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 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 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 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 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 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 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 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)
