def execute(cls, choices, galaxyFn=None, username=''):
genome, history = choices[:2]
track, catColumn, numHeaderLines = choices[3], choices[4], choices[5]
suffix, catSuffix = choices[6], choices[7]
private = True if choices[-1]=='Yes' else False
GalaxyInterface.integrateTrackFromHistory(genome, history.split(':'), track.split(':'), privateAccess=private, username=username)
#ensurePathExists(NONSTANDARD_DATA_PATH+'/'+'/'.join( [genome]+track.split(':')+['fName.txt'] ) )
StandTrackFiles.runParserClass([genome, track, 'PlainCopier', 'direction=std_to_coll', 'allSubTypes=False', 'subTypeDepth=1'], printUsageWhenError=False)
StandTrackFiles.runParserClass([genome, track, 'SplitFileToSubDirs', 'direction=coll_to_coll', 'allSubTypes=False', \
'subTypeDepth=1', 'subTypeCol='+catColumn, 'numHeaderLines='+numHeaderLines, \
'suffix=.%s' % suffix, 'catSuffix=.%s' % catSuffix], printUsageWhenError=False)
StandTrackFiles.runParserClass([genome, track, 'PlainCopier', 'direction=coll_to_std', 'allSubTypes=True', 'subTypeDepth=1'], printUsageWhenError=False)
GalaxyInterface.startPreProcessing(genome, track, username)
def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices, galaxyFn)
with stdout_redirector(open(galaxyFn, "w", 0)):
core = HtmlCore()
core.append(GalaxyInterface.getHtmlBeginForRuns(galaxyFn))
core.append(
GalaxyInterface.getHtmlForToggles(withRunDescription=False))
core.styleInfoBegin(styleClass='debug')
core.paragraph(
'GalaxyInterface.startPreProcessing({}, {}, {})'.format(
choices.genome, choices.track, username))
print core
if choices.parsingError == cls.MOVE_TO_PARSING_ERROR_CHOICE:
finished = False
while not finished:
DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS = True
try:
GalaxyInterface.startPreProcessing(
choices.genome, choices.track, username)
finished = True
except (PreprocessWarning, PreprocessError) as e:
print e
match = re.search("trackName=\"([^\"]+)\"", str(e))
if match:
trackName = match.group(1).split(':')
PlainMover().parseFiles(choices.genome,
trackName,
direction='std_to_error')
else: # cls.DO_NOTHING_CHOICE
GalaxyInterface.startPreProcessing(choices.genome,
choices.track, username)
core = HtmlCore()
core.styleInfoEnd()
core.script('done = true;')
core.end()
print core
def execute(choices, galaxyFn=None, username=''):
'''Is called when execute-button is pushed by web-user.
Should print output as HTML to standard out, which will be directed to a results page in Galaxy history. If getOutputFormat is anything else than HTML, the output should be written to the file with path galaxyFn.gtr
If needed, StaticFile can be used to get a path where additional files can be put (e.g. generated image files).
choices is a list of selections made by web-user in each options box.
'''
print 'Executing...'
print choices
print choices[-1]
genome = choices[0]
trackNames = choices[1].split(':')
ucscFileName = trackNames[-2]
for cellType in InstallUcscTool.cellTypes:
if ucscFileName.find(cellType) > -1:
print 'CellType and fileName: ', cellType, ucscFileName
break
internalTrackPath = choices[2].split(':')
bedfil, suffix = None, None
metaData = None
if trackNames[0] == 'ucsc':
ucscObj = UcscHandler()
print InstallUcscTool.trackNames
if len(trackNames) == 3:
lastLevelForTrackList = ucscObj.getFinalLevelTrackNames(
genome, trackNames)
else:
lastLevelForTrackList = [trackNames[-2]]
trackNames = trackNames[:-2]
for i in lastLevelForTrackList:
bedfil, metaData = ucscObj.getBedData(genome,
trackNames + [i, 'bed'])
print 'downloaded %s' % i
print bedfil[:35]
time.sleep(0.5)
# path = createOrigPath(genome, internalTrackPath+[i])
path = createOrigPath(genome, internalTrackPath)
origFn = path + os.sep + internalTrackPath[-1] + '.bed'
ensurePathExists(origFn)
open(origFn, 'w').write(bedfil)
os.chmod(origFn, 0664)
# InstallUcscTool.storeTrackInfo(genome, internalTrackPath+[i], metaData)
InstallUcscTool.storeTrackInfo(genome, internalTrackPath,
metaData)
else:
path = createOrigPath(genome, trackNames)
if os.path.isdir(path):
filenames = os.listdir(path)
else:
fileName = os.listdir(path)[0]
print fileName
suffix = fileName.split('.')[-1]
bedfil = open(path + os.sep + fileName, 'r').read()
path = createOrigPath(genome, internalTrackPath)
suffix = trackNames[-1] if not suffix else suffix
origFn = path + os.sep + internalTrackPath[-1] + '.' + suffix
ensurePathExists(origFn)
open(origFn, 'w').write(bedfil)
os.chmod(origFn, 0664)
GalaxyInterface.startPreProcessing(genome, internalTrackPath, username)
