return 'On hold'
else:
return 'Queued'
- elif c['state'] == 'Complete' and c['exit_code'] != 0
+ elif c['state'] == 'Complete' and c['exit_code'] != 0:
return 'Failed'
elif c['state'] == 'Running':
if c['runtime_status'].get('error', None):
child_containers = {c["container_uuid"]: c for c in child_requests["items"]}
cancelled_child_containers = api.containers().list(filters=[
["exit_code", "!=", "0"],
- ["uuid", "in", child_containers.keys()]], limit=1000).execute()
+ ["uuid", "in", list(child_containers.keys())]], limit=1000).execute()
for c in cancelled_child_containers["items"]:
print("%s (%s)" % (child_containers[c["uuid"]]["name"], child_containers[c["uuid"]]["uuid"]))
{% endcodeblock %}
container_request = api.container_requests().get(uuid=container_request_uuid).execute()
collection = arvados.collection.CollectionReader(container_request["log_uuid"])
for c in collection:
- print(collection.open(c).read())
+ if isinstance(collection.find(c), arvados.arvfile.ArvadosFile):
+ print(collection.open(c).read())
{% endcodeblock %}
-h2. Create a collection sharing link
+h2(#sharing_link). Create a collection sharing link
{% codeblock as python %}
import arvados
content = reader.read(128*1024)
print("Finished downloading %s" % filename)
{% endcodeblock %}
+
+h2. Copy files from a collection a new collection
+
+{% codeblock as python %}
+import arvados.collection
+
+source_collection = "x1u39-4zz18-krzg64ufvehgitl"
+target_project = "x1u39-j7d0g-67q94einb8ptznm"
+target_name = "Files copied from source_collection"
+files_to_copy = ["folder1/sample1/sample1_R1.fastq",
+ "folder1/sample2/sample2_R1.fastq"]
+
+source = arvados.collection.CollectionReader(source_collection)
+target = arvados.collection.Collection()
+
+for f in files_to_copy:
+ target.copy(f, "", source_collection=source)
+
+target.save_new(name=target_name, owner_uuid=target_project)
+print("Created collection %s" % target.manifest_locator())
+{% endcodeblock %}