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 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.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not choices.targetTrack and not choices.refTrackCollection:
return ToolGuideController.getHtml(
cls.toolId,
[ToolGuideConfig.TRACK_INPUT, ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
if not choices.targetTrack:
return ToolGuideController.getHtml(cls.toolId,
[ToolGuideConfig.TRACK_INPUT],
choices.isBasic)
if not choices.refTrackCollection:
return ToolGuideController.getHtml(cls.toolId,
[ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(
choices.refTrackCollection)
if errorString:
return errorString
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = GeneralGuiTool._checkTrack(choices, 'targetTrack',
'genome')
if errorString:
return errorString
refGSuite = getGSuiteFromGalaxyTN(choices.refTrackCollection)
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.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.
'''
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(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 ' ' in choices[0]:
return 'Genome short name should not contain spaces.'
basePath = GenomeImporter.getBasePathSequence(choices[0])
if os.path.exists(basePath):
return "Genome sequence path already exists: %s. Rename genome or delete directory to proceed." \
% basePath
if any(c.strip() == '' for c in choices[0:2]):
return "Genome abbreviation and name boxes must be filled."
if choices[2] == 'URL':
if choices[3].strip() == '':
return "Sequence URL box must be filled."
else:
error = GeneralGuiTool._checkTrack(choices, trackChoiceIndex=4, genomeChoiceIndex=None, \
filetype='FASTA', validateFirstLine=True)
if error:
return error
# test if the URLs are alive
if choices[2] == 'URL':
urls = choices[3].strip().split()
urlError = validateURLs(urls)
if urlError:
return urlError
taxonomyUrl = choices[8].strip()
if taxonomyUrl != '':
urlError = validateURL(taxonomyUrl)
if urlError:
return urlError
import re
emails = [v for v in re.split('[ ,\n\t\r]+', choices[10])]
for email in emails:
if not ('@' in email and '.' in email):
#pass
#if len([v for v in choices[8].replace(os.linesep, ' ').replace(',', ' ').split(' ') if not v =='' and v.find('@')<0])>0:
return 'There is an invalid format (%s) inside the E-mail address field' % email
ucscError = validateUcscValues([choices[x] for x in [13, 14, 15]])
if ucscError:
return ucscError
if choices[16] == 'from URL':
if choices[17].strip() == '':
return "Genome annotation URL box must be filled."
elif choices[16] == 'from history':
error = GeneralGuiTool._checkTrack(choices, trackChoiceIndex=18, genomeChoiceIndex=None, \
filetype='FASTA', validateFirstLine=True)
if error:
return error
# test if the URLs are alive
if choices[16] == 'from URL':
urls = choices[17].strip().split()
urlError = validateURLs(urls)
if urlError:
return urlError
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
