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, 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
Example #3
0
 def validate_run(self, log, info, exit_code, stdout):
     if "Warning - no spectra searched" in stdout:
         raise RuntimeError("No spectra in mzXML!")
     check_stdout(log, stdout)
     check_exitcode(log, exit_code)
     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
Example #5
0
    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, 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):
     validation.check_exitcode(log, exit_code)
     validation.check_xml(log, info['PROTXML'])
     return info
Example #9
0
 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