[ARVADOS] created: 278ab6f51df6163e49eedd16afc8bfa907522ce8

[Git user]

        at  278ab6f51df6163e49eedd16afc8bfa907522ce8 (commit)


commit 278ab6f51df6163e49eedd16afc8bfa907522ce8
Author: radhika <radhika at curoverse.com>
Date:   Wed Jan 4 04:20:01 2017 -0500

    10110: arv-copy workflows

diff --git a/sdk/python/arvados/commands/arv_copy.py b/sdk/python/arvados/commands/arv_copy.py
index 1f72635..71820b3 100755
--- a/sdk/python/arvados/commands/arv_copy.py
+++ b/sdk/python/arvados/commands/arv_copy.py
@@ -33,6 +33,7 @@ import arvados.keep
 import arvados.util
 import arvados.commands._util as arv_cmd
 import arvados.commands.keepdocker
+import ruamel.yaml as yaml
 
 from arvados.api import OrderedJsonModel
 from arvados._version import __version__
@@ -144,6 +145,9 @@ def main():
         set_src_owner_uuid(src_arv.pipeline_templates(), args.object_uuid, args)
         result = copy_pipeline_template(args.object_uuid,
                                         src_arv, dst_arv, args)
+    elif t == 'Workflow':
+        set_src_owner_uuid(src_arv.workflows(), args.object_uuid, args)
+        result = copy_workflow(args.object_uuid, src_arv, dst_arv, args)
     else:
         abort("cannot copy object {} of type {}".format(args.object_uuid, t))
 
@@ -405,6 +409,50 @@ def copy_pipeline_template(pt_uuid, src, dst, args):
 
     return dst.pipeline_templates().create(body=pt, ensure_unique_name=True).execute(num_retries=args.retries)
 
+# copy_workflow(wf_uuid, src, dst, args)
+#
+#    Copies a workflow identified by wf_uuid from src to dst.
+#
+#    If args.recursive is True, also copy any collections
+#      referenced in the workflow definition yaml.
+#
+#    The owner_uuid of the new workflow is set to any given
+#      project_uuid or the user who copied the template.
+#
+#    Returns the copied workflow object.
+#
+def copy_workflow(wf_uuid, src, dst, args):
+    # fetch the workflow from the source instance
+    wf = src.workflows().get(uuid=wf_uuid).execute(num_retries=args.retries)
+
+    if args.recursive:
+        wf_def = yaml.safe_load(wf["definition"])
+        if wf_def is not None:
+            colls = []
+            graph = wf_def.get('$graph', None)
+            if graph is not None:
+                workflow_collections(graph, colls)
+            else:
+                workflow_collections(wf_def, colls)
+            copy_collections(colls, src, dst, args)
+
+    del wf['uuid']
+    wf['owner_uuid'] = args.project_uuid
+
+    return dst.workflows().create(body=wf).execute(num_retries=args.retries)
+
+def workflow_collections(obj, colls):
+    if isinstance(obj, dict):
+        loc = obj.get('location', None)
+        if loc is not None:
+            if loc.startswith("keep:"):
+                colls.append(loc[5:])
+        for x in obj:
+            workflow_collections(obj[x], colls)
+    if isinstance(obj, list):
+        for x in obj:
+            workflow_collections(x, colls)
+
 # copy_collections(obj, src, dst, args)
 #
 #    Recursively copies all collections referenced by 'obj' from src

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