def getOptionsBoxResults(cls, prevChoices):
#if prevChoices.source.find('HyperBrowser') > -1:
# return
#if prevChoices.showResults in [None,'No']:
# return
if not prevChoices.source or prevChoices.transfer == 'Yes' or prevChoices.outputType != 'Select tracks manually':
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
if prevChoices.source.find('HyperBrowser') > -1:
return gsm.getTrackFileList(prevChoices.search,
prevChoices.subCategory,
'HyperBrowser')
else:
source = prevChoices.source.split('[')[0].strip()
# # allFileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems()]
# # fileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems() if selected]
##allDataTypes = [x.split('[')[0].strip() for x,selected in prevChoices.dataType.iteritems()]
#dataTypes = [x.split('[')[0].strip() for x,selected in prevChoices.dataType.iteritems() if selected]
dataTypes = [prevChoices.dataType.split('[')[0].strip()]
##Was made to speadup so that there will be no filetype comparisons,
##but deactivated for now since there is hardcoded filtering in
##prevChoices.fileType
#if len(allFileTypes) == len(fileTypes):
# fileTypes = []
#return '__rawStr__',gsm.getTrackFileList(prevChoices.search, prevChoices.subCategory,source,dataTypes)
return gsm.getTrackFileList(prevChoices.search,
prevChoices.subCategory, source,
dataTypes)
def getOptionsBoxSource(cls, prevChoices):
if prevChoices.subCategory in [None, '--Select--']:
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
items = gsm.getItems(prevChoices.search, prevChoices.subCategory)
##return [str(item) for item in items]
sourceTupleList = gsm.getDataSources(items)
sourceList = []
countAll = 0
for src, count in sourceTupleList:
sourceList.append(src + ' [' + str(count) + ' files found]')
countAll += count
if len(sourceList) > 1:
sourceList.insert(
0, 'All databases [' + str(countAll) + ' files found]')
##Asked to be removed by Sveinung. Commenting it out (maybe it will be reused later)
# HBGsuite = quick.gsuite.GSuiteHbIntegration.getSubtracksAsGSuite('hg19', ['Sample data', 'Chromatin catalog', prevChoices.search, prevChoices.subCategory])
# if HBGsuite.numTracks() > 0:
# sourceList.append('HyperBrowser['+str(HBGsuite.numTracks())+']')
return sourceList
def getOptionsBoxOutputType(cls, prevChoices):
#if prevChoices.source.find('HyperBrowser') > -1:
# return
if not prevChoices.source or prevChoices.transfer == 'Yes' or prevChoices.source.find('HyperBrowser') == -1 \
and not prevChoices.dataType:
#and len([x for x,selected in prevChoices.dataType.iteritems() if selected]) == 0:
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
source = prevChoices.source.split('[')[0].strip()
if prevChoices.source.find('HyperBrowser') > -1:
#fileTypes = []
dataTypes = []
else:
#fileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems() if selected]
#dataTypes = [x.split('[')[0].strip() for x,selected in prevChoices.dataType.iteritems() if selected]
dataTypes = [prevChoices.dataType.split('[')[0].strip()]
count = gsm.getGSuite(prevChoices.search,
prevChoices.subCategory,
source,
dataTypes,
filterFileSuffix=True).numTracks()
choicesList = [
'Keep all tracks as selected above [' + str(count) + ']',
'Select tracks manually'
]
##if prevChoices.source.find('HyperBrowser') == -1:
choicesList.extend(
['Select 10 random tracks', 'Select 50 random tracks'])
# # if gsm.dataSourceExists(source):
# # choicesList.append('Transfer selection to advanced mode for further fine-tuning')
return choicesList
def getRedirectURL(cls, choices):
gsm = TrackGlobalSearchModule(cls.useSqlite)
sourceTool,attr_val_dict = gsm.getSourceToolURLParams(choices.search,\
choices.subCategory,\
choices.source.split('[')[0].strip())
return cls.createGenericGuiToolURL('hb_track_source_test_tool',
sourceTool, attr_val_dict)
def getOptionsBoxResultsTable(
cls, prevChoices): #To display results in HTML table
if not prevChoices.source or prevChoices.transfer == 'Yes' or prevChoices.source.find('HyperBrowser') == -1 \
and not prevChoices.dataType:
#and len([x for x,selected in prevChoices.dataType.iteritems() if selected]) == 0:
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
source = prevChoices.source.split('[')[0].strip()
#dataTypes = [x.split('[')[0].strip() for x,selected in prevChoices.dataType.iteritems() if selected]
dataTypes = [prevChoices.dataType.split('[')[0].strip()]
rowDicts = None
if prevChoices.outputType in [
None, 'select 10 random tracks', 'select 50 random tracks'
]:
return
elif 'all tracks' in prevChoices.outputType:
rowDicts = gsm.getRowsDicts(prevChoices.search,prevChoices.subCategory,source,dataTypes,\
filterFileSuffix = True)
elif prevChoices.outputType == 'Select tracks manually':
rowDicts = gsm.getRowsDicts(prevChoices.search,prevChoices.subCategory,source,dataTypes,\
selectedFileIDs = prevChoices.results, filterFileSuffix = True)
htmlTableDict = {}
if rowDicts:
for row in rowDicts:
if 'url' in row:
filename = row['url'].split('/')[-1]
elif 'uri' in row:
filename = row['uri'].split('/')[-1]
elif '_url' in row:
filename = row['_url'].split('/')[-1]
else:
filename = '<No filename>'
rowList = []
for attr in cls.RESULT_COLS:
if attr in row:
rowList.append(unicode(row[attr]))
htmlTableDict[filename] = rowList
if len(htmlTableDict) == 0:
return
html = HtmlCore()
html.tableFromDictionary(htmlTableDict, columnNames = ['File name'] + cls.RESULT_COLS_HEADER,\
tableId='t1', expandable=True)
return '__rawstr__', unicode(html)
def getOptionsBoxDataType(cls, prevChoices):
if not prevChoices.source or prevChoices.source.find(
'HyperBrowser') > -1 or prevChoices.transfer == 'Yes':
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
items = gsm.getItems(prevChoices.search, prevChoices.subCategory)
source = prevChoices.source.split('[')[0].strip()
datatypes = gsm.getDataTypes(items, source)
countAll = 0
for dt, count in datatypes.iteritems():
countAll += count
##Change requested by Sveinung for simplicity
#return OrderedDict([(dataType + ' ['+str(count)+']',True) for dataType,count in datatypes.iteritems()])
#return ['All data types ['+str(countAll)+' files found]'] + \
return [
dataType + ' [' + str(count) + ' files found]'
for dataType, count in datatypes.iteritems()
]
def getOptionsBoxSubCategory(cls, prevChoices):
if prevChoices.search == '--Select--':
return
gsm = TrackGlobalSearchModule(cls.useSqlite)
return ['--Select--'] + gsm.getSubCategories(prevChoices.search)
def getOptionsBoxSearch(cls, prevChoices):
gsm = TrackGlobalSearchModule(cls.useSqlite)
return ['--Select--'] + gsm.getCategories()
def execute(cls, choices, galaxyFn=None, username=''):
if not choices.source:
return
source = choices.source.split('[')[0].strip()
fileTypes = []
gsm = TrackGlobalSearchModule(cls.useSqlite)
desc = choices.subCategory
if choices.source.find('HyperBrowser') == -1:
#items = gsm.getItems(choices.search,choices.subCategory)
# # allFileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems()]
# # fileTypes = [x.split('[')[0] for x,selected in prevChoices.filetype.iteritems() if selected]
##allDataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems()]
#dataTypes = [x.split('[')[0].strip() for x,selected in choices.dataType.iteritems() if selected]
dataTypes = [choices.dataType.split('[')[0].strip()]
##Was made to speadup so that there will be no filetype comparisons,
##but deactivated for now since there is hardcoded filtering in
##prevChoices.fileType
#if len(allFileTypes) == len(fileTypes):
# fileTypes = []
if 'all tracks' in choices.outputType:
remoteGSuite = gsm.getGSuite(choices.search,
choices.subCategory,
source,
dataTypes,
filterFileSuffix=True)
elif choices.outputType == 'Select tracks manually':
remoteGSuite = gsm.getGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,selectedFileIDs = choices.results)
elif choices.outputType == 'Select 10 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 10)
elif choices.outputType == 'Select 50 random tracks':
remoteGSuite = gsm.getRandomGSuite(choices.search,choices.subCategory,source,dataTypes,\
filterFileSuffix = True,count = 50)
if choices.downloadAndPreprocess == 'Yes' and choices.source.find(
'HyperBrowser') == -1:
trackCount = remoteGSuite.numTracks()
progressViewer = \
ProgressViewer([('Download tracks', trackCount),
('Preprocess tracks', trackCount)], galaxyFn)
#from gold.gsuite.GSuiteDownloader import GSuiteMultipleGalaxyFnDownloader
#gSuiteDownloader = GSuiteMultipleGalaxyFnDownloader()
#localGSuite, errorLocalGSuite = \
# gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
# (remoteGSuite, progressViewer, cls.extraGalaxyFn)
from gold.gsuite.GSuiteDownloader import GSuiteSingleGalaxyFnDownloader
from quick.gsuite.GSuiteHbIntegration import \
writeGSuiteHiddenTrackStorageHtml
gSuiteDownloader = GSuiteSingleGalaxyFnDownloader()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', desc)]
localGSuite, errorLocalGSuite = \
gSuiteDownloader.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites \
(remoteGSuite, progressViewer, hiddenStorageFn, [])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
progressViewer.updateProgressObjectElementCount(
'Preprocess tracks', localGSuite.numTracks())
gSuitePreprocessor = GSuitePreprocessor()
preProcessedGSuite, errorPreProcessGSuite = \
gSuitePreprocessor.visitAllGSuiteTracksAndReturnOutputAndErrorGSuites\
(localGSuite, progressViewer)
#preProcessedGSuite, errorPreProcessGSuite = localGSuite.preProcessAllLocalTracksAndReturnOutputAndErrorGSuites(progressViewer)
GSuiteComposer.composeToFile(
remoteGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('remote', desc)])
GSuiteComposer.composeToFile(
errorLocalGSuite, cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nodownload', desc)])
GSuiteComposer.composeToFile(
localGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName('primary', desc)])
GSuiteComposer.composeToFile(
errorPreProcessGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'nopreprocessed', desc)])
GSuiteComposer.composeToFile(
preProcessedGSuite,
cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'preprocessed', desc)])
else:
GSuiteComposer.composeToFile(remoteGSuite, galaxyFn)