This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
-*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html*
+{% include 'tutorial_expectations' %}
In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt.
We query the "links" resource to find humans that report the selected trait. Links are directional connections between Arvados data items, for example, from a human to their reported traits.
<notextile>
-<pre><code>>>> <span class="userinput">trait_query = {
- 'link_class': 'human_trait',
- 'tail_kind': 'arvados#human',
- 'head_uuid': non_melanoma_cancer
- }
+<pre><code>>>> <span class="userinput">trait_filter = [
+ ['link_class', '=', 'human_trait'],
+ ['tail_uuid', 'is_a', 'arvados#human'],
+ ['head_uuid', '=', non_melanoma_cancer],
+ ]
</code></pre>
</notextile>
-* @'link_class'@ queries for links that describe the traits of a particular human.
-* @'tail_kind'@ queries for links where the tail of the link is a human.
-* @'head_uuit'@ queries for links where the head of the link is a specific data item.
+* @['link_class', '=', 'human_trait']@ filters on links that connect phenotype traits to individuals in the database.
+* @['tail_uuid', 'is_a', 'arvados#human']@ filters that the "tail" must be a "human" database object.
+* @['head_uuid', '=', non_melanoma_cancer]@ filters that the "head" of the link must connect to the "trait" database object non_melanoma_cancer .
The query will return links that match all three conditions.
<notextile>
-<pre><code>>>> <span class="userinput">trait_links = arvados.api().links().list(limit=1000, where=trait_query).execute()</span>
+<pre><code>>>> <span class="userinput">trait_links = arvados.api().links().list(limit=1000, filters=trait_filter).execute()</span>
</code></pre>
</notextile>
* @arvados.api()@ gets an object that provides access to the Arvados API server
* @.links()@ gets an object that provides access to the "links" resource on the Arvados API server
-* @.list(limit=1000, where=query)@ constructs a query to elements of the "links" resource that match the criteria discussed above, with a limit of 1000 entries returned
+* @.list(limit=1000, filters=trait_filter)@ constructs a query to elements of the "links" resource that match the criteria discussed above, with a limit of 1000 entries returned
* @.execute()@ executes the query and returns the result, which we assign to "trait_links"
<notextile>
h2. Find Personal Genome Project identifiers from Arvados UUIDs
<notextile>
-<pre><code>>>> <span class="userinput">human_query = {
- "link_class": "identifier",
- "head_uuid": human_uuids
- }</span>
->>> <span class="userinput">pgpid_links = arvados.api('v1').links().list(limit=1000, where=human_query).execute()</span>
+<pre><code>>>> <span class="userinput">human_filters = [
+ ["link_class", "=", "identifier"],
+ ["head_uuid", "in", human_uuids]
+ ]</span>
+>>> <span class="userinput">pgpid_links = arvados.api('v1').links().list(limit=1000, filters=human_filters).execute()</span>
>>> <span class="userinput">map(lambda l: l['name'], pgpid_links['items'])</span>
[u'hu01024B', u'hu11603C', u'hu15402B', u'hu174334', u'hu1BD549', u'hu237A50',
u'hu34A921', u'hu397733', u'hu414115', u'hu43860C', u'hu474789', u'hu553620',
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:
<notextile>
-<pre><code>>>> <span class="userinput">provenance_links = arvados.api().links().list(limit=1000, where={
- "link_class": "provenance",
- "name": "provided",
- "tail_uuid": human_uuids
- }).execute()
+<pre><code>>>> <span class="userinput">provenance_links = arvados.api().links().list(limit=1000, filters=[
+ ["link_class", "=", "provenance"],
+ ["name", "=", "provided"],
+ ["tail_uuid", "in", human_uuids]
+ ]).execute()
collection_uuids = map(lambda l: l['head_uuid'], provenance_links['items'])
# build map of human uuid -> PGP ID
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={
- "uuid": collection_uuids
- }).execute()
+collections = arvados.api('v1').collections().list(filters=[
+ ["uuid", "in", collection_uuids]
+ ]).execute()
# print PGP public profile links with file locators
for c in collections['items']:
projects / arvados.git / blobdiff