def validate_run(self, log, info, run_code, out):
if "No decoys with label DECOY_ were found" in out:
raise RuntimeError("No DECOY_s found in fasta. Please use other fasta!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log,stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['SPLIB'])
validation.check_file(log, info['TSV'])
validation.check_xml(log, info['TRAML'])
return info
def validate_run(self, log, info, exit_code, out):
validation.check_exitcode(log, exit_code)
if 'Valid models = 0' in out:
raise RuntimeError('No valid model found')
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, out):
validation.check_exitcode(log, exit_code)
if 'Valid models = 0' in out:
raise RuntimeError('No valid model found')
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, run_code, out):
for line in out.splitlines():
if "OpenMS peak type estimation indicates that this is not profile data!" in line:
raise RuntimeError("Found centroid data but LFQ must be run on profile mode data!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info['FEATUREXML'])
return info
def validate_run(self, log, info, run_code, out):
if "No decoys with label DECOY_ were found" in out:
raise RuntimeError(
"No DECOY_s found in fasta. Please use other fasta!")
validation.check_stdout(log, out)
validation.check_exitcode(log, run_code)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if exit_code == -8:
raise RuntimeError("iProphet failed most probably because too few peptides were found in the search before")
for line in stdout.splitlines():
if 'fin: error opening' in line:
raise RuntimeError("Could not read the input file " + line)
validation.check_exitcode(log, exit_code)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
for msg in ['Error:','did not find any InterProphet results in input data!',
'no data - quitting',
'WARNING: No database referenced']:
if msg in stdout:
raise RuntimeError('ProteinProphet error [%s]' % msg)
validation.check_xml(log, info[Keys.PROTXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log,stdout)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
for msg in [
'Error:',
'did not find any InterProphet results in input data!',
'no data - quitting', 'WARNING: No database referenced'
]:
if msg in stdout:
raise RuntimeError('ProteinProphet error [%s]' % msg)
validation.check_xml(log, info[Keys.PROTXML])
return info
def validate_run(self, log, info, exit_code, stdout):
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
#https://groups.google.com/forum/#!topic/spctools-discuss/dV8LSaE60ao
shutil.move(info[Keys.PEPXML], info[Keys.PEPXML]+'.broken')
fout = open(info[Keys.PEPXML],'w')
for line in open(info[Keys.PEPXML]+'.broken').readlines():
if 'spectrumNativeID' in line:
line = re.sub('spectrumNativeID="[^"]*"', '', line)
fout.write(line)
fout.close()
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log,stdout)
if exit_code:
log.warn("exit_code is %s", exit_code)
mzxml = info[Keys.MZXML]
log.warn("maybe the input file %s does not exist any more. check this !" % mzxml)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
if "CometMemAlloc" in stdout:
#print to stdout to reach gUSE rescue functionality. ugly, no?
print "MemoryError"
raise RuntimeError("The job run out of RAM!")
check_stdout(log, stdout)
if exit_code:
log.warn("exit_code is %s", exit_code)
mzxml = info[Keys.MZXML]
log.warn(
"maybe the input file %s does not exist any more. check this !"
% mzxml)
check_exitcode(log, exit_code)
check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log, stdout)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, run_code, out):
validation.check_exitcode(log, run_code)
validation.check_file(log, info['PROTCSV'])
validation.check_file(log, info['PEPCSV'])
validation.check_xml(log, info['CONSENSUSXML'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_xml(log, info['PROTXML'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_stdout(log,stdout)
validation.check_xml(log, info[Keys.PEPXML])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_xml(log, info['PROTXML'])
return info
def validate_run(self, log, info, run_code, out):
validation.check_exitcode(log, run_code)
validation.check_file(log, info['PROTCSV'])
validation.check_file(log, info['PEPCSV'])
validation.check_xml(log, info['CONSENSUSXML'])
return info
