X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/7f108bc7e00604fd0e346b044c05579bfa380e9a..1eed3583ea85b3384a97eeef4971a4385e6d7c96:/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 2adb986a5e..ff3bcf90e0 100644
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -12,24 +12,24 @@ SPDX-License-Identifier: CC-BY-SA-3.0
 
 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"]
@@ -40,26 +40,251 @@ container_dict = {c["uuid"]: c for c in containers}
 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 = 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>
+{% endcodeblock %}
 
 h2. Get output of a CWL workflow
 
-<code>
+{% 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>
+{% endcodeblock %}
 
-h2. Run a CWL workflow from a workflow record
+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 = "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 = 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 = "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 = 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 = 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 = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
+parent_container_uuid = container_request["container_uuid"]
+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 = api.containers().list(filters=[
+    ["exit_code", "!=", "0"],
+    ["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 %}
+
+h2. Get log of a child request
+
+{% codeblock as python %}
+import arvados
+import arvados.collection
+api = arvados.api()
+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:
+    if isinstance(collection.find(c), arvados.arvfile.ArvadosFile):
+        print(collection.open(c).read())
+{% endcodeblock %}
+
+h2(#sharing_link). Create a collection sharing link
+
+{% codeblock as python %}
+import arvados
+api = arvados.api()
+download="https://your.download.server"
+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"]))
+{% 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 to 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 %}
+
+h2. Copy files from a collection to another collection
+
+{% codeblock as python %}
+import arvados.collection
+
+source_collection = "x1u39-4zz18-krzg64ufvehgitl"
+target_collection = "x1u39-4zz18-67q94einb8ptznm"
+files_to_copy = ["folder1/sample1/sample1_R1.fastq",
+                 "folder1/sample2/sample2_R1.fastq"]
+
+source = arvados.collection.CollectionReader(source_collection)
+target = arvados.collection.Collection(target_collection)
+
+for f in files_to_copy:
+    target.copy(f, "", source_collection=source)
+
+target.save()
+{% endcodeblock %}
+
+h2. Listing records with paging
+
+Use the @arvados.util.keyset_list_all@ helper method to iterate over all the records matching an optional filter.  This method handles paging internally and returns results incrementally using a Python iterator.  The first parameter of the method takes a @list@ method of an Arvados resource (@collections@, @container_requests@, etc).
+
+{% codeblock as python %}
+import arvados.util
+
+api = arvados.api()
+for c in arvados.util.keyset_list_all(api.collections().list, filters=[["name", "like", "%sample123%"]]):
+    print("got collection " + c["uuid"])
+{% endcodeblock %}