print(collection.open("cwl.output.json").read())
{% endcodeblock %}
+h2. Get state of a CWL workflow
+
+{% codeblock as python %}
+import arvados
+def get_cr_state(cr_uuid):
+ api = arvados.api()
+ cr = api.container_requests().get(uuid=cr_uuid).execute()
+ if cr['container_uuid'] is None:
+ return cr['state']
+ c = api.containers().get(uuid=cr['container_uuid']).execute()
+ if cr['state'] == 'Final' and c['state'] != 'Complete':
+ return 'Cancelled'
+ elif c['state'] in ['Locked', 'Queued']:
+ if c['priority'] == 0:
+ return 'On hold'
+ else:
+ return 'Queued'
+ elif c['state'] == 'Complete' and c['exit_code'] != 0
+ return 'Failed'
+ elif c['state'] == 'Running':
+ if c['runtime_status'].get('error', None):
+ return 'Failing'
+ elif c['runtime_status'].get('warning', None):
+ return 'Warning'
+ return c['state']
+container_request_uuid = 'qr1hi-xvhdp-zzzzzzzzzzzzzzz'
+print(get_cr_state(container_request_uuid))
+{% endcodeblock %}
+
h2. List input of child requests
{% codeblock as python %}
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 %}