def execute(self):
self.stdoutToHistory()
#print self.params
#tracks = self.params['track1'].split(':')
username = self.params['userEmail'] if self.params.has_key('userEmail') else ''
track = self.params['track1'] if self.params.has_key('track1') else []
print 'GalaxyInterface.startPreProcessing', (self.genome, track, username)
GalaxyInterface.startPreProcessing(self.genome, track, username)
def execute(self):
self.stdoutToHistory()
#print self.params
#tracks = self.params['track1'].split(':')
username = self.params['userEmail'] if self.params.has_key(
'userEmail') else ''
track = self.params['track1'] if self.params.has_key('track1') else []
print 'GalaxyInterface.startPreProcessing', (self.genome, track,
username)
GalaxyInterface.startPreProcessing(self.genome, track, username)
def reinstallGenomes(genomeList, username, genomeListIsFn='True', verbose='False'):
"genomeList username genomeListIsFn=True verbose=False"
from quick.application.GalaxyInterface import GalaxyInterface
from gold.util.CustomExceptions import PreprocessError
from quick.extra.StandardizeTrackFiles import PlainMover
from config.Config import DebugConfig
genomeListIsFn = ast.literal_eval(genomeListIsFn)
verbose = ast.literal_eval(verbose)
prevPassOnPreprocessExceptions = DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS
prevVerbose = DebugConfig.VERBOSE
DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS = True
DebugConfig.VERBOSE = verbose
track_cats = ['Sequence:DNA', 'Genome build properties', 'Genes and gene subsets', 'Sample data']
if genomeListIsFn:
genomes = [_.strip() for _ in open(genomeList)]
else:
genomes = genomeList.split(',')
for genome in genomes:
genome = genome.strip()
print genome
if GenomeInfo(genome).installed and GenomeInfo._queryShelveWithKey(genome, 'r', old=False) is not None:
# Trigger installation double-check
gi = GenomeInfo(genome)
gi.installed = False
gi.store()
if gi.isInstalled():
print '\n**Genome "{}" was alread installed in the new shelve. Skipping!**\n'.format(genome)
continue
for track_cat in track_cats:
try:
GalaxyInterface.startPreProcessing(genome, track_cat.split(':'), username)
except PreprocessError, e:
traceback.print_exc()
print
match = re.search(r'trackName="([^"]+)"', str(e))
if match:
trackName = match.group(1).split(':')
PlainMover.parseFiles(genome, trackName, 'std_to_error')
print '\n\n**Moved track "{}" to "parsingErrorTracks" file structure**\n'.format(':'.join(trackName))
genome_info = GenomeInfo(genome)
installed = genome_info.flagAsInstalled(username)
if installed:
print '\n**Genome "{}" was reinstalled successfully!**\n'.format(genome)
else:
print '\n**Genome "{}" was not reinstalled!**\n'.format(genome)
