h2. Cancel a container request
-<code>
+{% codeblock as python %}
import arvados
arvados.api().container_requests().update(uuid=container_request_uuid, body={"priority": 0}).execute()
-</code>
+{% endcodeblock %}
h2. Cancel all container requests
-<code>
+{% codeblock as python %}
import arvados
api = arvados.api()
result = api.container_requests().list(filters=[["state", "=", "Committed"], ["priority", ">", "0"]]).execute()["items"]
for container_request in result:
api.container_requests().update(uuid=container_request["uuid"], body={"priority": 0}).execute()
-</code>
+{% endcodeblock %}
h2. List completed container requests
-<code>
+{% codeblock as python %}
import arvados
api = arvados.api()
result = api.container_requests().list(filters=[["name", "like", name], ["state", "=", "Final"]]).execute()["items"]
for container_request in result:
container = container_dict[container_request["container_uuid"]]
print("%s, %s, %s" % (container_request["uuid"], container_request["name"], "Success" if container["exit_code"] == 0 else "Failed"))
-</code>
+{% endcodeblock %}
h2. Get input of a CWL workflow
-<code>
+{% codeblock as python %}
import arvados
api = arvados.api()
+container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
container_request = arvados.api().container_requests().get(uuid=container_request_uuid).execute()
print(container_request["mounts"]["/var/lib/cwl/cwl.input.json"])
-</code>
+{% endcodeblock %}
h2. Get output of a CWL workflow
-<code>
+{% codeblock as python %}
import arvados
import arvados.collection
api = arvados.api()
+container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
container_request = arvados.api().container_requests().get(uuid=container_request_uuid).execute()
collection = arvados.collection.CollectionReader(container_request["output_uuid"])
print(collection.open("cwl.output.json").read())
-</code>
+{% endcodeblock %}
-h2. Run a CWL workflow from a workflow record
+h2. List input of child requests
+
+{% codeblock as python %}
+import arvados
+api = arvados.api()
+parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax
+container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_container_uuid = container_request["container_uuid"]
+child_requests = arvados.api().container_requests().list(filters=[
+ ["requesting_container_uuid", "=", parent_container_uuid],
+ ["name", "like", namefilter]]).execute()
+for c in child_requests["items"]:
+ print("%s" % c["name"])
+ for m in c["mounts"].values():
+ if "portable_data_hash" in m:
+ print(" %s" % m["portable_data_hash"])
+{% endcodeblock %}
+
+h2. List output of child requests
+
+{% codeblock as python %}
+import arvados
+api = arvados.api()
+parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax
+container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_container_uuid = container_request["container_uuid"]
+child_requests = arvados.api().container_requests().list(filters=[
+ ["requesting_container_uuid", "=", parent_container_uuid],
+ ["name", "like", namefilter]]).execute()
+output_uuids = [c["output_uuid"] for c in child_requests["items"]]
+collections = arvados.api().collections().list(filters=[["uuid", "in", output_uuids]]).execute()
+uuid_to_pdh = {c["uuid"]: c["portable_data_hash"] for c in collections["items"]}
+for c in child_requests["items"]:
+ print("%s -> %s" % (c["name"], uuid_to_pdh[c["output_uuid"]]))
+{% endcodeblock %}
+
+h2. List failed child requests
+
+{% codeblock as python %}
+import arvados
+api = arvados.api()
+parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_container_uuid = container_request["container_uuid"]
+child_requests = arvados.api().container_requests().list(filters=[
+ ["requesting_container_uuid", "=", parent_container_uuid]], limit=1000).execute()
+child_containers = {c["container_uuid"]: c for c in child_requests["items"]}
+cancelled_child_containers = arvados.api().containers().list(filters=[
+ ["exit_code", "!=", "0"],
+ ["uuid", "in", 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 %}
+
+h2. Get log of a child request
+
+{% codeblock as python %}
+import arvados
+import arvados.collection
+api = arvados.api()
+container_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+container_request = arvados.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())
+{% endcodeblock %}
+
+h2. Create a collection sharing link
+
+{% codeblock as python %}
+import arvados
+api = arvados.api()
+download="https://your.download.server"
+collection_uuid="qr1hi-4zz18-zzzzzzzzzzzzzzz"
+token = api.api_client_authorizations().create(body={"api_client_authorization":{"scopes": [
+ "GET /arvados/v1/collections/%s" % collection_uuid,
+ "GET /arvados/v1/collections/%s/" % collection_uuid,
+ "GET /arvados/v1/keep_services/accessible"]}}).execute()
+print("%s/c=%s/t=%s/_/" % (download, collection_uuid, token["api_token"]))
+{% endcodeblock %}
+
+h2. Combine two or more collections
+
+Note, if two collections have files of the same name, the contents will be concatenated in the resulting manifest.
+
+{% codeblock as python %}
+import arvados
+import arvados.collection
+api = arvados.api()
+project_uuid = "qr1hi-tpzed-zzzzzzzzzzzzzzz"
+collection_uuids = ["qr1hi-4zz18-aaaaaaaaaaaaaaa", "qr1hi-4zz18-bbbbbbbbbbbbbbb"]
+combined_manifest = ""
+for u in collection_uuids:
+ c = api.collections().get(uuid=u).execute()
+ combined_manifest += c["manifest_text"]
+newcol = arvados.collection.Collection(combined_manifest)
+newcol.save_new(name="My combined collection", owner_uuid=project_uuid)
+{% endcodeblock %}
projects / arvados.git / blobdiff