def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GSuiteTrack, GalaxyGSuiteTrack
from quick.application.UserBinSource import GlobalBinSource
from quick.extra.ProgressViewer import ProgressViewer
from quick.extra.TrackExtractor import TrackExtractor
genome = choices.genome
fullGenomeBins = GlobalBinSource(genome)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
progressViewer = ProgressViewer(
[(cls.PROGRESS_PROCESS_DESCRIPTION, len(gSuite))], galaxyFn)
outGSuite = GSuite()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', datasetInfo=choices.gsuite)]
fileNameSet = set()
for track in gSuite.allTracks():
fileName = cls._getUniqueFileName(fileNameSet, track.trackName)
title = track.title
attributes = track.attributes
fi = cls._getFileFormatInfo(choices, gSuite, genome, track)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix=fi.suffix)
gSuiteTrack = GSuiteTrack(uri,
title=title,
genome=genome,
attributes=attributes)
TrackExtractor.extractOneTrackManyRegsToOneFile(
track.trackName,
fullGenomeBins,
gSuiteTrack.path,
fileFormatName=fi.fileFormatName,
globalCoords=True,
asOriginal=fi.asOriginal,
allowOverlaps=fi.allowOverlaps)
outGSuite.addTrack(gSuiteTrack)
progressViewer.update()
primaryFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'primary', datasetInfo=choices.gsuite)]
GSuiteComposer.composeToFile(outGSuite, primaryFn)
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
return [
HistElement(
getGSuiteHistoryOutputName('nopreprocessed',
datasetInfo=choices.history),
'gsuite'),
HistElement(
getGSuiteHistoryOutputName('preprocessed',
datasetInfo=choices.history),
'gsuite')
]
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
from gold.gsuite.GSuiteConstants import GSUITE_SUFFIX, GSUITE_STORAGE_SUFFIX
fileList = [HistElement(getGSuiteHistoryOutputName(
'nomanipulate', datasetInfo=choices.history), GSUITE_SUFFIX)]
fileList += [HistElement(getGSuiteHistoryOutputName(
'primary', cls.OUTPUT_DESCRIPTION, choices.history), GSUITE_SUFFIX)]
fileList += [HistElement(getGSuiteHistoryOutputName(
'storage', cls.OUTPUT_DESCRIPTION, choices.history),
GSUITE_STORAGE_SUFFIX, hidden=True)]
return fileList
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
histList = []
histList.append(
HistElement(
getGSuiteHistoryOutputName('primary',
datasetInfo=choices.gsuite),
GSuiteConstants.GSUITE_SUFFIX))
histList.append(
HistElement(getGSuiteHistoryOutputName('storage',
datasetInfo=choices.gsuite),
GSuiteConstants.GSUITE_SUFFIX,
hidden=True))
return histList
def getExtraHistElements(cls, choices):
desc = cls.OUTPUT_GSUITE_DESCRIPTION
return [HistElement(getGSuiteHistoryOutputName(
'nointersect', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'primary', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'nopreprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'preprocessed', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName(
'storage', description=desc, datasetInfo=choices.gSuite),
GSuiteConstants.GSUITE_STORAGE_SUFFIX, hidden=True)]
def getOutputName(cls, choices):
if choices.track:
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
description = ', splitted on column: %s' % choices.attr
return getGSuiteHistoryOutputName('primary', description,
choices.track)
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
from gold.gsuite.GSuiteConstants import GSUITE_STORAGE_SUFFIX, GSUITE_SUFFIX
desc = cls._getOutputHistoryDescription(choices)
fileList = [
HistElement(getGSuiteHistoryOutputName('primary', desc),
GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('storage', desc),
GSUITE_STORAGE_SUFFIX,
hidden=True)
]
# if choices.archive:
#for archivedFile in cls._getArchiveReader(choices):
# fileList.append( HistElement(archivedFile.title, archivedFile.suffix, hidden=True) )
return fileList
def getExtraHistElements(cls, choices):
from quick.webtools.GeneralGuiTool import HistElement
fileList = [
HistElement(
getGSuiteHistoryOutputName('nodownload',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(
getGSuiteHistoryOutputName('primary',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
if choices.preProcess == 'Yes':
fileList += [
HistElement(
getGSuiteHistoryOutputName('nopreprocessed',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(
getGSuiteHistoryOutputName('preprocessed',
datasetInfo=choices.history),
GSUITE_SUFFIX)
]
fileList += [
HistElement(getGSuiteHistoryOutputName(
'storage', datasetInfo=choices.history),
GSUITE_STORAGE_SUFFIX,
hidden=True)
]
# if choices.history:
#from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
#gSuite = getGSuiteFromGalaxyTN(choices.history)
#
#for track in gSuite.allTracks():
# from gold.gsuite.GSuiteDownloader import getTitleAndSuffixWithCompressionSuffixesRemoved
# title, suffix = getTitleAndSuffixWithCompressionSuffixesRemoved(track)
# fileList.append( HistElement(title, suffix, hidden=True) )
return fileList
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
from gold.gsuite.GSuiteArchiver import ArchiveToGalaxyGSuiteTrackIterator, \
convertArchiveToGSuite
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
from quick.extra.ProgressViewer import ProgressViewer
from quick.util.debug import DebugUtil
# DebugUtil.insertBreakPoint(username=username, currentUser='******')
archive = cls._getArchiveReader(choices)
trackCount = sum(1 for file in archive)
desc = cls._getOutputHistoryDescription(choices)
progressViewer = ProgressViewer([('Extract tracks', trackCount)],
galaxyFn)
storeHierarchy = choices.storeHierarchy == 'Yes'
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', desc)]
archiveToGSuiteTrackIter = \
ArchiveToGalaxyGSuiteTrackIterator(archive, hiddenStorageFn, storeHierarchy)
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
gSuite = convertArchiveToGSuite(archiveToGSuiteTrackIter,
progressViewer)
GSuiteComposer.composeToFile(
gSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('primary', desc)])
def getOutputName(cls, choices):
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
from quick.util.CommonFunctions import prettyPrintTrackName
if choices.genome:
parentTrack = choices.parentTrack.split(':')
if parentTrack == ['']:
description = 'All tracks'
else:
description = prettyPrintTrackName(parentTrack)
return getGSuiteHistoryOutputName('preprocessed', description)
def getOutputName(cls, choices):
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
from proto.CommonFunctions import extractNameFromDatasetInfo
selected = [
extractNameFromDatasetInfo(val)
for val in choices.history.values() if val is not None
]
description = selected[0] + \
' + %s more' % (len(selected)-1) if len(selected) > 1 else ''
return getGSuiteHistoryOutputName('primary', description)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuitePreprocessor import GSuitePreprocessor
from quick.extra.ProgressViewer import ProgressViewer
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
inGSuite = getGSuiteFromGalaxyTN(choices.history)
if choices.genome != inGSuite.genome:
inGSuite.setGenomeOfAllTracks(choices.genome)
progressViewer = ProgressViewer(
[('Preprocess tracks', inGSuite.numTracks())], galaxyFn)
gSuitePreprocessor = GSuitePreprocessor()
outGSuite, errorGSuite = gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(inGSuite, progressViewer)
#outGSuite, errorGSuite = inGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites()
nopreprocFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nopreprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(errorGSuite, nopreprocFn)
preprocFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'preprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(outGSuite, preprocFn)
def getExtraHistElements(cls, choices):
from gold.gsuite.GSuiteConstants import GSUITE_SUFFIX, GSUITE_STORAGE_SUFFIX
fileList = []
if choices.outputType and choices.downloadAndPreprocess == 'Yes' and \
choices.source.find('HyperBrowser') == -1 and \
choices.transfer != 'Yes':
from quick.webtools.GeneralGuiTool import HistElement
desc = unidecode(choices.subCategory)
fileList += \
[HistElement(getGSuiteHistoryOutputName('remote', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('nodownload', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('primary', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('nopreprocessed', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('preprocessed', desc), GSUITE_SUFFIX),
HistElement(getGSuiteHistoryOutputName('storage', desc), GSUITE_STORAGE_SUFFIX,
hidden=True)]
return fileList
def getOptionsBoxHistoryElementsInfo(cls, prevChoices):
if not prevChoices.dataType:
return
desc = prevChoices.subCategory
core = HtmlCore()
core.styleInfoBegin(styleClass='infomessagesmall')
core.paragraph(
'This tool will create seven history elements (one of which is hidden):'
)
descriptionList = \
[('%s' % getGSuiteHistoryOutputName('storage', desc),
'hidden history element containing the actual downloaded track data. Should '
'in most cases be ignored'),
('%s' % getGSuiteHistoryOutputName('preprocessed', desc),
'use this in the analysis tool of choice'),
('%s' % getGSuiteHistoryOutputName('nopreprocessed', desc),
'preprocessing fails due to some issues with the track data. Some '
'manipulation is probably needed before one tries preprocessing again'),
('%s' % getGSuiteHistoryOutputName('primary', desc),
'use this if you need to manipulate the raw track data using a manipulation '
'tool. The GSuite resulting from manipulation needs to be preprocessed '
'before analysis'),
('%s' % getGSuiteHistoryOutputName('nodownload', desc),
'in some cases the downloading of tracks fails, but might work if one tries again'),
('%s' % getGSuiteHistoryOutputName('remote', desc),
'this refers to the original files available at a remote server. Use this '
'if one for some reason needs to re-download all the tracks'),
('%s' % getGSuiteHistoryOutputName('progress', desc),
'click the eye icon of this element to show the progress of the import')]
for label, description in descriptionList:
core.descriptionLine(label, description)
core.styleInfoEnd()
return '__rawstr__', unicode(core)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
DebugMixin._setDebugModeIfSelected(choices)
genome = choices.genome
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
# fullCategory = AnalysisManager.combineMainAndSubCategories(choices.analysisCategory, 'Basic')
fullCategory = AnalysisManager.combineMainAndSubCategories(
'Descriptive statistics', 'Basic')
tracks = list(gSuite.allTracks())
analysisName = choices.analysis
# selectedAnalysis = GSuiteSingleValueAnalysisPerTrackTool \
# ._resolveAnalysisFromName(gSuite.genome, fullCategory, tracks[0].trackName, analysisName)
selectedAnalysis = cls.ANALYSIS_PRETTY_NAME_TO_ANALYSIS_SPEC_MAPPING[
choices.analysis]
regSpec, binSpec = UserBinMixin.getRegsAndBinsSpec(choices)
analysisBins = GalaxyInterface._getUserBinSource(regSpec,
binSpec,
genome=genome)
# paramName, paramValues = selectedAnalysis.getFirstOptionKeyAndValues()
# if paramName and paramValues:
# if len(paramValues) == 1:
# selectedAnalysis.addParameter(paramName, paramValues[0])
# else:
# selectedAnalysis.addParameter(paramName, choices.paramOne)
tableDict = OrderedDict()
for track in tracks:
tableDict[track.title] = OrderedDict()
result = doAnalysis(selectedAnalysis, analysisBins, [track])
resultDict = result.getGlobalResult()
if 'Result' in resultDict:
track.setAttribute(analysisName.lower(),
str(resultDict['Result']))
tableDict[
track.title][analysisName] = strWithNatLangFormatting(
resultDict['Result'])
else:
for attrName, attrVal in resultDict.iteritems():
attrNameExtended = analysisName + ':' + attrName
track.setAttribute(attrNameExtended.lower(), str(attrVal))
tableDict[track.title][
attrNameExtended] = strWithNatLangFormatting(attrVal)
# assert isinstance(resultDict['Result'], (int, basestring, float)), type(resultDict['Result'])
core = HtmlCore()
core.begin()
core.header('Results: ' + analysisName)
def _produceTable(core, tableDict=None, tableId=None):
return core.tableFromDictOfDicts(tableDict,
firstColName='Track title',
tableId=tableId,
expandable=True,
visibleRows=20,
presorted=0)
tableId = 'results_table'
tableFile = GalaxyRunSpecificFile([tableId, 'table.tsv'], galaxyFn)
tabularHistElementName = 'Raw results: ' + analysisName
gsuiteFile = GalaxyRunSpecificFile(
[tableId, 'input_with_results.gsuite'], galaxyFn)
GSuiteComposer.composeToFile(gSuite, gsuiteFile.getDiskPath())
gsuiteHistElementName = \
getGSuiteHistoryOutputName('result', ', ' + analysisName, choices.gsuite)
core.tableWithImportButtons(
tabularFile=True,
tabularFn=tableFile.getDiskPath(),
tabularHistElementName=tabularHistElementName,
gsuiteFile=True,
gsuiteFn=gsuiteFile.getDiskPath(),
gsuiteHistElementName=gsuiteHistElementName,
produceTableCallbackFunc=_produceTable,
tableDict=tableDict,
tableId=tableId)
core.end()
print core
def getOutputName(cls, choices):
if choices.history:
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
return getGSuiteHistoryOutputName('same', ', subset of tracks',
choices.history)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GalaxyGSuiteTrack, GSuiteTrack
from gold.gsuite.GSuiteComposer import composeToFile
from gold.gsuite.GSuiteFunctions import getTitleWithSuffixReplaced
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
from quick.extra.ProgressViewer import ProgressViewer
from quick.util.CommonFunctions import ensurePathExists
gSuite = getGSuiteFromGalaxyTN(choices.history)
outGSuite = GSuite()
errorGSuite = GSuite()
progressViewer = ProgressViewer(
[('Manipulate tracks', gSuite.numTracks())], galaxyFn)
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', cls.OUTPUT_DESCRIPTION, choices.history)]
for track in gSuite.allTracks():
newSuffix = cls._getSuffix(choices, track)
fileName = os.path.basename(track.path)
fileName = changeSuffixIfPresent(fileName,
oldSuffix=track.suffix,
newSuffix=newSuffix)
title = getTitleWithSuffixReplaced(track.title, newSuffix)
try:
if fileName.endswith('.' + newSuffix):
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn, extraFileName=fileName)
else:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix=newSuffix)
gSuiteTrack = GSuiteTrack(uri,
title=title,
genome=track.genome,
attributes=track.attributes)
trackFn = gSuiteTrack.path
ensurePathExists(trackFn)
cls._runOperation(choices, track.path, trackFn)
outGSuite.addTrack(gSuiteTrack)
except Exception as e:
track.comment = 'An error occurred for the following track: ' + str(
e).partition('\n')[0]
errorGSuite.addTrack(track)
progressViewer.update()
primaryFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'primary', cls.OUTPUT_DESCRIPTION, choices.history)]
composeToFile(outGSuite, primaryFn)
errorFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nomanipulate', datasetInfo=choices.history)]
composeToFile(errorGSuite, errorFn)
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def getOutputName(cls, choices):
return getGSuiteHistoryOutputName('progress', cls.OUTPUT_DESCRIPTION,
choices.history)
def getOutputName(cls, choices):
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
description = cls._getAttrSelectionDescription(choices)
return getGSuiteHistoryOutputName('primary', description)
def getOutputName(cls, choices=None):
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
return getGSuiteHistoryOutputName('primary',
description=cls.GSUITE_DESCRIPTION,
datasetInfo=choices.gsuite)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GSuiteTrack, HbGSuiteTrack
from gold.origdata.TrackGenomeElementSource import TrackViewListGenomeElementSource
from gold.origdata.FileFormatComposer import getComposerClsFromFileSuffix
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from quick.application.ExternalTrackManager import ExternalTrackManager
from quick.application.GalaxyInterface import GalaxyInterface
from quick.application.UserBinSource import UserBinSource
from quick.extra.TrackExtractor import TrackExtractor
genome = choices.genome
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
if choices.withOverlaps == cls.NO_OVERLAPS:
if choices.trackSource == cls.FROM_HISTORY_TEXT:
filterTrackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices.trackHistory)
else:
filterTrackName = choices.track.split(':')
else:
if choices.trackSource == cls.FROM_HISTORY_TEXT:
regSpec = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.trackHistory)
binSpec = ExternalTrackManager.extractFnFromGalaxyTN(choices.trackHistory)
else:
regSpec = 'track'
binSpec = choices.track
userBinSource = UserBinSource(regSpec, binSpec, genome)
desc = cls.OUTPUT_GSUITE_DESCRIPTION
emptyFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('nointersect', description=desc, datasetInfo=choices.gSuite)]
primaryFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('primary', description=desc, datasetInfo=choices.gSuite)]
errorFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('nopreprocessed', description=desc, datasetInfo=choices.gSuite)]
preprocessedFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('preprocessed', description=desc, datasetInfo=choices.gSuite)]
hiddenStorageFn = cls.extraGalaxyFn \
[getGSuiteHistoryOutputName('storage', description=desc, datasetInfo=choices.gSuite)]
analysisDef = '-> TrackIntersectionStat'
# analysisDef = '-> TrackIntersectionWithValStat'
numTracks = gSuite.numTracks()
progressViewer = ProgressViewer([(cls.PROGRESS_INTERSECT_MSG, numTracks),
(cls.PROGRESS_PREPROCESS_MSG, numTracks)], galaxyFn)
emptyGSuite = GSuite()
primaryGSuite = GSuite()
for track in gSuite.allTracks():
newSuffix = cls.OUTPUT_TRACKS_SUFFIX
extraFileName = os.path.sep.join(track.trackName)
extraFileName = changeSuffixIfPresent(extraFileName, newSuffix=newSuffix)
title = getTitleWithSuffixReplaced(track.title, newSuffix)
primaryTrackUri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn, extraFileName=extraFileName,
suffix=newSuffix if not extraFileName.endswith(newSuffix) else '')
primaryTrack = GSuiteTrack(primaryTrackUri, title=title,
genome=track.genome, attributes=track.attributes)
if choices.withOverlaps == cls.NO_OVERLAPS:
res = GalaxyInterface.runManual([track.trackName, filterTrackName], analysisDef, '*', '*',
genome=genome, galaxyFn=galaxyFn, username=username)
trackViewList = [res[key]['Result'] for key in sorted(res.keys())]
tvGeSource = TrackViewListGenomeElementSource(genome, trackViewList)
composerCls = getComposerClsFromFileSuffix(cls.OUTPUT_TRACKS_SUFFIX)
composerCls(tvGeSource).composeToFile(primaryTrack.path)
else:
TrackExtractor.extractOneTrackManyRegsToOneFile( \
track.trackName, userBinSource, primaryTrack.path, fileFormatName=cls.OUTPUT_TRACKS_SUFFIX, \
globalCoords=True, asOriginal=False, allowOverlaps=True)
# Temporary hack until better solution for empty result tracks have been implemented
from gold.origdata.GenomeElementSource import GenomeElementSource
geSource = GenomeElementSource(primaryTrack.path, genome=genome, suffix=cls.OUTPUT_TRACKS_SUFFIX)
try:
geSource.parseFirstDataLine()
primaryGSuite.addTrack(primaryTrack)
except Exception, e: # Most likely empty file
primaryTrack.comment = e.message
emptyGSuite.addTrack(primaryTrack)
numTracks -= 1
progressViewer.updateProgressObjectElementCount(
cls.PROGRESS_PREPROCESS_MSG, numTracks)
#
progressViewer.update()
def getOutputName(cls, choices):
return getGSuiteHistoryOutputName('progress', description=cls.OUTPUT_GSUITE_DESCRIPTION,
datasetInfo=choices.gSuite)
def getOutputName(cls, choices):
description = cls._getOutputHistoryDescription(choices)
return getGSuiteHistoryOutputName('progress', description)
def getOutputName(cls, choices):
return getGSuiteHistoryOutputName('progress',
datasetInfo=choices.gsuite)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
from gold.gsuite.GSuitePreprocessor import GSuitePreprocessor
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
from quick.extra.ProgressViewer import ProgressViewer
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
inGSuite = getGSuiteFromGalaxyTN(choices.history)
trackCount = inGSuite.numTracks()
progressViewer = ProgressViewer(
[('Download tracks', trackCount)] +
([('Preprocess tracks',
trackCount)] if choices.preProcess == 'Yes' else []), galaxyFn)
#from gold.gsuite.GSuiteDownloader import GSuiteMultipleGalaxyFnDownloader
#gSuiteDownloader = GSuiteMultipleGalaxyFnDownloader()
#outGSuite, errorGSuite = \
# gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites(inGSuite, progressViewer, cls.extraGalaxyFn)
from gold.gsuite.GSuiteDownloader import GSuiteSingleGalaxyFnDownloader
gSuiteDownloader = GSuiteSingleGalaxyFnDownloader()
hiddenStorageFn = cls.extraGalaxyFn\
[getGSuiteHistoryOutputName('storage', datasetInfo=choices.history)]
outGSuite, errorGSuite = \
gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites \
(inGSuite, progressViewer, hiddenStorageFn, [])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
#outGSuite, errorGSuite = \
# inGSuite.downloadAllRemoteTracksAsMultipleDatasetsAndReturnOutputAndErrorGSuites(cls.extraGalaxyFn, progressViewer)
#outGSuite, errorGSuite = \
# inGSuite.downloadAllRemoteTracksAsSingleDatasetAndReturnOutputAndErrorGSuites(galaxyFn, ['cell', 'title'], progressViewer=progressViewer)
errorFn = cls.extraGalaxyFn\
[getGSuiteHistoryOutputName('nodownload', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(errorGSuite, errorFn)
outGSuite.setGenomeOfAllTracks(choices.genome)
downloadFn = cls.extraGalaxyFn\
[getGSuiteHistoryOutputName('primary', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(outGSuite, downloadFn)
if choices.preProcess == 'Yes':
progressViewer.updateProgressObjectElementCount(
'Preprocess tracks', outGSuite.numTracks())
gSuitePreprocessor = GSuitePreprocessor()
outGSuite, errorGSuite = gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(outGSuite, progressViewer)
#outGSuite, errorGSuite = outGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites(progressViewer)
noPreprocessedFn = cls.extraGalaxyFn\
[getGSuiteHistoryOutputName('nopreprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(errorGSuite, noPreprocessedFn)
preprocessedFn = cls.extraGalaxyFn\
[getGSuiteHistoryOutputName('preprocessed', datasetInfo=choices.history)]
GSuiteComposer.composeToFile(outGSuite, preprocessedFn)
def getOutputName(cls, choices):
if choices.gsuite:
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
return getGSuiteHistoryOutputName('same', ', metadata edited',
choices.gsuite)
def execute(cls, choices, galaxyFn=None, username=''):
if not choices.source:
return
source = choices.source.split('[')[0].strip()
fileTypes = []
gsm = TrackGlobalSearchModule(cls.useSqlite)
desc = choices.subCategory
if choices.source.find('HyperBrowser') == -1:
#items = gsm.getItems(choices.search,choices.subCategory)
# # allFileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems()]
# # fileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems() if selected]
##allDataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems()]
#dataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems() if selected]
dataTypes = [choices.dataType.split('[')[0].strip()]
##Was made to speadup so that there will be no filetype comparisons,
##but deactivated for now since there is hardcoded filtering in
##prevChoices.fileType
#if len(allFileTypes) == len(fileTypes):
# fileTypes = []
if 'all tracks' in choices.outputType:
remoteGSuite = gsm.getGSuite(choices.search,
choices.subCategory,
source,
dataTypes,
filterFileSuffix=True)
elif choices.outputType == 'Select tracks manually':
remoteGSuite = gsm.getGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,selectedFileIDs = choices.results)
elif choices.outputType == 'Select 10 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 10)
elif choices.outputType == 'Select 50 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 50)
if choices.downloadAndPreprocess == 'Yes' and choices.source.find(
'HyperBrowser') == -1:
trackCount = remoteGSuite.numTracks()
progressViewer = \
ProgressViewer([('Download tracks', trackCount),
('Preprocess tracks', trackCount)], galaxyFn)
#from gold.gsuite.GSuiteDownloader import GSuiteMultipleGalaxyFnDownloader
#gSuiteDownloader = GSuiteMultipleGalaxyFnDownloader()
#localGSuite, errorLocalGSuite = \
# gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
# (remoteGSuite, progressViewer, cls.extraGalaxyFn)
from gold.gsuite.GSuiteDownloader import GSuiteSingleGalaxyFnDownloader
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
gSuiteDownloader = GSuiteSingleGalaxyFnDownloader()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', desc)]
localGSuite, errorLocalGSuite = \
gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites \
(remoteGSuite, progressViewer, hiddenStorageFn, [])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
progressViewer.updateProgressObjectElementCount(
'Preprocess tracks', localGSuite.numTracks())
gSuitePreprocessor = GSuitePreprocessor()
preProcessedGSuite, errorPreProcessGSuite = \
gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(localGSuite, progressViewer)
#preProcessedGSuite, errorPreProcessGSuite = localGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites(progressViewer)
GSuiteComposer.composeToFile(
remoteGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('remote', desc)])
GSuiteComposer.composeToFile(
errorLocalGSuite, cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nodownload', desc)])
GSuiteComposer.composeToFile(
localGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('primary', desc)])
GSuiteComposer.composeToFile(
errorPreProcessGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nopreprocessed', desc)])
GSuiteComposer.composeToFile(
preProcessedGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'preprocessed', desc)])
else:
GSuiteComposer.composeToFile(remoteGSuite, galaxyFn)
def getOutputName(cls, choices):
if choices.downloadAndPreprocess == 'Yes': # and choices.source.find('HyperBrowser') == -1:
return getGSuiteHistoryOutputName('progress', choices.subCategory)
else:
return getGSuiteHistoryOutputName('primary', choices.subCategory)
def getOutputName(cls, choices):
from quick.gsuite.GSuiteHbIntegration import getGSuiteHistoryOutputName
return getGSuiteHistoryOutputName('primary', ', tracks exported',
choices.gsuite)
