{% codeblock as python %}
import arvados
api = arvados.api()
-container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+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 %}
import arvados
import arvados.collection
api = arvados.api()
-container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+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())
elif c['runtime_status'].get('warning', None):
return 'Warning'
return c['state']
-container_request_uuid = 'qr1hi-xvhdp-zzzzzzzzzzzzzzz'
+container_request_uuid = 'zzzzz-xvhdp-zzzzzzzzzzzzzzz'
print(get_cr_state(container_request_uuid))
{% endcodeblock %}
{% 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 = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
{% 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 = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
{% codeblock as python %}
import arvados
api = arvados.api()
-parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+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=[
import arvados
import arvados.collection
api = arvados.api()
-container_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+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:
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,
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()
import arvados
import arvados.collection
-project_uuid = "qr1hi-j7d0g-zzzzzzzzzzzzzzz"
+project_uuid = "zzzzz-j7d0g-zzzzzzzzzzzzzzz"
collection_name = "My collection"
filename = "file1.txt"
import arvados
import arvados.collection
-collection_uuid = "qr1hi-4zz18-zzzzzzzzzzzzzzz"
+collection_uuid = "zzzzz-4zz18-zzzzzzzzzzzzzzz"
filename = "file1.txt"
api = arvados.api()
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"]
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 %}