X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ddaa9596ebf94aa7b6ee720e06ceccd2d7dc43fc..a31420c0b77005cbe44f90d312c9091ca7f07fdf:/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 ff8b8052e5..eda6563d7a 100644
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -81,7 +81,7 @@ def get_cr_state(cr_uuid):
             return 'On hold'
         else:
             return 'Queued'
-    elif c['state'] == 'Complete' and c['exit_code'] != 0
+    elif c['state'] == 'Complete' and c['exit_code'] != 0:
         return 'Failed'
     elif c['state'] == 'Running':
         if c['runtime_status'].get('error', None):
@@ -144,7 +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 %}
@@ -159,7 +159,8 @@ 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(#sharing_link). Create a collection sharing link
@@ -236,13 +237,13 @@ with c.open(filename, "rb") as reader:
 print("Finished downloading %s" % filename)
 {% endcodeblock %}
 
-h2. Copy files from a collection a new collection
+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"
+source_collection = "zzzzz-4zz18-zzzzzzzzzzzzzzz"
+target_project = "zzzzz-j7d0g-zzzzzzzzzzzzzzz"
 target_name = "Files copied from source_collection"
 files_to_copy = ["folder1/sample1/sample1_R1.fastq",
                  "folder1/sample2/sample2_R1.fastq"]
@@ -256,3 +257,44 @@ for f in files_to_copy:
 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 = "zzzzz-4zz18-zzzzzzzzzzzzzzz"
+target_collection = "zzzzz-4zz18-aaaaaaaaaaaaaaa"
+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. Delete a file from an existing collection
+
+{% codeblock as python %}
+import arvados
+
+c = arvados.collection.Collection("zzzzz-4zz18-zzzzzzzzzzzzzzz")
+c.remove("file2.txt")
+c.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 %}