[ARVADOS] updated: 1f3035cfe645741753e45ff8d3cf43a3fc5b2385

[git at public.curoverse.com]

Summary of changes:
 sdk/cli/bin/arv-copy         | 55 ++++++++++++++++++++++++++++++++++++++++++--
 sdk/python/arvados/config.py |  2 ++
 2 files changed, 55 insertions(+), 2 deletions(-)

       via  1f3035cfe645741753e45ff8d3cf43a3fc5b2385 (commit)
      from  143bbe8d10d826b05357a531de6aa2a14f4cffb9 (commit)

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commit 1f3035cfe645741753e45ff8d3cf43a3fc5b2385
Author: Tim Pierce <twp at curoverse.com>
Date:   Tue Sep 2 13:29:11 2014 -0400

    3699: support pipeline templates
    
    arv-copy can work on pipeline templates.

diff --git a/sdk/cli/bin/arv-copy b/sdk/cli/bin/arv-copy
index b076782..25a8b50 100755
--- a/sdk/cli/bin/arv-copy
+++ b/sdk/cli/bin/arv-copy
@@ -1,5 +1,21 @@
 #! /usr/bin/env python
 
+# arv-copy [--recursive] [--no-recursive] object-uuid src dst
+#
+# Copies an object from Arvados instance src to instance dst.
+#
+# By default, arv-copy recursively copies any dependent objects
+# necessary to make the object functional in the new instance
+# (e.g. for a pipeline instance, arv-copy copies the pipeline
+# template, input collection, docker images, git repositories). If
+# --no-recursive is given, arv-copy copies only the single record
+# identified by object-uuid.
+#
+# The user must have files $HOME/.config/arvados/{src}.conf and
+# $HOME/.config/arvados/{dst}.conf with valid login credentials for
+# instances src and dst.  If either of these files is not found,
+# arv-copy will issue an error.
+
 import argparse
 import hashlib
 import os
@@ -19,7 +35,7 @@ def main():
 
     parser.add_argument('--recursive', dest='recursive', action='store_true')
     parser.add_argument('--no-recursive', dest='recursive', action='store_false')
-    parser.add_argument('pipeline_instance_uuid')
+    parser.add_argument('object_uuid')
     parser.add_argument('source_arvados')
     parser.add_argument('destination_arvados')
     parser.set_defaults(recursive=True)
@@ -31,6 +47,16 @@ def main():
     dst_arv = api_for_instance(args.destination_arvados)
 
     # And now for the copying.
+    t = uuid_type(args.object_uuid)
+    if t == 'collection':
+        copy_collection(args.object_uuid, src=src_arv, dst=dst_arv)
+    elif t == 'pipeline_instance':
+        copy_pipeline_instance(args.object_uuid, src=src_arv, dst=dst_arv)
+    elif t == 'pipeline_template':
+        new_pt = copy_pipeline_template(args.object_uuid, src=src_arv, dst=dst_arv)
+        print new_pt
+    else:
+        abort("cannot copy object {} of type {}".format(args.object_uuid, t))
 
     exit(0)
 
@@ -51,11 +77,36 @@ 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,
+                             cache=False)
     else:
         abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name))
     return client
 
+def copy_collection(obj_uuid, src=None, dst=None):
+    raise NotImplementedError
+
+def copy_pipeline_instance(obj_uuid, src=None, dst=None):
+    raise NotImplementedError
+
+def copy_pipeline_template(obj_uuid, src=None, dst=None):
+    # fetch the pipeline template from the source instance
+    old_pt = src.pipeline_templates().get(uuid=obj_uuid).execute()
+    old_pt['name'] = old_pt['name'] + ' copy'
+    del old_pt['uuid']
+    del old_pt['owner_uuid']
+    return dst.pipeline_templates().create(body=old_pt).execute()
+
+uuid_type_map = {
+    "4zz18": "collection",
+    "d1hrv": "pipeline_instance",
+    "p5p6p": "pipeline_template",
+}
+
+def uuid_type(object_uuid):
+    type_str = object_uuid.split('-')[1]
+    return uuid_type_map.get(type_str, None)
+
 def abort(msg, code=1):
     print >>sys.stderr, "arv-copy:", msg
     exit(code)
diff --git a/sdk/python/arvados/config.py b/sdk/python/arvados/config.py
index 211e6f5..c3b9b40 100644
--- a/sdk/python/arvados/config.py
+++ b/sdk/python/arvados/config.py
@@ -30,6 +30,8 @@ def load(config_file):
     cfg = {}
     with open(config_file, "r") as f:
         for config_line in f:
+            if re.match('^\s*$', config_line):
+                continue
             if re.match('^\s*#', config_line):
                 continue
             var, val = config_line.rstrip().split('=', 2)

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