def createGalaxyTnFromExternalTn(cls, externalTN):
# Hack to support ConvertPrimaryGsuiteToLocalPathsTool
from config.Config import EXT_RESULTS_PATH
assert externalTN[0] == 'external'
assert len(externalTN) == 5
resultsPathDirs = EXT_RESULTS_PATH.rstrip(os.path.sep).split(
os.path.sep)
assert resultsPathDirs[-1] == URL_PREFIX.strip('/')
instance = externalTN[1]
# Hack
if instance == 'dev2':
instance = 'developer'
resultsPathDirs[-1] = instance
extResultsFilesPath = os.path.sep.join(resultsPathDirs + ['files'])
galaxyFn = protoFunctions.getGalaxyFnFromAnyDatasetId(
externalTN[3], galaxyFilePath=extResultsFilesPath)
filePath = protoFunctions.getGalaxyFilesFilename(
galaxyFn, [externalTN[4]])
if not os.path.exists(filePath):
raise ValueError(
'Original track file {} does not exist'.format(filePath))
fileSuffix = getFileSuffix(filePath)
return cls.constructGalaxyTnFromSuitedFn(filePath,
fileEnding=fileSuffix,
name=externalTN[4])
def tableFromDictionary(self,
dataDict,
columnNames=None,
sortable=True,
tableId=None,
expandable=False,
visibleRows=6,
presorted=None,
**kwargs):
"""Render a table from data in dataDict. Each key in dataDict is a row title,
each value is a list of values, each corresponding to the column given with columnNames.
If presorted is set to a number and tableId != None and sortable == True, that column will be presorted (using a hacky solution using jquery.
"""
from proto import CommonFunctions
dataDictOfLists = CommonFunctions.convertToDictOfLists(dataDict)
if presorted is not None and presorted > -1:
assert isinstance(presorted, int), 'presorted must be int'
from quick.util import CommonFunctions
dataDictOfLists = CommonFunctions.smartSortDictOfLists(
dataDictOfLists, sortColumnIndex=presorted)
tableClass = 'colored bordered'
if expandable:
tableClass += ' expandable'
self.tableHeader(headerRow=columnNames,
sortable=sortable,
tableId=tableId,
tableClass=tableClass,
**kwargs)
for key, val in dataDictOfLists.iteritems():
if isinstance(val, list):
self.tableLine([key] + val, **kwargs)
else:
self.tableLine([key] + [val], **kwargs)
self.tableFooter(expandable=expandable,
tableId=tableId,
numRows=len(dataDict),
visibleRows=visibleRows,
**kwargs)
return self
def getGalaxyFnFromEncodedDatasetId(encodedId):
return protoFunctions.getGalaxyFnFromEncodedDatasetId(encodedId)
def getEncodedDatasetIdFromPlainGalaxyId(plainId):
return protoFunctions.getEncodedDatasetIdFromPlainGalaxyId(plainId)
def getEncodedDatasetIdFromGalaxyFn(cls, galaxyFn):
return protoFunctions.getEncodedDatasetIdFromGalaxyFn(galaxyFn)
def extractIdFromGalaxyFn(fn):
return protoFunctions.extractIdFromGalaxyFn(fn)
def extractFnFromGalaxyTN(cls, galaxyTN):
return protoFunctions.extractFnFromDatasetInfo(galaxyTN)
def createGalaxyFilesFn(galaxyFn, filename):
return protoFunctions.createGalaxyFilesFn(galaxyFn, filename)
def getGalaxyFilesFilename(cls, galaxyFn, id):
"""
id is the relative file hierarchy, encoded as a list of strings
"""
return protoFunctions.getGalaxyFilesFilename(galaxyFn, id)
def getGalaxyFilesDir(galaxyFn):
return protoFunctions.getGalaxyFilesDir(galaxyFn)