def getStdTrackNameFromGalaxyTN(cls, galaxyTN):
assert(galaxyTN[0].lower() == 'galaxy')
assert(galaxyTN[1].lower() in getSupportedFileSuffixes())
fn = cls.extractFnFromGalaxyTN(galaxyTN)
id = cls.extractIdFromGalaxyFn(fn)
name = galaxyTN[-1]
return ExternalTrackManager.createStdTrackName(id, name)
def getOptionsBoxTrack(prevChoices): # Alternatively: getOptionsBox2()
'''
See getOptionsBoxFirstKey().
prevChoices is a namedtuple of selections made by the user in the
previous input boxes (that is, a namedtuple containing only one element
in this case). The elements can accessed either by index, e.g.
prevChoices[0] for the result of input box 1, or by key, e.g.
prevChoices.key (case 2).
'''
if prevChoices.genome:
return GeneralGuiTool.getHistorySelectionElement(
*getSupportedFileSuffixes())
def getStdTrackNameFromGalaxyTN(cls,
galaxyTN,
allowUnsupportedSuffixes=False):
if isinstance(galaxyTN, basestring):
galaxyTN = galaxyTN.split(':')
assert galaxyTN[0].lower() == 'galaxy', str(galaxyTN)
if not allowUnsupportedSuffixes and not galaxyTN[1].lower(
) in getSupportedFileSuffixes():
raise InvalidFormatError('File type "%s" is not supported.' %
galaxyTN[1].lower())
fn = cls.extractFnFromGalaxyTN(galaxyTN)
id = cls.extractIdFromGalaxyFn(fn)
name = galaxyTN[-1]
return ExternalTrackManager.createStdTrackName(id, name)
def extractFileSuffixFromGalaxyTN(galaxyTN):
suffix = galaxyTN[1]
if not suffix in getSupportedFileSuffixes():
raise ShouldNotOccurError('Filetype ' + suffix + ' not supported.')
return suffix
def getOptionsBoxHistory(prevChoices):
if prevChoices.trackSource == 'history':
from gold.application.DataTypes import getSupportedFileSuffixes
return tuple(['__history__'] + getSupportedFileSuffixes())
def _allTracksHasOriginalFormat(cls, gSuite, genome):
for track in gSuite.allTracks():
if not TrackInfo(genome, track.trackName).fileType in \
getSupportedFileSuffixes():
return False
return True
def getFileSuffix(fn):
from gold.application.DataTypes import getSupportedFileSuffixes
for suffix in getSupportedFileSuffixes():
if '.' in suffix and fn.endswith('.' + suffix):
return suffix
return os.path.splitext(fn)[1].replace('.','')
def extractFileSuffixFromGalaxyTN(galaxyTN,
allowUnsupportedSuffixes=False):
fileSuffixFilterList = None if allowUnsupportedSuffixes else getSupportedFileSuffixes(
)
return protoFunctions.extractFileSuffixFromDatasetInfo\
(galaxyTN, fileSuffixFilterList=fileSuffixFilterList)