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.
'''
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(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.
'''
genome = choices[1] if choices[0] == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
errorStr = GeneralGuiTool._checkHistoryTrack(choices, 2, genome,
'first GTrack')
if errorStr:
return errorStr
errorStr = GeneralGuiTool._checkHistoryTrack(choices, 3, genome,
'second GTrack')
if errorStr:
return errorStr
if choices[2] == choices[3]:
return 'Please select two different GTrack files.'
if len(choices[4]) == 0:
return 'Error: the GTrack files do not contain common intersecting factors (positional information or "id" column).'
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.
'''
genome = choices[1] if choices[0] == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
errorStr = GeneralGuiTool._checkHistoryTrack(choices, 2, GtrackGenomeElementSource, genome, 'first GTrack')
if errorStr:
return errorStr
errorStr = GeneralGuiTool._checkHistoryTrack(choices, 3, GtrackGenomeElementSource, genome, 'second GTrack')
if errorStr:
return errorStr
if choices[2] == choices[3]:
return 'Please select two different GTrack files.'
if len(choices[4]) == 0:
return 'Error: the GTrack files do not contain common intersecting factors (positional information or "id" column).'
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.
'''
errorString = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_TYPES,
allowedTrackTypes=cls.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
if choices.genome:
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
return None
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 validateAndReturnErrors(cls, choices):
errorString = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=cls.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
def validateAndReturnErrors(choices):
errorStr = GeneralGuiTool._checkGenome(choices.genome)
if errorStr:
return errorStr
if not choices.seqs:
return 'Please enter at least one sequence'
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.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.location == GSuiteConstants.REMOTE:
return 'All tracks in GSuite file are remote. ' \
'Please download the tracks of the GSuite file before preprocessing.'
errorStr = cls._validateGenome(choices)
if errorStr:
return errorStr
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS)
if errorStr:
return errorStr
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.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats = cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations = cls.GSUITE_ALLOWED_LOCATIONS)
if errorStr:
return errorStr
if choices.operation:
if choices.operation == cls.NO_OPERATION_TEXT:
return 'Please select an operation to perform on the input tracks'
else:
try:
cls._runOperationOnExampleDataAndReturnOutput(choices)
except Exception as e:
return 'An error occured testing operation "%s": ' % choices.operation + str(e)
if choices.changeSuffix == 'Yes' and choices.suffix.strip() == '':
return 'Please select a file suffix'
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.
'''
from gold.gsuite.GSuiteConstants import UNKNOWN, MULTIPLE
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
if not gSuite.isPreprocessed():
return 'Selected GSuite file is not preprocess. Please preprocess ' \
'the GSuite file before continuing the analysis.'
if gSuite.trackType in [UNKNOWN]:
return 'The track type of the GSuite file is not known. The track type ' \
'is needed for doing analysis.'
if gSuite.trackType in [MULTIPLE]:
return 'All tracks in the GSuite file needs to be of the same track ' \
'type. Multiple track types are not supported.'
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 = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
allowedLocations=GSuiteExportToHistoryTool.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=GSuiteExportToHistoryTool.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=GSuiteExportToHistoryTool.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
if choices.changeFormat == cls.OUTPUT_FORMAT_CONVERT and choices.outputFormat is None:
return 'There are no common supported file formats that all selected tracks can be converted to.'
def _validateGenome(cls, choices, validateBinaryTracksIfPresent=True):
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from quick.application.ProcTrackOptions import ProcTrackOptions
allGSuiteGalaxyTNs = [
getattr(choices, key) for key in cls.GSUITE_FILE_OPTIONS_BOX_KEYS
]
if all(allGSuiteGalaxyTNs):
if (not cls._allowGenomeOverride(choices)
) and cls._getNumUniquelySpecifiedGenomes(choices) > 1:
return cls.ERROR_GENOME_BUILD_MISMATCH + ', '.join(
cls._getGsuiteGenomes(choices))
errorStr = GeneralGuiTool._checkGenome(choices.genome)
if errorStr:
return errorStr
if not cls._allowMultipleGenomes(
choices) and choices.genome == GSuiteConstants.MULTIPLE:
return cls.ERROR_MULTIPLE_GENOMES_NOT_ALLOWED
if validateBinaryTracksIfPresent:
for galaxyTN in allGSuiteGalaxyTNs:
gSuite = getGSuiteFromGalaxyTN(galaxyTN)
if gSuite.fileFormat == GSuiteConstants.PREPROCESSED and gSuite.location == GSuiteConstants.LOCAL:
for gSuiteTrack in gSuite.allTracks():
if not ProcTrackOptions.isValidTrack(
choices.genome, gSuiteTrack.trackName,
True):
return cls.ERROR_PREPROCESSED_TRACK_INVALID % gSuiteTrack.title
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.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.history)
if choices.rowIndices:
try:
selectedIndices = CommonFunctionsForTools.processIndicesString(
choices.rowIndices)
maxIndex = max(selectedIndices)
if maxIndex > (gSuite.numTracks()):
return 'Selected row index %i is too high. GSuite contains %i tracks.' % (
maxIndex, gSuite.numTracks())
except:
return 'Please enter valid indices string (e.g. 1-10, 12, 14)'
if gSuite.numTracks() == 0:
return 'GSuite file contains no tracks'
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(choices):
if choices.source == 'Tabular file from history':
if choices.history in [None, '']:
return 'Error: Please select a tabular file from your history. You may need to change the format of your history items to "tabular" or other tabular formats.'
else:
if choices.input == '':
return 'Please type or paste the contents of a tabular file into the input box.'
if choices.numSkipLines is not None:
try:
int(choices.numSkipLines.strip())
except:
return 'Error: please type a correct number of lines to skip ("%s")' % choices.numSkipLines.strip()
fileContentsInfo = TabularToGtrackTool._getFileContentsInfo(choices)
if fileContentsInfo and fileContentsInfo.error is not None:
return fileContentsInfo.error
if choices.selectGenome == 'Yes':
genome = choices.genome
if genome in [None, '']:
return 'Please select a genome build.'
else:
genome = None
if choices.handleSeqId == 'Yes, auto-correct to the best match in the genome build':
if choices.selectGenome != 'Yes':
return 'To auto-correct the sequence ids, you need to specify a genome build.'
if choices.cropCrossingSegments == 'Yes':
if choices.selectGenome != 'Yes':
return 'To crop segments crossing sequence ends, you need to specify a genome build.'
if choices.columnSelection == 'Base columns on existing GTrack file':
return GeneralGuiTool._checkHistoryTrack(choices, 'colSpecFile', genome, 'GTrack')
headers = TabularToGtrackTool._getHeaders(choices)
if not 'seqid' in headers:
return "Error: the 'seqid' column is mandatory but is missing."
if 'edges' in headers and not 'id' in choices:
return "Error: the 'id' column is missing, but is mandatory since the 'edges' column has been selected."
if choices.createDense == 'Yes' and not 'start' in headers:
return 'The start column must be defined in order to create dense track types.'
if choices.trackType is None:
return 'Error: the columns selected do not define a GTrack track type. Please refer to the GTrack specification for more information.'
elif any(x in choices.trackType.lower() for x in ['function', 'partition', 'base pairs']) and choices.createDense == 'No':
denseTracksBasis = {'Function (F)': 'Valued Points (VP)', 'Step Function (SF)': 'Valued Segments (VS)',
'Genome Partition (GP)': 'Segments (S)', 'Linked Base Pairs (LBP)': 'Points (P)'}
trackType, trackTypeBasis = choices.trackType, denseTracksBasis[choices.trackType]
return 'Error: to create track type "%s", you must use select columns corresponing to track type "%s" and ' % (trackType, trackTypeBasis) + \
'select "Yes" for "Create dense track type". For linked track types, select the appropriate "linked" or "edges" columns.'
return None
def getOptionsBoxQueryTrack(prevChoices):
"""
Defines the type and contents of the input box. User selections are
returned to the tools in the prevChoices and choices attributes to other
methods. These are lists of results, one for each input box (in the
order specified by getInputBoxOrder()).
The input box is defined according to the following syntax:
Selection box: ['choice1','choice2']
- Returns: string
Text area: 'textbox' | ('textbox',1) | ('textbox',1,False)
- Tuple syntax: (contents, height (#lines) = 1, read only flag = False)
- The contents is the default value shown inside the text area
- Returns: string
Raw HTML code: '__rawstr__', 'HTML code'
- This is mainly intended for read only usage. Even though more advanced
hacks are possible, it is discouraged.
Password field: '__password__'
- Returns: string
Genome selection box: '__genome__'
- Returns: string
Track selection box: '__track__'
- Requires genome selection box.
- Returns: colon-separated string denoting track name
History selection box: ('__history__',) | ('__history__', 'bed', 'wig')
- Only history items of specified types are shown.
- Returns: colon-separated string denoting galaxy track name, as
specified in ExternalTrackManager.py.
History check box list: ('__multihistory__', ) | ('__multihistory__', 'bed', 'wig')
- Only history items of specified types are shown.
- Returns: OrderedDict with galaxy id as key and galaxy track name
as value if checked, else None.
Hidden field: ('__hidden__', 'Hidden value')
- Returns: string
Table: [['header1','header2'], ['cell1_1','cell1_2'], ['cell2_1','cell2_2']]
- Returns: None
Check box list: OrderedDict([('key1', True), ('key2', False), ('key3', False)])
- Returns: OrderedDict from key to selection status (bool).
:param prevChoices:
"""
return GeneralGuiTool.getHistorySelectionElement(
*getSupportedFileSuffixesForPointsAndSegments()
)
def getOptionsBoxGsuite(prevChoices): # Alternatively: getOptionsBox2()
'''
See getOptionsBoxFirstKey().
prevChoices is a namedtuple of selections made by the user in the
previous input boxes (that is, a namedtuple containing only one element
in this case). The elements can accessed either by index, e.g.
prevChoices[0] for the result of input box 1, or by key, e.g.
prevChoices.key (case 2).
'''
return GeneralGuiTool.getHistorySelectionElement('gsuite')
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.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorStr:
return errorStr
def getOptionsBoxRefTrack(prevChoices): # Alternatively: getOptionsBox2()
'''
See getOptionsBoxFirstKey().
prevChoices is a namedtuple of selections made by the user in the
previous input boxes (that is, a namedtuple containing only one element
in this case). The elements can accessed either by index, e.g.
prevChoices[0] for the result of input box 1, or by key, e.g.
prevChoices.key (case 2).
'''
if prevChoices.gSuite and prevChoices.normStrat and prevChoices.normStrat in [NormalizeTracksInGSuiteTool.NORM_STRAT_TMM]:
return GeneralGuiTool.getHistorySelectionElement('gtrack', 'bed')
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.
'''
genome = choices[1] if choices[0] == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
return GeneralGuiTool._checkHistoryTrack(choices, 2, genome, 'GTrack')
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.
'''
genome = choices[1] if choices[0] == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
return GeneralGuiTool._checkHistoryTrack(choices, 2, GtrackGenomeElementSource, genome, 'GTrack')
def validateAndReturnErrors(choices):
genome = choices.genome if choices.selectGenome == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
error = GeneralGuiTool._checkHistoryTrack(choices, 'history', GenomeElementSource, genome)
if error:
return error
if choices.conversion is None:
suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices.history.split(':'))
return 'No conversions available for the selected file. Please make ' \
'sure that the file type is correct. Current file type: %s' % suffix
def getOptionsBoxHistElement(
prevChoices): # Alternatively: getOptionsBox1()
'''
Defines the type and contents of the input box. User selections are
returned to the tools in the prevChoices and choices attributes to other
methods. These are lists of results, one for each input box (in the
order specified by getInputBoxOrder()).
The input box is defined according to the following syntax:
Selection box: ['choice1','choice2']
- Returns: string
Text area: 'textbox' | ('textbox',1) | ('textbox',1,False)
- Tuple syntax: (contents, height (#lines) = 1, read only flag = False)
- The contents is the default value shown inside the text area
- Returns: string
Password field: '__password__'
- Returns: string
Genome selection box: '__genome__'
- Returns: string
Track selection box: '__track__'
- Requires genome selection box.
- Returns: colon-separated string denoting track name
History selection box: ('__history__',) | ('__history__', 'bed', 'wig')
- Only history items of specified types are shown.
- Returns: colon-separated string denoting galaxy track name, as
specified in ExternalTrackManager.py.
History check box list: ('__multihistory__', ) | ('__multihistory__', 'bed', 'wig')
- Only history items of specified types are shown.
- Returns: OrderedDict with galaxy id as key and galaxy track name
as value if checked, else None.
Hidden field: ('__hidden__', 'Hidden value')
- Returns: string
Table: [['header1','header2'], ['cell1_1','cell1_2'], ['cell2_1','cell2_2']]
- Returns: None
Check box list: OrderedDict([('key1', True), ('key2', False), ('key3', False)])
- Returns: OrderedDict from key to selection status (bool).
'''
#should accept only gtrack suite (but user may not be aware of the types, a file uploaded with Upload file galaxy tool will upload a gsuite as txt by default)
return GeneralGuiTool.getHistorySelectionElement('gsuite')
def validateAndReturnErrors(choices):
genome = choices.genome if choices.selectGenome == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
error = GeneralGuiTool._checkHistoryTrack(choices, 'history', genome)
if error:
return error
if choices.conversion is None:
suffix = ExternalTrackManager.extractFileSuffixFromGalaxyTN(
choices.history.split(':'))
return 'No conversions available for the selected file. Please make ' \
'sure that the file type is correct. Current file type: %s' % suffix
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.selectGenome == 'Yes':
errorStr = GeneralGuiTool._checkGenome(choices.genome)
if errorStr:
return errorStr
if not any(val is not None for val in choices.history.values()):
return 'Please select at least one history element'
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.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
if not choices.selectColumns is None and len(choices.selectColumns) == 0:
return 'GSuite file contains only standard columns'
def getOptionsBoxGSuiteRef(cls, prevChoices):
'''
See getOptionsBoxFirstKey().
prevChoices is a namedtuple of selections made by the user in the
previous input boxes (that is, a namedtuple containing only one element
in this case). The elements can accessed either by index, e.g.
prevChoices[0] for the result of input box 1, or by key, e.g.
prevChoices.key (case 2).
'''
#TODO: boris 20141102, return reference track gsuite element if
#appropriate feature extraction strategy is selected
if prevChoices.similarityTech == cls.SIMILARITY_RELATIONS_TO_OTHER \
or prevChoices.similarityTech == cls.REGIONS_CLUSTERING:
return GeneralGuiTool.getHistorySelectionElement('gsuite')
else:
return None
def validateAndReturnErrors(choices):
if choices.source == 'Tabular file from history':
if choices.history is None:
return 'Error: The history does not contain any tabular files. You may need to change the format of your history items to "tabular" or other tabular formats.'
else:
if choices.input == '':
return 'Please type or paste the contents of a tabular file into the input box.'
if choices.numSkipLines is not None:
try:
int(choices.numSkipLines.strip())
except:
return 'Error: please type a correct number of lines to skip ("%s")' % choices.numSkipLines.strip()
fileContentsInfo = TabularToGtrackTool._getFileContentsInfo(choices)
if fileContentsInfo.error is not None:
return fileContentsInfo.error
genome = choices.genome if choices.selectGenome == 'Yes' else None
if genome == '':
return 'Please select a genome build.'
if choices.handleSeqId == 'Yes, auto-correct to the best match in the genome build':
if choices.selectGenome != 'Yes':
return 'To auto-correct the sequence ids, you need to specify a genome build.'
if choices.columnSelection == 'Base columns on existing GTrack file':
from gold.origdata.GtrackGenomeElementSource import GtrackGenomeElementSource
return GeneralGuiTool._checkHistoryTrack(choices, 'colSpecFile', GtrackGenomeElementSource, genome, 'GTrack')
headers = TabularToGtrackTool._getHeaders(choices)
if not 'seqid' in headers:
return "Error: the 'seqid' column is mandatory but is missing."
if 'edges' in headers and not 'id' in choices:
return "Error: the 'id' column is missing, but is mandatory since the 'edges' column has been selected."
if choices.trackType is None:
return 'Error: the columns selected do not define a GTrack track type. Please refer to the GTrack specification for more information.'
elif any(x in choices.trackType.lower() for x in ['function', 'partition', 'base pairs']):
from gold.application.LogSetup import logLackOfSupport
logLackOfSupport('Track type "%s" is not yet supported by TabularToGtrackTool.' % choices.trackType)
return 'Error: the track type "%s" is not yet fully supported by this tool.' % choices.trackType
return None
def validateAndReturnErrors(cls, choices=None):
errorStr = GeneralGuiTool._checkGSuiteFile(choices.gSuite)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS
)
if errorStr:
return errorStr
def validateAndReturnErrors(cls, choices):
errorString = GeneralGuiTool._checkGSuiteFile(choices.gSuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite)
if errorString:
return errorString
columnY = choices.columnY
if isinstance(columnY, dict):
if not True in columnY.values():
errorString = 'Check at least one value for y-Axis'
return errorString
def getOptionsBoxLdGraphTrack():
return GeneralGuiTool.getHistorySelectionElement('gtrack')
def getOptionsBoxLdTrack(choices):
return GeneralGuiTool.getHistorySelectionElement('gtrack')
def getOptionsBoxGSuite():
return GeneralGuiTool.getHistorySelectionElement('gsuite')
