h2. Cancel a container request
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
arvados.api().container_requests().update(uuid=container_request_uuid, body={"priority": 0}).execute()
-</code></pre>
+{% endcodeblock %}
h2. Cancel all container requests
-<pre><code>import arvados
+{% 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></pre>
+{% endcodeblock %}
h2. List completed container requests
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
result = api.container_requests().list(filters=[["name", "like", name], ["state", "=", "Final"]]).execute()["items"]
container_uuids = [cr["container_uuid"] for cr in result]
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></pre>
+{% endcodeblock %}
h2. Get input of a CWL workflow
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
-container_request = arvados.api().container_requests().get(uuid=container_request_uuid).execute()
+container_request_uuid="zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+container_request = api.container_requests().get(uuid=container_request_uuid).execute()
print(container_request["mounts"]["/var/lib/cwl/cwl.input.json"])
-</code></pre>
+{% endcodeblock %}
h2. Get output of a CWL workflow
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
import arvados.collection
api = arvados.api()
-container_request = arvados.api().container_requests().get(uuid=container_request_uuid).execute()
+container_request_uuid="zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+container_request = 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></pre>
+{% 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 = 'zzzzz-xvhdp-zzzzzzzzzzzzzzz'
+print(get_cr_state(container_request_uuid))
+{% endcodeblock %}
h2. List input of child requests
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
-parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-namefilter = "bwa%"
-container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
-child_requests = arvados.api().container_requests().list(filters=[
+child_requests = api.container_requests().list(filters=[
["requesting_container_uuid", "=", parent_container_uuid],
["name", "like", namefilter]]).execute()
for c in child_requests["items"]:
for m in c["mounts"].values():
if "portable_data_hash" in m:
print(" %s" % m["portable_data_hash"])
-</code></pre>
+{% endcodeblock %}
h2. List output of child requests
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
-parent_request_uuid = "qr1hi-xvhdp-61y7cjymnhyp7yu"
-namefilter = "bwa%"
-container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
-child_requests = arvados.api().container_requests().list(filters=[
+child_requests = 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()
+collections = 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"]]))
-</code></pre>
+{% endcodeblock %}
h2. List failed child requests
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
-parent_request_uuid = "qr1hi-xvhdp-3d8f1zatx1xio36"
-container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
-child_requests = arvados.api().container_requests().list(filters=[
+child_requests = 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=[
+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"]))
-</code></pre>
+{% endcodeblock %}
h2. Get log of a child request
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
import arvados.collection
api = arvados.api()
-container_request_uuid = "qr1hi-xvhdp-3d8f1zatx1xio36"
-container_request = arvados.api().container_requests().get(uuid=container_request_uuid).execute()
+container_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+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())
-</code></pre>
+ 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
-<pre><code>import arvados
+{% codeblock as python %}
+import arvados
api = arvados.api()
download="https://your.download.server"
-collection_uuid="your-4zz18-collectionuuid"
+collection_uuid="zzzzz-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"]))
-</code></pre>
+{% 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 = "zzzzz-tpzed-zzzzzzzzzzzzzzz"
+collection_uuids = ["zzzzz-4zz18-aaaaaaaaaaaaaaa", "zzzzz-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 %}
+
+h2. Upload a file into a new collection
+
+{% codeblock as python %}
+import arvados
+import arvados.collection
+
+project_uuid = "zzzzz-j7d0g-zzzzzzzzzzzzzzz"
+collection_name = "My collection"
+filename = "file1.txt"
+
+api = arvados.api()
+c = arvados.collection.Collection()
+with open(filename, "rb") as reader:
+ with c.open(filename, "wb") as writer:
+ content = reader.read(128*1024)
+ while content:
+ writer.write(content)
+ content = reader.read(128*1024)
+c.save_new(name=collection_name, owner_uuid=project_uuid)
+print("Saved %s to %s" % (collection_name, c.manifest_locator()))
+{% endcodeblock %}
+
+h2. Download a file from a collection
+
+{% codeblock as python %}
+import arvados
+import arvados.collection
+
+collection_uuid = "zzzzz-4zz18-zzzzzzzzzzzzzzz"
+filename = "file1.txt"
+
+api = arvados.api()
+c = arvados.collection.CollectionReader(collection_uuid)
+with c.open(filename, "rb") as reader:
+ with open(filename, "wb") as writer:
+ content = reader.read(128*1024)
+ while content:
+ writer.write(content)
+ 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 %}
projects / arvados.git / blobdiff