def main():
    script_details = script_utils.parse_docs(transform.__doc__)

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])

    parser.add_argument('--workspace_service_url',
                        help=script_details["Args"]["workspace_service_url"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--workspace_name',
                        help=script_details["Args"]["workspace_name"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument("--object_name", 
                        help=script_details["Args"]["object_name"], 
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--output_file_name',
                        help=script_details["Args"]["output_file_name"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)
    parser.add_argument('--input_directory',
                        help=script_details["Args"]["input_directory"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument("--working_directory", 
                        help=script_details["Args"]["working_directory"], 
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument("--has_replicates", 
                        help=script_details["Args"]["has_replicates"], 
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--input_mapping',
                        help=script_details["Args"]["input_mapping"],
                        action='store', type=unicode, nargs='?', default=None,
                        required=False)

    # custom arguments specific to this uploader
    parser.add_argument('--format_type',
                        help=script_details["Args"]["format_type"],
                        action='store', type=str, required=False)

    args, unknown = parser.parse_known_args()

    logger = script_utils.stderrlogger(__file__)

    logger.debug(args)
    try:
        transform(workspace_service_url=args.workspace_service_url,
                  workspace_name=args.workspace_name,
                  object_name=args.object_name,
                  output_file_name=args.output_file_name,
                  input_directory=args.input_directory,
                  working_directory=args.working_directory,
                  has_replicates=args.has_replicates,
                  input_mapping=args.input_mapping,
                  format_type=args.format_type,
                  logger=logger)
    except Exception as e:
        logger.exception(e)
        sys.exit(1)
            validated = False
            break
        else:
            logger.info("Validation passed on {0}".format(input_file_name))
            checked = True

    if not validated:
        raise Exception("Validation failed!")
    elif not checked:
        raise Exception("No files were found that had a valid fasta or fastq extension.")
    else:
        logger.info("Validation passed.")


if __name__ == "__main__":
    script_details = script_utils.parse_docs(validate.__doc__)

    import argparse

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],                                     
                                     epilog=script_details["Authors"])
    parser.add_argument("--input_directory", help=script_details["Args"]["input_directory"], type=str, nargs="?", required=True)
    parser.add_argument("--working_directory", help=script_details["Args"]["working_directory"], type=str, nargs="?", required=True)

    args, unknown = parser.parse_known_args()

    returncode = 0

    try:
        validate(input_directory = args.input_directory, 
Esempio n. 3
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        logger.info(stdout)

    if stderr is not None and len(stderr) > 0:
        logger.error(
            "Transformation from KBaseGenomes.Genome to Genbank.Genome failed on {0}"
            .format(object_name))
        logger.error(stderr)
        sys.exit(1)

    logger.info(
        "Transformation from KBaseGenomes.Genome to Genbank.Genome completed.")
    sys.exit(0)


if __name__ == "__main__":
    script_details = script_utils.parse_docs(transform.__doc__)

    parser = script_utils.ArgumentParser(
        prog=__file__,
        description=script_details["Description"],
        epilog=script_details["Authors"])
    parser.add_argument("--shock_service_url",
                        help=script_details["Args"]["shock_service_url"],
                        action="store",
                        type=str,
                        nargs='?',
                        required=False)
    parser.add_argument("--workspace_service_url",
                        help=script_details["Args"]["workspace_service_url"],
                        action="store",
                        type=str,
Esempio n. 4
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def main():
    script_details = script_utils.parse_docs(transform.__doc__)

    import argparse

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])

    parser.add_argument('--shock_service_url',
                        help=script_details["Args"]["shock_service_url"],
                        action='store',
                        type=str,
                        nargs='?',
                        required=True)
    parser.add_argument('--handle_service_url',
                        help=script_details["Args"]["handle_service_url"],
                        action='store',
                        type=str,
                        nargs='?',
                        default=None,
                        required=False)
    parser.add_argument('--input_directory',
                        help=script_details["Args"]["input_directory"],
                        action='store',
                        type=str,
                        nargs='?',
                        required=True)
    parser.add_argument('--working_directory',
                        help=script_details["Args"]["working_directory"],
                        action='store',
                        type=str,
                        nargs='?',
                        required=True)
    parser.add_argument('--output_file_name',
                        help=script_details["Args"]["output_file_name"],
                        action='store',
                        type=str,
                        nargs='?',
                        default=None,
                        required=False)
    parser.add_argument('--shock_id',
                        help=script_details["Args"]["shock_id"],
                        action='store',
                        type=str,
                        nargs='?',
                        default=None,
                        required=False)
    parser.add_argument('--handle_id',
                        help=script_details["Args"]["handle_id"],
                        action='store',
                        type=str,
                        nargs='?',
                        default=None,
                        required=False)

    parser.add_argument('--input_mapping',
                        help=script_details["Args"]["input_mapping"],
                        action='store',
                        type=unicode,
                        nargs='?',
                        default=None,
                        required=False)

    # custom arguments specific to this uploader
    parser.add_argument('--polarity',
                        help=script_details["Args"]["polarity"],
                        action='store',
                        type=int,
                        required=False)
    parser.add_argument('--group',
                        help=script_details["Args"]["group"],
                        action='store',
                        type=str,
                        required=False)
    parser.add_argument('--inclusion_order',
                        help=script_details["Args"]["inclusion_order"],
                        action='store',
                        type=int,
                        required=False)
    parser.add_argument('--retention_correction',
                        help=script_details["Args"]["retention_correction"],
                        action='store',
                        type=float,
                        required=False)
    parser.add_argument('--atlases',
                        help=script_details["Args"]["atlases"],
                        action='store',
                        type=str,
                        nargs='?',
                        required=False)
    parser.add_argument('--mzml_file_name',
                        help=script_details["Args"]["mzml_file_name"],
                        action='store',
                        type=str,
                        required=False)
    parser.add_argument('--normalization_factor',
                        help=script_details["Args"]["normalization_factor"],
                        action='store',
                        type=float,
                        required=False)

    args, unknown = parser.parse_known_args()

    logger = script_utils.stderrlogger(__file__)

    logger.debug(args)
    try:
        transform(shock_service_url=args.shock_service_url,
                  handle_service_url=args.handle_service_url,
                  output_file_name=args.output_file_name,
                  input_directory=args.input_directory,
                  working_directory=args.working_directory,
                  shock_id=args.shock_id,
                  handle_id=args.handle_id,
                  input_mapping=args.input_mapping,
                  mzml_file_name=args.mzml_file_name,
                  polarity=args.polarity,
                  atlases=args.atlases,
                  group=args.group,
                  inclusion_order=args.inclusion_order,
                  normalization_factor=args.normalization_factor,
                  retention_correction=args.retention_correction,
                  logger=logger)
    except Exception as e:
        logger.exception(e)
        sys.exit(1)
    # This generates the json for the object
    objectString = simplejson.dumps(contig_set_dict, sort_keys=True, indent=4)

    logger.info("ContigSet data structure creation completed.  Writing out JSON.")

    output_file_path = os.path.join(working_directory,output_file_name) 
    with open(output_file_path, "w") as outFile:
        outFile.write(objectString)
    
    logger.info("Conversion completed.")


# called only if script is run from command line
if __name__ == "__main__":
    script_details = script_utils.parse_docs(transform.__doc__)    

    import argparse

    parser = argparse.ArgumentParser(prog=__file__, 
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])
                                     
    parser.add_argument('--shock_service_url', 
                        help=script_details["Args"]["shock_service_url"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--handle_service_url', 
                        help=script_details["Args"]["handle_service_url"], 
                        action='store', type=str, nargs='?', default=None, required=False)
    parser.add_argument('--input_directory', 
                        help=script_details["Args"]["input_directory"], 
        except biokbase.workspace.client.ServerError as err:
            print "ASSEMBLY SAVE FAILED ON genome " + str(
                assembly_name) + " ERROR: " + str(err)
            raise
        except:
            print "ASSEMBLY SAVE FAILED ON genome " + str(
                assembly_name) + " GENERAL_EXCEPTION: " + str(
                    sys.exc_info()[0])
            raise

    logger.info("Conversion completed.")


# called only if script is run from command line
if __name__ == "__main__":
    script_details = script_utils.parse_docs(upload_assembly.__doc__)

    import argparse

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])

    parser.add_argument('--shock_service_url',
                        help=script_details["Args"]["shock_service_url"],
                        action='store',
                        type=str,
                        nargs='?',
                        required=True)
    parser.add_argument('--handle_service_url',
                        help=script_details["Args"]["handle_service_url"],
                 "name": assembly_name, 
                 "provenance":assembly_provenance}]}) 
            assembly_not_saved = False 
        except biokbase.workspace.client.ServerError as err: 
            print "ASSEMBLY SAVE FAILED ON genome " + str(assembly_name) + " ERROR: " + str(err) 
            raise 
        except: 
            print "ASSEMBLY SAVE FAILED ON genome " + str(assembly_name) + " GENERAL_EXCEPTION: " + str(sys.exc_info()[0]) 
            raise 
    
    logger.info("Conversion completed.")


# called only if script is run from command line
if __name__ == "__main__":
    script_details = script_utils.parse_docs(upload_assembly.__doc__)    

    import argparse

    parser = argparse.ArgumentParser(prog=__file__, 
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])
                                     
    parser.add_argument('--shock_service_url', 
                        help=script_details["Args"]["shock_service_url"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--handle_service_url', 
                        help=script_details["Args"]["handle_service_url"], 
                        action='store', type=str, nargs='?', default=None, required=True)
    parser.add_argument('--workspace_name', nargs='?', help='workspace name to populate', required=True)
    parser.add_argument('--workspace_service_url', action='store', type=str, nargs='?', required=True) 
Esempio n. 8
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def main():
    script_details = script_utils.parse_docs(transform.__doc__)

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])

    parser.add_argument('--workspace_service_url',
                        help=script_details["Args"]["workspace_service_url"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--workspace_name',
                        help=script_details["Args"]["workspace_name"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument("--object_name", 
                        help=script_details["Args"]["object_name"], 
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--output_file_name',
                        help=script_details["Args"]["output_file_name"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)
    parser.add_argument('--input_directory',
                        help=script_details["Args"]["input_directory"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument("--working_directory", 
                        help=script_details["Args"]["working_directory"], 
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--input_mapping',
                        help=script_details["Args"]["input_mapping"],
                        action='store', type=unicode, nargs='?', default=None,
                        required=False)

    # custom arguments specific to this uploader
    parser.add_argument('--format_type',
                        help=script_details["Args"]["format_type"],
                        action='store', type=str, required=False)
    parser.add_argument('--genome_object_name',
                        help=script_details["Args"]["genome_object_name"],
                        action='store', type=str, required=False)
    parser.add_argument('--fill_missing_values',
                        help=script_details["Args"]["fill_missing_values"],
                        action='store', type=int, required=False)
    parser.add_argument('--data_type',
                        help=script_details["Args"]["data_type"],
                        action='store', type=str, required=False)
    parser.add_argument('--data_scale',
                        help=script_details["Args"]["data_scale"],
                        action='store', type=str, required=False)

    args, unknown = parser.parse_known_args()

    logger = script_utils.stderrlogger(__file__)

    logger.debug(args)
    try:
        transform(workspace_service_url=args.workspace_service_url,
                  workspace_name=args.workspace_name,
                  object_name=args.object_name,
                  output_file_name=args.output_file_name,
                  input_directory=args.input_directory,
                  working_directory=args.working_directory,
                  input_mapping=args.input_mapping,
                  format_type=args.format_type,
                  genome_object_name=args.genome_object_name,
                  fill_missing_values=args.fill_missing_values,
                  data_type=args.data_type,
                  data_scale=args.data_scale,
                  logger=logger)
    except Exception as e:
        logger.exception(e)
        sys.exit(1)
def main():
    """
    KBase Convert task manager for converting between KBase objects.
    
    Step 1 - Run a converter to pull the source object and save the destination object.
    
    Args:
        workspace_service_url: URL for a KBase Workspace service where KBase objects 
                               are stored.
        ujs_service_url: URL for a User and Job State service to report task progress
                         back to the user.
        shock_service_url: URL for a KBase SHOCK data store service for storing files 
                           and large reference data.
        handle_service_url: URL for a KBase Handle service that maps permissions from 
                            the Workspace to SHOCK for KBase types that specify a Handle 
                            reference instead of a SHOCK reference.
        source_workspace_name: The name of the source workspace.
        destination_workspace_name: The name of the destination workspace.
        source_object_name: The source object name.
        destination_object_name: The destination object name.
        source_kbase_type: The KBase Workspace type string that indicates the module
                           and type of the object being created.                       
        destination_kbase_type: The KBase Workspace type string that indicates the module
                                and type of the object being created.
        optional_arguments: This is a JSON string containing optional parameters that can
                            be passed in for custom behavior per conversion.
        ujs_job_id: The job id from the User and Job State service that can be used to
                    report status on task progress back to the user.
        job_details: This is a JSON string that passes in the script specific command
                     line options for a given conversion type.  The service pulls
                     these config settings from a script config created by the developer
                     of the conversion script and passes that into the AWE job that
                     calls this script.
        working_directory: The working directory on disk where files can be created and
                           will be cleaned when the job ends with success or failure.
        keep_working_directory: A flag to tell the script not to delete the working
                                directory, which is mainly for debugging purposes.
    
    Returns:
        Literal return value is 0 for success and 1 for failure.
        
        Actual data output is one or more Workspace objects saved to a user's workspace. 
        
    Authors:
        Matt Henderson, Gavin Price            
    """

    logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
    logger.info("Executing KBase Convert tasks")
    
    script_details = script_utils.parse_docs(main.__doc__)
    
    logger.debug(script_details["Args"])
    
    parser = script_utils.ArgumentParser(description=script_details["Description"],
                                     epilog=script_details["Authors"])
    # provided by service config
    parser.add_argument('--workspace_service_url', 
                        help=script_details["Args"]["workspace_service_url"], 
                        action='store', 
                        required=True)
    parser.add_argument('--ujs_service_url', 
                        help=script_details["Args"]["ujs_service_url"], 
                        action='store', 
                        required=True)
    
    # optional because not all KBase Workspace types contain a SHOCK or Handle reference
    parser.add_argument('--shock_service_url', 
                        help=script_details["Args"]["shock_service_url"], 
                        action='store', 
                        default=None)
    parser.add_argument('--handle_service_url', 
                        help=script_details["Args"]["handle_service_url"], 
                        action='store', 
                        default=None)

    # workspace info for pulling the data
    parser.add_argument('--source_workspace_name', 
                        help=script_details["Args"]["source_workspace_name"], 
                        action='store', 
                        required=True)
    parser.add_argument('--source_object_name', 
                        help=script_details["Args"]["source_object_name"], 
                        action='store', 
                        required=True)

    # workspace info for saving the data
    parser.add_argument('--destination_workspace_name', 
                        help=script_details["Args"]["destination_workspace_name"], 
                        action='store', 
                        required=True)
    parser.add_argument('--destination_object_name', 
                        help=script_details["Args"]["destination_object_name"], 
                        action='store', 
                        required=True)

    # the types that we are transforming between, currently assumed one to one 
    parser.add_argument('--source_kbase_type', 
                        help=script_details["Args"]["source_kbase_type"], 
                        action='store', 
                        required=True)
    parser.add_argument('--destination_kbase_type', 
                        help=script_details["Args"]["destination_kbase_type"], 
                        action='store', 
                        required=True)

    # any user options provided, encoded as a jason string                           
    parser.add_argument('--optional_arguments', 
                        help=script_details["Args"]["optional_arguments"], 
                        action='store', 
                        default='{}')

    # Used if you are restarting a previously executed job?
    parser.add_argument('--ujs_job_id', 
                        help=script_details["Args"]["ujs_job_id"], 
                        action='store', 
                        default=None, 
                        required=False)

    # config information for running the validate and transform scripts
    parser.add_argument('--job_details', 
                        help=script_details["Args"]["job_details"], 
                        action='store', 
                        default=None)

    # the working directory is where all the files for this job will be written, 
    # and normal operation cleans it after the job ends (success or fail)
    parser.add_argument('--working_directory', 
                        help=script_details["Args"]["working_directory"], 
                        action='store', 
                        default=None, 
                        required=True)
    parser.add_argument('--keep_working_directory', 
                        help=script_details["Args"]["keep_working_directory"], 
                        action='store_true')

    # ignore any extra arguments
    args, unknown = parser.parse_known_args()
            
    kb_token = os.environ.get('KB_AUTH_TOKEN')
    ujs = UserAndJobState(url=args.ujs_service_url, token=kb_token)

    est = datetime.datetime.utcnow() + datetime.timedelta(minutes=3)
    if args.ujs_job_id is not None:
        ujs.update_job_progress(args.ujs_job_id, kb_token, "KBase Data Convert started", 
                                1, est.strftime('%Y-%m-%dT%H:%M:%S+0000'))

    # parse all the json strings from the argument list into dicts
    # TODO had issues with json.loads and unicode strings, workaround was using simplejson and base64
    
    args.optional_arguments = simplejson.loads(base64.urlsafe_b64decode(args.optional_arguments))
    args.job_details = simplejson.loads(base64.urlsafe_b64decode(args.job_details))
    
    if not os.path.exists(args.working_directory):
        os.mkdir(args.working_directory)

    if args.ujs_job_id is not None:
        ujs.update_job_progress(args.ujs_job_id, kb_token, 
                                "Converting from {0} to {1}".format(args.source_kbase_type,args.destination_kbase_type), 
                                1, est.strftime('%Y-%m-%dT%H:%M:%S+0000') )

    # Step 1 : Convert the objects
    try:
        logger.info(args)
    
        convert_args = args.job_details["transform"]
        convert_args["optional_arguments"] = args.optional_arguments
        convert_args["working_directory"] = args.working_directory
        convert_args["workspace_service_url"] = args.workspace_service_url
        convert_args["source_workspace_name"] = args.source_workspace_name
        convert_args["source_object_name"] = args.source_object_name
        convert_args["destination_workspace_name"] = args.destination_workspace_name
        convert_args["destination_object_name"] = args.destination_object_name
        
        logger.info(convert_args)
        
        task_output = handler_utils.run_task(logger, convert_args)
        
        if task_output["stdout"] is not None:
            logger.debug("STDOUT : " + str(task_output["stdout"]))
        
        if task_output["stderr"] is not None:
            logger.debug("STDERR : " + str(task_output["stderr"]))        
    except Exception, e:
        handler_utils.report_exception(logger, 
                         {"message": 'ERROR : Conversion from {0} to {1}'.format(args.source_kbase_type,args.destination_kbase_type),
                          "exc": e,
                          "ujs": ujs,
                          "ujs_job_id": args.ujs_job_id,
                          "token": kb_token,
                         },
                         {"keep_working_directory": args.keep_working_directory,
                          "working_directory": args.working_directory})

        ujs.complete_job(args.ujs_job_id,
                         kb_token,
                         "Convert to {0} failed.".format(
                             args.destination_workspace_name), 
                         str(e),
                         None)
Esempio n. 10
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    stdout, stderr = tool_process.communicate()

    if len(stderr) > 0:
        logger.error("Validation failed on {0}".format(fileName))
    else:
        logger.info("Validation passed on {0}".format(fileName))
        validated = True

    if not validated:
        raise Exception("Validation failed!")
    else:
        logger.info("Validation passed.")


if __name__ == "__main__":
    script_details = script_utils.parse_docs(validate.__doc__)

    import argparse

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])
    parser.add_argument("--input_file_name",
                        help=script_details["Args"]["input_file_name"],
                        type=str,
                        nargs="?",
                        required=True)
    parser.add_argument("--working_directory",
                        help=script_details["Args"]["working_directory"],
                        type=str,
                        nargs="?",
Esempio n. 11
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        handler_utils.report_exception(logger, error_object, cleanup_details)

        ujs.complete_job(ujs_job_id, 
                         kb_token, 
                         "Download from {0} failed.".format(workspace_name), 
                         traceback.format_exc(), 
                         None)
        sys.exit(1)                                  



if __name__ == "__main__":
    logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
    
    script_details = script_utils.parse_docs(download_taskrunner.__doc__)
        
    parser = script_utils.ArgumentParser(description=script_details["Description"],
                                         epilog=script_details["Authors"])
    # provided by service config
    parser.add_argument('--workspace_service_url', 
                        help=script_details["Args"]["workspace_service_url"], 
                        action='store', 
                        required=True)
    parser.add_argument('--ujs_service_url', 
                        help=script_details["Args"]["ujs_service_url"], 
                        action='store', 
                        required=True)
    
    # optional because not all KBase Workspace types contain a SHOCK or Handle reference
    parser.add_argument('--shock_service_url', 
Esempio n. 12
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def main():
    """
    KBase Convert task manager for converting between KBase objects.
    
    Step 1 - Run a converter to pull the source object and save the destination object.
    
    Args:
        workspace_service_url: URL for a KBase Workspace service where KBase objects 
                               are stored.
        ujs_service_url: URL for a User and Job State service to report task progress
                         back to the user.
        shock_service_url: URL for a KBase SHOCK data store service for storing files 
                           and large reference data.
        handle_service_url: URL for a KBase Handle service that maps permissions from 
                            the Workspace to SHOCK for KBase types that specify a Handle 
                            reference instead of a SHOCK reference.
        source_workspace_name: The name of the source workspace.
        destination_workspace_name: The name of the destination workspace.
        source_object_name: The source object name.
        destination_object_name: The destination object name.
        source_kbase_type: The KBase Workspace type string that indicates the module
                           and type of the object being created.                       
        destination_kbase_type: The KBase Workspace type string that indicates the module
                                and type of the object being created.
        optional_arguments: This is a JSON string containing optional parameters that can
                            be passed in for custom behavior per conversion.
        ujs_job_id: The job id from the User and Job State service that can be used to
                    report status on task progress back to the user.
        job_details: This is a JSON string that passes in the script specific command
                     line options for a given conversion type.  The service pulls
                     these config settings from a script config created by the developer
                     of the conversion script and passes that into the AWE job that
                     calls this script.
        working_directory: The working directory on disk where files can be created and
                           will be cleaned when the job ends with success or failure.
        keep_working_directory: A flag to tell the script not to delete the working
                                directory, which is mainly for debugging purposes.
        debug: Run the taskrunner in debug mode for local execution in a virtualenv.
    
    Returns:
        Literal return value is 0 for success and 1 for failure.
        
        Actual data output is one or more Workspace objects saved to a user's workspace. 
        
    Authors:
        Matt Henderson, Gavin Price            
    """

    logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
    logger.info("Executing KBase Convert tasks")
    
    script_details = script_utils.parse_docs(main.__doc__)
    
    logger.debug(script_details["Args"])
    
    parser = script_utils.ArgumentParser(description=script_details["Description"],
                                         epilog=script_details["Authors"])
    # provided by service config
    parser.add_argument('--workspace_service_url', 
                        help=script_details["Args"]["workspace_service_url"], 
                        action='store', 
                        required=True)
    parser.add_argument('--ujs_service_url', 
                        help=script_details["Args"]["ujs_service_url"], 
                        action='store', 
                        required=True)
    
    # optional because not all KBase Workspace types contain a SHOCK or Handle reference
    parser.add_argument('--shock_service_url', 
                        help=script_details["Args"]["shock_service_url"], 
                        action='store', 
                        default=None)
    parser.add_argument('--handle_service_url', 
                        help=script_details["Args"]["handle_service_url"], 
                        action='store', 
                        default=None)

    # workspace info for pulling the data
    parser.add_argument('--source_workspace_name', 
                        help=script_details["Args"]["source_workspace_name"], 
                        action='store', 
                        required=True)
    parser.add_argument('--source_object_name', 
                        help=script_details["Args"]["source_object_name"], 
                        action='store', 
                        required=True)

    # workspace info for saving the data
    parser.add_argument('--destination_workspace_name', 
                        help=script_details["Args"]["destination_workspace_name"], 
                        action='store', 
                        required=True)
    parser.add_argument('--destination_object_name', 
                        help=script_details["Args"]["destination_object_name"], 
                        action='store', 
                        required=True)

    # the types that we are transforming between, currently assumed one to one 
    parser.add_argument('--source_kbase_type', 
                        help=script_details["Args"]["source_kbase_type"], 
                        action='store', 
                        required=True)
    parser.add_argument('--destination_kbase_type', 
                        help=script_details["Args"]["destination_kbase_type"], 
                        action='store', 
                        required=True)

    # any user options provided, encoded as a jason string                           
    parser.add_argument('--optional_arguments', 
                        help=script_details["Args"]["optional_arguments"], 
                        action='store', 
                        default='{}')

    # Used if you are restarting a previously executed job?
    parser.add_argument('--ujs_job_id', 
                        help=script_details["Args"]["ujs_job_id"], 
                        action='store', 
                        default=None, 
                        required=False)

    # config information for running the validate and transform scripts
    parser.add_argument('--job_details', 
                        help=script_details["Args"]["job_details"], 
                        action='store', 
                        default=None)

    # the working directory is where all the files for this job will be written, 
    # and normal operation cleans it after the job ends (success or fail)
    parser.add_argument('--working_directory', 
                        help=script_details["Args"]["working_directory"], 
                        action='store', 
                        default=None, 
                        required=True)
    parser.add_argument('--keep_working_directory', 
                        help=script_details["Args"]["keep_working_directory"], 
                        action='store_true')

    # turn on debugging options for script developers running locally
    parser.add_argument('--debug', 
                        help=script_details["Args"]["debug"], 
                        action='store_true')

    args = None
    try:
        args = parser.parse_args()
    except Exception, e:
        logger.debug("Caught exception parsing arguments!")
        logger.exception(e)
        sys.exit(1)
Esempio n. 13
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def main():
    """
    KBase Convert task manager for converting between KBase objects.
    
    Step 1 - Run a converter to pull the source object and save the destination object.
    
    Args:
        workspace_service_url: URL for a KBase Workspace service where KBase objects 
                               are stored.
        ujs_service_url: URL for a User and Job State service to report task progress
                         back to the user.
        shock_service_url: URL for a KBase SHOCK data store service for storing files 
                           and large reference data.
        handle_service_url: URL for a KBase Handle service that maps permissions from 
                            the Workspace to SHOCK for KBase types that specify a Handle 
                            reference instead of a SHOCK reference.
        source_workspace_name: The name of the source workspace.
        destination_workspace_name: The name of the destination workspace.
        source_object_name: The source object name.
        destination_object_name: The destination object name.
        source_kbase_type: The KBase Workspace type string that indicates the module
                           and type of the object being created.                       
        destination_kbase_type: The KBase Workspace type string that indicates the module
                                and type of the object being created.
        optional_arguments: This is a JSON string containing optional parameters that can
                            be passed in for custom behavior per conversion.
        ujs_job_id: The job id from the User and Job State service that can be used to
                    report status on task progress back to the user.
        job_details: This is a JSON string that passes in the script specific command
                     line options for a given conversion type.  The service pulls
                     these config settings from a script config created by the developer
                     of the conversion script and passes that into the AWE job that
                     calls this script.
        working_directory: The working directory on disk where files can be created and
                           will be cleaned when the job ends with success or failure.
        keep_working_directory: A flag to tell the script not to delete the working
                                directory, which is mainly for debugging purposes.
        debug: Run the taskrunner in debug mode for local execution in a virtualenv.
    
    Returns:
        Literal return value is 0 for success and 1 for failure.
        
        Actual data output is one or more Workspace objects saved to a user's workspace. 
        
    Authors:
        Matt Henderson, Gavin Price            
    """

    logger = script_utils.stderrlogger(__file__, level=logging.DEBUG)
    logger.info("Executing KBase Convert tasks")

    script_details = script_utils.parse_docs(main.__doc__)

    logger.debug(script_details["Args"])

    parser = script_utils.ArgumentParser(
        description=script_details["Description"],
        epilog=script_details["Authors"])
    # provided by service config
    parser.add_argument('--workspace_service_url',
                        help=script_details["Args"]["workspace_service_url"],
                        action='store',
                        required=True)
    parser.add_argument('--ujs_service_url',
                        help=script_details["Args"]["ujs_service_url"],
                        action='store',
                        required=True)

    # optional because not all KBase Workspace types contain a SHOCK or Handle reference
    parser.add_argument('--shock_service_url',
                        help=script_details["Args"]["shock_service_url"],
                        action='store',
                        default=None)
    parser.add_argument('--handle_service_url',
                        help=script_details["Args"]["handle_service_url"],
                        action='store',
                        default=None)

    # workspace info for pulling the data
    parser.add_argument('--source_workspace_name',
                        help=script_details["Args"]["source_workspace_name"],
                        action='store',
                        required=True)
    parser.add_argument('--source_object_name',
                        help=script_details["Args"]["source_object_name"],
                        action='store',
                        required=True)

    # workspace info for saving the data
    parser.add_argument(
        '--destination_workspace_name',
        help=script_details["Args"]["destination_workspace_name"],
        action='store',
        required=True)
    parser.add_argument('--destination_object_name',
                        help=script_details["Args"]["destination_object_name"],
                        action='store',
                        required=True)

    # the types that we are transforming between, currently assumed one to one
    parser.add_argument('--source_kbase_type',
                        help=script_details["Args"]["source_kbase_type"],
                        action='store',
                        required=True)
    parser.add_argument('--destination_kbase_type',
                        help=script_details["Args"]["destination_kbase_type"],
                        action='store',
                        required=True)

    # any user options provided, encoded as a jason string
    parser.add_argument('--optional_arguments',
                        help=script_details["Args"]["optional_arguments"],
                        action='store',
                        default='{}')

    # Used if you are restarting a previously executed job?
    parser.add_argument('--ujs_job_id',
                        help=script_details["Args"]["ujs_job_id"],
                        action='store',
                        default=None,
                        required=False)

    # config information for running the validate and transform scripts
    parser.add_argument('--job_details',
                        help=script_details["Args"]["job_details"],
                        action='store',
                        default=None)

    # the working directory is where all the files for this job will be written,
    # and normal operation cleans it after the job ends (success or fail)
    parser.add_argument('--working_directory',
                        help=script_details["Args"]["working_directory"],
                        action='store',
                        default=None,
                        required=True)
    parser.add_argument('--keep_working_directory',
                        help=script_details["Args"]["keep_working_directory"],
                        action='store_true')

    # turn on debugging options for script developers running locally
    parser.add_argument('--debug',
                        help=script_details["Args"]["debug"],
                        action='store_true')

    args = None
    try:
        args = parser.parse_args()
    except Exception, e:
        logger.debug("Caught exception parsing arguments!")
        logger.exception(e)
        sys.exit(1)
def main():
    script_details = script_utils.parse_docs(transform.__doc__)

    import argparse

    parser = argparse.ArgumentParser(prog=__file__,
                                     description=script_details["Description"],
                                     epilog=script_details["Authors"])

    parser.add_argument('--shock_service_url',
                        help=script_details["Args"]["shock_service_url"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--handle_service_url',
                        help=script_details["Args"]["handle_service_url"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)
    parser.add_argument('--input_directory',
                        help=script_details["Args"]["input_directory"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--working_directory',
                        help=script_details["Args"]["working_directory"],
                        action='store', type=str, nargs='?', required=True)
    parser.add_argument('--output_file_name',
                        help=script_details["Args"]["output_file_name"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)
    parser.add_argument('--shock_id',
                        help=script_details["Args"]["shock_id"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)
    parser.add_argument('--handle_id',
                        help=script_details["Args"]["handle_id"],
                        action='store', type=str, nargs='?', default=None,
                        required=False)

    parser.add_argument('--input_mapping',
                        help=script_details["Args"]["input_mapping"],
                        action='store', type=unicode, nargs='?', default=None,
                        required=False)

    # custom arguments specific to this uploader
    parser.add_argument('--polarity',
                        help=script_details["Args"]["polarity"],
                        action='store', type=int, required=False)
    parser.add_argument('--group',
                        help=script_details["Args"]["group"],
                        action='store', type=str, required=False)
    parser.add_argument('--inclusion_order',
                        help=script_details["Args"]["inclusion_order"],
                        action='store', type=int, required=False)
    parser.add_argument('--retention_correction',
                        help=script_details["Args"]["retention_correction"],
                        action='store', type=float, required=False)
    parser.add_argument('--atlases',
                        help=script_details["Args"]["atlases"],
                        action='store', type=str, nargs='?',
                        required=False)
    parser.add_argument('--mzml_file_name',
                        help=script_details["Args"]["mzml_file_name"],
                        action='store', type=str, required=False)
    parser.add_argument('--normalization_factor',
                        help=script_details["Args"]["normalization_factor"],
                        action='store', type=float, required=False)

    args, unknown = parser.parse_known_args()

    logger = script_utils.stderrlogger(__file__)

    logger.debug(args)
    try:
        transform(shock_service_url=args.shock_service_url,
                  handle_service_url=args.handle_service_url,
                  output_file_name=args.output_file_name,
                  input_directory=args.input_directory,
                  working_directory=args.working_directory,
                  shock_id=args.shock_id,
                  handle_id=args.handle_id,
                  input_mapping=args.input_mapping,
                  mzml_file_name=args.mzml_file_name,
                  polarity=args.polarity,
                  atlases=args.atlases,
                  group=args.group,
                  inclusion_order=args.inclusion_order,
                  normalization_factor=args.normalization_factor,
                  retention_correction=args.retention_correction,
                  logger=logger)
    except Exception as e:
        logger.exception(e)
        sys.exit(1)