def testComposeLocalUrlGenomeAttributesNonAscii(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome=u'hg18ø',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', u'nø')])))
gSuite.addTrack(
GSuiteTrack(
HbGSuiteTrack.generateURI(trackName=[u'track', u'nøme']),
genome='hg38',
attributes=OrderedDict([('two', 'yes')])))
gSuite.setCustomHeader('my header', u'bø!')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'##my header: b%C3%B8!\n' \
'###uri\ttitle\tfile_format\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\tunknown\thg18%C3%B8\tyes\t.\n' \
'file:/path/to/file2\tfile2\tunknown\thg19\t.\tn%C3%B8\n' \
'hb:/track/n%C3%B8me\tn%C3%B8me\tpreprocessed\thg38\t.\tyes\n'
self.assertEquals(targetOutput, output)
def generateSynGSuite(cls, dataOut, galaxyFn, genome):
outGSuite = GSuite()
g = SimulationPointIter()
newData = ''
chrNum = 0
for chr in dataOut:
# fileName = 'syn-chr' + 'iInterR-' + str(chr[0]) + 'st-' + str(chr[1]) + 'end-' + str(
# chr[2]) + 'iInterR-' + str(chr[3]) + 'iIntraR-' + str(chr[4]) + 'prob-' + str(chr[5]) + '--' + str(
# chrNum)
fileName = 'syn-' + str(chr[0]) + ',' + str(chr[1]) + ',' + str(chr[2]) + ',' + str(chr[3]) +',' + str(chr[4]) +',' + str(chr[5])
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=galaxyFn,
extraFileName=fileName,
suffix='bed')
gSuiteTrack = GSuiteTrack(uri)
outFn = gSuiteTrack.path
ensurePathExists(outFn)
g.createChrTrack(genome, chr[0], PointIter, outFn, chr[3], chr[4], chr[5], chr[1], chr[2])
with open(outFn, 'r') as outputFile:
newData += ''.join(outputFile.readlines())
chrNum += 1
if chrNum == len(dataOut):
with open(outFn, 'w') as outputFile:
outputFile.write(newData)
outGSuite.addTrack(GSuiteTrack(uri, title=''.join(fileName), genome=genome))
GSuiteComposer.composeToFile(outGSuite, cls.extraGalaxyFn['synthetic GSuite'])
def testQuoteInURLRemote(self):
for scheme, cls in [('ftp', FtpGSuiteTrack), ('http', HttpGSuiteTrack),
('https', HttpsGSuiteTrack),
('rsync', RsyncGSuiteTrack)]:
uri = cls.generateURI(
netloc='server.com%7C',
path='/path/to/file_with%20%3B%22%5B',
suffix='bed%7C%2F',
query='search=%2Aab&track=My%3Atrack+name%3B%22%5B%3Ahierarchy',
doQuote=False)
track = GSuiteTrack(uri)
self.assertEquals(
scheme +
'://server.com%7C/path/to/file_with%20%3B%22%5B;bed%7C%2F?search=%2Aab&track=My%3Atrack+name%3B%22%5B%3Ahierarchy',
uri)
self.assertEquals(scheme, track.scheme)
self.assertEquals(
scheme +
'://server.com%7C/path/to/file_with%20%3B%22%5B;bed%7C%2F?search=%2Aab&track=My%3Atrack+name%3B%22%5B%3Ahierarchy',
track.uri)
self.assertEquals('server.com|', track.netloc)
self.assertEquals('/path/to/file_with ;"[', track.path)
self.assertEquals('hierarchy', track.title)
self.assertEquals('bed|/', track.suffix)
self.assertEquals('search=*ab&track=My:track name;"[:hierarchy',
track.query)
self.assertEquals(['My', 'track name;"[', 'hierarchy'],
track.trackName)
uri = cls.generateURI(
netloc='server.com|',
path='/path/to/file_with ;"[',
suffix='btrack|/',
trackName=['My', 'track name;"[', 'hierarchy'],
doQuote=True)
track = GSuiteTrack(uri)
self.assertEquals(
scheme +
'://server.com%7C/path/to/file_with%20%3B%22%5B;btrack%7C%2F?track=My%3Atrack+name%3B%22%5B%3Ahierarchy',
uri)
self.assertEquals(scheme, track.scheme)
self.assertEquals(
scheme +
'://server.com%7C/path/to/file_with%20%3B%22%5B;btrack%7C%2F?track=My%3Atrack+name%3B%22%5B%3Ahierarchy',
track.uri)
self.assertEquals('server.com|', track.netloc)
self.assertEquals('/path/to/file_with ;"[', track.path)
self.assertEquals('hierarchy', track.title)
self.assertEquals('btrack|/', track.suffix)
self.assertEquals('track=My:track name;"[:hierarchy', track.query)
self.assertEquals(
['My', 'track name;"[', 'hierarchy'], track.trackName
) # Temporarily, should be fixed if remote BTracks are supported
def testSimpleTitleDuplicate(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed'))
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/other/path/to/file1.bed'))
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/third/path/to/file1.bed'))
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/last/path/to/file1.bed'))
self.assertEqual(
['file1.bed', 'file1.bed (2)', 'file1.bed (3)', 'file1.bed (4)'],
gSuite.allTrackTitles())
def setUp(self):
GSuiteTestWithMockEncodingFuncs.setUp(self)
self.track1 = GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track1', genome='hg18',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')]))
self.track2 = GSuiteTrack('hb:/track/name/hierarchy',
title='Track2', genome='hg18')
self.track3 = GSuiteTrack('galaxy:/ad123dd12fg;btrack',
title='Track3', genome='hg18',
attributes=OrderedDict([('view', 'signal'),
('antibody', 'cMyb')]))
def _getUriForDownloadedAndUncompressedTrackPossiblyCached(
self, gSuiteTrack, galaxyFn, uncomprSuffix, extraFileName=None):
from gold.gsuite.GSuiteTrackCache import GSUITE_TRACK_CACHE
cache = GSUITE_TRACK_CACHE
if cache.isCached(gSuiteTrack):
cachedUri = cache.getCachedGalaxyUri(gSuiteTrack)
if os.path.exists(GSuiteTrack(cachedUri).path):
return cache.getCachedGalaxyUri(gSuiteTrack)
if extraFileName:
from quick.application.ExternalTrackManager import ExternalTrackManager
outGalaxyFn = ExternalTrackManager.createGalaxyFilesFn(
galaxyFn, extraFileName)
ensurePathExists(outGalaxyFn)
if extraFileName.endswith('.' + uncomprSuffix):
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=galaxyFn, extraFileName=extraFileName)
else:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=galaxyFn,
extraFileName=extraFileName,
suffix=uncomprSuffix)
else:
outGalaxyFn = galaxyFn
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=outGalaxyFn,
suffix=uncomprSuffix)
uncompressorAndDownloader = GSuiteTrackUncompressorAndDownloader()
uncompressorAndDownloader.visit(gSuiteTrack, outGalaxyFn)
if cache.shouldBeCached(gSuiteTrack):
cache.cache(gSuiteTrack, uri)
return uri
def visitGalaxyGSuiteTrack(self, gSuiteTrack):
self.genericVisit(gSuiteTrack)
from quick.application.ExternalTrackManager import ExternalTrackManager
from gold.description.TrackInfo import TrackInfo
if gSuiteTrack.hasExtraFileName():
baseFileName = os.path.basename(gSuiteTrack.uriWithoutSuffix)
else:
baseFileName = gSuiteTrack.title
galaxyTN = ExternalTrackManager.constructGalaxyTnFromSuitedFn(
gSuiteTrack.path, fileEnding=gSuiteTrack.suffix, name=baseFileName)
trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
gSuiteTrack.genome,
galaxyTN,
printErrors=False,
printProgress=False,
renameExistingTracksIfNeeded=False)
trackType = TrackInfo(gSuiteTrack.genome,
trackName).trackFormatName.lower()
hbUri = HbGSuiteTrack.generateURI(trackName=trackName)
return GSuiteTrack(hbUri,
title=gSuiteTrack.title,
trackType=trackType,
genome=gSuiteTrack.genome,
attributes=gSuiteTrack.attributes,
comment=gSuiteTrack.comment)
def testCreateGalaxyGSuiteTrack(self):
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn='/path/to/dataset_12345.dat',
extraFileName='specific_file',
trackName=['trackname'],
suffix='btrack',
doQuote=False)
track = GSuiteTrack(uri,
title='MyTrack',
fileFormat='preprocessed',
trackType='points',
genome='mm9',
attributes=OrderedDict([('extra', 'yes')]))
self.assertEquals(
'galaxy:/9085014203344132088/specific_file;btrack?track=trackname',
uri)
self.assertEquals('galaxy', track.scheme)
self.assertEquals(
'galaxy:/9085014203344132088/specific_file;btrack?track=trackname',
track.uri)
self.assertEquals(None, track.netloc)
self.assertEquals(
'/path/to/dataset_9085014203344132088_files/specific_file',
track.path)
self.assertEquals('track=trackname', track.query)
self.assertEquals('btrack', track.suffix)
self.assertEquals('MyTrack', track.title)
self.assertEquals(['trackname'], track.trackName)
self.assertEquals('local', track.location)
self.assertEquals('preprocessed', track.fileFormat)
self.assertEquals('points', track.trackType)
self.assertEquals('mm9', track.genome)
self.assertEquals(OrderedDict([('extra', 'yes')]), track.attributes)
def testCreateFileGSuiteTrack(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file',
suffix='btrack',
trackName=['trackname'],
doQuote=False)
track = GSuiteTrack(uri,
title='MyTrack',
trackType='segments',
genome='unknown',
attributes=OrderedDict([('extra', 'no')]))
self.assertEquals('file:/path/to/file;btrack?track=trackname', uri)
self.assertEquals('file', track.scheme)
self.assertEquals('file:/path/to/file;btrack?track=trackname',
track.uri)
self.assertEquals(None, track.netloc)
self.assertEquals('/path/to/file', track.path)
self.assertEquals('track=trackname', track.query)
self.assertEquals('btrack', track.suffix)
self.assertEquals('MyTrack', track.title)
self.assertEquals(['trackname'], track.trackName)
self.assertEquals('local', track.location)
self.assertEquals('preprocessed', track.fileFormat)
self.assertEquals('segments', track.trackType)
self.assertEquals('unknown', track.genome)
self.assertEquals(OrderedDict([('extra', 'no')]), track.attributes)
def execute(cls, choices, galaxyFn=None, username=''):
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GalaxyGSuiteTrack, GSuiteTrack
import gold.gsuite.GSuiteComposer as GSuiteComposer
from quick.application.ExternalTrackManager import ExternalTrackManager
genome = choices.genome if choices.selectGenome == 'Yes' else None
selectedHistories = [
key for key, val in choices.history.iteritems() if val is not None
]
gSuite = GSuite()
for histGalaxyId in selectedHistories:
galaxyTrackName = choices.history[histGalaxyId].split(':')
histGalaxyFn = ExternalTrackManager.extractFnFromGalaxyTN(
galaxyTrackName)
histName = ExternalTrackManager.extractNameFromHistoryTN(
galaxyTrackName)
histSuffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
galaxyTrackName)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=histGalaxyFn,
suffix=histSuffix)
gSuite.addTrack(GSuiteTrack(uri, title=histName, genome=genome))
GSuiteComposer.composeToFile(gSuite, galaxyFn)
def __iter__(self):
for archivedFileInfo in self._archive:
# galaxyFn = self._titleToGalaxyFnDict.get(archivedFileInfo.title)
# if not galaxyFn:
# raise ShouldNotOccurError('Galaxy filename not found for file with title: ' + archivedFile.title)
extraFileName = os.sep.join((archivedFileInfo.directories if self._storeHierarchy else []) +\
[archivedFileInfo.baseFileName])
if self._storeHierarchy:
attributeList = OrderedDict([('dir_level_%s' % (i+1), directory) \
for i,directory in enumerate(archivedFileInfo.directories)])
else:
attributeList = OrderedDict()
uri = GalaxyGSuiteTrack.generateURI(self._galaxyFn,
extraFileName=extraFileName)
gSuiteTrack = GSuiteTrack(uri,
title=archivedFileInfo.baseFileName,
attributes=attributeList)
outFn = gSuiteTrack.path
ensurePathExists(outFn)
with open(outFn, 'w') as outFile:
inFile = self._archive.openFile(archivedFileInfo.path)
outFile.write(inFile.read())
inFile.close()
yield gSuiteTrack
def _createPreprocessedGsuiteTrack(self,
gSuiteTrack,
baseFileName,
doEncodeId,
urlPrefix=None):
from quick.application.ExternalTrackManager import ExternalTrackManager as ETM
from gold.description.TrackInfo import TrackInfo
self.genericVisit(gSuiteTrack)
galaxyTN = ETM.constructGalaxyTnFromSuitedFn(
gSuiteTrack.path, fileEnding=gSuiteTrack.suffix, name=baseFileName)
trackName = ETM.getPreProcessedTrackFromGalaxyTN(
gSuiteTrack.genome,
galaxyTN,
printErrors=False,
printProgress=False,
renameExistingTracksIfNeeded=False,
doEncodeId=doEncodeId,
urlPrefix=urlPrefix)
trackType = TrackInfo(gSuiteTrack.genome,
trackName).trackFormatName.lower()
hbUri = HbGSuiteTrack.generateURI(trackName=trackName)
return GSuiteTrack(hbUri,
title=gSuiteTrack.title,
trackType=trackType,
genome=gSuiteTrack.genome,
attributes=gSuiteTrack.attributes,
comment=gSuiteTrack.comment)
def execute(cls, choices, galaxyFn=None, username=''):
basisTrackNameAsList = choices.basisTrack.split(':')
extractionOptions = dict(
GalaxyInterface.getTrackExtractionOptions(choices.genome,
basisTrackNameAsList))
extractionFormat = extractionOptions[
choices.extFormatLbl] if extractionOptions else None
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for gsTrack in gsuite.allTracks():
# outputTrackFn = cls.extraGalaxyFn[gsTrack.title]
# print '<br>\n<br>\n output track filename: ', outputTrackFn
# print 'path: ', gsTrack.path
# print 'parsed uri: ', gsTrack._parsedUri
newTrackFileName = gsTrack.title + '.' + extractionFormat
outGalaxyFn = ExternalTrackManager.createGalaxyFilesFn(
galaxyFn, newTrackFileName)
ensurePathExists(outGalaxyFn)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn,
extraFileName=newTrackFileName)
GalaxyInterface.parseExtFormatAndExtractTrackManyBins(
choices.genome, basisTrackNameAsList, gsTrack.suffix,
gsTrack.path, True, choices.extFormatLbl, outGalaxyFn)
outGSuite.addTrack(
GSuiteTrack(uri,
title=gsTrack.title,
fileFormat=gsTrack.fileFormat,
trackType=gsTrack.trackType,
genome=choices.genome,
attributes=gsTrack.attributes))
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def _parseTrackLine(trackLine, colNames, headerVars):
colVals = trackLine.split('\t')
if len(colVals) != len(colNames):
raise InvalidFormatError('The number of columns in track line: %s ' % (repr(trackLine)) +
'is not equal to the number of columns in the '
'column specification line (%s != %s)' %
(len(colVals), len(colNames)))
from copy import copy
remainingColNames = copy(colNames)
assert colNames[0] == URI_COL
kwArgs = {}
for colSpec in ALL_STD_COL_SPECS:
val = _popValueFromColValsAndNamesIfPresent(colVals, remainingColNames, colSpec.colName)
if val is not None:
kwArgs[colSpec.memberName] = val
elif colSpec.headerName in headerVars:
if headerVars[colSpec.headerName] != MULTIPLE:
kwArgs[colSpec.memberName] = headerVars[colSpec.headerName]
attributes = OrderedDict(zip(remainingColNames, colVals))
for key, val in attributes.iteritems():
if val == '.':
del attributes[key]
kwArgs['attributes'] = attributes
try:
track = GSuiteTrack(**kwArgs)
except InvalidFormatError as e:
errorMsg = 'Error in track line %s:\n' % repr(trackLine) + e.message
raise InvalidFormatError(errorMsg)
return track
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 getTitleAndSuffixWithCompressionSuffixesRemoved(gSuiteTrack):
gSuiteReq = GSuiteRequirements(allowedLocations=[LOCAL, REMOTE],
allowedFileFormats=[PREPROCESSED, PRIMARY, UNKNOWN])
gSuiteReq.check(gSuiteTrack)
title, suffix, path = gSuiteTrack.title, gSuiteTrack.suffix, gSuiteTrack.path
if suffix:
for compSuffix in COMPRESSION_SUFFIXES:
reduceLen = len(compSuffix)+1
if suffix.lower() == compSuffix:
if path.endswith('.' + compSuffix):
path = path[:-reduceLen]
suffix = getFileSuffix(path)
else:
if isinstance(gSuiteTrack, SearchQueryForSuffixGSuiteTrack):
tempGSuiteTrack = GSuiteTrack(gSuiteTrack.uri.replace('.' + compSuffix, ''), title='')
suffix = tempGSuiteTrack.suffix
else:
suffix = None # Impossible to find uncompressed suffix
elif suffix.lower().endswith('.' + compSuffix):
suffix = suffix[:-reduceLen] # e.g. suffix = 'bed.gz' -> 'bed'
else:
continue
title = getTitleWithSuffixReplaced(title, '')
break
return title, suffix
def execute(cls, choices, galaxyFn=None, username=''):
from quick.util.CommonFunctions import getFileSuffix
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import registerGSuiteTrackClass, GSuiteTrack, FileGSuiteTrack
registerGSuiteTrackClass(FileGSuiteTrack)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for track in gSuite.allTracks():
path = track.path
suffix = track.suffix if track.suffix != getFileSuffix(
path) else ''
uri = FileGSuiteTrack.generateURI(path=path, suffix=suffix)
newTrack = GSuiteTrack(uri,
title=track.title,
trackType=track.trackType,
genome=track.genome,
attributes=track.attributes)
outGSuite.addTrack(newTrack)
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def testCreateRemoteGSuiteTrack(self):
for scheme, cls in [('ftp', FtpGSuiteTrack), ('http', HttpGSuiteTrack),
('https', HttpsGSuiteTrack), ('rsync', RsyncGSuiteTrack)]:
uri = cls.generateURI(netloc='server.com', path='/path/to/file',
suffix='btrack', trackName=['trackname'], doQuote=False)
track = GSuiteTrack(uri, title='MyTrack', fileFormat='preprocessed',
trackType='segments', genome='TestGenome',
attributes=OrderedDict([('extra', 'yes')]))
self.assertEquals(scheme + '://server.com/path/to/file;btrack?track=trackname',
uri)
self.assertEquals(scheme, track.scheme)
self.assertEquals(scheme + '://server.com/path/to/file;btrack?track=trackname',
track.uri)
self.assertEquals('server.com', track.netloc)
self.assertEquals('/path/to/file', track.path)
self.assertEquals('track=trackname', track.query)
self.assertEquals('btrack', track.suffix)
self.assertEquals('MyTrack', track.title)
self.assertEquals(['trackname'], track.trackName)
self.assertEquals('remote', track.location)
self.assertEquals('preprocessed', track.fileFormat)
self.assertEquals('segments', track.trackType)
self.assertEquals('TestGenome', track.genome)
self.assertEquals(OrderedDict([('extra', 'yes')]), track.attributes)
def testIncorrectTrackType(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file')
# track = GSuiteTrack(uri, trackType='segment')
self.assertRaises(InvalidFormatError, GSuiteTrack, uri, trackType='segment')
track = GSuiteTrack(uri)
# track.trackType = 'segment'
self.assertRaises(InvalidFormatError, track.__setattr__, 'trackType', 'segment')
def testIncorrectFileFormatGalaxy(self):
uri = GalaxyGSuiteTrack.generateURI(galaxyFn='/path/to/file')
# track = GSuiteTrack(uri, fileFormat='doc')
self.assertRaises(InvalidFormatError, GSuiteTrack, uri, fileFormat='doc')
track = GSuiteTrack(uri)
# track.fileFormat = 'doc'
self.assertRaises(InvalidFormatError, track.__setattr__, 'fileFormat', 'doc')
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 (cls, e.g. generated image files). choices is a list
of selections made by web-user in each options box.
Mandatory unless isRedirectTool() returns True.
"""
#TODO: add functionality for single gtrack within-track randomization
print 'Executing...'
inputGsuite = getGSuiteFromGalaxyTN(choices.gs)
outputGSuite = GSuite()
genome = inputGsuite.genome
ts = factory.getFlatTracksTS(genome, choices.gs)
randIndex = 0
bins = GlobalBinSource(genome)
if choices.randType == TsRandAlgReg.BETWEEN_TRACKS_CATEGORY and \
choices.category not in [None, 'None']:
ts = ts.getSplittedByCategoryTS(choices.category)
randomizedTs = TrackStructureV2()
for subTsKey, subTs in ts.items():
tvProvider = cls.createTrackViewProvider(
choices, subTs, bins, genome)
randomizedTs[subTsKey] = getRandomizedVersionOfTs(
subTs, tvProvider, randIndex)
randomizedTs = randomizedTs.getFlattenedTS()
else:
tvProvider = cls.createTrackViewProvider(choices, ts, bins, genome)
randomizedTs = getRandomizedVersionOfTs(ts, tvProvider, randIndex)
for singleTrackTs in randomizedTs.getLeafNodes():
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=galaxyFn,
extraFileName=os.path.sep.join(singleTrackTs.track.trackName) +
'.randomized',
suffix='bed')
title = singleTrackTs.metadata.pop('title')
gSuiteTrack = GSuiteTrack(uri,
title=title + '.randomized',
fileFormat='primary',
trackType='segments',
genome=genome,
attributes=singleTrackTs.metadata)
outputGSuite.addTrack(gSuiteTrack)
singleTrackTs.metadata['trackFilePath'] = gSuiteTrack.path
spec = AnalysisSpec(TsWriterStat)
res = doAnalysis(spec, bins, randomizedTs)
GSuiteComposer.composeToFile(outputGSuite, galaxyFn)
def testComposeRemoteOnlyUrl(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1'))
gSuite.addTrack(GSuiteTrack('http://server.other.com/path/to/file2'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: unknown\n' \
'###uri\ttitle\n' \
'ftp://server.somewhere.com/path/to/file1\tfile1\n' \
'http://server.other.com/path/to/file2\tfile2\n'
self.assertEquals(targetOutput, output)
def testQuoteInURLHb(self):
uri = HbGSuiteTrack.generateURI(trackName=['My', 'track name;"[', 'hierarchy'],
doQuote=True)
track = GSuiteTrack(uri)
self.assertEquals('hb:/My/track%20name%3B%22%5B/hierarchy', track.uri)
self.assertEquals('hb', track.scheme)
self.assertEquals('hb:/My/track%20name%3B%22%5B/hierarchy', track.uri)
self.assertEquals(['My', 'track name;"[', 'hierarchy'], track.trackName)
self.assertEquals('hierarchy', track.title)
def testComposeUrlTitleLocationTrackType(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1',
title='Track1',
trackType='points'))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2', trackType='segments'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: unknown\n' \
'##track type: multiple\n' \
'##genome: unknown\n' \
'###uri\ttitle\ttrack_type\n' \
'ftp://server.somewhere.com/path/to/file1\tTrack1\tpoints\n' \
'file:/path/to/file2\tfile2\tsegments\n'
self.assertEquals(targetOutput, output)
def testComposeRemoteUrlGenomeFileFormat(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
genome='hg18'))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2',
genome='hg18'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'###uri\ttitle\tfile_format\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tfile1.bed\tprimary\n' \
'http://server.other.com/path/to/file2\tfile2\tunknown\n'
self.assertEquals(targetOutput, output)
def testComposeLocalUrlGenomeAttributes(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome='hg18',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', 'no')])))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'###uri\ttitle\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\thg18\tyes\t.\n' \
'file:/path/to/file2\tfile2\thg19\t.\tno\n'
self.assertEquals(targetOutput, output)
def testFullCompose(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2.bed',
title='Track2',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyc')])))
gSuite.addTrack(
GSuiteTrack('https://server.other.com/path/to/file3.bed',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('rsync://server.other.com/path/to/file4;wig',
title='Track4',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.addTrack(GSuiteTrack('hb:/track/name/hierarchy', title='Track'))
gSuite.addTrack(
GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track name7',
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
gSuite.setGenomeOfAllTracks('hg18')
gSuite.setCustomHeader('My header', 'Some value')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'##my header: Some value\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack\tprimary\tk562\tcMyb\t.\n' \
'http://server.other.com/path/to/file2.bed\tTrack2\tprimary\tGM12878\tcMyc\t.\n' \
'https://server.other.com/path/to/file3.bed\tfile3.bed\tprimary\tGM12878\tcMyb\t.\n' \
'rsync://server.other.com/path/to/file4;wig\tTrack4\tprimary\tNHFL\t.\t.\n' \
'hb:/track/name/hierarchy\tTrack (2)\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack (3)\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
self.assertEquals(targetOutput, output)
def visitRemoteGSuiteTrack(self, gSuiteTrack, galaxyFn, colHierarchyList):
import os
self.genericVisit(gSuiteTrack, galaxyFn, colHierarchyList)
uncomprTitle, uncomprSuffix = getTitleAndSuffixWithCompressionSuffixesRemoved(
gSuiteTrack)
rawFileName = getTitleWithCompressionSuffixesRemoved(
GSuiteTrack(gSuiteTrack.uri))
duplicateIdx = getDuplicateIdx(uncomprTitle)
rawFileName = renameBaseFileNameWithDuplicateIdx(
rawFileName, duplicateIdx)
memberHierarchyList = []
for colName in colHierarchyList:
memberName = colName
for colSpec in OPTIONAL_STD_COL_SPECS:
if not colSpec.deprecated:
if colName == colSpec.colName:
memberName = colSpec.memberName
memberHierarchyList.append(memberName)
extraFileName = os.path.sep.join([
getattr(gSuiteTrack, memberName)
for memberName in memberHierarchyList
] + [rawFileName])
uri = self._getUriForDownloadedAndUncompressedTrackPossiblyCached(
gSuiteTrack, galaxyFn, uncomprSuffix, extraFileName)
return GSuiteTrack(uri,
title=uncomprTitle,
fileFormat=gSuiteTrack.fileFormat,
trackType=gSuiteTrack.trackType,
genome=gSuiteTrack.genome,
attributes=gSuiteTrack.attributes)
def testQuoteInURLFile(self):
uri = FileGSuiteTrack.generateURI(path='/path/to/file_with ;"[', suffix='btrack',
trackName=['My', 'track ;"[', 'name'], doQuote=True)
track = GSuiteTrack(uri, fileFormat='preprocessed', trackType='segments')
self.assertEquals('file:/path/to/file_with%20%3B%22%5B;btrack?'
'track=My%3Atrack+%3B%22%5B%3Aname', uri)
self.assertEquals('file', track.scheme)
self.assertEquals('file:/path/to/file_with%20%3B%22%5B;btrack?'
'track=My%3Atrack+%3B%22%5B%3Aname', track.uri)
self.assertEquals('/path/to/file_with ;"[', track.path)
self.assertEquals('name', track.title)
self.assertEquals('track=My:track ;"[:name', track.query)
self.assertEquals(['My', 'track ;"[', 'name'], track.trackName)
self.assertEquals('btrack', track.suffix)
def testCreateGSuiteTrackDefaults(self):
track = GSuiteTrack('ftp://server/path/to/file')
self.assertEquals('ftp', track.scheme)
self.assertEquals('ftp://server/path/to/file', track.uri)
self.assertEquals('server', track.netloc)
self.assertEquals('/path/to/file', track.path)
self.assertEquals(None, track.query)
self.assertEquals(None, track.suffix)
self.assertEquals('file', track.title)
self.assertEquals(None, track.trackName)
self.assertEquals('remote', track.location)
self.assertEquals('unknown', track.fileFormat)
self.assertEquals('unknown', track.trackType)
self.assertEquals('unknown', track.genome)
self.assertEquals(OrderedDict(), track.attributes)
