X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c69d271455a0550cda8e56ab6a4685fe3d7d91ea..e71aee834568e3bd058f21bff714621073fd5385:/doc/sdk/python/cookbook.html.textile.liquid diff --git a/doc/sdk/python/cookbook.html.textile.liquid b/doc/sdk/python/cookbook.html.textile.liquid index 4a6c453cae..82741c3ea6 100644 --- a/doc/sdk/python/cookbook.html.textile.liquid +++ b/doc/sdk/python/cookbook.html.textile.liquid @@ -47,8 +47,8 @@ h2. Get input of a CWL workflow {% 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() +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"]) {% endcodeblock %} @@ -58,22 +58,51 @@ h2. Get output of a CWL workflow 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() +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()) {% 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 {% codeblock as python %} import arvados api = arvados.api() -parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz" +parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax -container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute() +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"]: @@ -88,15 +117,15 @@ h2. List output of child requests {% codeblock as python %} import arvados api = arvados.api() -parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz" +parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz" namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax -container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute() +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"]])) @@ -107,15 +136,15 @@ 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_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"])) {% endcodeblock %} @@ -126,20 +155,21 @@ h2. Get log of a child request 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() +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()) + 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 api = arvados.api() download="https://your.download.server" -collection_uuid="qr1hi-4zz18-zzzzzzzzzzzzzzz" +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, @@ -155,8 +185,8 @@ Note, if two collections have files of the same name, the contents will be conca import arvados import arvados.collection api = arvados.api() -project_uuid = "qr1hi-tpzed-zzzzzzzzzzzzzzz" -collection_uuids = ["qr1hi-4zz18-aaaaaaaaaaaaaaa", "qr1hi-4zz18-bbbbbbbbbbbbbbb"] +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() @@ -171,7 +201,7 @@ h2. Upload a file into a new collection import arvados import arvados.collection -project_uuid = "qr1hi-j7d0g-zzzzzzzzzzzzzzz" +project_uuid = "zzzzz-j7d0g-zzzzzzzzzzzzzzz" collection_name = "My collection" filename = "file1.txt" @@ -193,7 +223,7 @@ h2. Download a file from a collection import arvados import arvados.collection -collection_uuid = "qr1hi-4zz18-zzzzzzzzzzzzzzz" +collection_uuid = "zzzzz-4zz18-zzzzzzzzzzzzzzz" filename = "file1.txt" api = arvados.api() @@ -206,3 +236,24 @@ with c.open(filename, "rb") as reader: 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 %}