def WaitForAssembly(proglist):
''' Checking the status of the assembler, and waiting for it to finish if
it is still running. '''
# Verify that assembly is submitted
if proglist.Exists('Assembler'):
status = proglist['Assembler'].GetStatus()
if status == 'Executing':
printDebug("\nWaiting for Assembly to finish...") #DEBUG
proglist['Assembler'].WaitOn(pattern='Done', ePattern='Error')
status = proglist['Assembler'].GetStatus()
# THE SUCCESS OF THE ASSEMBLY IS VALIDATED
if status == 'Done':
printNsave(template_line%'The Assembly was finished...')
# Retrieve contigs path
contig_data = RetrieveContigsInfo(args.usr, args.token, isolateID)
if contig_data is not None:
path, fid = contig_data
# Removing the gz extension
if path[-3:]=='.gz': path = path[:-3]
# Checking if the file exists as normal or gzipped file
if os.path.exists(path):
paths.add_path('contigs', path)
elif os.path.exists(path+'.gz'):
paths.add_path('contigs', path+'.gz')
else:
printDebug("Contigs could not be found! (%s)"%(path))
printNsave(template_line%'The contigs file could not be found!')
status = 'Failure'
proglist['Assembler'].status = status
else:
printNsave(template_line%'No suitable contigs was created by the assembler!')
status = 'Failure'
proglist['Assembler'].status = status
if status == 'Done': return True, fid
else: return False, None
else:
return True, None
proglist.Add2List(assembler)
printNsave(template_line%'Assembler was executed according to plan...')
else:
# Validate that only 1 file was submitted
if len(inputFiles) != 1:
printDebug("Error: Invalid number of contig files (%s)\n"%(len(inputFiles)))
sys.exit(1)
# Validate that the uploaded file is fasta
if CheckFileType(inputFiles[0]) != 'fasta':
printDebug("Error: Invalid contigs format (%s)!\nOnly the fasta format is recognised as a proper contig format.\n"%
(CheckFileType(inputFiles[0])))
sys.exit(1)
# Add mySQL entry for the contigs
fid = AddFile2DB(isolateID, None, args.usr, 'contigs', inputFiles[0], 'Preassembled contigs')
# Add the contigs path to the paths object
paths.add_path('contigs', inputFiles[0])
# SPECIES TYPING
predicted_species = 'unknown'
if 'KmerFinder' in speciestyping: # KmerFinder
kmerfinder = program(name='KmerFinder',
ptype=None, path=paths['programRoot']+'KmerFinder-2.1.py',
workDir=paths['services'], ssh=False, toQueue=False, wait=False,
args=['--iid', isolateID,
'--ip', args.ip,
'--usr', args.usr,
'--token', args.token,
'-s', args.KFscoring,
'-d', args.KFdatabase
]
)
