16306: Merge branch 'master'

[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 1c0f4500d3f97585fc8bee0afdc162b81f731817..75c51ee5a8126c57b9b23bc95d9cffdcf7fc027c 100644 (file)
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -81,18 +81,13 @@ def get_cr_state(cr_uuid):
             return 'On hold'
         else:
             return 'Queued'
-    elif c['state'] == 'Complete':
-        if c['exit_code'] == 0:
-            return c['state']
-        else:
-            return 'Failed'
+    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'
-        else:
-            return c['state']
     return c['state']
 container_request_uuid = 'qr1hi-xvhdp-zzzzzzzzzzzzzzz'
 print(get_cr_state(container_request_uuid))
@@ -149,7 +144,7 @@ child_requests = api.container_requests().list(filters=[
 child_containers = {c["container_uuid"]: c for c in child_requests["items"]}
 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 %}
@@ -164,10 +159,11 @@ container_request_uuid = "qr1hi-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
@@ -240,3 +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 %}