def _getTempChromosomeNames(galaxyTn):
if isinstance(galaxyTn, basestring):
galaxyTn = galaxyTn.split(":")
tempinfofile = ExternalTrackManager.extractFnFromGalaxyTN(galaxyTn)
#abbrv=GenomeImporter.getGenomeAbbrv(tempinfofile)
#return os.linesep.join(GenomeInfo(abbrv).sourceChrNames)
return os.linesep.join(GenomeImporter.getChromosomeNames(tempinfofile))
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.installedBy = username
gi.timeOfInstallation = datetime.now()
gi.store()
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... with choices %s'%str(choices)
abbrv = choices[0]
name = choices[1]
#Should test that the genome is not in hyperbrowser.
gi = GenomeInfo(abbrv)
if gi.hasOrigFiles():
sys.stderr.write(
"Genome " + abbrv +
" is already in the Genomic HyperBrowser. Remove the old first."
)
else:
gi.fullName = name
if choices[2] == 'URL':
urls = choices[3].split()
gi.sourceUrls = urls
for url in urls:
try:
GenomeImporter.downloadGenomeSequence(abbrv, url)
except InvalidFormatError:
return
else:
basePath = GenomeImporter.getBasePathSequence(abbrv)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[4].split(':'))
fnDest = basePath + os.path.sep + abbrv + '.fa'
ensurePathExists(fnDest)
copyfile(fnSource, fnDest)
if choices[16] == 'from URL':
urls = choices[3].split()
gi.sourceUrls = urls
for url in urls:
try:
GenomeImporter.downloadGffFile(abbrv, url)
except InvalidFormatError:
return
elif choices[16] == 'from history':
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[18].split(':'))
fnDest = GenomeImporter.getCollectedPathGFF(abbrv)
ensurePathExists(fnDest)
copyfile(fnSource, fnDest)
chrs = GenomeImporter.extractChromosomesFromGenome(abbrv)
#gi.sourceChrNames = chrs
gi.installedBy = username
gi.genomeBuildSource = choices[5]
gi.genomeBuildName = choices[6]
gi.species = choices[7]
gi.speciesTaxonomyUrl = choices[8]
gi.assemblyDetails = choices[9]
gi.privateAccessList = [
v.strip()
for v in choices[10].replace(os.linesep, ' ').replace(
',', ' ').split(' ') if v.find('@') > 0
]
gi.isPrivate = (choices[11] != 'All')
gi.isExperimental = (choices[12] != 'All')
gi.ucscClade = choices[13]
gi.ucscGenome = choices[14]
gi.ucscAssembly = choices[15]
galaxyFile = open(galaxyFn, "w")
galaxyFile.write('Genome abbreviation: ' + abbrv + os.linesep)
galaxyFile.write('Genome full name: ' + name + os.linesep)
galaxyFile.write('Track name: ' +
':'.join(GenomeInfo.getSequenceTrackName(abbrv)) +
os.linesep)
galaxyFile.write('Temp chromosome names: ' + ' || '.join(chrs) +
os.linesep)
#GenomeImporter.saveTempInfo(abbrv, name, chrs)
#print 'Chromosomes: '+chrs
gi.store()
def validateAndReturnErrors(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 ' ' in choices[0]:
return 'Genome short name should not contain spaces.'
basePath = GenomeImporter.getBasePathSequence(choices[0])
if os.path.exists(basePath):
return "Genome sequence path already exists: %s. Rename genome or delete directory to proceed." \
% basePath
if any(c.strip() == '' for c in choices[0:2]):
return "Genome abbreviation and name boxes must be filled."
if choices[2] == 'URL':
if choices[3].strip() == '':
return "Sequence URL box must be filled."
else:
error = GeneralGuiTool._checkTrack(choices, trackChoiceIndex=4, genomeChoiceIndex=None, \
filetype='FASTA', validateFirstLine=True)
if error:
return error
# test if the URLs are alive
if choices[2] == 'URL':
urls = choices[3].strip().split()
urlError = validateURLs(urls)
if urlError:
return urlError
taxonomyUrl = choices[8].strip()
if taxonomyUrl != '':
urlError = validateURL(taxonomyUrl)
if urlError:
return urlError
import re
emails = [v for v in re.split('[ ,\n\t\r]+', choices[10])]
for email in emails:
if not ('@' in email and '.' in email):
#pass
#if len([v for v in choices[8].replace(os.linesep, ' ').replace(',', ' ').split(' ') if not v =='' and v.find('@')<0])>0:
return 'There is an invalid format (%s) inside the E-mail address field' % email
ucscError = validateUcscValues([choices[x] for x in [13, 14, 15]])
if ucscError:
return ucscError
if choices[16] == 'from URL':
if choices[17].strip() == '':
return "Genome annotation URL box must be filled."
elif choices[16] == 'from history':
error = GeneralGuiTool._checkTrack(choices, trackChoiceIndex=18, genomeChoiceIndex=None, \
filetype='FASTA', validateFirstLine=True)
if error:
return error
# test if the URLs are alive
if choices[16] == 'from URL':
urls = choices[17].strip().split()
urlError = validateURLs(urls)
if urlError:
return urlError