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 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 Shortcuts(preferences.Page):
def __init__(self, dialog):
super(Shortcuts, self).__init__(dialog)
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.scheme = SchemeSelector(self)
layout.addWidget(self.scheme)
self.tree = QTreeWidget(self)
self.tree.setHeaderLabels([_("Command"), _("Shortcut")])
self.tree.setRootIsDecorated(False)
self.tree.setColumnCount(2)
self.tree.setAllColumnsShowFocus(True)
self.tree.setAnimated(True)
layout.addWidget(self.tree)
self.edit = QPushButton(
icons.get("preferences-desktop-keyboard-shortcuts"), '')
layout.addWidget(self.edit)
# signals
self.scheme.currentChanged.connect(self.slotSchemeChanged)
self.scheme.changed.connect(self.changed)
self.tree.currentItemChanged.connect(self.slotCurrentItemChanged)
self.tree.itemDoubleClicked.connect(self.editCurrentItem)
self.edit.clicked.connect(self.editCurrentItem)
# make a dict of all actions with the actions as key and the names as
# value, with the collection prepended (for loading/saving)
win = dialog.parent()
allactions = {}
for collection in actioncollectionmanager.manager(
win).actionCollections():
for name, action in collection.actions().items():
allactions[action] = (collection, name)
# keep a list of actions not in the menu structure
left = list(allactions.keys())
def add_actions(menuitem, actions):
"""Add actions to a QTreeWidgetItem."""
for a in actions:
if a.menu():
item = build_menu_item(a)
if item.childCount():
menuitem.addChild(item)
elif a in left:
left.remove(a)
menuitem.addChild(ShortcutItem(a, *allactions[a]))
menuitem.setFlags(Qt.ItemIsEnabled) # disable selection
def build_menu_item(action):
"""Return a QTreeWidgetItem with children for all the actions in the submenu."""
menuitem = QTreeWidgetItem()
text = qutil.removeAccelerator(action.text())
menuitem.setText(0, _("Menu {name}").format(name=text))
add_actions(menuitem, action.menu().actions())
return menuitem
# present the actions nicely ordered as in the menus
for a in win.menuBar().actions():
menuitem = build_menu_item(a)
if menuitem.childCount():
self.tree.addTopLevelItem(menuitem)
# sort leftover actions
left.sort(key=lambda i: i.text())
# show actions that are left, grouped by collection
titlegroups = {}
for a in left[:]: # copy
collection, name = allactions[a]
if collection.title():
titlegroups.setdefault(collection.title(), []).append(a)
left.remove(a)
for title in sorted(titlegroups):
item = QTreeWidgetItem(["{0}:".format(title)])
for a in titlegroups[title]:
item.addChild(ShortcutItem(a, *allactions[a]))
self.tree.addTopLevelItem(item)
item.setFlags(Qt.ItemIsEnabled) # disable selection
# show other actions that were not in the menus
item = QTreeWidgetItem([_("Other commands:")])
for a in left:
if a.text() and not a.menu():
item.addChild(ShortcutItem(a, *allactions[a]))
if item.childCount():
self.tree.addTopLevelItem(item)
item.setFlags(Qt.ItemIsEnabled) # disable selection
self.tree.expandAll()
item = self.tree.topLevelItem(0).child(0)
if _lastaction:
# find the previously selected item
for i in self.items():
if i.name == _lastaction:
item = i
break
self.tree.setCurrentItem(item)
self.tree.resizeColumnToContents(0)
def items(self):
"""Yield all the items in the actions tree."""
def children(item):
for i in range(item.childCount()):
c = item.child(i)
if c.childCount():
for c1 in children(c):
yield c1
else:
yield c
for c in children(self.tree.invisibleRootItem()):
yield c
def item(self, collection, name):
for item in self.items():
if item.collection.name == collection and item.name == name:
return item
def saveSettings(self):
self.scheme.saveSettings("shortcut_scheme", "shortcut_schemes",
"shortcuts")
for item in self.items():
for scheme in self.scheme.schemes():
item.save(scheme)
item.clearSettings()
item.switchScheme(self.scheme.currentScheme())
def loadSettings(self):
self.scheme.loadSettings("shortcut_scheme", "shortcut_schemes")
# clear the settings in all the items
for item in self.items():
item.clearSettings()
item.switchScheme(self.scheme.currentScheme())
def slotSchemeChanged(self):
"""Called when the Scheme combobox is changed by the user."""
for item in self.items():
item.switchScheme(self.scheme.currentScheme())
def slotCurrentItemChanged(self, item):
if isinstance(item, ShortcutItem):
self.edit.setText(
_("&Edit Shortcut for \"{name}\"").format(name=item.text(0)))
self.edit.setEnabled(True)
global _lastaction
_lastaction = item.name
else:
self.edit.setText(_("(no shortcut)"))
self.edit.setEnabled(False)
def import_(self, filename):
from . import import_export
import_export.importShortcut(filename, self, self.scheme)
def export(self, name, filename):
from . import import_export
try:
import_export.exportShortcut(self, self.scheme.currentScheme(),
name, filename)
except (IOError, OSError) as e:
QMessageBox.critical(
self, _("Error"),
_("Can't write to destination:\n\n{url}\n\n{error}").format(
url=filename, error=e.strerror))
def findShortcutConflict(self, shortcut):
"""Find the possible shortcut conflict and return the conflict name."""
if shortcut:
item = self.tree.currentItem()
if not isinstance(item, ShortcutItem):
return None
scheme = self.scheme.currentScheme()
for i in self.items():
a = i.action(scheme)
if i != item and a.shortcuts():
for s1 in a.shortcuts():
if s1.matches(shortcut) or shortcut.matches(s1):
return qutil.removeAccelerator(a.text())
return None
def editCurrentItem(self):
item = self.tree.currentItem()
if not isinstance(item, ShortcutItem):
return
dlg = ShortcutEditDialog(self, self.findShortcutConflict)
scheme = self.scheme.currentScheme()
action = item.action(scheme)
default = item.defaultShortcuts() or None
if dlg.editAction(action, default):
shortcuts = action.shortcuts()
# check for conflicts
conflicting = []
for i in self.items():
if i is not item:
for s1, s2 in itertools.product(i.shortcuts(scheme),
shortcuts):
if s1.matches(s2) or s2.matches(s1):
conflicting.append(i)
if conflicting:
for i in conflicting:
l = i.shortcuts(scheme)
for s1 in list(l): # copy
for s2 in shortcuts:
if s1.matches(s2) or s2.matches(s1):
l.remove(s1)
i.setShortcuts(l, scheme)
# store the shortcut
item.setShortcuts(shortcuts, scheme)
self.changed.emit()
class Shortcuts(preferences.Page):
def __init__(self, dialog):
super(Shortcuts, self).__init__(dialog)
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.scheme = SchemeSelector(self)
layout.addWidget(self.scheme)
self.tree = QTreeWidget(self)
self.tree.setHeaderLabels([_("Command"), _("Shortcut")])
self.tree.setRootIsDecorated(False)
self.tree.setColumnCount(2)
self.tree.setAllColumnsShowFocus(True)
self.tree.setAnimated(True)
layout.addWidget(self.tree)
self.edit = QPushButton(icons.get("preferences-desktop-keyboard-shortcuts"), '')
layout.addWidget(self.edit)
# signals
self.scheme.currentChanged.connect(self.slotSchemeChanged)
self.scheme.changed.connect(self.changed)
self.tree.currentItemChanged.connect(self.slotCurrentItemChanged)
self.tree.itemDoubleClicked.connect(self.editCurrentItem)
self.edit.clicked.connect(self.editCurrentItem)
# make a dict of all actions with the actions as key and the names as
# value, with the collection prepended (for loading/saving)
win = dialog.parent()
allactions = {}
for collection in actioncollectionmanager.manager(win).actionCollections():
for name, action in collection.actions().items():
allactions[action] = (collection, name)
# keep a list of actions not in the menu structure
left = allactions.keys()
def add_actions(menuitem, actions):
"""Add actions to a QTreeWidgetItem."""
for a in actions:
if a.menu():
item = build_menu_item(a)
if item.childCount():
menuitem.addChild(item)
elif a in left:
left.remove(a)
menuitem.addChild(ShortcutItem(a, *allactions[a]))
menuitem.setFlags(Qt.ItemIsEnabled) # disable selection
def build_menu_item(action):
"""Return a QTreeWidgetItem with children for all the actions in the submenu."""
menuitem = QTreeWidgetItem()
text = qutil.removeAccelelator(action.text())
menuitem.setText(0, _("Menu {name}").format(name=text))
add_actions(menuitem, action.menu().actions())
return menuitem
# present the actions nicely ordered as in the menus
for a in win.menuBar().actions():
menuitem = build_menu_item(a)
if menuitem.childCount():
self.tree.addTopLevelItem(menuitem)
# sort leftover actions
left.sort(key=lambda i: i.text())
# show actions that are left, grouped by collection
titlegroups = {}
for a in left[:]: # copy
collection, name = allactions[a]
if collection.title():
titlegroups.setdefault(collection.title(), []).append(a)
left.remove(a)
for title in sorted(titlegroups):
item = QTreeWidgetItem(["{0}:".format(title)])
for a in titlegroups[title]:
item.addChild(ShortcutItem(a, *allactions[a]))
self.tree.addTopLevelItem(item)
item.setFlags(Qt.ItemIsEnabled) # disable selection
# show other actions that were not in the menus
item = QTreeWidgetItem([_("Other commands:")])
for a in left:
if a.text() and not a.menu():
item.addChild(ShortcutItem(a, *allactions[a]))
if item.childCount():
self.tree.addTopLevelItem(item)
item.setFlags(Qt.ItemIsEnabled) # disable selection
self.tree.expandAll()
item = self.tree.topLevelItem(0).child(0)
if _lastaction:
# find the previously selected item
for i in self.items():
if i.name == _lastaction:
item = i
break
self.tree.setCurrentItem(item)
self.tree.resizeColumnToContents(0)
def items(self):
"""Yield all the items in the actions tree."""
def children(item):
for i in range(item.childCount()):
c = item.child(i)
if c.childCount():
for c1 in children(c):
yield c1
else:
yield c
for c in children(self.tree.invisibleRootItem()):
yield c
def saveSettings(self):
self.scheme.saveSettings("shortcut_scheme", "shortcut_schemes", "shortcuts")
for item in self.items():
for scheme in self.scheme.schemes():
item.save(scheme)
item.clearSettings()
item.switchScheme(self.scheme.currentScheme())
def loadSettings(self):
self.scheme.loadSettings("shortcut_scheme", "shortcut_schemes")
# clear the settings in all the items
for item in self.items():
item.clearSettings()
item.switchScheme(self.scheme.currentScheme())
def slotSchemeChanged(self):
"""Called when the Scheme combobox is changed by the user."""
for item in self.items():
item.switchScheme(self.scheme.currentScheme())
def slotCurrentItemChanged(self, item):
if isinstance(item, ShortcutItem):
self.edit.setText(
_("&Edit Shortcut for \"{name}\"").format(name=item.text(0)))
self.edit.setEnabled(True)
global _lastaction
_lastaction = item.name
else:
self.edit.setText(_("(no shortcut)"))
self.edit.setEnabled(False)
def editCurrentItem(self):
item = self.tree.currentItem()
if not isinstance(item, ShortcutItem):
return
try:
dlg = self._editdialog
except AttributeError:
dlg = self._editdialog = ShortcutEditDialog(self)
scheme = self.scheme.currentScheme()
action = item.action(scheme)
default = item.defaultShortcuts()
if dlg.editAction(action, default):
shortcuts = action.shortcuts()
# check for conflicts
conflicting = []
for i in self.items():
if i is not item:
for s1, s2 in itertools.product(i.shortcuts(scheme), shortcuts):
if s1.matches(s2) or s2.matches(s1):
conflicting.append(i)
if conflicting:
# show a question dialog
msg = [_("This shortcut conflicts with the following command:",
"This shortcut conflicts with the following commands:", len(conflicting))]
msg.append('<br/>'.join(i.text(0) for i in conflicting))
msg.append(_("Remove the shortcut from that command?",
"Remove the shortcut from those commands?", len(conflicting)))
msg = '<p>{0}</p>'.format('</p><p>'.join(msg))
res = QMessageBox.warning(self, _("Shortcut Conflict"), msg,
QMessageBox.Yes | QMessageBox.No | QMessageBox.Cancel)
if res == QMessageBox.Yes:
# remove from conflicting
for i in conflicting:
l = i.shortcuts(scheme)
for s1 in list(l): # copy
for s2 in shortcuts:
if s1.matches(s2) or s2.matches(s1):
l.remove(s1)
i.setShortcuts(l, scheme)
elif res == QMessageBox.No:
# remove from ourselves
for i in conflicting:
for s1 in list(shortcuts): # copy
for s2 in i.shortcuts(scheme):
if s1.matches(s2) or s2.matches(s1):
shortcuts.remove(s1)
else:
return # cancelled
# store the shortcut
item.setShortcuts(shortcuts, scheme)
self.changed.emit()
def expandAll(self):
self._treeDepth = 10000
QTreeWidget.expandAll(self)
def __init__(self, term, parent=None):
super(FeeDialog, self).__init__(parent)
self.term = term
self.sid = term
terms = self.pullOnes('terms', self.term)
session = self.pullOnes('session', terms['sessionID'])
self.termname = str(session['name'])+' '+terms['name']+' Term Report'
self.pagetitle = self.termname
ko = 0
Form1 = QFormLayout()
Form2 = QFormLayout()
#title
self.title = QLabel("Set Fees")
self.titleData = QComboBox()
self.titleData.setObjectName("name")
#self.titleData.setPlaceHolderText("e.g. 2019 FIRST TERM RESULT")
tree = QTreeWidget()
tree.setItemDelegate(Delegate())
tree.setHeaderLabel("Which grading system will you be using?")
tree1 = QTreeWidget()
tree1.setHeaderLabel("Choose Assessments and Classes")
tree2 = QTreeWidget()
tree2.setHeaderLabel("Report Card Settings")
self.ass_arr = {}
parent = QTreeWidgetItem(tree1)
parent.setText(0, "Select Assessments")
parent.setFlags(parent.flags() | Qt.ItemIsTristate | Qt.ItemIsUserCheckable)
arr = self.pullCas()
if arr and len(arr) > 0:
for val in arr:
dt = self.pullOne(val['name'])
child = QTreeWidgetItem(parent)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(dt['name']).upper())
self.ass_arr[val['name']] = child
if (val['active'] == 0):
child.setCheckState(0, Qt.Unchecked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.cla_arr ={}
parent1 = QTreeWidgetItem(tree1)
parent1.setText(0, "Select Class")
parent1.setFlags(parent1.flags() | Qt.ItemIsTristate | Qt.ItemIsUserCheckable)
arr = self.pullClass()
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent1)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(val['name']).upper())
self.cla_arr[val['id']] = child
if (val['active'] == 0):
child.setCheckState(0, Qt.Unchecked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.gra_arr = {}
parent2 = QTreeWidgetItem(tree)
parent2.setText(0, "Select Grade")
arr = self.pullGrade()
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent2)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(val['name']).upper())
self.gra_arr[val['id']] = child
if (val['active'] == 0):
child.setCheckState(0, Qt.Unchecked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.set_arr= {}
parent3 = QTreeWidgetItem(tree2)
parent3.setText(0, "Include ...")
parent3.setFlags(parent3.flags() | Qt.ItemIsTristate | Qt.ItemIsUserCheckable)
arr ={
1:'School Number',
2:'Class Position',
3:'Class Unit Position',
4:'Total (100%)',
5:'Total',
6:'Grading',
7:'Subject Average',
8:'Ranking',
9:'Ranking and Student Population',
10:'Student Passport',
11:'School Logo',
12:'School Address',
13:'Students Address',
14:'Attendance',
15:'Fees Owed',
16:'Test/Assesments'
}
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent3)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(arr[val]).upper())
self.set_arr[val] = child
child.setCheckState(0, Qt.Unchecked)
child1 = QTreeWidgetItem(parent3)
child1.setFlags(child1.flags() | Qt.ItemIsUserCheckable)
child1.setText(0, 'AFFECTIVE DOMAIN REPORT')
self.set_arr['aff'] = child1
child1.setCheckState(0, Qt.Unchecked)
child2 = QTreeWidgetItem(child1)
child2.setFlags(child2.flags() | Qt.ItemIsTristate | Qt.ItemIsUserCheckable)
child2.setText(0, 'TABLE')
self.set_arr['afftable'] = child2
child2.setCheckState(0, Qt.Unchecked)
child3 = QTreeWidgetItem(child1)
child3.setFlags(child3.flags() | Qt.ItemIsUserCheckable)
child3.setText(0, 'GRAPH')
self.set_arr['affgraph'] = child3
child3.setCheckState(0, Qt.Unchecked)
child4 = QTreeWidgetItem(parent3)
child4.setFlags(child4.flags() | Qt.ItemIsTristate | Qt.ItemIsUserCheckable)
child4.setText(0, 'PYSCHOMOTOR DOMAIN REPORT')
self.set_arr['psy'] = child4
child4.setCheckState(0, Qt.Unchecked)
child5 = QTreeWidgetItem(child4)
child5.setFlags(child5.flags() | Qt.ItemIsUserCheckable)
child5.setText(0, 'TABLE')
self.set_arr['psytable'] = child5
child5.setCheckState(0, Qt.Unchecked)
child6 = QTreeWidgetItem(child4)
child6.setFlags(child6.flags() | Qt.ItemIsUserCheckable)
child6.setText(0, 'GRAPH')
self.set_arr['psygraph'] = child6
child6.setCheckState(0, Qt.Unchecked)
tree.expandAll()
tree1.expandAll()
tree2.expandAll()
#tree.show()
self.l5 = QLabel("Theme Color")
self.pbc = QPushButton()
self.pbc.setObjectName("Pickcolor")
self.pbc.setText("Click to change")
self.le5 = QLineEdit()
self.le5.setObjectName("Showcolor")
self.le5.setText("#000000")
self.pbc.setStyleSheet("background-color: black; color: white")
self.connect(self.pbc, SIGNAL("clicked()"), lambda: self.color_picker())
self.l6 = QLabel("Pick Theme Font")
self.pbf = QPushButton()
self.pbf.setObjectName("Pickfont")
self.pbf.setText("Click to Change")
self.le6 = QLineEdit()
self.le6.setObjectName("Showcolor")
self.le6.setText("#000000")
self.pbf.setStyleSheet("background-color: black; color: white")
self.connect(self.pbf, SIGNAL("clicked()"), lambda: self.font_picker())
self.lv_box = QHBoxLayout()
self.lv_box.addWidget(self.pbc)
self.lv_box.addWidget(self.le5)
self.lv_box1 = QHBoxLayout()
self.lv_box1.addWidget(self.pbf)
self.lv_box1.addWidget(self.le6)
Form1.addRow(self.title, self.titleData)
Form2.addRow(self.l5, self.lv_box)
Form2.addRow(self.l6, self.lv_box1)
Gbo = QGridLayout()
Gbo.addLayout(Form1, 0, 0, 1, 2)
Gbo.addWidget(tree, 1, 0)
Gbo.addWidget(tree1, 1, 1)
Gbo.addWidget(tree2, 2, 0)
Gbo.addLayout(Form2, 2, 1)
groupBox1 = QGroupBox('Academic Report Setup')
groupBox1.setLayout(Gbo)
self.pb = QPushButton()
self.pb.setObjectName("Add")
self.pb.setText("Save")
self.pb1 = QPushButton()
self.pb1.setObjectName("Cancel")
self.pb1.setText("Cancel")
self.pb2 = QPushButton()
self.pb2.setObjectName("Save")
self.pb2.setText("Save and Keep Template")
self.lTemplate = QLineEdit()
self.lTemplate.setPlaceholderText('Template Name')
self.rTemplate = QLabel()
self.rTemplate.setText('')
hbo = QHBoxLayout()
hbo.addWidget(self.pb1)
hbo.addStretch()
hbo.addWidget(self.lTemplate)
hbo.addWidget(self.pb2)
hbo.addWidget(self.rTemplate)
hbo.addStretch()
hbo.addWidget(self.pb)
groupBox2 = QGroupBox('')
groupBox2.setLayout(hbo)
grid = QGridLayout()
grid.addWidget(groupBox1, 0, 0)
grid.addWidget(groupBox2, 1, 0)
self.setLayout(grid)
self.connect(self.pb, SIGNAL("clicked()"), lambda: self.button_click(self))
self.connect(self.pb2, SIGNAL("clicked()"), lambda: self.button_template(self))
self.connect(self.pb1, SIGNAL("clicked()"), lambda: self.button_close(self))
self.setWindowTitle(self.pagetitle)
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 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 Preferences(QDialog):
configuration = {}
weight = 0
def __init__(self, parent=None):
super(Preferences, self).__init__(parent, Qt.Dialog)
self.setWindowTitle(translations.TR_PREFERENCES_TITLE)
self.setMinimumSize(QSize(800, 600))
self.setMaximumSize(QSize(0, 0))
vbox = QVBoxLayout(self)
hbox = QHBoxLayout()
vbox.setContentsMargins(0, 0, 5, 5)
hbox.setContentsMargins(0, 0, 0, 0)
self.tree = QTreeWidget()
self.tree.header().setHidden(True)
self.tree.setSelectionMode(QTreeWidget.SingleSelection)
self.tree.setAnimated(True)
self.tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
self.tree.setFixedWidth(200)
self.stacked = QStackedLayout()
hbox.addWidget(self.tree)
hbox.addLayout(self.stacked)
vbox.addLayout(hbox)
hbox_footer = QHBoxLayout()
self._btnSave = QPushButton(translations.TR_SAVE)
self._btnCancel = QPushButton(translations.TR_CANCEL)
hbox_footer.addSpacerItem(QSpacerItem(1, 0, QSizePolicy.Expanding))
hbox_footer.addWidget(self._btnCancel)
hbox_footer.addWidget(self._btnSave)
vbox.addLayout(hbox_footer)
self.connect(self.tree, SIGNAL("itemSelectionChanged()"),
self._change_current)
self.connect(self._btnCancel, SIGNAL("clicked()"), self.close)
self.connect(self._btnSave, SIGNAL("clicked()"),
self._save_preferences)
self.load_ui()
self.tree.setCurrentItem(self.tree.topLevelItem(0))
def _save_preferences(self):
self.emit(SIGNAL("savePreferences()"))
self.close()
def load_ui(self):
sections = sorted(
list(Preferences.configuration.keys()),
key=lambda item: Preferences.configuration[item]['weight'])
for section in sections:
text = Preferences.configuration[section]['text']
Widget = Preferences.configuration[section]['widget']
widget = Widget(self)
area = QScrollArea()
area.setWidgetResizable(True)
area.setWidget(widget)
index = self.stacked.addWidget(area)
item = QTreeWidgetItem([text])
item.setData(0, Qt.UserRole, index)
self.tree.addTopLevelItem(item)
#Sort Item Children
subcontent = Preferences.configuration[section].get(
'subsections', {})
subsections = sorted(list(subcontent.keys()),
key=lambda item: subcontent[item]['weight'])
for sub in subsections:
text = subcontent[sub]['text']
Widget = subcontent[sub]['widget']
widget = Widget(self)
area = QScrollArea()
area.setWidgetResizable(True)
area.setWidget(widget)
index = self.stacked.addWidget(area)
subitem = QTreeWidgetItem([text])
subitem.setData(0, Qt.UserRole, index)
item.addChild(subitem)
self.tree.expandAll()
def _change_current(self):
item = self.tree.currentItem()
index = item.data(0, Qt.UserRole)
self.stacked.setCurrentIndex(index)
@classmethod
def register_configuration(cls,
section,
widget,
text,
weight=None,
subsection=None):
if weight is None:
Preferences.weight += 1
weight = Preferences.weight
if not subsection:
Preferences.configuration[section] = {
'widget': widget,
'weight': weight,
'text': text
}
else:
config = Preferences.configuration.get(section, {})
if not config:
config[section] = {'widget': None, 'weight': 100}
subconfig = config.get('subsections', {})
subconfig[subsection] = {
'widget': widget,
'weight': weight,
'text': text
}
config['subsections'] = subconfig
Preferences.configuration[section] = config
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 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 = [("Data", Orange.data.Table, "SetData", widget.Default),
("Reference", Orange.data.Table, "SetRefData")]
outputs = [("Selected Data", Orange.data.Table, widget.Default),
("Unselected Data", 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.",
default=False,
autoDefault=False)
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 Data", None)
self.send("Unselected Data", 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
if vars:
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))
else:
imax = -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)
if len(self.geneAttrCandidates) == 0:
self.useAttrNames = True
self.geneAttrIndex = -1
else:
self.geneAttrIndex = min(self.geneAttrIndex,
len(self.geneAttrCandidates) - 1)
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:
assert 0 <= self.geneAttrIndex < len(self.geneAttrCandidates)
geneAttr = self.geneAttrCandidates[self.geneAttrIndex]
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 Data", data)
elif self.geneAttrCandidates:
assert 0 <= self.geneAttrIndex < len(self.geneAttrCandidates)
geneAttr = self.geneAttrCandidates[self.geneAttrIndex]
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 Data", selected)
self.send("Unselected Data", other)
else:
self.send("Selected Data", None)
self.send("Unselected Data", 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 OWKEGGPathwayBrowser(OWWidget):
settingsList = ["organismIndex", "geneAttrIndex", "autoCommit",
"autoResize", "useReference", "useAttrNames",
"showOrthology"]
contextHandlers = {
"": DomainContextHandler(
"",
[ContextField("organismIndex",
DomainContextHandler.Required +
DomainContextHandler.IncludeMetaAttributes),
ContextField("geneAttrIndex",
DomainContextHandler.Required +
DomainContextHandler.IncludeMetaAttributes),
ContextField("useAttrNames",
DomainContextHandler.Required +
DomainContextHandler.IncludeMetaAttributes)]
)
}
def __init__(self, parent=None, signalManager=None, name="KEGG Pathways"):
OWWidget.__init__(self, parent, signalManager, name, wantGraph=True)
self.inputs = [("Examples", Orange.data.Table, self.SetData),
("Reference", Orange.data.Table, self.SetRefData)]
self.outputs = [("Selected Examples", Orange.data.Table),
("Unselected Examples", Orange.data.Table)]
self.organismIndex = 0
self.geneAttrIndex = 0
self.autoCommit = False
self.autoResize = True
self.useReference = False
self.useAttrNames = 0
self.showOrthology = True
self.loadSettings()
self.organismCodes = []
self._changedFlag = False
self.controlArea.setMaximumWidth(250)
box = OWGUI.widgetBox(self.controlArea, "Info")
self.infoLabel = OWGUI.widgetLabel(box, "No data on input\n")
# Organism selection.
box = OWGUI.widgetBox(self.controlArea, "Organism")
self.organismComboBox = OWGUI.comboBox(
box, self, "organismIndex",
items=[],
callback=self.Update,
addSpace=True,
debuggingEnabled=0,
tooltip="Select the organism of the input genes")
# Selection of genes attribute
box = OWGUI.widgetBox(self.controlArea, "Gene attribute")
self.geneAttrCandidates = VariableListModel(parent=self)
self.geneAttrCombo = OWGUI.comboBox(
box, self, "geneAttrIndex", callback=self.Update)
self.geneAttrCombo.setModel(self.geneAttrCandidates)
OWGUI.checkBox(box, self, "useAttrNames",
"Use variable names",
disables=[(-1, self.geneAttrCombo)],
callback=self.Update)
self.geneAttrCombo.setDisabled(bool(self.useAttrNames))
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "useReference",
"From signal",
box="Reference",
callback=self.Update)
OWGUI.separator(self.controlArea)
OWGUI.checkBox(self.controlArea, self, "showOrthology",
"Show pathways in full orthology",
box="Orthology",
callback=self.UpdateListView)
OWGUI.checkBox(self.controlArea, self, "autoResize",
"Resize to fit",
box="Image",
callback=self.UpdatePathwayViewTransform)
box = OWGUI.widgetBox(self.controlArea, "Cache Control")
OWGUI.button(box, self, "Clear cache",
callback=self.ClearCache,
tooltip="Clear all locally cached KEGG data.")
OWGUI.separator(self.controlArea)
box = OWGUI.widgetBox(self.controlArea, "Selection")
cb = OWGUI.checkBox(box, self, "autoCommit", "Commit on update")
button = OWGUI.button(box, self, "Commit", callback=self.Commit,
default=True)
OWGUI.setStopper(self, button, cb, "_changedFlag", self.Commit)
OWGUI.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(spliter)
spliter.addWidget(self.listView)
self.listView.setAllColumnsShowFocus(1)
self.listView.setColumnCount(4)
self.listView.setHeaderLabels(["Pathway", "P value",
"Genes", "Reference"])
self.listView.setSelectionMode(QTreeWidget.SingleSelection)
self.listView.setSortingEnabled(True)
self.listView.setMaximumHeight(200)
self.connect(self.listView,
SIGNAL("itemSelectionChanged()"),
self.UpdatePathwayView)
self.connect(self.graphButton,
SIGNAL("clicked()"),
self.saveGraph)
select = QAction(
"Select All", self,
shortcut=QKeySequence.SelectAll
)
select.triggered.connect(self.selectAll)
self.addAction(select)
self.data = None
self.refData = None
self.resize(800, 600)
self.connect(self,
SIGNAL("widgetStateChanged(QString, int, QString)"),
self.onStateChange)
self.has_new_data = False
self.has_new_reference_set = False
self._executor = ThreadExecutor()
self.setEnabled(False)
self.setBlocking(True)
QTimer.singleShot(0, self._initialize)
self.infoLabel.setText("Fetching organism definitions\n")
def _initialize(self):
# First try to import slumber to see if we can even use the
# kegg module.
try:
import slumber
except ImportError:
QMessageBox.warning(self,
"'slumber' library required.",
'<p>Please install '
'<a href="http://pypi.python.org/pypi/slumber">slumber</a> '
'library to use KEGG Pathways widget.</p>'
)
self.infoLabel.setText(
'<p>Please install '
'<a href="http://pypi.python.org/pypi/slumber">slumber</a> '
'library to use KEGG Pathways widget.</p>'
)
self.error(0, "Missing slumber/requests library")
return
progress = 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 = map(genome.org_code_to_entry_key, essential + common)
genome.pre_cache(keys, progress_callback=progress)
return (keys, genome)
self._genomeTask = task = Task(function=get_genome)
task.finished.connect(self._initializeOrganisms)
self.progressBarInit()
self._executor.submit(task)
def _initializeOrganisms(self):
self.progressBarFinished()
try:
keys, genome = self._genomeTask.result()
except Exception as err:
self.error(0, str(err))
return
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.setEnabled(True)
self.setBlocking(False)
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):
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.getmetas().values()
vars = [var for var in vars
if isinstance(var, (Orange.feature.String,
Orange.feature.Discrete))]
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.has_new_data = True
def SetRefData(self, data=None):
self.refData = data
self.information(1)
self.has_new_reference_set = True
def handleNewSignals(self):
if self.has_new_data or (self.has_new_reference_set and \
self.useReference):
self.Update()
self.has_new_data = False
self.has_new_reference_set = 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.sort(lambda a, b: cmp(a[1][1], b[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 = 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 = methodinvoke(self, "setProgress", (float,))
self._enrichTask = 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)
self.progressBarFinished()
try:
pathways, org, unique_genes, unique_ref_genes = \
self._enrichTask.result()
except Exception:
raise
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()
@pyqtSlot(float)
def setProgress(self, value):
self.progressBarValue = value
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 e[geneAttr].isSpecial()]
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
if self.autoCommit:
self.Commit()
else:
self._changedFlag = True
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:
selectedVars = [self.data.domain[self.uniqueGenesDict[gene]]
for gene in selectedGenes]
newDomain = Orange.data.Domain(selectedVars, 0)
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)]
selectedExamples = []
otherExamples = []
for ex in 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):
selectedExamples.append(ex)
else:
otherExamples.append(ex)
if selectedExamples:
selectedExamples = Orange.data.Table(selectedExamples)
else:
selectedExamples = None
if otherExamples:
otherExamples = Orange.data.Table(otherExamples)
else:
otherExamples = None
self.send("Selected Examples", selectedExamples)
self.send("Unselected Examples", otherExamples)
else:
self.send("Selected Examples", None)
self.send("Unselected Examples", None)
def ClearCache(self):
from ..kegg import caching
try:
caching.clear_cache()
except Exception, ex:
QMessageBox.warning(self, "Cache clear", ex.args[0])
class mainwindow(QtGui.QMainWindow):
'''主窗体'''
def __init__(self):
super(mainwindow, self).__init__()
self.setWindowTitle('组件设计工具')
self.setWindowIcon(QIcon(':/image/组件设计工具.png'))
self.setMinimumWidth(1024)
self.setMinimumHeight(800)
self.showMaximized()
self.menuBar().show()
self.createMenus()
#self.setWindowFlags(QtCore.Qt.WindowMinimizeButtonHint)
labelSizePolicy = QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
editSizePolicy = QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Fixed)
cwVLayout = QVBoxLayout()
cwHLayout = QHBoxLayout()
lLayout = QVBoxLayout()
rLayout = QVBoxLayout()
self.lw = QListWidget()
self.lw.setSelectionMode(QAbstractItemView.SingleSelection)
lLayout.addWidget(self.lw)
self.lw.itemSelectionChanged.connect(self.on_select)
lGroup = QGroupBox('项目列表')
lGroup.setLayout(lLayout)
cwHLayout.addWidget(lGroup, 2)
lGroup.setContentsMargins(0, 12, 0, 22)
tLayout = QVBoxLayout()
bLayout = QHBoxLayout()
self.tGroup = QGroupBox('配置信息')
self.bGroup = QGroupBox('生成代码')
self.tGroup.setLayout(tLayout)
self.tGroup.setEnabled(False)
self.bGroup.setLayout(bLayout)
self.bGroup.setEnabled(False)
cwHLayout.addWidget(self.tGroup, 8)
cwVLayout.addLayout(cwHLayout)
cwVLayout.addWidget(self.bGroup)
self.tw_config = QTreeWidget()
headerLabels = QStringList()
headerLabels.append(' 项目')
headerLabels.append(' 值')
self.tw_config.setHeaderLabels(headerLabels)
self.tw_config.setColumnWidth(0, 312)
self.tw_config.setColumnWidth(1, 660)
thLayout = QHBoxLayout()
thLayout.setContentsMargins(0, 6, 0, 0)
thLayout.addSpacing(10)
modify_btn = QPushButton('') #修改
modify_btn.setObjectName('modify_btn')
modify_btn.clicked.connect(self.on_modify)
del_btn = QPushButton('') #删除
del_btn.setObjectName('del_btn')
del_btn.clicked.connect(self.on_del)
thLayout.addWidget(modify_btn)
thLayout.addWidget(del_btn)
thLayout.addStretch(0)
tLayout.addLayout(thLayout)
tLayout.addWidget(self.tw_config)
bhLayout = QHBoxLayout()
lable1 = QLabel('工程名称：')
lable1.setSizePolicy(labelSizePolicy)
self.et_project_name = QLineEdit()
self.et_project_name.setSizePolicy(editSizePolicy)
bhLayout.addWidget(lable1)
bhLayout.addWidget(self.et_project_name)
bhLayout.addSpacing(16)
lable2 = QLabel('工程位置：')
lable2.setSizePolicy(labelSizePolicy)
self.et_project_location = QLineEdit()
self.et_project_location.setReadOnly(True)
self.et_project_location.setSizePolicy(editSizePolicy)
btn_location = QPushButton('') #打开
btn_location.setObjectName('btn_location')
btn_location.setSizePolicy(labelSizePolicy)
btn_location.clicked.connect(self.getProjectLocation)
bhLayout.addWidget(lable2)
bhLayout.addWidget(self.et_project_location)
bhLayout.addSpacing(10)
bhLayout.addWidget(btn_location)
#bhLayout.addStretch(0)
gen_btn = QPushButton('') # 生成
gen_btn.setObjectName('gen_btn')
gen_btn.setSizePolicy(labelSizePolicy)
gen_btn.clicked.connect(self.on_gen)
bhLayout.addSpacing(45)
bhLayout.addWidget(gen_btn)
bLayout.addLayout(bhLayout)
bLayout.setContentsMargins(10, 24, 22, 34)
statusBar = self.statusBar()
sBH = QHBoxLayout()
copyright = QLabel('')
copyright.setAlignment(QtCore.Qt.AlignCenter)
copyright.setStyleSheet("color:#acacac")
statusBar.setMinimumHeight(30)
statusBar.addWidget(copyright, 10)
cw = QWidget()
cw.setLayout(cwVLayout)
self.setCentralWidget(cw)
self._initByConfig()
self.setMinimumSize(400, 200)
def _initByConfig(self):
'''初始化'''
pass
def createMenus(self):
'''创建菜单'''
self.ToolBar = self.addToolBar('')
self.ToolBar.setMinimumHeight(54)
newBtn = QToolButton()
newBtn.setText('创建项目')
newBtn.setIcon(QIcon(':/image/创建项目.png'))
newBtn.setToolButtonStyle(3)
newBtn.setFixedWidth(99)
OpenBtn = QToolButton()
OpenBtn.setText('打开项目')
OpenBtn.setIcon(QIcon(':/image/打开.png'))
OpenBtn.setToolButtonStyle(3)
OpenBtn.setFixedWidth(99)
AboutBtn = QToolButton()
AboutBtn.setText('关于')
AboutBtn.setIcon(QIcon(':/image/关于.png'))
AboutBtn.setToolButtonStyle(3)
AboutBtn.setFixedWidth(99)
HelpBtn = QToolButton()
HelpBtn.setText('帮助')
HelpBtn.setIcon(QIcon(':/image/帮助.png'))
HelpBtn.setToolButtonStyle(3)
HelpBtn.setFixedWidth(99)
newBtn.clicked.connect(self.on_new)
OpenBtn.clicked.connect(self.on_open)
AboutBtn.clicked.connect(self.on_about)
HelpBtn.clicked.connect(self.on_help)
self.ToolBar.addWidget(newBtn)
self.ToolBar.addWidget(OpenBtn)
self.ToolBar.addWidget(AboutBtn)
self.ToolBar.addWidget(HelpBtn)
self.ToolBar.setMovable(False)
self.ToolBar.setVisible(True)
def on_help(self):
app.g_pwd = os.getcwd()
if not (QtGui.QDesktopServices.openUrl(
QUrl.fromLocalFile(app.g_pwd + os.sep + 'image' + os.sep +
'help.pdf'))):
print app.g_pwd + os.sep + '/image/help.pdf'
QMessageBox.critical(None, "Failure", "Cannot open help manual")
def on_about(self):
abt = AboutDlg()
abt.exec_()
def on_new(self):
'''新建向导'''
app.g_configurations = Configuration() # 用来渲染的配置数据
dlg = wizard.MyWizard()
if dlg.exec_():
app.g_configurations.initialized = True
app.g_projects.append(app.g_configurations)
content = app.g_configurations.toJson()
self.path = QFileDialog.getSaveFileName(
self, "选择模板保存的路径",
app.g_pwd + os.sep + "configurations" + os.sep +
app.g_configurations.project_name.encode('utf-8') + ".json",
"Config (*.json)")
fileInfo = QFileInfo(self.path)
if not self.path.isEmpty():
path = app.QString2str(self.path)
with open(path, 'w+') as f:
f.write(content)
self.addConfig(fileInfo.baseName(), fileInfo.filePath(),
content)
#self.lw.addItem(app.g_configurations.project_name)
def getProjectLocation(self):
'''获取项目路径'''
path = QFileDialog.getExistingDirectory()
path = QDir.fromNativeSeparators(path)
self.et_project_location.setText(path)
def on_open(self):
'''打开现有配置'''
fileName = QFileDialog.getOpenFileName(
self, "选择现有模板", app.g_pwd + os.sep + "configurations",
"Config (*.json)")
if fileName.isEmpty():
return
self.path = fileName
with open(app.QString2str(fileName), 'r') as f:
content = f.read()
fileInfo = QFileInfo(fileName)
if not fileInfo.exists():
return
config = Configuration()
config.fromJson(content)
config.allone_dir = os.getenv('ALLONEDIR', '../..').replace('\\', '/')
self.addConfig(fileInfo.baseName(), fileInfo.filePath(), content)
self.on_select()
def on_del(self):
self.tw_config.clear()
self.bGroup.setEnabled(False)
self.tGroup.setEnabled(False)
index = self.lw.currentRow()
self.lw.takeItem(index)
def on_select(self):
'''选取配置'''
item = self.lw.currentItem()
if item != None:
content = item.data(QtCore.Qt.UserRole).toString()
config = Configuration()
config.fromJson(app.QString2str(content))
self.currentConfig = config
self.showConfigInfo(self.currentConfig)
self.bGroup.setEnabled(True)
self.path = item.data(QtCore.Qt.UserRole + 1).toString()
# index = self.lw.currentRow()
# if index < len(app.g_projects):
# self.currentConfig = app.g_projects[index]
# self.showConfigInfo(self.currentConfig)
# self.bGroup.setEnabled(True)
def addConfig(self, fileName, filePath, config):
item = QListWidgetItem(fileName)
item.setData(QtCore.Qt.UserRole, config)
item.setData(QtCore.Qt.UserRole + 1, filePath)
self.lw.addItem(item)
self.lw.setCurrentRow(0)
def showConfigInfo(self, cf):
'''显示配置信息'''
self.tw_config.clear()
self.et_project_name.setText(cf.project_name)
self.et_project_location.setText(cf.project_location)
sr = QStringList()
sr.append('信息')
root1 = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('Qt库')
root2 = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('模块')
root3a = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('第三方库')
root3b = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('接口')
root4 = QTreeWidgetItem(sr)
self.tw_config.addTopLevelItem(root1)
self.tw_config.addTopLevelItem(root2)
self.tw_config.addTopLevelItem(root3a)
self.tw_config.addTopLevelItem(root3b)
self.tw_config.addTopLevelItem(root4)
sr1c00 = QStringList()
sr1c00.append("项目名称")
sr1c00.append(cf.project_name)
r1c00 = QTreeWidgetItem(sr1c00)
root1.addChild(r1c00)
# sr1c0 = QStringList()
# sr1c0.append("项目位置")
# sr1c0.append(cf.project_location)
# r1c0 = QTreeWidgetItem(sr1c0)
# root1.addChild(r1c0)
sr1c1 = QStringList()
sr1c1.append("组件类型")
sr1c1.append(cf.component_type)
r1c1 = QTreeWidgetItem(sr1c1)
root1.addChild(r1c1)
sr1c2 = QStringList()
sr1c2.append("源模板")
sr1c2.append(cf.template_source)
r1c2 = QTreeWidgetItem(sr1c2)
root1.addChild(r1c2)
sr1c3 = QStringList()
sr1c3.append("平台类型")
tmp_pt = ""
if cf.platform_type & configuration.PT_WIN32:
tmp_pt += "win32;"
if cf.platform_type & configuration.PT_LINUX:
tmp_pt += "linux"
sr1c3.append(tmp_pt)
r1c3 = QTreeWidgetItem(sr1c3)
root1.addChild(r1c3)
sr1c4 = QStringList()
sr1c4.append("平台级别")
sr1c4.append(cf.platform_version)
r1c4 = QTreeWidgetItem(sr1c4)
root1.addChild(r1c4)
sr1c5 = QStringList()
sr1c5.append("资源文件")
if cf.resourcesFile == "True":
sr1c5.append("添加")
else:
sr1c5.append("未添加")
r1c5 = QTreeWidgetItem(sr1c5)
root1.addChild(r1c5)
sr1c6 = QStringList()
sr1c6.append("翻译文件")
if cf.translateFile == "True":
sr1c6.append("添加")
else:
sr1c6.append("未添加")
r1c6 = QTreeWidgetItem(sr1c6)
root1.addChild(r1c6)
for qt in cf.qt_libs:
sr2 = QStringList()
sr2.append(qt['name'])
sr2.append(qt['qt'])
r2 = QTreeWidgetItem(sr2)
root2.addChild(r2)
for module in cf.modules:
sr3a = QStringList()
sr3a.append(module['name'])
sr3a.append(module['description'])
r3a = QTreeWidgetItem(sr3a)
root3a.addChild(r3a)
# sr3b = QStringList()
# sr3b.append('ALLONE_DIR')
# sr3b.append(os.getenv('ALLONEDIR','../..')) # 第二个参数是默认值
# r3b = QTreeWidgetItem(sr3b)
# root3b.addChild(r3b)
for info in cf.thirdpart_lib:
sr3b = QStringList()
sr3b.append(info['libname'])
sr3b.append(info['libpath'])
r3b = QTreeWidgetItem(sr3b)
root3b.addChild(r3b)
for key in cf.interfaces.keys():
sr4 = QStringList()
sr4.append(key)
if cf.interfaces[key]:
sr4.append('实现')
else:
sr4.append('未实现')
r4 = QTreeWidgetItem(sr4)
root4.addChild(r4)
self.tw_config.expandAll()
self.tw_config.header().resizeSection(0, 300)
self.tGroup.setEnabled(True)
def on_modify(self):
'''修改配置'''
if self.currentConfig:
app.g_configurations = copy.copy(self.currentConfig)
dlg = wizard.MyWizard()
if dlg.exec_():
item = self.lw.currentItem()
if item != None:
content = app.g_configurations.toJson()
item.setData(QtCore.Qt.UserRole, content)
path = item.data(QtCore.Qt.UserRole + 1).toString()
if not path.isEmpty():
path = app.QString2str(path)
with open(path, 'w+') as f:
f.write(content)
self.on_select()
def on_gen(self):
'''生成工程'''
if not self.currentConfig:
return
#获取工程名及有效路径
project_name = self.et_project_name.text()
project_location = self.et_project_location.text()
qdir = QDir(project_location)
if not qdir.exists():
if not qdir.mkpath(project_location):
QMessageBox.warning(self, '警告', '路径无效！')
return
project_location = qdir.absolutePath()
if not project_location.endsWith(
'/') and not project_location.endsWith('\\'):
project_location += os.sep
project_location.replace('\\', '/')
if project_name.isEmpty() or project_location.isEmpty():
QMessageBox.warning(self, '警告', '项目名称或路径不能为空！')
return
self.currentConfig.project_name = app.QString2str(project_name)
self.currentConfig.project_location = app.QString2str(project_location)
content = self.currentConfig.toJson()
fileInfo = QFileInfo(self.path)
if not self.path.isEmpty():
path = app.QString2str(self.path)
with open(path, 'w+') as f:
f.write(content)
item = self.lw.currentItem()
item.setData(QtCore.Qt.UserRole, content)
template_name = self.currentConfig.template_source
template_dir = app.g_pwd + os.sep + 'templates' + os.sep + template_name.encode(
'utf-8')
with open(template_dir + os.sep + 'config.json', 'r') as f:
self.currentConfig.config_content = f.read()
ret_json = app.render(self.currentConfig.config_content,
config=self.currentConfig)
self.currentConfig.config = json.loads(ret_json)
for file in self.currentConfig.config['files']:
sourcepath = template_dir + os.sep + file['source'].encode('utf-8')
targetdir = self.currentConfig.project_location + self.currentConfig.project_name
targetpath = targetdir + os.sep + file['target']
fi = QFileInfo(targetpath)
qdir = fi.absoluteDir()
if not qdir.exists():
qdir.mkpath(fi.absolutePath())
with open(sourcepath, 'r') as f:
content = f.read()
content = app.render(content, config=self.currentConfig) #渲染文件
with open(targetpath, 'w+') as f:
f.write(content.encode('utf-8'))
QMessageBox.information(self, '提示', '生成成功！')
class mainwindow(QtGui.QMainWindow):
'''主窗体'''
def __init__(self):
super(mainwindow,self).__init__()
self.setWindowTitle('组件设计工具')
self.showMaximized()
self.menuBar().show()
self.createMenus()
cwHLayout = QHBoxLayout()
lLayout = QVBoxLayout()
rLayout = QVBoxLayout()
self.lw = QListWidget()
self.lw.setSelectionMode(QAbstractItemView.SingleSelection )
lLayout.addWidget(self.lw)
self.lw.itemSelectionChanged.connect(self.on_select)
lGroup = QGroupBox('项目列表')
lGroup.setLayout(lLayout)
cwHLayout.addWidget(lGroup,2)
cwHLayout.addLayout(rLayout,8)
tLayout = QVBoxLayout()
bLayout = QVBoxLayout()
tGroup = QGroupBox('配置信息')
self.bGroup = QGroupBox('生成代码')
tGroup.setLayout(tLayout)
self.bGroup.setLayout(bLayout)
self.bGroup.setEnabled(False)
rLayout.addWidget(tGroup)
rLayout.addWidget(self.bGroup)
self.tw_config = QTreeWidget()
headerLabels = QStringList()
headerLabels.append('项目')
headerLabels.append('值')
self.tw_config.setHeaderLabels(headerLabels)
thLayout = QHBoxLayout()
thLayout.addStretch(0)
modify_btn = QPushButton('修改')
modify_btn.clicked.connect(self.on_modify)
del_btn = QPushButton('删除')
del_btn.clicked.connect(self.on_del)
thLayout.addWidget(modify_btn)
thLayout.addWidget(del_btn)
tLayout.addWidget(self.tw_config)
tLayout.addLayout(thLayout)
bhLayout = QHBoxLayout()
bhLayout.addStretch(0)
gen_btn = QPushButton('生成')
gen_btn.clicked.connect(self.on_gen)
bhLayout.addWidget(gen_btn)
row1 = QHBoxLayout()
lable1 = QLabel('工程名称：')
self.et_project_name = QLineEdit()
row1.addSpacing(10)
row1.addWidget(lable1)
row1.addWidget(self.et_project_name)
row1.addStretch(0)
row2 = QHBoxLayout()
lable2 = QLabel('工程位置：')
self.et_project_location = QLineEdit()
self.et_project_location.setReadOnly(True)
btn_location = QPushButton('...')
btn_location.setFixedWidth(50)
btn_location.clicked.connect(self.getProjectLocation)
row2.addSpacing(10)
row2.addWidget(lable2)
row2.addWidget(self.et_project_location)
row2.addWidget(btn_location)
row2.addStretch(0)
bLayout.addLayout(row1)
bLayout.addLayout(row2)
bLayout.addLayout(bhLayout)
cw = QWidget()
cw.setLayout(cwHLayout)
self.setCentralWidget(cw)
self._initByConfig()
self.setMinimumSize(400,200)
def _initByConfig(self):
'''初始化'''
pass
def createMenus(self):
'''创建菜单'''
menueBar = self.menuBar()
menuSys = menueBar.addMenu('系统')
actNew = menuSys.addAction('新建工程')
actOpen = menuSys.addAction('打开工程')
actNew.triggered.connect(self.on_new)
actOpen.triggered.connect(self.on_open)
menueBar.addMenu(menuSys)
def on_new(self):
'''新建向导'''
app.g_configurations = Configuration() # 用来渲染的配置数据
dlg = wizard.MyWizard()
if dlg.exec_():
app.g_configurations.initialized = True
app.g_projects.append(app.g_configurations)
content = app.g_configurations.toJson()
path = QFileDialog.getSaveFileName(self,"选择模板保存的路径",
app.g_pwd + os.sep + "configurations" + os.sep + app.g_configurations.project_name + ".json"
,"Config (*.json)")
if not path.isEmpty():
path = app.QString2str(path)
with open(path,'w+') as f:
f.write(content)
self.lw.addItem(app.g_configurations.project_name)
def getProjectLocation(self):
'''获取项目路径'''
path = QFileDialog.getExistingDirectory()
path = QDir.fromNativeSeparators(path)
self.et_project_location.setText(path)
def on_open(self):
'''打开现有配置'''
fileName = QFileDialog.getOpenFileName(self,"选择现有模板",app.g_pwd + os.sep + "configurations","Config (*.json)")
if fileName.isEmpty():
return
with open(app.QString2str(fileName), 'r') as f:
content = f.read()
config = Configuration()
config.fromJson(content)
app.g_projects.append(config)
self.lw.addItem(config.project_name)
def on_del(self):
index = self.lw.currentRow()
if index < app.g_projects:
self.bGroup.setEnabled(False)
self.lw.takeItem(index)
config = app.g_projects[index]
app.g_projects.remove(config)
self.tw_config.clear()
return
def on_select(self):
'''选取配置'''
index = self.lw.currentRow()
if index < app.g_projects:
self.bGroup.setEnabled(True)
self.currentConfig = app.g_projects[index]
self.showConfigInfo(self.currentConfig)
def showConfigInfo(self,cf):
'''显示配置信息'''
self.tw_config.clear()
self.et_project_name.setText(cf.project_name)
self.et_project_location.setText(cf.project_location)
sr = QStringList()
sr.append('信息')
root1 = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('Qt库')
root2 = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('模块')
root3 = QTreeWidgetItem(sr)
sr = QStringList()
sr.append('接口')
root4 = QTreeWidgetItem(sr)
self.tw_config.addTopLevelItem(root1)
self.tw_config.addTopLevelItem(root2)
self.tw_config.addTopLevelItem(root3)
self.tw_config.addTopLevelItem(root4)
sr1c00 = QStringList()
sr1c00.append("项目名称")
sr1c00.append(cf.project_name)
r1c00 = QTreeWidgetItem(sr1c00)
root1.addChild(r1c00)
# sr1c0 = QStringList()
# sr1c0.append("项目位置")
# sr1c0.append(cf.project_location)
# r1c0 = QTreeWidgetItem(sr1c0)
# root1.addChild(r1c0)
sr1c1 = QStringList()
sr1c1.append("组件类型")
sr1c1.append(cf.component_type)
r1c1 = QTreeWidgetItem(sr1c1)
root1.addChild(r1c1)
sr1c2 = QStringList()
sr1c2.append("源模板")
sr1c2.append(cf.template_source)
r1c2 = QTreeWidgetItem(sr1c2)
root1.addChild(r1c2)
sr1c3 = QStringList()
sr1c3.append("平台类型")
tmp_pt = ""
if cf.platform_type & configuration.PT_WIN32:
tmp_pt += "win32;"
if cf.platform_type & configuration.PT_LINUX:
tmp_pt += "linux"
sr1c3.append(tmp_pt)
r1c3 = QTreeWidgetItem(sr1c3)
root1.addChild(r1c3)
sr1c4 = QStringList()
sr1c4.append("平台级别")
sr1c4.append(cf.platform_version)
r1c4 = QTreeWidgetItem(sr1c4)
root1.addChild(r1c4)
for qt in cf.qt_libs:
sr2 = QStringList()
sr2.append(qt['name'])
sr2.append(qt['qt'])
r2 = QTreeWidgetItem(sr2)
root2.addChild(r2)
for module in cf.modules:
sr3 = QStringList()
sr3.append(module['name'])
sr3.append(module['description'])
r3 = QTreeWidgetItem(sr3)
root3.addChild(r3)
for key in cf.interfaces.keys():
sr4 = QStringList()
sr4.append(key)
if cf.interfaces[key]:
sr4.append('实现')
else:
sr4.append('未实现')
r4 = QTreeWidgetItem(sr4)
root4.addChild(r4)
self.tw_config.expandAll()
self.tw_config.header().resizeSection(0,300)
def on_modify(self):
'''修改配置'''
if self.currentConfig:
app.g_configurations = copy.copy(self.currentConfig)
dlg = wizard.MyWizard()
if dlg.exec_():
index = self.lw.currentRow()
if index < app.g_projects:
self.currentConfig = app.g_configurations
app.g_projects[index] = self.currentConfig
self.showConfigInfo(self.currentConfig)
def on_gen(self):
'''生成工程'''
if not self.currentConfig:
return
#获取工程名及有效路径
project_name = self.et_project_name.text()
project_location = self.et_project_location.text()
qdir = QDir(project_location)
if not qdir.exists():
if not qdir.mkpath(project_location):
QMessageBox.warning(self, '警告', '路径无效！')
return
project_location = qdir.absolutePath()
if not project_location.endsWith('/') and not project_location.endsWith('\\'):
project_location += os.sep
if project_name.isEmpty() or project_location.isEmpty():
QMessageBox.warning(self, '警告', '项目名称或路径不能为空！')
return
self.currentConfig.project_name = app.QString2str(project_name)
self.currentConfig.project_location = app.QString2str(project_location)
template_name = self.currentConfig.template_source
template_dir = app.g_pwd + os.sep + 'templates' + os.sep + template_name
with open(template_dir + os.sep + 'config.json', 'r') as f:
self.currentConfig.config_content = f.read()
ret_json = app.render(self.currentConfig.config_content, config=self.currentConfig)
self.currentConfig.config = json.loads(ret_json)
for file in self.currentConfig.config['files']:
sourcepath = template_dir + os.sep + file['source']
targetdir = self.currentConfig.project_location + self.currentConfig.project_name
targetpath = targetdir + os.sep + file['target']
fi = QFileInfo(targetpath)
qdir = fi.absoluteDir()
if not qdir.exists():
qdir.mkpath(fi.absolutePath())
with open(sourcepath, 'r') as f:
content = f.read()
content = app.render(content, config=self.currentConfig) #渲染文件
with open(targetpath, 'w+') as f:
f.write(content.encode('utf-8'))
QMessageBox.information(self,'提示','生成成功！')
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 GmApp(QMainWindow):
def __init__(self):
super(QMainWindow, self).__init__()
self.setWindowTitle("GuloMail by GulonSoft")
self.setWindowIcon(QIcon("g-square.png"))
self.createActions()
self.createStatusBar()
self.createMenus()
self.createToolbars()
self.createWidgets()
self.createLayouts()
def createActions(self):
self.newAction=QAction("&New", self, shortcut=QKeySequence.New, statusTip="New")
self.sendReceiveAction=QAction("Send / &Receive", self, shortcut="F9", statusTip="Send / Receive")
self.printAction=QAction("&Print...", self, shortcut="Ctrl+P", statusTip="Print")
self.quitAction=QAction("&Quit", self, shortcut="Ctrl+Q", statusTip="Quit", triggered=self.close)
self.copyAction=QAction("&Copy", self, statusTip="Copy", shortcut=QKeySequence.Copy)
self.deleteAction=QAction("&Delete", self, statusTip="Delete Message")
self.nextAction=QAction("Next &Unread Message", self, shortcut="Ctrl+]", statusTip="Next unread message")
self.previousAction=QAction("P&revious Unread Message", self, shortcut="Ctrl+[", statusTip="Previous unread message")
self.replyAction=QAction("&Reply", self, shortcut="Ctrl+R", statusTip="Reply to sender", triggered=self.reply)
self.replyToAllAction=QAction("Reply to &All", self, shortcut="Ctrl+Shift+R", statusTip="Reply to all", triggered=self.replyToAll)
self.forwardAction=QAction("&Forward", self, shortcut="Ctrl+F", statusTip="Forward")
self.junkAction=QAction("Junk", self, shortcut="Ctrl+J", statusTip="Mark as Junk")
self.notJunkAction=QAction("Not junk", self, shortcut="Shift+Ctrl+J", statusTip="Mark as Not Junk")
self.contentsAction=QAction("&Contents", self, statusTip="Help Contents", shortcut="F1", triggered=self.helpContents)
self.aboutAction=QAction("&About", self, statusTip="About GuloMail", triggered=self.about)
self.cancelAction=QAction("&Cancel", self, statusTip="Cancel")
def createStatusBar(self):
self.statusBar()
def createMenus(self):
self.fileMenu=self.menuBar().addMenu("&File")
self.fileMenu.addAction(self.newAction)
self.fileMenu.addAction(self.sendReceiveAction)
self.fileMenu.addAction(self.printAction)
self.fileMenu.addAction(self.quitAction)
self.editMenu=self.menuBar().addMenu("&Edit")
self.editMenu.addAction(self.copyAction)
self.editMenu.addAction(self.deleteAction)
self.viewMenu=self.menuBar().addMenu("&View")
self.folderMenu=self.menuBar().addMenu("F&older")
self.messageMenu=self.menuBar().addMenu("&Message")
self.goToMenu=self.messageMenu.addMenu("&Go To")
self.goToMenu.addAction(self.nextAction)
self.goToMenu.addAction(self.previousAction)
self.messageMenu.addAction(self.replyAction)
self.messageMenu.addAction(self.replyToAllAction)
self.messageMenu.addAction(self.forwardAction)
self.markAsMenu=self.messageMenu.addMenu("Mar&k as...")
self.markAsMenu.addAction(self.junkAction)
self.markAsMenu.addAction(self.notJunkAction)
self.searchMenu=self.menuBar().addMenu("&Search")
self.helpMenu=self.menuBar().addMenu("&Help")
self.helpMenu.addAction(self.contentsAction)
self.helpMenu.addAction(self.aboutAction)
def createToolbars(self):
self.toolbar=self.addToolBar('Main Toolbar')
self.toolbar.setMovable(False)
self.toolbar.addAction(self.newAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.sendReceiveAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.replyAction)
self.toolbar.addAction(self.replyToAllAction)
self.toolbar.addAction(self.forwardAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.printAction)
self.toolbar.addAction(self.deleteAction)
self.toolbar.addAction(self.junkAction)
self.toolbar.addAction(self.notJunkAction)
self.toolbar.addAction(self.cancelAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.previousAction)
self.toolbar.addAction(self.nextAction)
def createWidgets(self):
## Message Table
self.table=QTableView()
self.table.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table.setGridStyle(Qt.NoPen)
self.model = QStandardItemModel(8, 3, self)
self.model.setHeaderData(0, Qt.Horizontal, "From")
self.model.setHeaderData(1, Qt.Horizontal, "Subject")
self.model.setHeaderData(2, Qt.Horizontal, "Received")
self.table.setModel(self.model)
self.selectionModel = QItemSelectionModel(self.model)
self.selectionModel.SelectionFlag=0x0020
self.table.setSelectionModel(self.selectionModel)
self.table.horizontalHeader().setStretchLastSection(True)
self.table.verticalHeader().setVisible(False)
self.table.setSortingEnabled(True)
self.table.setAlternatingRowColors(True)
## Folder Tree View
self.folderTree=QTreeWidget()
self.folderTree.setColumnCount(1)
self.folderTree.setHeaderLabel(QString('Folders'))
self.treeItem=QTreeWidgetItem()
self.treeItem.setText(0, 'Folders')
self.inbox=QTreeWidgetItem()
self.inbox.setText(0, 'Inbox')
self.deletedItems=QTreeWidgetItem()
self.deletedItems.setText(0, 'Deleted Items')
self.drafts=QTreeWidgetItem()
self.drafts.setText(0, 'Drafts')
self.junk=QTreeWidgetItem()
self.junk.setText(0, 'Junk')
self.outbox=QTreeWidgetItem()
self.outbox.setText(0, 'Outbox')
self.sent=QTreeWidgetItem()
self.sent.setText(0, 'Sent')
self.treeItem.addChild(self.inbox)
self.treeItem.addChild(self.deletedItems)
self.treeItem.addChild(self.drafts)
self.treeItem.addChild(self.junk)
self.treeItem.addChild(self.outbox)
self.treeItem.addChild(self.sent)
self.folderTree.addTopLevelItem(self.treeItem)
self.folderTree.expandAll()
self.folderTree.setAnimated(True)
self.folderTree.setMaximumWidth(150)
## Temp. placeholders
self.textEdit=QTextEdit()
self.textEdit2=QTextEdit()
def createLayouts(self):
self.mainSplitter=QSplitter()
self.setCentralWidget(self.mainSplitter)
self.mainSplitter.addWidget(self.folderTree)
self.messageSplitter=QSplitter(Qt.Vertical)
self.messageSplitter.addWidget(self.table)
self.messageSplitter.addWidget(self.textEdit2)
self.mainSplitter.addWidget(self.messageSplitter)
def helpContents(self):
print "Help"
def reply(self):
print "Reply"
def replyToAll(self):
print "Reply To All"
def about(self):
text=QString("GuloMail v0.1\n\n")
text.append("GuloMail is a freeware email client written in Python using PyQt4 (Python bindings for Nokia's Qt)\n\n")
text.append(QChar(0x00A9))
text.append("GulonSoft 2010\nhttp://www.gulon.co.uk/")
QMessageBox.about(self, "About GuloMail", text)
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 Preferences(QDialog):
configuration = {}
weight = 0
def __init__(self, parent=None):
super(Preferences, self).__init__(parent, Qt.Dialog)
self.setWindowTitle(translations.TR_PREFERENCES_TITLE)
self.setMinimumSize(QSize(800, 600))
self.setMaximumSize(QSize(0, 0))
vbox = QVBoxLayout(self)
hbox = QHBoxLayout()
vbox.setContentsMargins(0, 0, 5, 5)
hbox.setContentsMargins(0, 0, 0, 0)
self.tree = QTreeWidget()
self.tree.header().setHidden(True)
self.tree.setSelectionMode(QTreeWidget.SingleSelection)
self.tree.setAnimated(True)
self.tree.header().setHorizontalScrollMode(
QAbstractItemView.ScrollPerPixel)
self.tree.header().setResizeMode(0, QHeaderView.ResizeToContents)
self.tree.header().setStretchLastSection(False)
self.tree.setFixedWidth(200)
self.stacked = QStackedLayout()
hbox.addWidget(self.tree)
hbox.addLayout(self.stacked)
vbox.addLayout(hbox)
hbox_footer = QHBoxLayout()
self._btnSave = QPushButton(translations.TR_SAVE)
self._btnCancel = QPushButton(translations.TR_CANCEL)
hbox_footer.addSpacerItem(QSpacerItem(1, 0, QSizePolicy.Expanding))
hbox_footer.addWidget(self._btnCancel)
hbox_footer.addWidget(self._btnSave)
vbox.addLayout(hbox_footer)
self.connect(self.tree, SIGNAL("itemSelectionChanged()"),
self._change_current)
self.connect(self._btnCancel, SIGNAL("clicked()"), self.close)
self.connect(self._btnSave, SIGNAL("clicked()"),
self._save_preferences)
self.load_ui()
self.tree.setCurrentItem(self.tree.topLevelItem(0))
def _save_preferences(self):
self.emit(SIGNAL("savePreferences()"))
self.close()
def load_ui(self):
sections = sorted(list(Preferences.configuration.keys()),
key=lambda item: Preferences.configuration[item]['weight'])
for section in sections:
text = Preferences.configuration[section]['text']
Widget = Preferences.configuration[section]['widget']
widget = Widget(self)
area = QScrollArea()
area.setWidgetResizable(True)
area.setWidget(widget)
index = self.stacked.addWidget(area)
item = QTreeWidgetItem([text])
item.setData(0, Qt.UserRole, index)
self.tree.addTopLevelItem(item)
#Sort Item Children
subcontent = Preferences.configuration[section].get(
'subsections', {})
subsections = sorted(list(subcontent.keys()),
key=lambda item: subcontent[item]['weight'])
for sub in subsections:
text = subcontent[sub]['text']
Widget = subcontent[sub]['widget']
widget = Widget(self)
area = QScrollArea()
area.setWidgetResizable(True)
area.setWidget(widget)
index = self.stacked.addWidget(area)
subitem = QTreeWidgetItem([text])
subitem.setData(0, Qt.UserRole, index)
item.addChild(subitem)
self.tree.expandAll()
def _change_current(self):
item = self.tree.currentItem()
index = item.data(0, Qt.UserRole)
self.stacked.setCurrentIndex(index)
@classmethod
def register_configuration(cls, section, widget, text, weight=None,
subsection=None):
if weight is None:
Preferences.weight += 1
weight = Preferences.weight
if not subsection:
Preferences.configuration[section] = {'widget': widget,
'weight': weight, 'text': text}
else:
config = Preferences.configuration.get(section, {})
if not config:
config[section] = {'widget': None, 'weight': 100}
subconfig = config.get('subsections', {})
subconfig[subsection] = {'widget': widget, 'weight': weight,
'text': text}
config['subsections'] = subconfig
Preferences.configuration[section] = config
def __init__(self, term, row, parent=None):
super(EditReportDialog, self).__init__(parent)
self.term = term
self.sid = term
self.row = row
terms = self.pullOnes('terms', self.term)
datas = self.pullOnes('datas', self.row)
session = self.pullOnes('session', terms['sessionID'])
self.termname = str(
session['name']) + ' ' + terms['name'] + ' Term Report'
self.pagetitle = self.termname
ko = 0
#prepare data
d = datas['description']
d = d.split(':::')
_title = d[0]
_theme = d[1]
_font = d[2]
_ass = d[3]
_gra = d[4]
_set = d[5]
_ass_list = _ass.split('::')
_gra_list = _gra.split('::')
_set_list = _set.split('::')
_cla_list = _set.split('::')
layout1 = QGridLayout()
Form1 = QFormLayout()
Form2 = QFormLayout()
#title
self.title = QLabel("Report Title")
self.titleData = QLineEdit()
self.titleData.setObjectName("name")
self.titleData.setText(_title)
tree = QTreeWidget()
tree.setItemDelegate(Delegate())
tree.setHeaderLabel("Which grading system will you be using?")
tree1 = QTreeWidget()
tree1.setHeaderLabel("Choose Assessments and classes")
tree2 = QTreeWidget()
tree2.setHeaderLabel("Report Card Settings")
self.ass_arr = {}
parent = QTreeWidgetItem(tree1)
parent.setText(0, "Select Assessments")
parent.setFlags(parent.flags() | Qt.ItemIsTristate
| Qt.ItemIsUserCheckable)
arr = self.pullCas()
if arr and len(arr) > 0:
for val in arr:
dt = self.pullOne(val['name'])
child = QTreeWidgetItem(parent)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(dt['name']).upper())
self.ass_arr[val['id']] = child
if str(val['id']) in _ass_list:
child.setCheckState(0, Qt.Checked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.cla_arr = {}
parent1 = QTreeWidgetItem(tree1)
parent1.setText(0, "Select Class")
parent1.setFlags(parent1.flags() | Qt.ItemIsTristate
| Qt.ItemIsUserCheckable)
arr = self.pullClass()
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent1)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(val['name']).upper())
self.cla_arr[val['id']] = child
va = str(val['id'])
if (va in _cla_list):
child.setCheckState(0, Qt.Checked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.gra_arr = {}
parent2 = QTreeWidgetItem(tree)
parent2.setText(0, "Select Grade")
arr = self.pullGrade()
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent2)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(val['name']).upper())
self.gra_arr[val['id']] = child
if str(val['id']) in _gra_list:
child.setCheckState(0, Qt.Checked)
else:
child.setCheckState(0, Qt.Unchecked)
ko += 1
self.set_arr = {}
parent3 = QTreeWidgetItem(tree2)
parent3.setText(0, "Include ...")
parent3.setFlags(parent3.flags() | Qt.ItemIsTristate
| Qt.ItemIsUserCheckable)
arr = {
1: 'School Number',
2: 'Class Position',
3: 'Class Unit Position',
4: 'Total (100%)',
5: 'Total',
6: 'Grading',
7: 'Subject Average',
8: 'Ranking',
9: 'Ranking and Student Population',
10: 'Student Passport',
11: 'School Logo',
12: 'School Address',
13: 'Students Address',
14: 'Attendance',
15: 'Fees Owed',
16: 'Test/Assesments'
}
if arr and len(arr) > 0:
for val in arr:
child = QTreeWidgetItem(parent3)
child.setFlags(child.flags() | Qt.ItemIsUserCheckable)
child.setText(0, str(arr[val]).upper())
self.set_arr[val] = child
if str(val) in _set_list:
child.setCheckState(0, Qt.Checked)
else:
child.setCheckState(0, Qt.Unchecked)
child1 = QTreeWidgetItem(parent3)
child1.setFlags(child1.flags() | Qt.ItemIsUserCheckable)
child1.setText(0, 'AFFECTIVE DOMAIN REPORT')
self.set_arr['aff'] = child1
if 'aff' in _set_list:
child1.setCheckState(0, Qt.Checked)
else:
child1.setCheckState(0, Qt.Unchecked)
child2 = QTreeWidgetItem(child1)
child2.setFlags(child2.flags() | Qt.ItemIsTristate
| Qt.ItemIsUserCheckable)
child2.setText(0, 'TABLE')
self.set_arr['afftable'] = child2
if 'afftable' in _set_list:
child2.setCheckState(0, Qt.Checked)
else:
child2.setCheckState(0, Qt.Unchecked)
child3 = QTreeWidgetItem(child1)
child3.setFlags(child3.flags() | Qt.ItemIsUserCheckable)
child3.setText(0, 'GRAPH')
self.set_arr['affgraph'] = child3
if 'affgraph' in _set_list:
child3.setCheckState(0, Qt.Checked)
else:
child3.setCheckState(0, Qt.Unchecked)
child4 = QTreeWidgetItem(parent3)
child4.setFlags(child4.flags() | Qt.ItemIsTristate
| Qt.ItemIsUserCheckable)
child4.setText(0, 'PYSCHOMOTOR DOMAIN REPORT')
self.set_arr['psy'] = child4
if 'psy' in _set_list:
child4.setCheckState(0, Qt.Checked)
else:
child4.setCheckState(0, Qt.Unchecked)
child5 = QTreeWidgetItem(child4)
child5.setFlags(child5.flags() | Qt.ItemIsUserCheckable)
child5.setText(0, 'TABLE')
self.set_arr['psytable'] = child5
if 'psytable' in _set_list:
child5.setCheckState(0, Qt.Checked)
else:
child5.setCheckState(0, Qt.Unchecked)
child6 = QTreeWidgetItem(child4)
child6.setFlags(child6.flags() | Qt.ItemIsUserCheckable)
child6.setText(0, 'GRAPH')
self.set_arr['psygraph'] = child6
if 'psygraph' in _set_list:
child6.setCheckState(0, Qt.Checked)
else:
child6.setCheckState(0, Qt.Unchecked)
tree.expandAll()
tree1.expandAll()
tree2.expandAll()
#tree.show()
self.l5 = QLabel("Theme Color")
self.pbc = QPushButton()
self.pbc.setObjectName("Pickcolor")
self.pbc.setText("Click to change")
self.le5 = QLineEdit()
self.le5.setObjectName("Showcolor")
self.le5.setText(_theme)
self.pbc.setStyleSheet("background-color: " + _theme +
"; color: white")
self.connect(self.pbc, SIGNAL("clicked()"),
lambda: self.color_picker())
self.l6 = QLabel("Pick Theme Font")
self.pbf = QPushButton()
self.pbf.setObjectName("Pickfont")
self.pbf.setText(_font)
self.le6 = QLineEdit()
self.le6.setObjectName("Showcolor")
self.le6.setText("#000000")
self.pbf.setStyleSheet("color: black")
self.connect(self.pbf, SIGNAL("clicked()"), lambda: self.font_picker())
self.lv_box = QHBoxLayout()
self.lv_box.addWidget(self.pbc)
self.lv_box.addWidget(self.le5)
self.lv_box1 = QHBoxLayout()
self.lv_box1.addWidget(self.pbf)
self.lv_box1.addWidget(self.le6)
Form1.addRow(self.title, self.titleData)
Form2.addRow(self.l5, self.lv_box)
Form2.addRow(self.l6, self.lv_box1)
Gbo = QGridLayout()
Gbo.addLayout(Form1, 0, 0, 1, 2)
Gbo.addWidget(tree, 1, 0)
Gbo.addWidget(tree1, 1, 1)
Gbo.addWidget(tree2, 2, 0)
Gbo.addLayout(Form2, 2, 1)
groupBox1 = QGroupBox('Academic Report Setup')
groupBox1.setLayout(Gbo)
self.pb = QPushButton()
self.pb.setObjectName("Add")
self.pb.setText("Add Assessment")
self.pb1 = QPushButton()
self.pb1.setObjectName("Cancel")
self.pb1.setText("Cancel")
hbo = QHBoxLayout()
hbo.addWidget(self.pb1)
hbo.addStretch()
hbo.addWidget(self.pb)
groupBox2 = QGroupBox('')
groupBox2.setLayout(hbo)
grid = QGridLayout()
grid.addWidget(groupBox1, 0, 0)
grid.addWidget(groupBox2, 1, 0)
self.setLayout(grid)
self.connect(self.pb, SIGNAL("clicked()"),
lambda: self.button_click(self))
self.connect(self.pb1, SIGNAL("clicked()"),
lambda: self.button_close(self))
self.setWindowTitle(self.pagetitle)
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 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()
def expandAll(self):
self._treeDepth=10000
QTreeWidget.expandAll(self)
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 GmApp(QMainWindow):
def __init__(self):
super(QMainWindow, self).__init__()
self.setWindowTitle("GuloMail by GulonSoft")
self.setWindowIcon(QIcon("g-square.png"))
self.createActions()
self.createStatusBar()
self.createMenus()
self.createToolbars()
self.createWidgets()
self.createLayouts()
def createActions(self):
self.newAction = QAction("&New",
self,
shortcut=QKeySequence.New,
statusTip="New")
self.sendReceiveAction = QAction("Send / &Receive",
self,
shortcut="F9",
statusTip="Send / Receive")
self.printAction = QAction("&Print...",
self,
shortcut="Ctrl+P",
statusTip="Print")
self.quitAction = QAction("&Quit",
self,
shortcut="Ctrl+Q",
statusTip="Quit",
triggered=self.close)
self.copyAction = QAction("&Copy",
self,
statusTip="Copy",
shortcut=QKeySequence.Copy)
self.deleteAction = QAction("&Delete",
self,
statusTip="Delete Message")
self.nextAction = QAction("Next &Unread Message",
self,
shortcut="Ctrl+]",
statusTip="Next unread message")
self.previousAction = QAction("P&revious Unread Message",
self,
shortcut="Ctrl+[",
statusTip="Previous unread message")
self.replyAction = QAction("&Reply",
self,
shortcut="Ctrl+R",
statusTip="Reply to sender",
triggered=self.reply)
self.replyToAllAction = QAction("Reply to &All",
self,
shortcut="Ctrl+Shift+R",
statusTip="Reply to all",
triggered=self.replyToAll)
self.forwardAction = QAction("&Forward",
self,
shortcut="Ctrl+F",
statusTip="Forward")
self.junkAction = QAction("Junk",
self,
shortcut="Ctrl+J",
statusTip="Mark as Junk")
self.notJunkAction = QAction("Not junk",
self,
shortcut="Shift+Ctrl+J",
statusTip="Mark as Not Junk")
self.contentsAction = QAction("&Contents",
self,
statusTip="Help Contents",
shortcut="F1",
triggered=self.helpContents)
self.aboutAction = QAction("&About",
self,
statusTip="About GuloMail",
triggered=self.about)
self.cancelAction = QAction("&Cancel", self, statusTip="Cancel")
def createStatusBar(self):
self.statusBar()
def createMenus(self):
self.fileMenu = self.menuBar().addMenu("&File")
self.fileMenu.addAction(self.newAction)
self.fileMenu.addAction(self.sendReceiveAction)
self.fileMenu.addAction(self.printAction)
self.fileMenu.addAction(self.quitAction)
self.editMenu = self.menuBar().addMenu("&Edit")
self.editMenu.addAction(self.copyAction)
self.editMenu.addAction(self.deleteAction)
self.viewMenu = self.menuBar().addMenu("&View")
self.folderMenu = self.menuBar().addMenu("F&older")
self.messageMenu = self.menuBar().addMenu("&Message")
self.goToMenu = self.messageMenu.addMenu("&Go To")
self.goToMenu.addAction(self.nextAction)
self.goToMenu.addAction(self.previousAction)
self.messageMenu.addAction(self.replyAction)
self.messageMenu.addAction(self.replyToAllAction)
self.messageMenu.addAction(self.forwardAction)
self.markAsMenu = self.messageMenu.addMenu("Mar&k as...")
self.markAsMenu.addAction(self.junkAction)
self.markAsMenu.addAction(self.notJunkAction)
self.searchMenu = self.menuBar().addMenu("&Search")
self.helpMenu = self.menuBar().addMenu("&Help")
self.helpMenu.addAction(self.contentsAction)
self.helpMenu.addAction(self.aboutAction)
def createToolbars(self):
self.toolbar = self.addToolBar('Main Toolbar')
self.toolbar.setMovable(False)
self.toolbar.addAction(self.newAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.sendReceiveAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.replyAction)
self.toolbar.addAction(self.replyToAllAction)
self.toolbar.addAction(self.forwardAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.printAction)
self.toolbar.addAction(self.deleteAction)
self.toolbar.addAction(self.junkAction)
self.toolbar.addAction(self.notJunkAction)
self.toolbar.addAction(self.cancelAction)
self.toolbar.addSeparator()
self.toolbar.addAction(self.previousAction)
self.toolbar.addAction(self.nextAction)
def createWidgets(self):
## Message Table
self.table = QTableView()
self.table.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table.setGridStyle(Qt.NoPen)
self.model = QStandardItemModel(8, 3, self)
self.model.setHeaderData(0, Qt.Horizontal, "From")
self.model.setHeaderData(1, Qt.Horizontal, "Subject")
self.model.setHeaderData(2, Qt.Horizontal, "Received")
self.table.setModel(self.model)
self.selectionModel = QItemSelectionModel(self.model)
self.selectionModel.SelectionFlag = 0x0020
self.table.setSelectionModel(self.selectionModel)
self.table.horizontalHeader().setStretchLastSection(True)
self.table.verticalHeader().setVisible(False)
self.table.setSortingEnabled(True)
self.table.setAlternatingRowColors(True)
## Folder Tree View
self.folderTree = QTreeWidget()
self.folderTree.setColumnCount(1)
self.folderTree.setHeaderLabel(QString('Folders'))
self.treeItem = QTreeWidgetItem()
self.treeItem.setText(0, 'Folders')
self.inbox = QTreeWidgetItem()
self.inbox.setText(0, 'Inbox')
self.deletedItems = QTreeWidgetItem()
self.deletedItems.setText(0, 'Deleted Items')
self.drafts = QTreeWidgetItem()
self.drafts.setText(0, 'Drafts')
self.junk = QTreeWidgetItem()
self.junk.setText(0, 'Junk')
self.outbox = QTreeWidgetItem()
self.outbox.setText(0, 'Outbox')
self.sent = QTreeWidgetItem()
self.sent.setText(0, 'Sent')
self.treeItem.addChild(self.inbox)
self.treeItem.addChild(self.deletedItems)
self.treeItem.addChild(self.drafts)
self.treeItem.addChild(self.junk)
self.treeItem.addChild(self.outbox)
self.treeItem.addChild(self.sent)
self.folderTree.addTopLevelItem(self.treeItem)
self.folderTree.expandAll()
self.folderTree.setAnimated(True)
self.folderTree.setMaximumWidth(150)
## Temp. placeholders
self.textEdit = QTextEdit()
self.textEdit2 = QTextEdit()
def createLayouts(self):
self.mainSplitter = QSplitter()
self.setCentralWidget(self.mainSplitter)
self.mainSplitter.addWidget(self.folderTree)
self.messageSplitter = QSplitter(Qt.Vertical)
self.messageSplitter.addWidget(self.table)
self.messageSplitter.addWidget(self.textEdit2)
self.mainSplitter.addWidget(self.messageSplitter)
def helpContents(self):
print "Help"
def reply(self):
print "Reply"
def replyToAll(self):
print "Reply To All"
def about(self):
text = QString("GuloMail v0.1\n\n")
text.append(
"GuloMail is a freeware email client written in Python using PyQt4 (Python bindings for Nokia's Qt)\n\n"
)
text.append(QChar(0x00A9))
text.append("GulonSoft 2010\nhttp://www.gulon.co.uk/")
QMessageBox.about(self, "About GuloMail", text)
