{% codeblock as python %}
import arvados
api = arvados.api()
-container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-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"])
{% endcodeblock %}
import arvados
import arvados.collection
api = arvados.api()
-container_request_uuid="qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-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())
{% 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 = '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 = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
+parent_request_uuid = "zzzzz-xvhdp-zzzzzzzzzzzzzzz"
namefilter = "bwa%" # the "like" filter uses SQL pattern match syntax
-container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
-child_requests = arvados.api().container_requests().list(filters=[
+child_requests = api.container_requests().list(filters=[
["requesting_container_uuid", "=", parent_container_uuid],
["name", "like", namefilter]]).execute()
for c in child_requests["items"]:
{% 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 = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+container_request = api.container_requests().get(uuid=parent_request_uuid).execute()
parent_container_uuid = container_request["container_uuid"]
-child_requests = arvados.api().container_requests().list(filters=[
+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 = arvados.api().collections().list(filters=[["uuid", "in", output_uuids]]).execute()
+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"]]))
{% codeblock as python %}
import arvados
api = arvados.api()
-parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-container_request = arvados.api().container_requests().get(uuid=parent_request_uuid).execute()
+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 = arvados.api().container_requests().list(filters=[
+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 = arvados.api().containers().list(filters=[
+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 %}
import arvados
import arvados.collection
api = arvados.api()
-container_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-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["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
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()
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 = "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"]
+
+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 = "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 %}
+
+h2. Querying the vocabulary definition
+
+The Python SDK provides facilities to interact with the "active metadata vocabulary":{{ site.baseurl }}/admin/metadata-vocabulary.html in the system. The developer can do key and value lookups in a case-insensitive manner:
+
+{% codeblock as python %}
+>>> from arvados import api, vocabulary
+>>> voc = vocabulary.load_vocabulary(api('v1'))
+>>> [k.identifier for k in set(voc.key_aliases.values())]
+['IDTAGCOLORS', 'IDTAGFRUITS', 'IDTAGCOMMENT', 'IDTAGIMPORTANCES', 'IDTAGCATEGORIES', 'IDTAGSIZES', 'IDTAGANIMALS']
+>>> voc['IDTAGSIZES'].preferred_label
+'Size'
+>>> [v.preferred_label for v in set(voc['size'].value_aliases.values())]
+['S', 'M', 'L', 'XL', 'XS']
+>>> voc['size']['s'].aliases
+['S', 'small']
+>>> voc['size']['Small'].identifier
+'IDVALSIZES2'
+{% endcodeblock %}
+
+h2. Translating between vocabulary identifiers and labels
+
+Client software might need to present properties to the user in a human-readable form or take input from the user without requiring them to remember identifiers. For these cases, there're a couple of conversion methods that take a dictionary as input like this:
+
+{% codeblock as python %}
+>>> voc.convert_to_labels({'IDTAGIMPORTANCES': 'IDVALIMPORTANCES1'})
+{'Importance': 'Critical'}
+>>> voc.convert_to_identifiers({'creature': 'elephant'})
+{'IDTAGANIMALS': 'IDVALANIMALS3'}
+{% endcodeblock %}
\ No newline at end of file
projects / arvados.git / blobdiff