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)
def execute(cls, 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 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...'
tempinfofile = ExternalTrackManager.extractFnFromGalaxyTN(
choices[0].split(":"))
abbrv = GenomeImporter.getGenomeAbbrv(tempinfofile)
gi = GenomeInfo(abbrv)
#chrNamesInFasta=gi.sourceChrNames
chrNamesInFasta = cls._getTempChromosomeNames(choices[0]).split(
os.linesep)
chromNamesDict = {}
chrDict = cls._getRenamedChrDictWithSelection(choices)
for i, key in enumerate(chrDict.keys()):
if chrDict[key]:
chromNamesDict[chrNamesInFasta[i]] = key
print 'All chromosomes chosen: ' + str(chromNamesDict)
stdChrDict = cls._getRenamedChrDictWithSelection(choices, stdChrs=True)
stdChrs = [x for x in stdChrDict if stdChrDict[x]]
print 'Standard chromosomes chosen: ' + ", ".join(stdChrs)
GenomeImporter.createGenome(abbrv,
gi.fullName,
chromNamesDict,
stdChrs,
username=username)
gi.flagAsInstalled(username)
print 'FAILED: Error occurred copying from %s to %s: ' % (
fromDir, toDir) + str(e).strip()
sys.exit(1)
for track in ProcTrackOptions.getSubtypes('TestGenome',
['GESourceTracks']):
ti = TrackInfo('TestGenome', ['GESourceTracks', track])
ti.trackName = [track]
ti.genome = 'ModelsForExternalTracks'
ti.store()
from quick.util.GenomeInfo import GenomeInfo
from datetime import datetime
gi = GenomeInfo('TestGenome')
gi.fullName = 'TestGenome'
gi.sourceUrls = ['http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr21.fa.gz', \
'http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chrM.fa.gz']
#gi.sourceChrNames = ['chr21', 'chrM']
gi.genomeBuildSource = 'NCBI'
gi.genomeBuildName = 'hg18'
gi.species = 'H**o Sapiens'
gi.speciesTaxonomyUrl = 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606'
gi.assemblyDetails = 'Chromosome 21 and M from the hg18 genome, used for testing purposes.'
gi.isPrivate = False
gi.privateAccessList = []
gi.isExperimental = False
gi.flagAsInstalled(username='******')
extractTestGenomeAndPreProcess(galaxy_dir)
