def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not (choices.queryGSuite and choices.refGSuite):
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.GSUITE_INPUT], choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(choices.queryGSuite)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteFile(choices.refGSuite)
if errorString:
return errorString
qGSuite = getGSuiteFromGalaxyTN(choices.queryGSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(qGSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(qGSuite)
if errorString:
return errorString
refGSuite = getGSuiteFromGalaxyTN(choices.refGSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(refGSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(refGSuite)
if errorString:
return errorString
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorString = cls._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = cls._checkGSuiteRequirements(
gSuite,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=cls.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
errorStr = cls._validateGenome(choices)
if errorStr:
return errorStr
errorString = GeneralGuiTool._checkGSuiteTrackListSize(
gSuite, minSize=cls.GSUITE_MIN_TRACK_COUNT)
if errorString:
return errorString
def validateAndReturnErrors(cls, choices):
errorString = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = GeneralGuiTool._checkTrack(choices, 'targetTrack', 'genome')
if errorString:
return errorString
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gsuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gsuite)
if errorString:
return errorString
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
errorString = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.history)
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite, allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite,
minSize=1)
if errorString:
return errorString
def validateAndReturnErrors(cls, choices):
genome = choices.genome
genomicRegionsSource = choices.genomicRegionsSource
genomicRegions = choices.genomicRegions
sourceTfs = choices.sourceTfs
tfTracks = choices.tfTracks
# Check genome
if genome == cls.SELECT:
return 'Please select a genome build.'
# Check that all boxes have data:
if genomicRegionsSource == AllTargetsOfTfs.SELECT:
return 'Please select a genomic region source.'
if not genomicRegions:
return 'Please select a genomic region.'
# Check tracks for Genomic Regions-History:
if genomicRegionsSource == 'History (user-defined)':
if len(genomicRegions.split(":")) > 1:
if genomicRegions.split(":")[1] == "gsuite":
errorString = GeneralGuiTool._checkGSuiteFile(
genomicRegions)
if errorString:
return errorString
else:
gSuite = getGSuiteFromGalaxyTN(genomicRegions)
sizeErrorString = GeneralGuiTool._checkGSuiteTrackListSize(
gSuite, 1, 1000)
if sizeErrorString:
return sizeErrorString
else:
reqErrorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
AllTargetsOfTfs.GSUITE_ALLOWED_FILE_FORMATS,
AllTargetsOfTfs.GSUITE_ALLOWED_LOCATIONS,
AllTargetsOfTfs.GSUITE_ALLOWED_TRACK_TYPES,
AllTargetsOfTfs.GSUITE_DISALLOWED_GENOMES)
if reqErrorString:
return reqErrorString
else:
errorString = GeneralGuiTool._checkTrack(
choices, 'genomicRegions', 'genome')
if errorString:
return errorString
if sourceTfs == AllTargetsOfTfs.SELECT:
return 'Please select a TF source.'
if not tfTracks:
return 'Please select a TF track.'
# Check tracks for TFs-History:
if sourceTfs == 'History (user-defined)':
tfErrorString = GeneralGuiTool._checkTrack(choices, 'tfTracks',
'genome')
if tfErrorString:
return tfErrorString
return None
def getOptionsBoxTfTracks(cls, prevChoices):
if prevChoices.sourceTfsDetails != cls.SELECT:
genome = prevChoices.genome
sourceTfs = prevChoices.sourceTfs
sourceTfsDetails = prevChoices.sourceTfsDetails
if sourceTfs == cls.SELECT:
return
elif sourceTfs == 'Hyperbrowser repository':
tfSourceTN = TfTrackNameMappings.getTfTrackNameMappings(
prevChoices.genome)[sourceTfsDetails]
subtypes = ProcTrackOptions.getSubtypes(
prevChoices.genome, tfSourceTN, True)
falses = ['False'] * len(subtypes)
return OrderedDict(zip(subtypes, falses))
elif sourceTfs == cls.REGIONS_FROM_HISTORY:
if isinstance(sourceTfsDetails, basestring):
galaxyTN = sourceTfsDetails.split(':')
if galaxyTN[
1] == "gsuite": #ExternalTrackManager.extractFileSuffixFromGalaxyTN(prevChoices.sourceTfsDetails, allowUnsupportedSuffixes=True) == "gsuite"
errorString = GeneralGuiTool._checkGSuiteFile(
sourceTfsDetails)
if not errorString:
gSuite = getGSuiteFromGalaxyTN(sourceTfsDetails)
sizeErrorString = GeneralGuiTool._checkGSuiteTrackListSize(
gSuite, 1, 1000)
if not sizeErrorString:
reqErrorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
AllTfsOfRegions.GSUITE_ALLOWED_FILE_FORMATS,
AllTfsOfRegions.GSUITE_ALLOWED_LOCATIONS,
AllTfsOfRegions.GSUITE_ALLOWED_TRACK_TYPES,
AllTfsOfRegions.GSUITE_DISALLOWED_GENOMES)
if not reqErrorString:
validity = 'Valid'
else:
return
else:
return
else:
return
if validity == 'Valid':
selectedTrackNames = []
gSuite = getGSuiteFromGalaxyTN(sourceTfsDetails)
for track in gSuite.allTracks():
selectedTrackNames.append(':'.join(
track.trackName))
falses = ['False'] * len(selectedTrackNames)
return OrderedDict(zip(selectedTrackNames, falses))
else:
tfTrackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
genome, galaxyTN)
return [':'.join(tfTrackName)]
else:
return
else:
return
else:
return
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not choices.histElement:
return ToolGuideController.getHtml(cls.toolId,
[ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(choices.histElement)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.histElement)
if choices.Analysis in (
MultiTrackAnalysisTool.LBL_FACTORS_OBSERVED_VS_EXPECTED,
MultiTrackAnalysisTool.LBL_HYPOTHESIS_TESTING_MULTI):
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite,
minSize=3,
maxSize=3)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
MultiTrackAnalysisTool.GSUITE_ALLOWED_FILE_FORMATS,
MultiTrackAnalysisTool.GSUITE_ALLOWED_LOCATIONS,
MultiTrackAnalysisTool.GSUITE_ALLOWED_TRACK_TYPES,
MultiTrackAnalysisTool.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
# regSpec, binSpec = UserBinSelector.getRegsAndBinsSpec(choices)
# if regSpec.strip() is '' or binSpec.strip() is '':
# return 'Region and bin must be specified'
# ubSource = GalaxyInterface._getUserBinSource(regSpec, binSpec, gSuite.genome)
#
# hasBins = False
# for bin in ubSource:
# hasBins = True
# break
#
# if not hasBins:
# return 'Zero analysis bins specified. This may be caused by entering an incorrect filtering condition, e.g. a mistyped chromosome.'
#
return None
def validateAndReturnErrors(choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
if choices[0] == 'From GSuite':
if not choices[1]:
return 'Please select a GSuite from history'
if choices[0] == 'From GSuite':
errorString = GeneralGuiTool._checkGSuiteFile(choices[1])
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices[1])
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite,
minSize=2)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
CreateBpsVennDIagram.GSUITE_ALLOWED_FILE_FORMATS,
CreateBpsVennDIagram.GSUITE_ALLOWED_LOCATIONS,
CreateBpsVennDIagram.GSUITE_ALLOWED_TRACK_TYPES,
CreateBpsVennDIagram.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
genome, trackNames = CreateBpsVennDIagram.getTrackNamesFromFormParameters(
choices)
ret = ''
# ret += 'coiches='+str(choices) + '<br/>'
# ret += 'genome='+genome+'<br/>'
# ret += 'trackNames='+str(trackNames)+'<br/><br/>'
if choices[3] != 'Several bed files' and choices[
0] == 'From repository':
if len(list(trackNames)) == 0:
return ret + 'Need one category.bed file as input'
if len(list(trackNames)) > 1:
return ret + 'Need just one category.bed file as input'
if len(list(trackNames)) > len(
CreateBpsVennDIagram.getPrimeList()):
return ret + 'To many files for tool, max number of files is ' + len(
CreateBpsVennDIagram.getPrimeList())
else:
if len(list(trackNames)) < 2:
return ret + 'Need at least two tracks (or bed files) as input'
# if ret:
# return ret
return None
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
if cls.exception:
return cls.exception
#check track
errorString = GeneralGuiTool._checkTrack(choices, 'targetTrack', 'targetTrackGenome')
if errorString:
return errorString
genome, tn, tf = GeneralGuiTool._getBasicTrackFormat(choices, 'targetTrack', 'targetTrackGenome')
errorString = ''
from os import linesep
if tf not in SegmentsOverlapVisualizationTool.TRACK_ALLOWED_TRACK_TYPES:
errorString += '%s is not a supported track type for this tool. Supported track types are ' %tf
errorString += str(SegmentsOverlapVisualizationTool.TRACK_ALLOWED_TRACK_TYPES) + linesep
return errorString
if choices.refTrackCollection is not None:
targetTrackGenome = choices.targetTrackGenome
errorString = GeneralGuiTool._checkGSuiteFile(choices.refTrackCollection)
if errorString:
return errorString
refGSuite = getGSuiteFromGalaxyTN(choices.refTrackCollection)
#check genome
errorString = GeneralGuiTool._checkGenomeEquality(targetTrackGenome, refGSuite.genome)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteRequirements \
(refGSuite,
SegmentsOverlapVisualizationTool.GSUITE_ALLOWED_FILE_FORMATS,
SegmentsOverlapVisualizationTool.GSUITE_ALLOWED_LOCATIONS,
SegmentsOverlapVisualizationTool.GSUITE_ALLOWED_TRACK_TYPES,
SegmentsOverlapVisualizationTool.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
#number of tracks
errorString = GeneralGuiTool._checkGSuiteTrackListSize(refGSuite, maxSize=10)
if errorString:
return errorString
else:
return None
def validateGSuite(cls, choices):
errorString = cls._checkGSuiteFile(choices.gSuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite,
allowedLocations=CommonClusteringFunctions.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=CommonClusteringFunctions.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=CommonClusteringFunctions.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite, 2)
if errorString:
return errorString
def validateAndReturnErrors(cls, choices):
genome = choices.genome
genomicRegions = choices.genomicRegions
genomicRegionsTracks = choices.genomicRegionsTracks
sourceTfs = choices.sourceTfs
sourceTfsDetails = choices.sourceTfsDetails
tfTracks = choices.tfTracks
# Check genome
if genome == cls.SELECT:
return 'Please select a genome build.'
# Check that all region boxes have data:
if genomicRegions == AllTfsOfRegions.SELECT:
return 'Please select a genomic region.'
if genomicRegionsTracks == AllTfsOfRegions.SELECT:
return 'Please select a genomic region track.'
# Check tracks for Genomic Regions-History:
if genomicRegions == AllTfsOfRegions.REGIONS_FROM_HISTORY:
errorString = GeneralGuiTool._checkTrack(choices,
'genomicRegionsTracks',
'genome')
if errorString:
return errorString
# Check that TF box has data:
if sourceTfs == AllTfsOfRegions.SELECT:
return 'Please select a TF source.'
# Check tracks for TFs-History:
if sourceTfs == AllTfsOfRegions.REGIONS_FROM_HISTORY:
if sourceTfsDetails == AllTfsOfRegions.SELECT:
return 'Please select a TF track.'
else:
if isinstance(sourceTfsDetails, basestring):
trackType = sourceTfsDetails.split(':')[1]
if trackType == "gsuite":
errorString = GeneralGuiTool._checkGSuiteFile(
sourceTfsDetails)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(sourceTfsDetails)
sizeErrorString = GeneralGuiTool._checkGSuiteTrackListSize(
gSuite, 1, 1000)
if sizeErrorString:
return sizeErrorString
reqErrorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
AllTfsOfRegions.GSUITE_ALLOWED_FILE_FORMATS,
AllTfsOfRegions.GSUITE_ALLOWED_LOCATIONS,
AllTfsOfRegions.GSUITE_ALLOWED_TRACK_TYPES,
AllTfsOfRegions.GSUITE_DISALLOWED_GENOMES)
if reqErrorString:
return reqErrorString
else:
errorString = GeneralGuiTool._checkTrack(
choices, 'sourceTfsDetails', 'genome')
if errorString:
return errorString
return None
