9766: Supports packing workflow, setting defaults, uploading dependent files/docker...

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 0d0d41611f08a54af26a81eb673e75f774228172..80734d2f7c8e41e45ce25b7bd38cba6094b071e3 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -23,6 +23,7 @@ from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from .arvtool import ArvadosCommandTool
 from .fsaccess import CollectionFsAccess
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from .arvtool import ArvadosCommandTool
 from .fsaccess import CollectionFsAccess

+from .arvworkflow import make_workflow

 
 from cwltool.process import shortname, UnsupportedRequirement
 from cwltool.pathmapper import adjustFileObjs
 
 from cwltool.process import shortname, UnsupportedRequirement
 from cwltool.pathmapper import adjustFileObjs


@@ -172,6 +173,9 @@ class ArvCwlRunner(object):
             # cwltool.main will write our return value to stdout.
             return tmpl.uuid
 
             # cwltool.main will write our return value to stdout.
             return tmpl.uuid
 

+        if kwargs.get("create_workflow") or kwargs.get("update_workflow"):
+            return make_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
+

         self.debug = kwargs.get("debug")
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 
         self.debug = kwargs.get("debug")
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 


@@ -335,6 +339,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
                         default=True, dest="submit")
     exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")
     exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
                         default=True, dest="submit")
     exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")

+    exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow.")
+    exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow.")

 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",


@@ -361,7 +367,7 @@ def main(args, stdout, stderr, api_client=None):
 
     job_order_object = None
     arvargs = parser.parse_args(args)
 
     job_order_object = None
     arvargs = parser.parse_args(args)

-    if arvargs.create_template and not arvargs.job_order:
+    if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:

         job_order_object = ({}, "")
 
     try:
         job_order_object = ({}, "")
 
     try: