def test_task(self):
results = []
task = Task(function=QThread.currentThread)
task.resultReady.connect(results.append)
task.start()
self.app.processEvents()
self.assertSequenceEqual(results, [QThread.currentThread()])
thread = QThread()
thread.start()
try:
task = Task(function=QThread.currentThread)
task.moveToThread(thread)
self.assertIsNot(task.thread(), QThread.currentThread())
self.assertIs(task.thread(), thread)
results = Future()
def record(value):
# record the result value and the calling thread
results.set_result((QThread.currentThread(), value))
task.resultReady.connect(record, Qt.DirectConnection)
task.start()
f = task.future()
emit_thread, thread_ = results.result(3)
self.assertIs(f.result(3), thread)
self.assertIs(emit_thread, thread)
self.assertIs(thread_, thread)
finally:
thread.quit()
thread.wait()
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 = GDS(gds_id)
data = gds.get_data(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 updateInfoItems(self):
self.warning(0)
if self.data is None:
return
if self.useAttr:
genes = [attr.name for attr in self.data.domain.attributes]
elif self.attributes:
attr = self.attributes[self.gene_attr]
genes = [
str(ex[attr]) for ex in self.data if not math.isnan(ex[attr])
]
else:
genes = []
if not genes:
self.warning(0, "Could not extract genes from input dataset.")
self.warning(1)
org = self.organisms[min(self.organism_index, len(self.organisms) - 1)]
source_name, info_getter = ("NCBI Info", ncbi_info)
self.error(0)
self.progressBarInit()
self.setBlocking(True)
self.setEnabled(False)
self.infoLabel.setText("Retrieving info records.\n")
self.genes = genes
task = Task(function=partial(
info_getter, org, genes, advance=methodinvoke(self, "advance", (
))))
self.itemsfuture = self.executor.submit(task)
task.finished.connect(self._onItemsCompleted)
def RetrieveFilesList(self):
self.retryButton.hide()
self.warning(0)
self.progress.setRange(0, 3)
task = Task(function=partial(retrieveFilesList, methodinvoke(self.progress, "advance")))
task.resultReady.connect(self.SetFilesList)
task.exceptionReady.connect(self.HandleError)
self.executor.submit(task)
self.setEnabled(False)
def commit(self):
include_neighborhood = self.include_neighborhood
query_genes = self.query_genes()
source = SOURCES[self.network_source]
if source.score_filter:
min_score = self.min_score
assert source.name == "STRING"
min_score = min_score * 1000
else:
min_score = None
taxid = self.taxid
progress = methodinvoke(self, "advance")
if self.geneinfo is None:
self.geneinfo = self.executor.submit(fetch_ncbi_geneinfo, taxid,
progress)
geneinfo_f = self.geneinfo
taxmap = source.tax_mapping
db_taxid = taxmap.get(taxid, taxid)
if db_taxid is None:
raise ValueError("invalid taxid for this network")
def fetch_network():
geneinfo = geneinfo_f.result()
ppidb = fetch_ppidb(source, db_taxid, progress)
return get_gene_network(ppidb,
geneinfo,
db_taxid,
query_genes,
include_neighborhood=include_neighborhood,
min_score=min_score,
progress=methodinvoke(
self, "set_progress", (float, )))
self.nettask = Task(function=fetch_network)
self.nettask.finished.connect(self._on_result_ready)
self.executor.submit(self.nettask)
self.setBlocking(True)
self.setEnabled(False)
self.progressBarInit()
self._invalidated = False
self._update_info()
def test_executor(self):
executor = ThreadExecutor()
f = executor.submit(QThread.currentThread)
self.assertIsNot(f.result(3), QThread.currentThread())
f = executor.submit(lambda: 1 / 0)
with self.assertRaises(ZeroDivisionError):
f.result()
results = []
task = Task(function=QThread.currentThread)
task.resultReady.connect(results.append, Qt.DirectConnection)
f = executor.submit_task(task)
self.assertIsNot(f.result(3), QThread.currentThread())
executor.shutdown()
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
# For now only support one alt source, with a checkbox
# In the future this can be extended to multiple selections
self.altSourceCheck = gui.checkBox(self.organismBox,
self,
"useAltSource",
"Show information from dictyBase",
callback=self.onAltSourceChange)
self.altSourceCheck.hide()
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
cb = gui.checkBox(box,
self,
"useAttr",
"Use attribute names",
callback=self.updateInfoItems)
cb.toggled[bool].connect(self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
# A label for dictyExpress link (Why oh god why???)
self.dictyExpressBox = gui.widgetBox(self.controlArea, "Dicty Express")
self.linkLabel = gui.widgetLabel(self.dictyExpressBox, "")
self.linkLabel.setOpenExternalLinks(False)
self.linkLabel.linkActivated.connect(self.onDictyExpressLink)
self.dictyExpressBox.hide()
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea,
selectionMode=QTreeView.ExtendedSelection,
rootIsDecorated=False,
uniformRowHeights=True,
sortingEnabled=True)
self.treeWidget.setItemDelegate(
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())))
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)
def __init__(self, parent=None, signalManager=None,
name="Databases update"):
OWWidget.__init__(self, parent, signalManager, name,
wantMainArea=False)
self.searchString = ""
fbox = gui.widgetBox(self.controlArea, "Filter")
self.completer = TokenListCompleter(
self, caseSensitivity=Qt.CaseInsensitive)
self.lineEditFilter = QLineEdit(textChanged=self.SearchUpdate)
self.lineEditFilter.setCompleter(self.completer)
fbox.layout().addWidget(self.lineEditFilter)
box = gui.widgetBox(self.controlArea, "Files")
self.filesView = QTreeWidget(self)
self.filesView.setHeaderLabels(
["", "Data Source", "Update", "Last Updated", "Size"])
self.filesView.setRootIsDecorated(False)
self.filesView.setUniformRowHeights(True)
self.filesView.setSelectionMode(QAbstractItemView.NoSelection)
self.filesView.setSortingEnabled(True)
self.filesView.sortItems(1, Qt.AscendingOrder)
self.filesView.setItemDelegateForColumn(
0, UpdateOptionsItemDelegate(self.filesView))
self.filesView.model().layoutChanged.connect(self.SearchUpdate)
box.layout().addWidget(self.filesView)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
self.updateButton = gui.button(
box, self, "Update all",
callback=self.UpdateAll,
tooltip="Update all updatable files",
)
self.downloadButton = gui.button(
box, self, "Download all",
callback=self.DownloadFiltered,
tooltip="Download all filtered files shown"
)
self.cancelButton = gui.button(
box, self, "Cancel", callback=self.Cancel,
tooltip="Cancel scheduled downloads/updates."
)
self.retryButton = gui.button(
box, self, "Reconnect", callback=self.RetrieveFilesList
)
self.retryButton.hide()
gui.rubber(box)
self.warning(0)
box = gui.widgetBox(self.controlArea, orientation="horizontal")
gui.rubber(box)
self.infoLabel = QLabel()
self.infoLabel.setAlignment(Qt.AlignCenter)
self.controlArea.layout().addWidget(self.infoLabel)
self.infoLabel.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.updateItems = []
self.resize(800, 600)
self.progress = ProgressState(self, maximum=3)
self.progress.valueChanged.connect(self._updateProgress)
self.progress.rangeChanged.connect(self._updateProgress)
self.executor = ThreadExecutor(
threadPool=QThreadPool(maxThreadCount=2)
)
task = Task(self, function=self.RetrieveFilesList)
task.exceptionReady.connect(self.HandleError)
task.start()
self._tasks = []
self._haveProgress = False
def updateAnnotations(self):
if self.data is None:
return
assert not self.__state & OWSetEnrichment.Initializing
self._cancelPending()
self._clearView()
self.information(0)
self.warning(0)
self.error(0)
if not self.genesinrows and len(self.geneAttrs) == 0:
self.error(0, "Input data contains no columns with gene names")
return
self.__state = OWSetEnrichment.RunningEnrichment
taxid = self.taxid_list[self.speciesIndex]
self.taxid = taxid
categories = self.selectedCategories()
clusterGenes = self.genesFromTable(self.data)
if self.referenceData is not None and self.useReferenceData:
referenceGenes = self.genesFromTable(self.referenceData)
else:
referenceGenes = None
self.currentAnnotatedCategories = categories
genematcher = self._genematcher()
self.progressBarInit()
## Load collections in a worker thread
# TODO: Use cached collections if already loaded and
# use ensure_genesetsdownloaded with progress report (OWSelectGenes)
collections = self._executor.submit(geneset.collections, *categories)
def refset_null():
"""Return the default background reference set"""
col = collections.result()
return reduce(operator.ior, (set(g.genes) for g in col), set())
def refset_ncbi():
"""Return all NCBI gene names"""
geneinfo = gene.NCBIGeneInfo(taxid)
return set(geneinfo.keys())
def namematcher():
matcher = genematcher.result()
match = matcher.set_targets(ref_set.result())
match.umatch = memoize(match.umatch)
return match
def map_unames():
matcher = namematcher.result()
query = list(filter(None, map(matcher.umatch, querynames)))
reference = list(
filter(None, map(matcher.umatch, ref_set.result())))
return query, reference
if self._nogenematching():
if referenceGenes is None:
ref_set = self._executor.submit(refset_null)
else:
ref_set = fulfill(referenceGenes)
else:
if referenceGenes == None:
ref_set = self._executor.submit(refset_ncbi)
else:
ref_set = fulfill(referenceGenes)
namematcher = self._executor.submit(namematcher)
querynames = clusterGenes
state = types.SimpleNamespace()
state.query_set = clusterGenes
state.reference_set = referenceGenes
state.namematcher = namematcher
state.query_count = len(set(clusterGenes))
state.reference_count = (len(set(referenceGenes))
if referenceGenes is not None else None)
state.cancelled = False
progress = methodinvoke(self, "_setProgress", (float, ))
info = methodinvoke(self, "_setRunInfo", (str, ))
@withtraceback
def run():
info("Loading data")
match = namematcher.result()
query, reference = map_unames()
gscollections = collections.result()
results = []
info("Running enrichment")
p = 0
for i, gset in enumerate(gscollections):
genes = set(filter(None, map(match.umatch, gset.genes)))
enr = set_enrichment(genes, reference, query)
results.append((gset, enr))
if state.cancelled:
raise UserInteruptException
pnew = int(100 * i / len(gscollections))
if pnew != p:
progress(pnew)
p = pnew
progress(100)
info("")
return query, reference, results
task = Task(function=run)
task.resultReady.connect(self.__on_enrichment_finished)
task.exceptionReady.connect(self.__on_enrichment_failed)
result = self._executor.submit(task)
state.results = result
self.state = state
self._updatesummary()
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 = gui.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
def __init__(
self,
parent=None,
):
super().__init__(self, parent)
self.selectionChangedFlag = False
self.__initialized = False
self.initfuture = None
self.itemsfuture = None
self.map_input_to_ensembl = None
self.infoLabel = gui.widgetLabel(
gui.widgetBox(self.controlArea, "Info", addSpace=True),
"Initializing\n")
self.organisms = None
self.organismBox = gui.widgetBox(self.controlArea,
"Organism",
addSpace=True)
self.organismComboBox = gui.comboBox(
self.organismBox,
self,
"organism_index",
callback=self._onSelectedOrganismChanged)
box = gui.widgetBox(self.controlArea, "Gene names", addSpace=True)
self.geneAttrComboBox = gui.comboBox(box,
self,
"gene_attr",
"Gene attribute",
callback=self.updateInfoItems)
self.geneAttrComboBox.setEnabled(not self.useAttr)
self.geneAttrCheckbox = gui.checkBox(box,
self,
"useAttr",
"Use column names",
callback=self.updateInfoItems)
self.geneAttrCheckbox.toggled[bool].connect(
self.geneAttrComboBox.setDisabled)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
gui.rubber(self.controlArea)
gui.lineEdit(self.mainArea,
self,
"search_string",
"Filter",
callbackOnType=True,
callback=self.searchUpdate)
self.treeWidget = QTreeView(self.mainArea)
self.treeWidget.setAlternatingRowColors(True)
self.treeWidget.setSortingEnabled(True)
self.treeWidget.setSelectionMode(QTreeView.ExtendedSelection)
self.treeWidget.setUniformRowHeights(True)
self.treeWidget.setRootIsDecorated(False)
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['NCBI ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.setItemDelegateForColumn(
HEADER_SCHEMA['Ensembl ID'],
gui.LinkStyledItemDelegate(self.treeWidget))
self.treeWidget.viewport().setMouseTracking(True)
self.mainArea.layout().addWidget(self.treeWidget)
box = gui.widgetBox(self.mainArea, "", orientation="horizontal")
gui.button(box, self, "Select Filtered", callback=self.selectFiltered)
gui.button(box,
self,
"Clear Selection",
callback=self.treeWidget.clearSelection)
self.geneinfo = []
self.cells = []
self.row2geneinfo = {}
self.data = None
# : (# input genes, # matches genes)
self.matchedInfo = 0, 0
self.setBlocking(True)
self.executor = ThreadExecutor(self)
self.progressBarInit()
task = Task(
function=partial(taxonomy.ensure_downloaded,
callback=methodinvoke(self, "advance", ())))
task.resultReady.connect(self.initialize)
task.exceptionReady.connect(self._onInitializeError)
self.initfuture = self.executor.submit(task)