コード例 #1
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  # Query job status
  status = appServicePort.queryStatus(queryStatusRequest(jobID))

# If execution is successful retrieve job outputs. 
if status._code == 8: # 8 = GramJob.STATUS_DONE

  # Create local directory to hold output files
  output_dir = 'meme_out'
  mkdir(output_dir);

  # Instantiate a collection of outputs
  outputs = appServicePort.getOutputs(getOutputsRequest(jobID))

  # Instantiate a request object for retrieving output files
  fileRequest = getOutputAsBase64ByNameRequest()

  # Retreive each output file and save to local directory.
  # MEME writes stdout and stderr to files that aren't listed
  # in the response, so we handle those separately.
  print "\tStandard Output:", outputs._stdOut
  localOutput = open(output_dir + '/' + "stdout.txt", "w")
  fileRequest._jobID = jobID
  fileRequest._fileName = "stdout.txt"
  content = appServicePort.getOutputAsBase64ByName(fileRequest)
  print >>localOutput, content
  localOutput.close()
  print "\tStandard Error:", outputs._stdErr
  localOutput = open(output_dir + '/' + "stderr.txt", "w")
  fileRequest._jobID = jobID
  fileRequest._fileName = "stderr.txt"
コード例 #2
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    sleep(30)

    # Query job status
    status = appServicePort.queryStatus(queryStatusRequest(jobID))

if status._code == 8:  # 8 = GramJob.STATUS_DONE

    # Create local directory to hold output files
    output_dir = 'fimo_out'
    mkdir(output_dir)

    # Find out what outputs were generated by the job
    outputs = appServicePort.getOutputs(getOutputsRequest(jobID))

    # Instantiate a request object for reteiving output files
    req = getOutputAsBase64ByNameRequest()

    # Retreive each output file and save to local directory.
    # MEME writes stdout and stderr to files that aren't listed
    # in the response, so we handle those separately.
    print "\tStandard Output:", outputs._stdOut
    output = open(output_dir + '/' + "stdout.txt", "w")
    req._jobID = resp._jobID
    req._fileName = "stdout.txt"
    content = appServicePort.getOutputAsBase64ByName(req)
    print >> output, content
    output.close()
    print "\tStandard Error:", outputs._stdErr
    output = open(output_dir + '/' + "stderr.txt", "w")
    req._jobID = jobID
    req._fileName = "stderr.txt"
コード例 #3
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ファイル: MemeClient.py プロジェクト: xfLee/denovochipseq
    # Query job status
    status = appServicePort.queryStatus(queryStatusRequest(jobID))

# If execution is successful retrieve job outputs.
if status._code == 8:  # 8 = GramJob.STATUS_DONE

    # Create local directory to hold output files
    output_dir = "meme_out"
    mkdir(output_dir)

    # Instantiate a collection of outputs
    outputs = appServicePort.getOutputs(getOutputsRequest(jobID))

    # Instantiate a request object for retrieving output files
    fileRequest = getOutputAsBase64ByNameRequest()

    # Retreive each output file and save to local directory.
    # MEME writes stdout and stderr to files that aren't listed
    # in the response, so we handle those separately.
    print "\tStandard Output:", outputs._stdOut
    localOutput = open(output_dir + "/" + "stdout.txt", "w")
    fileRequest._jobID = jobID
    fileRequest._fileName = "stdout.txt"
    content = appServicePort.getOutputAsBase64ByName(fileRequest)
    print >> localOutput, content
    localOutput.close()
    print "\tStandard Error:", outputs._stdErr
    localOutput = open(output_dir + "/" + "stderr.txt", "w")
    fileRequest._jobID = jobID
    fileRequest._fileName = "stderr.txt"
コード例 #4
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ファイル: BabelClient.py プロジェクト: SinSiXX/opaltoolkit
# Retrieve job outputs, if execution is successful
if status._code == 8: # 8 = GramJob.STATUS_DONE
    print "Retrieving Babel output metadata: "
    resp = appServicePort.getOutputs(getOutputsRequest(jobID))

    # Retrieve a listing of all output files
    print "\tStandard Output:", resp._stdOut, "\n", \
	  "\tStandard Error:", resp._stdErr
    if (resp._outputFile != None):
	for i in range(0, resp._outputFile.__len__()):
	    print "\t" + resp._outputFile[i]._name, ":", resp._outputFile[i]._url


    # Retrieve an output file as a Base64 encoded binary
    print "Downloading Babel output: "
    req = getOutputAsBase64ByNameRequest()
    req._jobID = jobID
    req._fileName = "stdout.txt"
    resp = appServicePort.getOutputAsBase64ByName(req)
    print resp

# Set up blocking job launch
req = launchJobBlockingRequest()
req._argList = "-ipdb benzene.pdb -h -opdb output.pdb"
inputFiles = []
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = 'benzene.pdb'
sampleFile = open("./etc/benzene.pdb", "r")
sampleFileString = sampleFile.read()
sampleFile.close()
inputFile._contents = sampleFileString