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.
'''
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(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.gSuite:
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.GSUITE_INPUT], True)
if choices.normStrat not in [cls.NORM_STRAT_RPKM]:
return 'Not implemented yet'
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.
'''
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not choices.histElement1 or not choices.histElement2:
return ToolGuideController.getHtml(cls.toolId,
[ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
gSuiteList = []
for desc, histElement in [('first', choices.histElement1),
('second', choices.histElement2)]:
errorString = cls._checkGSuiteFile(histElement)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(histElement)
errorString = cls._checkGSuiteTrackListSize\
(gSuite, minSize=cls.MIN_NUMBER_OF_TRACKS, maxSize=cls.MAX_NUMBER_OF_TRACKS)
if errorString:
return errorString
errorString = cls._checkGSuiteRequirements \
(gSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return 'Error in the %s GSuite file: ' % desc + errorString
gSuiteList.append(gSuite)
errorString = cls._checkGenomeEquality(
*[gSuite.genome for gSuite in gSuiteList])
if errorString:
return errorString
for i, desc, divideChoice, numClustersChoice in \
[(0, 'row', choices.divideRows, choices.numClustersRows),
(1, 'column', choices.divideCols, choices.numClustersCols)]:
if divideChoice == 'Yes':
try:
numClusters = int(numClustersChoice)
except:
return numClustersChoice + ' is not an integer (number)'
numTracks = gSuiteList[i].numTracks()
if numClusters < 1 or numClusters > (numTracks / 2):
return 'The number of cluster for the %s tracks must be between 1 and %s' \
% (desc, numTracks / 2)
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 not choices.gSuite:
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
return ToolGuideController.getHtml(cls.toolId,
[ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(choices.gSuite)
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
if choices.similarityTech == cls.SIMILARITY_RELATIONS_TO_OTHER \
or choices.similarityTech == cls.REGIONS_CLUSTERING:
if not choices.gSuiteRef:
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
return ToolGuideController.getHtml(
cls.toolId, [ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(choices.gSuiteRef)
if errorString:
return errorString
gSuiteRef = getGSuiteFromGalaxyTN(choices.gSuiteRef)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuiteRef,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
if choices.similarityTech in [
cls.SIMILARITY_POSITIONAL, cls.SIMILARITY_RELATIONS_TO_OTHER
]:
if not choices.featureSelection:
return 'Feature for similarity calculation has not been selected. ' \
'If no features are available for selection, the track types ' \
'if the clustering and reference tracks are too inconsistent. ' \
'Please remove the inconsistent tracks from the GSuite.'
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.
:param choices: Dict holding all current selections
"""
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not choices.queryTrack and not choices.gsuite:
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.TRACK_INPUT, ToolGuideConfig.GSUITE_INPUT],
choices.isBasic)
if not choices.queryTrack:
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.TRACK_INPUT], choices.isBasic)
if not choices.gsuite:
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.GSUITE_INPUT], choices.isBasic)
errorString = cls._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = cls._checkTrack(choices, 'queryTrack', 'genome')
if errorString:
return errorString
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = cls._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 = cls._checkGSuiteTrackListSize(gsuite)
if errorString:
return errorString
if choices.randStrat in [RAND_BY_UNIVERSE_TEXT]:
errorString = cls._checkTrack(choices, 'intensityTrack', 'genome')
if errorString:
return errorString
if choices.queryTrack and choices.intensityTrack:
basicTFQuery = cls._getBasicTrackFormat(choices, 'queryTrack')[-1]
basicTFIntensity = cls._getBasicTrackFormat(choices, 'intensityTrack')[-1]
if not all(_ == 'points' for _ in [basicTFQuery, basicTFIntensity]):
core = HtmlCore()
core.paragraph('The selected randomization strategy requires the query and '
'the universe track to both be of type "Points". One or both '
'of these tracks have the incorrect track type.')
core.descriptionLine('Current track type of query track', basicTFQuery)
core.descriptionLine('Current track type of universe track', basicTFIntensity)
core.paragraph('The only file formats (Galaxy datatypes) that '
'support the "Points" track type is "gtrack" and "bed.points". '
'To fix your input track(s), do as follows:')
core.orderedList([
'If you currently have a segment track (with segment lengths > 1), '
'please convert it into points tracks by using the tool "Expand or '
'contract points/segments" under the "Customize tracks" submenu.',
'If you currently have a "bed" file where all segments have '
'length one, possibly as the result of step 1, you will need to '
'change the Galaxy datatype to "point.bed". To do this, click the '
'"pencil" icon of the history element, select the "Datatypes" tab '
'and select "point.bed".'])
return str(core)
errorString = cls.validateUserBins(choices)
if errorString:
return errorString