X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/385f300ba44bc186aa679d5aba543260e8ffee1e..36ca0d3ede8554a229d6872b151b7e79ce959ba9:/doc/user/tutorials/tutorial-trait-search.textile diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.textile index 4f4ec9c2e3..0381d28f5d 100644 --- a/doc/user/tutorials/tutorial-trait-search.textile +++ b/doc/user/tutorials/tutorial-trait-search.textile @@ -29,11 +29,10 @@ If everything is set up correctly, you will be able to import the arvados SDK. notextile.
>>> import arvados
-This tutorial will also use the regular expression (re) and json python modules:
+This tutorial will also use the regular expression (re) python module:
>>> import re
->>> import json
>>> trait_query = json.dumps({
+>>> trait_query = {
'link_class': 'human_trait',
'tail_kind': 'arvados#human',
'head_uuid': non_melanoma_cancer
- })
+ }
>>> human_query = json.dumps({
+>>> human_query = {
"link_class": "identifier",
"head_uuid": human_uuids
- })
+ }
>>> pgpid_links = arvados.api('v1').links().list(limit=1000, where=human_query).execute()
>>> map(lambda l: l['name'], pgpid_links['items'])
[u'hu01024B', u'hu11603C', u'hu15402B', u'hu174334', u'hu1BD549', u'hu237A50',
@@ -151,11 +150,11 @@ h2. Find genomic data from specific humans
Now we want to find collections in Keep that were provided by these humans. We search the "links" resource for "provenance" links that point to subjects in list of humans with the non-melanoma skin cancer trait:
->>> provenance_links = arvados.api().links().list(limit=1000, where=json.dumps({
+>>> provenance_links = arvados.api().links().list(limit=1000, where={
"link_class": "provenance",
"name": "provided",
"tail_uuid": human_uuids
- })).execute()
+ }).execute()
collection_uuids = map(lambda l: l['head_uuid'], provenance_links['items'])
# build map of human uuid -> PGP ID
@@ -168,9 +167,9 @@ for p_link in provenance_links['items']:
pgpid[p_link['head_uuid']] = pgpid[p_link['tail_uuid']]
# get details (e.g., list of files) of each collection
-collections = arvados.api('v1').collections().list(where=json.dumps({
+collections = arvados.api('v1').collections().list(where={
"uuid": collection_uuids
- })).execute()
+ }).execute()
# print PGP public profile links with file locators
for c in collections['items']: