def updateStandardFoldersForAllGenomes():
for genomeinfo in GalaxyInterface.getAllGenomes():
genome = genomeinfo[1]
if genome == "hg18": #trengs dette?
genome = "hg18"
if genome == "TestGenome": ############### ta bort for aa oppdatere alle genomer.
updateOrCreateStandardFolders(genome)
def updateTrackFolderStatistics():
print('inne i updateTrackFolderStatistics')
#trackInfoShelve = safeshelve.open(SHELVE_FN, 'w')
for genomeinfo in GalaxyInterface.getAllGenomes():
genome = genomeinfo[1]
if genome=="hg18":
genome="hg18"
print "dirname=",genome
thisntracks=0
thisndirs=0
for startparenttrack in GalaxyInterface.getMainTrackNames(genome):
#print "startparenttrack=",startparenttrack
firstparenttrack=[startparenttrack[0]]
ndirs,ntracks = countSubTracks(genome,firstparenttrack , 0 )
thisndirs=thisndirs+ndirs
thisntracks=thisntracks+ntracks
# put counts into genomeinfo.shelve?
print('plan to update genomeinfo', genome, ' set number of folders to ', thisndirs, ' and number of tracks to ', thisntracks)
def updateTrackFolderStatistics():
print('inne i updateTrackFolderStatistics')
#trackInfoShelve = safeshelve.open(SHELVE_FN, 'w')
for genomeinfo in GalaxyInterface.getAllGenomes():
genome = genomeinfo[1]
if genome == "hg18":
genome = "hg18"
print "dirname=", genome
thisntracks = 0
thisndirs = 0
for startparenttrack in GalaxyInterface.getMainTrackNames(genome):
#print "startparenttrack=",startparenttrack
firstparenttrack = [startparenttrack[0]]
ndirs, ntracks = countSubTracks(genome, firstparenttrack, 0)
thisndirs = thisndirs + ndirs
thisntracks = thisntracks + ntracks
# put counts into genomeinfo.shelve?
print('plan to update genomeinfo', genome,
' set number of folders to ', thisndirs,
' and number of tracks to ', thisntracks)
def execute(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.
'''
genomesList = []
for v in GalaxyInterface.getAllGenomes(username):
if choices[3].get(v[0]):
if choices[3][v[0]] and isdir(createDirPath(choices[1].split(':'),v[1])):
genomesList.append(v[1])
#genomesList = [v[1] for v in GalaxyInterface.getAllGenomes(username) if choices[3][v[0]] and isdir(createDirPath(choices[1].split(':'),v[1]))]
#print 'Executing...'
genomes = [choices[0]] + genomesList
oldTn = choices[1]
newTn = choices[2]
for genome in genomes:
renameTrack(genome, oldTn.split(':'), newTn.split(':'))
print '%s renamed to %s in genome %s.' % (oldTn, newTn, genome)
