Merge branch 'master' into 6657-no-git-in-arv-copy

[arvados.git] / sdk / python / arvados / commands / arv_copy.py

diff --git a/sdk/python/arvados/commands/arv_copy.py b/sdk/python/arvados/commands/arv_copy.py
index 54d9798e401049c8273f90b597a8bb80d94ed1b0..e7eb5a9e2802ae8cede8ec2987f75cbcc8fba933 100755 (executable)
--- a/sdk/python/arvados/commands/arv_copy.py
+++ b/sdk/python/arvados/commands/arv_copy.py
@@ -32,6 +32,8 @@ import arvados.util
 import arvados.commands._util as arv_cmd
 import arvados.commands.keepdocker
 
+from arvados.api import OrderedJsonModel
+
 logger = logging.getLogger('arvados.arv-copy')
 
 # local_repo_dir records which git repositories from the Arvados source
@@ -180,7 +182,8 @@ def api_for_instance(instance_name):
         client = arvados.api('v1',
                              host=cfg['ARVADOS_API_HOST'],
                              token=cfg['ARVADOS_API_TOKEN'],
-                             insecure=api_is_insecure)
+                             insecure=api_is_insecure,
+                             model=OrderedJsonModel())
     else:
         abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name))
     return client
@@ -209,6 +212,12 @@ def copy_pipeline_instance(pi_uuid, src, dst, args):
     pi = src.pipeline_instances().get(uuid=pi_uuid).execute(num_retries=args.retries)
 
     if args.recursive:
+        # Check if git is available
+        try:
+            arvados.util.run_command(['git', '--help'])
+        except:
+            abort('git command is not available. Please ensure git is installed.')
+
         if not args.dst_git_repo:
             abort('--dst-git-repo is required when copying a pipeline recursively.')
         # Copy the pipeline template and save the copied template.
@@ -410,12 +419,10 @@ def create_collection_from(c, src, dst, args):
     for link_class in ("docker_image_repo+tag", "docker_image_hash"):
         docker_links = src.links().list(filters=[["head_uuid", "=", collection_uuid], ["link_class", "=", link_class]]).execute(num_retries=args.retries)['items']
 
-        for d in docker_links:
-            body={
-                'head_uuid': dst_collection['uuid'],
-                'link_class': link_class,
-                'name': d['name'],
-            }
+        for src_link in docker_links:
+            body = {key: src_link[key]
+                    for key in ['link_class', 'name', 'properties']}
+            body['head_uuid'] = dst_collection['uuid']
             body['owner_uuid'] = args.project_uuid
 
             lk = dst.links().create(body=body).execute(num_retries=args.retries)