), self.tr("Recursive") ]
self.testManager.setHeaderLabels(self.labels)
self.testManager.setIndentation(10)
self.testManager.setContextMenuPolicy(Qt.CustomContextMenu)
layoutCurrent = QVBoxLayout()
layoutCurrent.addWidget(self.dockToolbar)
layoutCurrent.addWidget(self.testManager)
self.currentBox.setLayout(layoutCurrent)
v_splitter = QSplitter(self)
v_splitter.addWidget( self.tabWaiting )
v_splitter.addWidget( self.currentBox )
topLayout.addWidget(v_splitter)
# history tree widget
self.historyBox = QGroupBox("History")
self.testHistory = QTreeWidget(self)
self.historyToolbar = QToolBar(self)
self.labels2 = [ self.tr("Id"), self.tr("Schedulation Type"), self.tr("Project") , self.tr("Name"),
self.tr("Sched at"), self.tr("Run start"), self.tr("Run end"), self.tr("Author"),
self.tr("Duration (in sec.)"), self.tr("Run Result") ]
self.testHistory.setHeaderLabels(self.labels2)
self.statsBox = QGroupBox("Summary")
self.nbRunningLabel = QLabel("0")
self.nbWaitingLabel = QLabel("0")
self.nbHistoryLabel = QLabel("0")
self.nbCompleteHistoryLabel = QLabel("0")
self.nbErrorHistoryLabel = QLabel("0")
self.nbKilledHistoryLabel = QLabel("0")
self.nbCancelledHistoryLabel = QLabel("0")
layout2 = QFormLayout()
layout2.addRow(QLabel("Running"), self.nbRunningLabel )
layout2.addRow(QLabel("Waiting"), self.nbWaitingLabel )
layout2.addRow( QLabel(""), QLabel("") )
layout2.addRow(QLabel("History"), self.nbHistoryLabel )
layout2.addRow(QLabel(" - COMPLETE"), self.nbCompleteHistoryLabel )
layout2.addRow(QLabel(" - ERROR"), self.nbErrorHistoryLabel )
layout2.addRow(QLabel(" - KILLED"), self.nbKilledHistoryLabel )
layout2.addRow(QLabel(" - CANCELLED"), self.nbCancelledHistoryLabel )
self.statsBox.setLayout(layout2)
layoutHistory = QVBoxLayout()
layoutHistory.addWidget(self.historyToolbar)
layoutHistory.addWidget(self.testHistory)
self.historyBox.setLayout(layoutHistory)
subLayout = QHBoxLayout()
subLayout.addWidget(self.historyBox)
subLayout.addWidget(self.statsBox)
frame_left = QFrame(self)
frame_left.setFrameShape(QFrame.NoFrame)
frame_left.setLayout(topLayout)
frame_right = QFrame(self)
frame_right.setFrameShape(QFrame.NoFrame)
frame_right.setLayout(subLayout)
topLayout.setContentsMargins(0,0,0,0)
subLayout.setContentsMargins(0,0,0,0)
splitter1 = QSplitter(Qt.Vertical)
splitter1.addWidget(frame_left)
splitter1.addWidget(frame_right)
layout.addWidget(splitter1)
self.setLayout(layout)
def createConnections(self):
"""
Create Qt Connections
"""
self.testWaiting.customContextMenuRequested.connect(self.onPopupMenuWaiting)
self.testWaiting.currentItemChanged.connect(self.onCurrentWaitingItemChanged)
self.testManager.customContextMenuRequested.connect(self.onPopupMenu)
self.testManager.currentItemChanged.connect(self.onCurrentItemChanged)
self.testWaiting.itemDoubleClicked.connect(self.onItemDoubleClicked)
def createActions (self):
"""
Actions defined:
* sort running task
* sort waiting task
* sort history task
* kill one task
* kill all tasks
* cancel one task
* cancel all task
* clear the history
* edit a waiting task
* refresh waiting tasks
* refresh running tasks
* partial refresh of the history
* complete refresh of the history
* disable a waiting task
* enable a waiting task
"""
self.sortAction = QtHelper.createAction(self, "Ascending Order", self.toggleSort, toggled = True,
icon = QIcon(":/ascending.png") )
self.sortHistoryAction = QtHelper.createAction(self, "Ascending Order", self.toggleSortHistory, toggled = True,
icon = QIcon(":/ascending.png") )
self.sortWaitingAction = QtHelper.createAction(self, "Ascending Order", self.toggleSortWaiting, toggled = True,
icon = QIcon(":/ascending.png") )
self.killAction = QtHelper.createAction(self, "&Kill", self.killTask, tip = 'Kill selected test',
icon = QIcon(":/process-kill.png") )
self.killAllAction = QtHelper.createAction(self, "&Kill All", self.killAllTasks, tip = 'Kill all running tests',
icon = QIcon(":/process-killall.png") )
self.cancelAction = QtHelper.createAction(self, "&Cancel", self.cancelTask, tip = 'Cancel selected test',
icon = QIcon(":/process-cancel.png") )
self.cancelAllAction = QtHelper.createAction(self, "&Cancel All", self.cancelAllTasks, tip = 'Cancel all waiting tests',
icon = QIcon(":/processes-cancelall.png") )
self.clearHistoryAction = QtHelper.createAction(self, "&Clear history", self.clearHistory, tip = 'Clear history',
icon = QIcon(":/trash.png"))
self.editWaitingAction = QtHelper.createAction(self, "&Edit", self.editWaiting, tip = 'Edit the selected task',
icon = QIcon(":/reschedule.png"))
self.refreshWaitingAction = QtHelper.createAction(self, "Waiting tasks", self.refreshWaitingList,
icon = QIcon(":/act-refresh.png"), tip="Refresh waiting tasks" )
self.refreshRunningAction = QtHelper.createAction(self, "Running tasks", self.refreshRunningList,
icon = QIcon(":/act-refresh.png"), tip="Refresh running tasks" )
self.partialRefreshHistoryAction = QtHelper.createAction(self, "Partial history", self.partialRefreshHistoryList,
icon = QIcon(":/act-half-refresh.png"), tip="Refresh partial history" )
self.refreshHistoryAction = QtHelper.createAction(self, "Full history", self.refreshHistoryList,
icon = QIcon(":/act-refresh.png"), tip="Refresh full history" )
self.disableAction = QtHelper.createAction(self, "&Disable", self.disableTask, tip = 'Disable task',
icon = QIcon(":/process-pause-icon.png") )
self.enableAction = QtHelper.createAction(self, "&Enable", self.enableTask, tip = 'Enable task',
icon = None)
def createToolbar(self):
"""
Toolbar creation
||----------||
|| Kill all ||
||----------||
"""
self.dockToolbar.setObjectName("Test Manager toolbar")
self.dockToolbar.addAction(self.sortAction)
self.dockToolbar.addAction(self.refreshRunningAction)
self.dockToolbar.addSeparator()
self.dockToolbar.addAction(self.killAction)
self.dockToolbar.addAction(self.killAllAction)
self.dockToolbar.addSeparator()
self.dockToolbar.setIconSize(QSize(16, 16))
#
self.historyToolbar.setObjectName("Test Manager History toolbar")
self.historyToolbar.addAction(self.sortHistoryAction)
self.historyToolbar.addAction(self.partialRefreshHistoryAction)
self.historyToolbar.addAction(self.refreshHistoryAction)
self.historyToolbar.addSeparator()
self.historyToolbar.addAction(self.clearHistoryAction)
self.historyToolbar.setIconSize(QSize(16, 16))
#
self.waitingToolbar.setObjectName("Test Manager Waiting toolbar")
self.waitingToolbar.addAction(self.sortWaitingAction)
self.waitingToolbar.addAction(self.refreshWaitingAction)
self.waitingToolbar.addSeparator()
self.waitingToolbar.addAction(self.editWaitingAction)
self.waitingToolbar.addAction(self.disableAction)
self.waitingToolbar.addAction(self.cancelAction)
self.waitingToolbar.addAction(self.cancelAllAction)
self.waitingToolbar.addSeparator()
self.waitingToolbar.setIconSize(QSize(16, 16))
def onItemDoubleClicked(self, item):
"""
On item double clicked in waiting task
"""
if item.taskEventType in [ UCI.SCHED_QUEUE_AT, UCI.SCHED_QUEUE ]:
pass
else:
self.editWaiting()
def getProjectName(self, prjId):
"""
Return the project name
"""
pname = "UNKNOWN"
if prjId == 0:
return "UNDEFINED"
for p in self.projects:
if int(p['project_id']) == int(prjId):
pname = p['name']
break
return pname
def refreshWaitingList(self):
"""
Refresh the waiting task list
"""
RCI.instance().waitingTasks()
def refreshRunningList(self):
"""
Refresh the running task list
"""
RCI.instance().runningTasks()
def partialRefreshHistoryList(self):
"""
Partial refresh of the history task list
"""
RCI.instance().historyTasks()
def refreshHistoryList(self):
"""
Refresh the history task list
"""
RCI.instance().historyTasksAll()
def onCurrentItemChanged(self, witem1, witem2):
"""
On current item changed
@param witem1:
@type witem1:
@param witem2:
@type witem2:
"""
# kill task available just for admin and tester
if UCI.RIGHTS_ADMIN in RCI.instance().userRights or UCI.RIGHTS_TESTER in RCI.instance().userRights :
if witem1 is not None:
if witem1.taskState == STATE_RUNNING :
self.itemCurrent = witem1
self.killAction.setEnabled(True)
else:
self.killAction.setEnabled(False)
def onCurrentWaitingItemChanged(self, witem1, witem2):
"""
On current waiting task item changed
@param witem1:
@type witem1:
@param witem2:
@type witem2:
"""
# kill task available just for admin and tester
if UCI.RIGHTS_ADMIN in RCI.instance().userRights or UCI.RIGHTS_TESTER in RCI.instance().userRights :
if witem1 is not None:
self.itemCurrent = witem1
self.cancelAction.setEnabled(True)
self.editWaitingAction.setEnabled(True)
self.disableAction.setEnabled(True)
else:
self.cancelAction.setEnabled(False)
self.editWaitingAction.setEnabled(False)
self.disableAction.setEnabled(False)
def disableTask(self):
"""
Disable a waiting task
"""
# if self.itemCurrent is not None:
for currentItem in self.testWaiting.selectedItems():
RCI.instance().rescheduleTask(taskId=currentItem.taskId, taskEnabled=False,
scheduleType=currentItem.taskEventType,
scheduleAt=currentItem.taskEventArgs,
scheduleRepeat=currentItem.taskEventNb,
probesEnabled=currentItem.taskWithoutProbes,
notificationsEnabled=currentItem.taskWithoutNotif,
debugEnabled=False, logsEnabled=currentItem.taskNoKeepTr,
fromTime=currentItem.taskEventFrom, toTime=currentItem.taskEventTo )
def enableTask(self):
"""
Enable a waiting task
"""
# if self.itemCurrent is not None:
for currentItem in self.testWaiting.selectedItems():
RCI.instance().rescheduleTask(taskId=currentItem.taskId, taskEnabled=True,
scheduleType=currentItem.taskEventType,
scheduleAt=currentItem.taskEventArgs,
scheduleRepeat=currentItem.taskEventNb,
probesEnabled=currentItem.taskWithoutProbes,
notificationsEnabled=currentItem.taskWithoutNotif,
debugEnabled=False, logsEnabled=currentItem.taskNoKeepTr,
fromTime=currentItem.taskEventFrom, toTime=currentItem.taskEventTo )
def editWaiting(self):
"""
Edit a waiting task
"""
if self.itemCurrent is not None:
if self.itemCurrent.taskEventType in [ UCI.SCHED_QUEUE_AT, UCI.SCHED_QUEUE ]:
pass
else:
dSched = ScheduleDialog.SchedDialog( self )
dSched.fillFields( schedType=self.itemCurrent.taskEventType, schedArgs=self.itemCurrent.taskEventArgs,
taskName=self.itemCurrent.taskEventName, taskId=self.itemCurrent.taskId,
schedNb=self.itemCurrent.taskEventNb, withoutProbes=self.itemCurrent.taskWithoutProbes,
enabled=self.itemCurrent.taskEventEnabled,
withoutNotifs=self.itemCurrent.taskWithoutNotif, noKeepTr=self.itemCurrent.taskNoKeepTr,
schedFrom=self.itemCurrent.taskEventFrom, schedTo=self.itemCurrent.taskEventTo )
if dSched.exec_() == QDialog.Accepted:
runAt, runType, runNb, withoutProbes, runEnabled, noTr, withoutNotifs, runFrom, runTo = dSched.getSchedtime()
RCI.instance().rescheduleTask(taskId=self.itemCurrent.taskId, taskEnabled=runEnabled, scheduleType=runType,
scheduleAt=runAt, scheduleRepeat=runNb,
probesEnabled=withoutProbes, notificationsEnabled=withoutNotifs,
debugEnabled=False, logsEnabled=noTr,
fromTime=runFrom, toTime=runTo )
def clearHistory(self):
"""
Call the server to clear the history
"""
reply = QMessageBox.question(self, "Clear tasks history", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
RCI.instance().clearHistory()
def testKilled(self):
"""
Test kiled
"""
self.itemCurrent = None
self.killAction.setEnabled(False)
def testCancelled(self):
"""
Test cancelled
"""
self.itemCurrent = None
self.cancelAction.setEnabled(False)
def active (self):
"""
Enables QTreeWidget
"""
self.waitingBox.setEnabled(True)
self.currentBox.setEnabled(True)
self.historyBox.setEnabled(True)
self.statsBox.setEnabled(True)
#
self.testManager.setEnabled(True)
self.testHistory.setEnabled(True)
self.testWaiting.setEnabled(True)
#
self.sortAction.setEnabled(True)
self.sortHistoryAction.setEnabled(True)
self.sortWaitingAction.setEnabled(True)
self.refreshWaitingAction.setEnabled(True)
self.refreshRunningAction.setEnabled(True)
self.refreshHistoryAction.setEnabled(True)
self.partialRefreshHistoryAction.setEnabled(True)
self.killAction.setEnabled(False)
self.cancelAction.setEnabled(False)
self.editWaitingAction.setEnabled(False)
if UCI.RIGHTS_ADMIN in RCI.instance().userRights:
self.killAllAction.setEnabled(True)
self.cancelAllAction.setEnabled(True)
self.clearHistoryAction.setEnabled(True)
self.disableAction.setEnabled(False)
self.enableAction.setEnabled(True)
def deactivate (self):
"""
Clears QTreeWidget and disables it
"""
self.waitingBox.setEnabled(False)
self.currentBox.setEnabled(False)
self.historyBox.setEnabled(False)
self.statsBox.setEnabled(False)
self.testWaiting.clear()
self.testWaiting.setEnabled(False)
self.testManager.clear()
self.testManager.setEnabled(False)
self.testHistory.clear()
self.testHistory.setEnabled(False)
self.testEnqueued.clear()
self.testHistory.setEnabled(False)
self.nbRunningLabel.setText("0")
self.nbWaitingLabel.setText("0")
self.nbHistoryLabel.setText("0")
self.nbCompleteHistoryLabel.setText("0")
self.nbErrorHistoryLabel.setText("0")
self.nbKilledHistoryLabel.setText("0")
self.nbCancelledHistoryLabel.setText("0")
self.itemCurrent = None
self.setDefaultActionsValues()
def setDefaultActionsValues (self):
"""
Set default values for qt actions
"""
self.sortAction.setEnabled(False)
self.sortHistoryAction.setEnabled(False)
self.sortWaitingAction.setEnabled(False)
self.killAction.setEnabled(False)
self.killAllAction.setEnabled(False)
self.cancelAction.setEnabled(False)
self.cancelAllAction.setEnabled(False)
self.editWaitingAction.setEnabled(False)
self.clearHistoryAction.setEnabled(False)
self.refreshWaitingAction.setEnabled(False)
self.refreshRunningAction.setEnabled(False)
self.refreshHistoryAction.setEnabled(False)
self.partialRefreshHistoryAction.setEnabled(False)
self.disableAction.setEnabled(False)
self.enableAction.setEnabled(False)
def loadProjects(self, data):
"""
Load all projects
"""
self.projects = data
def loadRunning (self, data):
"""
Loads running tasks
@param data:
@type data: dict
"""
self.nbRunningLabel.setText( str( len(data) ) )
for task in data:
if self.getProjectName(task['project-id']) == "UNKNOWN":
continue
taskItem = TaskRunningItem( task = task, parent= self.testManager )
# resize cols
for i in xrange(len(self.labels2) - 1):
self.testManager.resizeColumnToContents(i)
# change sort order
if self.ascendingOrder:
self.testWaiting.sortItems(2, Qt.AscendingOrder) # sort by sched time
self.testManager.sortItems(2, Qt.DescendingOrder)
def updateRunning(self, data):
"""
Update running tasks
@param data:
@type data:
"""
self.testManager.clear()
self.loadRunning( data=data )
def loadWaiting (self, data):
"""
Loads waiting tasks
@param data:
@type data: dict
"""
self.nbWaitingLabel.setText( str(len(data)) )
for task in data:
eventid, eventtype, eventargs, eventtime, eventname, author, realruntime, duration, result, eventnb, \
eventnbcur, eventenabled, withoutprobes, withoutnotif, nokeeptr, userid, projectid, eventfrom, eventto, groupid = task
if self.getProjectName(projectid) == "UNKNOWN":
continue
taskItem = TaskWaitingItem( task = task, parent= self.testWaiting )
# resize cols
for i in xrange(len(self.labels2) - 1):
self.testWaiting.resizeColumnToContents(i)
# change sort order
if self.ascendingOrderHistory:
self.testWaiting.sortItems(3, Qt.AscendingOrder)
self.testWaiting.sortItems(3, Qt.DescendingOrder)
def updateWaiting(self, data):
"""
Update waiting tasks
@param data:
@type data:
"""
self.testWaiting.clear()
self.loadWaiting( data=data )
def loadEnqueued (self, data):
"""
Loads enqueued tasks
@param data:
@type data: dict
"""
for (groupId, groupData) in data.items():
groupName, groupsTests = groupData
pluriel = ''
if len(groupsTests) > 1:
pluriel = ''
groupTask = TaskEnqueuedItem( parent=self.testEnqueued, text="%s - %s - (%s test%s)" % (groupId, groupName, len(groupsTests), pluriel) )
groupTask.setExpanded(True)
for gTest in groupsTests:
tDict = eval(gTest)
tst = "%s:%s.%s" % ( self.getProjectName(tDict['prj-id']), tDict['test-path'], tDict['test-extension'])
# set the icon according to the type of test
if tDict['test-extension'] == 'tux':
testIcon = QIcon(":/tux.png")
if tDict['test-extension'] == 'tax':
testIcon = QIcon(":/tax.png")
if tDict['test-extension'] == 'tsx':
testIcon = QIcon(":/tsx.png")
if tDict['test-extension'] == 'tpx':
testIcon = QIcon(":/tpx.png")
if tDict['test-extension'] == 'tgx':
testIcon = QIcon(":/tgx.png")
subTask = TaskEnqueuedItem(parent=groupTask, text=tst, icon=testIcon)
def updateEnqueued(self, data):
"""
Update enqueued tasks
@param data:
@type data:
"""
self.testEnqueued.clear()
self.loadEnqueued( data=data )
def loadHistory (self, data):
"""
Loads history tasks
@param data:
@type data: dict
"""
# Init counters
nbComplete = int(self.nbCompleteHistoryLabel.text())
nbError = int(self.nbErrorHistoryLabel.text())
nbKilled = int(self.nbKilledHistoryLabel.text())
nbCancelled = int(self.nbCancelledHistoryLabel.text())
for task in data:
dbid, eventtype, eventargs, eventtime, eventname, author, realruntime, duration, result, projectid = task
if self.getProjectName(projectid) == "UNKNOWN":
continue
taskItem = TaskHistoryItem( task = task, parent= self.testHistory )
if taskItem.taskEventResult == STATE_COMPLETE:
nbComplete += 1
if taskItem.taskEventResult == STATE_ERROR:
nbError += 1
if taskItem.taskEventResult == STATE_KILLED:
nbKilled += 1
if taskItem.taskEventResult == STATE_CANCELLED:
nbCancelled += 1
# resize cols
for i in xrange(len(self.labels2) - 1):
self.testHistory.resizeColumnToContents(i)
# change sort order by sched at
if self.ascendingOrderHistory:
self.testHistory.sortItems(0, Qt.AscendingOrder)
self.testHistory.sortItems(0, Qt.DescendingOrder)
# Update summary
nbHistory = int(self.nbHistoryLabel.text())
self.nbHistoryLabel.setText( str( len(data) + nbHistory ) )
self.nbCompleteHistoryLabel.setText( str(nbComplete) )
self.nbErrorHistoryLabel.setText( str(nbError) )
self.nbKilledHistoryLabel.setText( str(nbKilled) )
self.nbCancelledHistoryLabel.setText( str(nbCancelled) )
def updateHistory(self, data):
"""
Update history tasks
@param data:
@type data:
"""
# reset counters
self.nbHistoryLabel.setText("0")
self.nbCompleteHistoryLabel.setText("0")
self.nbErrorHistoryLabel.setText("0")
self.nbKilledHistoryLabel.setText("0")
self.nbCancelledHistoryLabel.setText("0")
#
self.testHistory.clear()
self.loadHistory( data=data )
def refreshRunningTask(self, data, action):
"""
Refresh running task
@param data:
@type data:
@param action:
@type action:
"""
if action == "add":
self.loadRunning(data=data)
elif action == "update":
self.updateRunning(data=data)
else:
pass # error
def refreshWaitingTask(self, data, action):
"""
Refresh waiting task
@param data:
@type data:
@param action:
@type action:
"""
if action == "update":
self.updateWaiting(data=data)
else:
pass # error
def refreshEnqueuedTask(self, data, action):
"""
Refresh enqueued task
@param data:
@type data:
@param action:
@type action:
"""
if action == "update":
self.updateEnqueued(data=data)
else:
pass # error
def refreshHistoryTask(self, data, action):
"""
Refresh history task
@param data:
@type data:
@param action:
@type action:
"""
if action == "add":
self.loadHistory(data=data)
elif action == "update":
self.updateHistory(data=data)
else:
pass # error
def onPopupMenu(self, pos):
"""
Display menu on right click
@param pos:
@type pos:
"""
self.menu = QMenu()
item = self.testManager.itemAt(pos)
if item:
self.itemCurrent = item
# kill task available just for admin and tester
if UCI.RIGHTS_ADMIN in RCI.instance().userRights or UCI.RIGHTS_TESTER in RCI.instance().userRights :
if item.taskState == STATE_RUNNING :
self.menu.addAction( self.killAction )
self.menu.popup(self.testManager.mapToGlobal(pos))
def onPopupMenuWaiting(self, pos):
"""
Display menu on right click
@param pos:
@type pos:
"""
self.menu = QMenu()
item = self.testWaiting.itemAt(pos)
if item:
self.itemCurrent = item
# kill task available just for admin and tester
if UCI.RIGHTS_ADMIN in RCI.instance().userRights or UCI.RIGHTS_TESTER in RCI.instance().userRights :
self.menu.addAction( self.editWaitingAction )
self.menu.addAction( self.cancelAction )
self.menu.addSeparator()
self.menu.addAction( self.disableAction )
self.menu.addAction( self.enableAction )
self.menu.popup(self.testWaiting.mapToGlobal(pos))
def cancelTask(self):
"""
Cancel the selected task
"""
items = self.testWaiting.selectedItems()
taskIds = []
for itm in items:
taskIds.append( itm.taskId )
reply = QMessageBox.question(self, "Cancel test(s)", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
RCI.instance().cancelTasks(taskIds=taskIds)
def cancelAllTasks(self):
"""
Cancel all tasks
"""
reply = QMessageBox.question(self, "Cancel all tests", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
RCI.instance().cancelTasksAll()
def killTask(self):
"""
Kill the selected task
"""
items = self.testManager.selectedItems()
taskIds = []
for itm in items:
taskIds.append( itm.taskId )
reply = QMessageBox.question(self, "Kill test", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
RCI.instance().killTasks(taskIds=taskIds)
def killAllTasks(self):
"""
Kill all tasks
"""
reply = QMessageBox.question(self, "Kill all tests", "Are you sure ?",
QMessageBox.Yes | QMessageBox.No )
if reply == QMessageBox.Yes:
RCI.instance().killTasksAll()
def toggleSort(self):
"""
Toggle sort of running task
"""
if not self.ascendingOrder:
self.testManager.sortItems(2, Qt.AscendingOrder)
self.ascendingOrder = True
else:
self.testManager.sortItems(2, Qt.DescendingOrder)
self.ascendingOrder = False
def toggleSortHistory(self):
"""
Toggle sort of the history
"""
if not self.ascendingOrderHistory:
self.testHistory.sortItems(0, Qt.AscendingOrder)
self.ascendingOrderHistory = True
else:
self.testHistory.sortItems(0, Qt.DescendingOrder)
self.ascendingOrderHistory = False
def toggleSortWaiting(self):
"""
Toggle sort of the waiting
"""
if not self.ascendingOrderWaiting:
self.testWaiting.sortItems(3, Qt.AscendingOrder)
self.ascendingOrderWaiting = True
else:
self.testWaiting.sortItems(3, Qt.DescendingOrder)
self.ascendingOrderWaiting = False
class OWGEODatasets(OWWidget):
name = "GEO Data Sets"
description = DESCRIPTION
icon = "../widgets/icons/GEODataSets.svg"
priority = PRIORITY
inputs = []
outputs = [("Expression Data", Orange.data.Table)]
settingsList = [
"outputRows", "mergeSpots", "gdsSelectionStates", "splitterSettings",
"currentGds", "autoCommit", "datasetNames"
]
outputRows = Setting(True)
mergeSpots = Setting(True)
gdsSelectionStates = Setting({})
currentGds = Setting(None)
datasetNames = Setting({})
splitterSettings = Setting((
b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xea\x00\x00\x00\xd7\x01\x00\x00\x00\x07\x01\x00\x00\x00\x02',
b'\x00\x00\x00\xff\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x01\xb5\x00\x00\x02\x10\x01\x00\x00\x00\x07\x01\x00\x00\x00\x01'
))
autoCommit = Setting(False)
def __init__(self, parent=None, signalManager=None, name=" GEO Data Sets"):
OWWidget.__init__(self, parent, signalManager, name)
self.selectionChanged = False
self.filterString = ""
self.datasetName = ""
## GUI
box = gui.widgetBox(self.controlArea, "Info", addSpace=True)
self.infoBox = gui.widgetLabel(box, "Initializing\n\n")
box = gui.widgetBox(self.controlArea, "Output", addSpace=True)
gui.radioButtonsInBox(box,
self,
"outputRows",
["Genes in rows", "Samples in rows"],
"Rows",
callback=self.commitIf)
gui.checkBox(box,
self,
"mergeSpots",
"Merge spots of same gene",
callback=self.commitIf)
gui.separator(box)
self.nameEdit = gui.lineEdit(
box,
self,
"datasetName",
"Data set name",
tooltip="Override the default output data set name",
callback=self.onNameEdited)
self.nameEdit.setPlaceholderText("")
if sys.version_info < (3, ):
box = gui.widgetBox(self.controlArea, "Commit", addSpace=True)
self.commitButton = gui.button(box,
self,
"Commit",
callback=self.commit)
cb = gui.checkBox(box, self, "autoCommit", "Commit on any change")
gui.setStopper(self, self.commitButton, cb, "selectionChanged",
self.commit)
else:
gui.auto_commit(self.controlArea,
self,
"autoCommit",
"Commit",
box="Commit")
self.commitIf = self.commit
gui.rubber(self.controlArea)
gui.widgetLabel(self.mainArea, "Filter")
self.filterLineEdit = QLineEdit(textChanged=self.filter)
self.completer = TokenListCompleter(self,
caseSensitivity=Qt.CaseInsensitive)
self.filterLineEdit.setCompleter(self.completer)
self.mainArea.layout().addWidget(self.filterLineEdit)
splitter = QSplitter(Qt.Vertical, self.mainArea)
self.mainArea.layout().addWidget(splitter)
self.treeWidget = QTreeView(splitter)
self.treeWidget.setSelectionMode(QTreeView.SingleSelection)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setEditTriggers(QTreeView.NoEditTriggers)
linkdelegate = LinkStyledItemDelegate(self.treeWidget)
self.treeWidget.setItemDelegateForColumn(1, linkdelegate)
self.treeWidget.setItemDelegateForColumn(8, linkdelegate)
self.treeWidget.setItemDelegateForColumn(
0, gui.IndicatorItemDelegate(self.treeWidget, role=Qt.DisplayRole))
proxyModel = MySortFilterProxyModel(self.treeWidget)
self.treeWidget.setModel(proxyModel)
self.treeWidget.selectionModel().selectionChanged.connect(
self.updateSelection)
self.treeWidget.viewport().setMouseTracking(True)
splitterH = QSplitter(Qt.Horizontal, splitter)
box = gui.widgetBox(splitterH, "Description")
self.infoGDS = gui.widgetLabel(box, "")
self.infoGDS.setWordWrap(True)
gui.rubber(box)
box = gui.widgetBox(splitterH, "Sample Annotations")
self.annotationsTree = QTreeWidget(box)
self.annotationsTree.setHeaderLabels(
["Type (Sample annotations)", "Sample count"])
self.annotationsTree.setRootIsDecorated(True)
box.layout().addWidget(self.annotationsTree)
self.annotationsTree.itemChanged.connect(
self.annotationSelectionChanged)
self._annotationsUpdating = False
self.splitters = splitter, splitterH
for sp, setting in zip(self.splitters, self.splitterSettings):
sp.splitterMoved.connect(self.splitterMoved)
sp.restoreState(setting)
self.searchKeys = [
"dataset_id", "title", "platform_organism", "description"
]
self.gds = []
self.gds_info = None
self.resize(1000, 600)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._executor = ThreadExecutor()
func = partial(get_gds_model,
methodinvoke(self, "_setProgress", (float, )))
self._inittask = Task(function=func)
self._inittask.finished.connect(self._initializemodel)
self._executor.submit(self._inittask)
self._datatask = None
@Slot(float)
def _setProgress(self, value):
self.progressBarValue = value
def _initializemodel(self):
assert self.thread() is QThread.currentThread()
model, self.gds_info, self.gds = self._inittask.result()
model.setParent(self)
proxy = self.treeWidget.model()
proxy.setFilterKeyColumn(0)
proxy.setFilterRole(TextFilterRole)
proxy.setFilterCaseSensitivity(False)
proxy.setFilterFixedString(self.filterString)
proxy.setSourceModel(model)
proxy.sort(0, Qt.DescendingOrder)
self.progressBarFinished()
self.setBlocking(False)
self.setEnabled(True)
filter_items = " ".join(gds[key] for gds in self.gds
for key in self.searchKeys)
tr_chars = ",.:;!?(){}[]_-+\\|/%#@$^&*<>~`"
tr_table = str.maketrans(tr_chars, " " * len(tr_chars))
filter_items = filter_items.translate(tr_table)
filter_items = sorted(set(filter_items.split(" ")))
filter_items = [item for item in filter_items if len(item) > 3]
self.completer.setTokenList(filter_items)
if self.currentGds:
current_id = self.currentGds["dataset_id"]
gdss = [(i, qunpack(proxy.data(proxy.index(i, 1), Qt.DisplayRole)))
for i in range(proxy.rowCount())]
current = [i for i, data in gdss if data and data == current_id]
if current:
current_index = proxy.index(current[0], 0)
self.treeWidget.selectionModel().select(
current_index,
QItemSelectionModel.Select | QItemSelectionModel.Rows)
self.treeWidget.scrollTo(current_index,
QTreeView.PositionAtCenter)
for i in range(8):
self.treeWidget.resizeColumnToContents(i)
self.treeWidget.setColumnWidth(
1, min(self.treeWidget.columnWidth(1), 300))
self.treeWidget.setColumnWidth(
2, min(self.treeWidget.columnWidth(2), 200))
self.updateInfo()
def updateInfo(self):
gds_info = self.gds_info
text = ("%i datasets\n%i datasets cached\n" %
(len(gds_info),
len(glob.glob(serverfiles.localpath("GEO") + "/GDS*"))))
filtered = self.treeWidget.model().rowCount()
if len(self.gds) != filtered:
text += ("%i after filtering") % filtered
self.infoBox.setText(text)
def updateSelection(self, *args):
current = self.treeWidget.selectedIndexes()
mapToSource = self.treeWidget.model().mapToSource
current = [mapToSource(index).row() for index in current]
if current:
self.currentGds = self.gds[current[0]]
self.setAnnotations(self.currentGds)
self.infoGDS.setText(self.currentGds.get("description", ""))
self.nameEdit.setPlaceholderText(self.currentGds["title"])
self.datasetName = \
self.datasetNames.get(self.currentGds["dataset_id"], "")
else:
self.currentGds = None
self.nameEdit.setPlaceholderText("")
self.datasetName = ""
self.commitIf()
def setAnnotations(self, gds):
self._annotationsUpdating = True
self.annotationsTree.clear()
annotations = defaultdict(set)
subsetscount = {}
for desc in gds["subsets"]:
annotations[desc["type"]].add(desc["description"])
subsetscount[desc["description"]] = str(len(desc["sample_id"]))
for type, subsets in annotations.items():
key = (gds["dataset_id"], type)
subsetItem = QTreeWidgetItem(self.annotationsTree, [type])
subsetItem.setFlags(subsetItem.flags() | Qt.ItemIsUserCheckable
| Qt.ItemIsTristate)
subsetItem.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked))
subsetItem.key = key
for subset in subsets:
key = (gds["dataset_id"], type, subset)
item = QTreeWidgetItem(
subsetItem, [subset, subsetscount.get(subset, "")])
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(
0, self.gdsSelectionStates.get(key, Qt.Checked))
item.key = key
self._annotationsUpdating = False
self.annotationsTree.expandAll()
for i in range(self.annotationsTree.columnCount()):
self.annotationsTree.resizeColumnToContents(i)
def annotationSelectionChanged(self, item, column):
if self._annotationsUpdating:
return
for i in range(self.annotationsTree.topLevelItemCount()):
item = self.annotationsTree.topLevelItem(i)
self.gdsSelectionStates[item.key] = item.checkState(0)
for j in range(item.childCount()):
child = item.child(j)
self.gdsSelectionStates[child.key] = child.checkState(0)
def filter(self):
filter_string = unicode(self.filterLineEdit.text())
proxyModel = self.treeWidget.model()
if proxyModel:
strings = filter_string.lower().strip().split()
proxyModel.setFilterFixedStrings(strings)
self.updateInfo()
def selectedSamples(self):
"""
Return the currently selected sample annotations.
The return value is a list of selected (sample type, sample value)
tuples.
.. note:: if some Sample annotation type has no selected values.
this method will return all values for it.
"""
samples = []
unused_types = []
used_types = []
for stype in childiter(self.annotationsTree.invisibleRootItem()):
selected_values = []
all_values = []
for sval in childiter(stype):
value = (str(stype.text(0)), str(sval.text(0)))
if self.gdsSelectionStates.get(sval.key, True):
selected_values.append(value)
all_values.append(value)
if selected_values:
samples.extend(selected_values)
used_types.append(str(stype.text(0)))
else:
# If no sample of sample type is selected we don't filter
# on it.
samples.extend(all_values)
unused_types.append(str(stype.text(0)))
return samples, used_types
def commitIf(self):
if self.autoCommit:
self.commit()
else:
self.selectionChanged = True
@Slot(int, int)
def progressCompleted(self, value, total):
if total > 0:
self.progressBarSet(100. * value / total, processEvents=False)
else:
pass
# TODO: report 'indeterminate progress'
def commit(self):
if self.currentGds:
self.error(0)
sample_type = None
self.progressBarInit(processEvents=None)
_, groups = self.selectedSamples()
if len(groups) == 1 and self.outputRows:
sample_type = groups[0]
self.setEnabled(False)
self.setBlocking(True)
progress = methodinvoke(self, "progressCompleted", (int, int))
def get_data(gds_id, report_genes, transpose, sample_type, title):
gds_ensure_downloaded(gds_id, progress)
gds = geo.GDS(gds_id)
data = gds.getdata(report_genes=report_genes,
transpose=transpose,
sample_type=sample_type)
data.name = title
return data
get_data = partial(get_data,
self.currentGds["dataset_id"],
report_genes=self.mergeSpots,
transpose=self.outputRows,
sample_type=sample_type,
title=self.datasetName
or self.currentGds["title"])
self._datatask = Task(function=get_data)
self._datatask.finished.connect(self._on_dataready)
self._executor.submit(self._datatask)
def _on_dataready(self):
self.setEnabled(True)
self.setBlocking(False)
self.progressBarFinished(processEvents=False)
try:
data = self._datatask.result()
except urlrequest.URLError as error:
self.error(0, ("Error while connecting to the NCBI ftp server! "
"'%s'" % error))
sys.excepthook(type(error), error, getattr(error, "__traceback__"))
return
finally:
self._datatask = None
data_name = data.name
samples, _ = self.selectedSamples()
self.warning(0)
message = None
if self.outputRows:
def samplesinst(ex):
out = []
for meta in data.domain.metas:
out.append((meta.name, ex[meta].value))
if data.domain.class_var.name != 'class':
out.append((data.domain.class_var.name,
ex[data.domain.class_var].value))
return out
samples = set(samples)
mask = [samples.issuperset(samplesinst(ex)) for ex in data]
data = data[numpy.array(mask, dtype=bool)]
if len(data) == 0:
message = "No samples with selected sample annotations."
else:
samples = set(samples)
domain = Orange.data.Domain([
attr for attr in data.domain.attributes
if samples.issuperset(attr.attributes.items())
], data.domain.class_var, data.domain.metas)
# domain.addmetas(data.domain.getmetas())
if len(domain.attributes) == 0:
message = "No samples with selected sample annotations."
stypes = set(s[0] for s in samples)
for attr in domain.attributes:
attr.attributes = dict(
(key, value) for key, value in attr.attributes.items()
if key in stypes)
data = Orange.data.Table(domain, data)
if message is not None:
self.warning(0, message)
data_hints.set_hint(data, "taxid", self.currentGds.get("taxid", ""),
10.0)
data_hints.set_hint(data, "genesinrows", self.outputRows, 10.0)
data.name = data_name
self.send("Expression Data", data)
model = self.treeWidget.model().sourceModel()
row = self.gds.index(self.currentGds)
model.setData(model.index(row, 0), " ", Qt.DisplayRole)
self.updateInfo()
self.selectionChanged = False
def splitterMoved(self, *args):
self.splitterSettings = [
bytes(sp.saveState()) for sp in self.splitters
]
def send_report(self):
self.report_items("GEO Dataset",
[("ID", self.currentGds['dataset_id']),
("Title", self.currentGds['title']),
("Organism", self.currentGds['sample_organism'])])
self.report_items("Data",
[("Samples", self.currentGds['sample_count']),
("Features", self.currentGds['feature_count']),
("Genes", self.currentGds['gene_count'])])
self.report_name("Sample annotations")
subsets = defaultdict(list)
for subset in self.currentGds['subsets']:
subsets[subset['type']].append(
(subset['description'], len(subset['sample_id'])))
self.report_html += "<ul>"
for type in subsets:
self.report_html += "<b>" + type + ":</b></br>"
for desc, count in subsets[type]:
self.report_html += 9 * " " + "<b>{}:</b> {}</br>".format(
desc, count)
self.report_html += "</ul>"
def onDeleteWidget(self):
if self._inittask:
self._inittask.future().cancel()
self._inittask.finished.disconnect(self._initializemodel)
if self._datatask:
self._datatask.future().cancel()
self._datatask.finished.disconnect(self._on_dataready)
self._executor.shutdown(wait=False)
super(OWGEODatasets, self).onDeleteWidget()
def onNameEdited(self):
if self.currentGds:
gds_id = self.currentGds["dataset_id"]
self.datasetNames[gds_id] = unicode(self.nameEdit.text())
self.commitIf()
class OWDatabasesUpdate(OWWidget):
name = "Databases update"
description = "Update local system biology databases."
icon = "../widgets/icons/Databases.svg"
priority = 10
inputs = []
outputs = []
want_main_area = False
def __init__(self, parent=None, signalManager=None,
name="Databases update", domains=None):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
self.accessCode = ""
self.domains = domains or DOMAINS
self.serverFiles = serverfiles.ServerFiles()
self.__in_progress_update = False
fbox = gui.widgetBox(self.controlArea, "Filter")
# The completer model token strings
self.completertokens = []
# A 'dynamic' completer item model will be updated with
# 'prefix {token}' where prefix is current 'active' filter list
# (the QCompleter only completes on one item in the model)
self.completermodel = QStringListModel(self)
self.completer = QCompleter(
self.completermodel, self,
caseSensitivity=Qt.CaseInsensitive
)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
gui.rubber(box)
gui.lineEdit(box, self, "accessCode", "Access Code",
orientation="horizontal",
callback=self.RetrieveFilesList)
self.retryButton = gui.button(
box, self, "Retry", callback=self.RetrieveFilesList
)
self.retryButton.hide()
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def RetrieveFilesList(self):
self.progress.setRange(0, 3)
self.serverFiles = serverfiles.ServerFiles(access_code=self.accessCode)
task = Task(function=partial(retrieveFilesList, self.serverFiles,
self.domains,
methodinvoke(self.progress, "advance")))
task.resultReady.connect(self.SetFilesList)
task.exceptionReady.connect(self.HandleError)
self.executor.submit(task)
self.setEnabled(False)
def SetFilesList(self, serverInfo):
"""
Set the files to show.
"""
self.setEnabled(True)
domains = serverInfo.keys()
if not domains:
if self.domains:
domains = self.domains
else:
domains = serverfiles.listdomains()
localInfo = dict([(dom, serverfiles.allinfo(dom)) for dom in domains])
all_tags = set()
self.filesView.clear()
self.updateItems = []
for item in join_info_dict(localInfo, serverInfo):
tree_item = UpdateTreeWidgetItem(item)
options_widget = UpdateOptionsWidget(item.state)
options_widget.item = item
options_widget.installClicked.connect(
partial(self.SubmitDownloadTask, item.domain, item.filename)
)
options_widget.removeClicked.connect(
partial(self.SubmitRemoveTask, item.domain, item.filename)
)
self.updateItems.append((item, tree_item, options_widget))
all_tags.update(item.tags)
self.filesView.addTopLevelItems(
[tree_item for _, tree_item, _ in self.updateItems]
)
for item, tree_item, options_widget in self.updateItems:
self.filesView.setItemWidget(tree_item, 0, options_widget)
# Add an update button if the file is updateable
if item.state == OUTDATED:
button = QToolButton(
None, text="Update",
maximumWidth=120,
maximumHeight=30
)
if sys.platform == "darwin":
button.setAttribute(Qt.WA_MacSmallSize)
button.clicked.connect(
partial(self.SubmitDownloadTask, item.domain,
item.filename)
)
self.filesView.setItemWidget(tree_item, 2, button)
self.progress.advance()
self.filesView.setColumnWidth(0, self.filesView.sizeHintForColumn(0))
for column in range(1, 4):
contents_hint = self.filesView.sizeHintForColumn(column)
header_hint = self.filesView.header().sectionSizeHint(column)
width = max(min(contents_hint, 400), header_hint)
self.filesView.setColumnWidth(column, width)
hints = [hint for hint in sorted(all_tags) if not hint.startswith("#")]
self.completertokens = hints
self.completermodel.setStringList(hints)
self.SearchUpdate()
self.UpdateInfoLabel()
self.toggleButtons()
self.cancelButton.setEnabled(False)
self.progress.setRange(0, 0)
def buttonCheck(self, selected_items, state, button):
for item in selected_items:
if item.state != state:
button.setEnabled(False)
else:
button.setEnabled(True)
break
def toggleButtons(self):
selected_items = [item for item, tree_item, _ in self.updateItems if not tree_item.isHidden()]
self.buttonCheck(selected_items, OUTDATED, self.updateButton)
self.buttonCheck(selected_items, AVAILABLE, self.downloadButton)
def HandleError(self, exception):
if isinstance(exception, IOError):
self.error(0,
"Could not connect to server! Press the Retry "
"button to try again.")
self.SetFilesList({})
else:
sys.excepthook(type(exception), exception.args, None)
self.progress.setRange(0, 0)
self.setEnabled(True)
def UpdateInfoLabel(self):
local = [item for item, tree_item, _ in self.updateItems
if item.state != AVAILABLE and not tree_item.isHidden()]
size = sum(float(item.size) for item in local)
onServer = [item for item, tree_item, _ in self.updateItems if not tree_item.isHidden()]
sizeOnServer = sum(float(item.size) for item in onServer)
text = ("%i items, %s (on server: %i items, %s)" %
(len(local),
sizeof_fmt(size),
len(onServer),
sizeof_fmt(sizeOnServer)))
self.infoLabel.setText(text)
def UpdateAll(self):
for item, tree_item, _ in self.updateItems:
if item.state == OUTDATED and not tree_item.isHidden():
self.SubmitDownloadTask(item.domain, item.filename)
def DownloadFiltered(self):
# TODO: submit items in the order shown.
for item, tree_item, _ in self.updateItems:
if not tree_item.isHidden() and item.state in \
[AVAILABLE, OUTDATED]:
self.SubmitDownloadTask(item.domain, item.filename)
def _updateCompleterPrefix(self, prefix, seperator=" "):
prefix = str(self.completer.completionPrefix())
tokens = self.completertokens
model = self.completer.model()
if not prefix.endswith(seperator) and seperator in prefix:
prefix, _ = prefix.rsplit(seperator, 1)
items = [prefix + seperator + item for item in tokens]
else:
items = tokens
old = set(str(item) for item in model.stringList())
if old != set(items):
model.setStringList(items)
def SearchUpdate(self, searchString=None):
self._updateCompleterPrefix(searchString)
strings = str(self.lineEditFilter.text()).split()
for item, tree_item, _ in self.updateItems:
hide = not all(UpdateItem_match(item, string)
for string in strings)
tree_item.setHidden(hide)
self.UpdateInfoLabel()
self.toggleButtons()
def SubmitDownloadTask(self, domain, filename):
"""
Submit the (domain, filename) to be downloaded/updated.
"""
self.cancelButton.setEnabled(True)
index = self.updateItemIndex(domain, filename)
_, tree_item, opt_widget = self.updateItems[index]
if self.accessCode:
sf = serverfiles.ServerFiles(access_code=self.accessCode)
else:
sf = serverfiles.ServerFiles()
task = DownloadTask(domain, filename, sf)
self.executor.submit(task)
self.progress.adjustRange(0, 100)
pb = ItemProgressBar(self.filesView)
pb.setRange(0, 100)
pb.setTextVisible(False)
task.advanced.connect(pb.advance)
task.advanced.connect(self.progress.advance)
task.finished.connect(pb.hide)
task.finished.connect(self.onDownloadFinished, Qt.QueuedConnection)
task.exception.connect(self.onDownloadError, Qt.QueuedConnection)
self.filesView.setItemWidget(tree_item, 2, pb)
# Clear the text so it does not show behind the progress bar.
tree_item.setData(2, Qt.DisplayRole, "")
pb.show()
# Disable the options widget
opt_widget.setEnabled(False)
self._tasks.append(task)
def EndDownloadTask(self, task):
future = task.future()
index = self.updateItemIndex(task.domain, task.filename)
item, tree_item, opt_widget = self.updateItems[index]
self.filesView.removeItemWidget(tree_item, 2)
opt_widget.setEnabled(True)
if future.cancelled():
# Restore the previous state
tree_item.setUpdateItem(item)
opt_widget.setState(item.state)
elif future.exception():
tree_item.setUpdateItem(item)
opt_widget.setState(item.state)
# Show the exception string in the size column.
tree_item.setData(
2, Qt.DisplayRole,
"Error occurred while downloading:" + str(future.exception())
)
else:
# get the new updated info dict and replace the the old item
info = serverfiles.info(item.domain, item.filename)
new_item = update_item_from_info(item.domain, item.filename,
info, info)
self.updateItems[index] = (new_item, tree_item, opt_widget)
tree_item.setUpdateItem(new_item)
opt_widget.setState(new_item.state)
self.UpdateInfoLabel()
def SubmitRemoveTask(self, domain, filename):
serverfiles.remove(domain, filename)
index = self.updateItemIndex(domain, filename)
item, tree_item, opt_widget = self.updateItems[index]
if item.info_server:
new_item = item._replace(state=AVAILABLE, local=None,
info_local=None)
else:
new_item = item._replace(local=None, info_local=None)
# Disable the options widget. No more actions can be performed
# for the item.
opt_widget.setEnabled(False)
tree_item.setUpdateItem(new_item)
opt_widget.setState(new_item.state)
self.updateItems[index] = (new_item, tree_item, opt_widget)
self.UpdateInfoLabel()
def Cancel(self):
"""
Cancel all pending update/download tasks (that have not yet started).
"""
for task in self._tasks:
task.future().cancel()
def onDeleteWidget(self):
self.Cancel()
self.executor.shutdown(wait=False)
OWWidget.onDeleteWidget(self)
def onDownloadFinished(self):
# on download completed/canceled/error
assert QThread.currentThread() is self.thread()
for task in list(self._tasks):
future = task.future()
if future.done():
self.EndDownloadTask(task)
self._tasks.remove(task)
if not self._tasks:
# Clear/reset the overall progress
self.progress.setRange(0, 0)
self.cancelButton.setEnabled(False)
def onDownloadError(self, exc_info):
sys.excepthook(*exc_info)
def updateItemIndex(self, domain, filename):
for i, (item, _, _) in enumerate(self.updateItems):
if item.domain == domain and item.filename == filename:
return i
raise ValueError("%r, %r not in update list" % (domain, filename))
def _updateProgress(self, *args):
rmin, rmax = self.progress.range()
if rmin != rmax:
if not self._haveProgress:
self._haveProgress = True
self.progressBarInit()
self.progressBarSet(self.progress.ratioCompleted() * 100)
# self.progressBarSet(self.progress.ratioCompleted() * 100,
# processEventsFlags=None)
if rmin == rmax:
self._haveProgress = False
self.progressBarFinished()
def progressBarSet(self, value):
if not self.__in_progress_update:
self.__in_progress_update = True
try:
OWWidget.progressBarSet(self, value)
finally:
self.__in_progress_update = False
class TreeSymbolsWidget(QDialog):
"""Class of Dialog for Tree Symbols"""
def __init__(self, parent=None):
super(TreeSymbolsWidget, self).__init__(parent,
Qt.WindowStaysOnTopHint)
vbox = QVBoxLayout(self)
vbox.setContentsMargins(0, 0, 0, 0)
vbox.setSpacing(0)
self.tree = QTreeWidget()
vbox.addWidget(self.tree)
self.tree.header().setHidden(True)
self.tree.setSelectionMode(self.tree.SingleSelection)
self.tree.setAnimated(True)
self.tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
self.actualSymbols = ('', {})
self.docstrings = {}
self.collapsedItems = {}
self.connect(self, SIGNAL("itemClicked(QTreeWidgetItem *, int)"),
self._go_to_definition)
self.connect(self, SIGNAL("itemActivated(QTreeWidgetItem *, int)"),
self._go_to_definition)
self.tree.setContextMenuPolicy(Qt.CustomContextMenu)
self.connect(self,
SIGNAL("customContextMenuRequested(const QPoint &)"),
self._menu_context_tree)
self.connect(self, SIGNAL("itemCollapsed(QTreeWidgetItem *)"),
self._item_collapsed)
self.connect(self, SIGNAL("itemExpanded(QTreeWidgetItem *)"),
self._item_expanded)
IDE.register_service('symbols_explorer', self)
ExplorerContainer.register_tab(translations.TR_TAB_SYMBOLS, self)
def install_tab(self):
"""Connect signals for goingdown"""
ide = IDE.get_service('ide')
self.connect(ide, SIGNAL("goingDown()"), self.close)
def _menu_context_tree(self, point):
"""Context menu"""
index = self.tree.indexAt(point)
if not index.isValid():
return
menu = QMenu(self)
f_all = menu.addAction(translations.TR_FOLD_ALL)
u_all = menu.addAction(translations.TR_UNFOLD_ALL)
menu.addSeparator()
u_class = menu.addAction(translations.TR_UNFOLD_CLASSES)
u_class_method = menu.addAction(
translations.TR_UNFOLD_CLASSES_AND_METHODS)
u_class_attr = menu.addAction(
translations.TR_UNFOLD_CLASSES_AND_ATTRIBUTES)
menu.addSeparator()
#save_state = menu.addAction(self.tr("Save State"))
self.connect(f_all, SIGNAL("triggered()"),
lambda: self.tree.collapseAll())
self.connect(u_all, SIGNAL("triggered()"),
lambda: self.tree.expandAll())
self.connect(u_class, SIGNAL("triggered()"), self._unfold_class)
self.connect(u_class_method, SIGNAL("triggered()"),
self._unfold_class_method)
self.connect(u_class_attr, SIGNAL("triggered()"),
self._unfold_class_attribute)
#self.connect(save_state, SIGNAL("triggered()"),
#self._save_symbols_state)
menu.exec_(QCursor.pos())
def _get_classes_root(self):
"""Return the root of classes"""
class_root = None
for i in range(self.tree.topLevelItemCount()):
item = self.tree.topLevelItem(i)
if item.isClass and not item.isClickable:
class_root = item
break
return class_root
def _unfold_class(self):
"""Method to Unfold Classes"""
self.tree.collapseAll()
classes_root = self._get_classes_root()
if not classes_root:
return
classes_root.setExpanded(True)
def _unfold_class_method(self):
"""Method to Unfold Methods"""
self.tree.expandAll()
classes_root = self._get_classes_root()
if not classes_root:
return
#for each class!
for i in range(classes_root.childCount()):
class_item = classes_root.child(i)
#for each attribute or functions
for j in range(class_item.childCount()):
item = class_item.child(j)
#METHODS ROOT!!
if not item.isMethod and not item.isClickable:
item.setExpanded(False)
break
def _unfold_class_attribute(self):
"""Method to Unfold Attributes"""
self.tree.expandAll()
classes_root = self._get_classes_root()
if not classes_root:
return
#for each class!
for i in range(classes_root.childCount()):
class_item = classes_root.child(i)
#for each attribute or functions
for j in range(class_item.childCount()):
item = class_item.child(j)
#ATTRIBUTES ROOT!!
if not item.isAttribute and not item.isClickable:
item.setExpanded(False)
break
def _save_symbols_state(self):
"""Method to Save a persistent Symbols state"""
#filename = self.actualSymbols[0]
#TODO: persist self.collapsedItems[filename] in QSettings
pass
def _get_expand(self, item):
"""
Returns True or False to be used as setExpanded() with the items
It method is based on the click that the user made in the tree
"""
name = self._get_unique_name(item)
filename = self.actualSymbols[0]
collapsed_items = self.collapsedItems.get(filename, [])
can_check = (not item.isClickable) or item.isClass or item.isMethod
if can_check and name in collapsed_items:
return False
return True
@staticmethod
def _get_unique_name(item):
"""
Returns a string used as unique name
"""
# className_Attributes/className_Functions
parent = item.parent()
if parent:
return "%s_%s" % (parent.text(0), item.text(0))
return "_%s" % item.text(0)
def update_symbols_tree(self, symbols, filename='', parent=None):
"""Method to Update the symbols on the Tree"""
if not parent:
if filename == self.actualSymbols[0] and \
self.actualSymbols[1] and not symbols:
return
if symbols == self.actualSymbols[1]:
# Nothing new then return
return
# we have new symbols refresh it
self.tree.clear()
self.actualSymbols = (filename, symbols)
self.docstrings = symbols.get('docstrings', {})
parent = self.tree
if 'attributes' in symbols:
globalAttribute = ItemTree(parent, [translations.TR_ATTRIBUTES])
globalAttribute.isClickable = False
globalAttribute.isAttribute = True
globalAttribute.setExpanded(self._get_expand(globalAttribute))
for glob in sorted(symbols['attributes']):
globItem = ItemTree(globalAttribute, [glob],
lineno=symbols['attributes'][glob])
globItem.isAttribute = True
globItem.setIcon(0, QIcon(":img/attribute"))
globItem.setExpanded(self._get_expand(globItem))
if 'functions' in symbols and symbols['functions']:
functionsItem = ItemTree(parent, [translations.TR_FUNCTIONS])
functionsItem.isClickable = False
functionsItem.isMethod = True
functionsItem.setExpanded(self._get_expand(functionsItem))
for func in sorted(symbols['functions']):
item = ItemTree(functionsItem, [func],
lineno=symbols['functions'][func]['lineno'])
tooltip = self.create_tooltip(
func, symbols['functions'][func]['lineno'])
item.isMethod = True
item.setIcon(0, QIcon(":img/function"))
item.setToolTip(0, tooltip)
item.setExpanded(self._get_expand(item))
self.update_symbols_tree(
symbols['functions'][func]['functions'], parent=item)
if 'classes' in symbols and symbols['classes']:
classItem = ItemTree(parent, [translations.TR_CLASSES])
classItem.isClickable = False
classItem.isClass = True
classItem.setExpanded(self._get_expand(classItem))
for claz in sorted(symbols['classes']):
line_number = symbols['classes'][claz]['lineno']
item = ItemTree(classItem, [claz], lineno=line_number)
item.isClass = True
tooltip = self.create_tooltip(claz, line_number)
item.setToolTip(0, tooltip)
item.setIcon(0, QIcon(":img/class"))
item.setExpanded(self._get_expand(item))
self.update_symbols_tree(symbols['classes'][claz]['members'],
parent=item)
def _go_to_definition(self, item):
"""Takes and item object and goes to definition on the editor"""
main_container = IDE.get_service('main_container')
if item.isClickable and main_container:
main_container.editor_go_to_line(item.lineno - 1)
def create_tooltip(self, name, lineno):
"""Takes a name and line number and returns a tooltip"""
doc = self.docstrings.get(lineno, None)
if doc is None:
doc = ''
else:
doc = '\n' + doc
tooltip = name + doc
return tooltip
def _item_collapsed(self, item):
"""When item collapsed"""
super(TreeSymbolsWidget, self).collapseItem(item)
can_check = (not item.isClickable) or item.isClass or item.isMethod
if can_check:
n = self._get_unique_name(item)
filename = self.actualSymbols[0]
self.collapsedItems.setdefault(filename, [])
if not n in self.collapsedItems[filename]:
self.collapsedItems[filename].append(n)
def _item_expanded(self, item):
"""When item expanded"""
super(TreeSymbolsWidget, self).expandItem(item)
n = self._get_unique_name(item)
filename = self.actualSymbols[0]
if n in self.collapsedItems.get(filename, []):
self.collapsedItems[filename].remove(n)
if not len(self.collapsedItems[filename]):
# no more items, free space
del self.collapsedItems[filename]
def clean(self):
"""
Reset the tree and reset attributes
"""
self.tree.clear()
self.collapsedItems = {}
def reject(self):
if self.parent() is None:
self.emit(SIGNAL("dockWidget(PyQt_PyObject)"), self)
def closeEvent(self, event):
"""On Close event handling"""
self.emit(SIGNAL("dockWidget(PyQt_PyObject)"), self)
event.ignore()
class DBDatabasesWidget(QWidget):
"""Displays a list of Databases"""
def __init__(self, parent=None):
QWidget.__init__(self, parent)
self.debug = False
self.db = None
self.setWindowTitle("Databases")
#s#elf.setWindowFlags(self.windowFlags() | QtCore.Qt.WindowStaysOnTopHint)
self.mainLayout = QVBoxLayout()
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(0)
self.setLayout(self.mainLayout)
#=============================================
## Top Toolbar
topBar = QToolBar()
topBar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.mainLayout.addWidget(topBar)
## Add the action buttons
topBar.addAction(Ico.icon(Ico.ServerAdd), "Add", self.on_server_add)
self.actionServerEdit = topBar.addAction(Ico.icon(Ico.ServerEdit),
"Edit", self.on_server_edit)
self.actionServerDelete = topBar.addAction(Ico.icon(Ico.ServerDelete),
"Delete",
self.on_server_delete)
#=============================================
## Tree
self.tree = QTreeWidget()
self.mainLayout.addWidget(self.tree)
self.tree.setHeaderLabels(["Server", "User", ""])
self.tree.setUniformRowHeights(True)
self.tree.setRootIsDecorated(False)
self.tree.setColumnWidth(C.widget, 20)
self.connect(self.tree, SIGNAL('itemSelectionChanged()'),
self.on_tree_selection_changed)
self.connect(self.tree,
SIGNAL('itemDoubleClicked (QTreeWidgetItem *,int)'),
self.on_tree_double_clicked)
self.buttGroup = QButtonGroup(self)
self.connect(self.buttGroup, SIGNAL("buttonClicked(QAbstractButton*)"),
self.on_open_server)
self.on_tree_selection_changed()
self.load_servers()
#=======================================
##== Tree Events
def on_tree_selection_changed(self):
disabled = self.tree.selectionModel().hasSelection() == False
self.actionServerEdit.setDisabled(disabled)
self.actionServerDelete.setDisabled(disabled)
def on_tree_double_clicked(self):
self.actionServerEdit.trigger()
#=======================================
## Server Actions
def on_server_add(self):
self.show_server_dialog(None)
def on_server_edit(self):
item = self.tree.currentItem()
if item == None:
return
server = str(item.text(C.server))
self.show_server_dialog(server)
def show_server_dialog(self, server=None):
d = DBServerDialog.DBServerDialog(self, server)
if d.exec_():
self.load_servers()
def on_open_server(self, butt):
self.emit(SIGNAL("open_server"), butt.property("server").toString())
def load_servers(self):
"""Load servers from :py:meth:`pyqtdb.XSettings.XSettings.get_servers` """
self.tree.clear()
for butt in self.buttGroup.buttons():
self.buttGroup.removeButton(butt)
for srv in G.settings.get_servers_list():
item = QTreeWidgetItem()
item.setText(C.server, srv['server'])
item.setText(C.user, srv['user'])
self.tree.addTopLevelItem(item)
butt = QToolButton()
butt.setIcon(Ico.icon(Ico.Connect))
butt.setProperty("server", srv['server'])
self.tree.setItemWidget(item, C.widget, butt)
self.buttGroup.addButton(butt)
def on_server_delete(self):
item = self.tree.currentItem()
if item == None:
return
srv = str(item.text(C.server))
G.settings.delete_server(srv)
self.load_servers()
