Exemple #1
0
def configure_workflow(workflow, ret_list, connection_galaxy):
    """
    Takes a workflow_uuid and associated data input map to return an expanded workflow 
    from core.models.workflow and workflow_data_input_map    
    """
    logger.debug("workflow.manager configure_workflow called")

    curr_workflow = workflow
    # gets galaxy internal id for specified workflow
    workflow_galaxy_id = curr_workflow.internal_id

    # gets dictionary version of workflow
    workflow_dict = connection_galaxy.get_workflow_dict(workflow_galaxy_id)

    # number of times to repeat workflow expansion
    repeat_num = len(ret_list)

    # creating base workflow to replicate input workflow
    new_workflow = createBaseWorkflow((workflow_dict["name"]))

    # checking to see what kind of workflow exists:
    # does it have  "annotation": "type=COMPACT", in the workflow annotation field
    work_type = getStepOptions(workflow_dict["annotation"])
    COMPACT_WORKFLOW = False

    for k, v in work_type.iteritems():
        if k.upper() == 'TYPE':
            try:
                if v[0].upper() == 'COMPACT':
                    COMPACT_WORKFLOW = True
            except:
                logger.exception("Malformed Workflow tag, cannot parse: %s" %
                                 (work_type))
                return

    # if workflow is tagged w/ type=COMPACT tag,
    if COMPACT_WORKFLOW:
        logger.debug(
            "workflow_manager.tasks.configure_workflow workflow processing: COMPACT"
        )
        new_workflow[
            "steps"], history_download, analysis_node_connections = createStepsCompact(
                ret_list, workflow_dict)
    else:
        logger.debug(
            "workflow_manager.tasks.configure_workflow workflow processing: EXPANSION"
        )
        # Updating steps in imported workflow X number of times
        new_workflow[
            "steps"], history_download, analysis_node_connections = createStepsAnnot(
                ret_list, workflow_dict)

    return new_workflow, history_download, analysis_node_connections
def configure_workflow(workflow, ret_list, connection_galaxy):
    """
    Takes a workflow_uuid and associated data input map to return an expanded workflow 
    from core.models.workflow and workflow_data_input_map    
    """
    logger.debug("workflow.manager configure_workflow called")

    curr_workflow = workflow
    # gets galaxy internal id for specified workflow
    workflow_galaxy_id = curr_workflow.internal_id

    # gets dictionary version of workflow
    workflow_dict = connection_galaxy.get_workflow_dict(workflow_galaxy_id)

    # number of times to repeat workflow expansion
    repeat_num = len(ret_list)
    
    # creating base workflow to replicate input workflow
    new_workflow = createBaseWorkflow( (workflow_dict["name"]) )
    
    # checking to see what kind of workflow exists:
    # does it have  "annotation": "type=COMPACT", in the workflow annotation field
    work_type = getStepOptions(workflow_dict["annotation"])
    COMPACT_WORKFLOW = False
    
    for k,v in work_type.iteritems():
        if k.upper() == 'TYPE':
            try:
                if v[0].upper() == 'COMPACT':
                    COMPACT_WORKFLOW = True
            except:
                logger.exception( "Malformed Workflow tag, cannot parse: %s" % (work_type) )
                return
        
    # if workflow is tagged w/ type=COMPACT tag, 
    if COMPACT_WORKFLOW:
        logger.debug("workflow_manager.tasks.configure_workflow workflow processing: COMPACT")
        new_workflow["steps"], history_download, analysis_node_connections = createStepsCompact(ret_list, workflow_dict)
    else:
        logger.debug("workflow_manager.tasks.configure_workflow workflow processing: EXPANSION")
        # Updating steps in imported workflow X number of times
        new_workflow["steps"], history_download, analysis_node_connections = createStepsAnnot(ret_list, workflow_dict);
          
    return new_workflow, history_download, analysis_node_connections
def configure_workflow(workflow_dict, ret_list):
    """Takes a workflow and associated data input map
    Returns an expanded workflow from core.models.workflow and
    workflow_data_input_map
    """
    logger.debug("workflow.manager configure_workflow called")
    # creating base workflow to replicate input workflow
    new_workflow = createBaseWorkflow(workflow_dict["name"])
    # checking to see what kind of workflow exists:
    # does it have  "annotation": "type=COMPACT", in the workflow annotation
    # field
    work_type = getStepOptions(workflow_dict["annotation"])
    COMPACT_WORKFLOW = False

    for k, v in work_type.iteritems():
        if k.upper() == 'TYPE':
            try:
                if v[0].upper() == 'COMPACT':
                    COMPACT_WORKFLOW = True
            except:
                logger.exception("Malformed workflow tag, cannot parse: %s",
                                 work_type)
                return
    # if workflow is tagged w/ type=COMPACT tag,
    if COMPACT_WORKFLOW:
        logger.debug(
            "workflow_manager.tasks.configure_workflow workflow processing: "
            "COMPACT")
        new_workflow["steps"], history_download, analysis_node_connections = \
            createStepsCompact(ret_list, workflow_dict)
    else:
        logger.debug(
            "workflow_manager.tasks.configure_workflow workflow processing: "
            "EXPANSION")
        # Updating steps in imported workflow X number of times
        new_workflow["steps"], history_download, analysis_node_connections = \
            createStepsAnnot(ret_list, workflow_dict)
    return new_workflow, history_download, analysis_node_connections