Merge branch '16129-scoped-token-doc' refs #16129

[arvados.git] / 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 c8ac5d1036ffb1b2939617895537bde9d8eba3de..bd7f64b33d068175b3219f1c962f671777fd3173 100644 (file)
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -64,6 +64,35 @@ 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 = 'qr1hi-xvhdp-zzzzzzzzzzzzzzz'
+print(get_cr_state(container_request_uuid))
+{% endcodeblock %}
+
 h2. List input of child requests
 
 {% codeblock as python %}
@@ -133,7 +162,7 @@ for c in collection:
     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
@@ -206,3 +235,24 @@ 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 %}