[ARVADOS] created: 1.3.0-1063-gee6ee144d

[Git user]

        at  ee6ee144d7dd86bbbe578be3b9072e11c73f41ef (commit)


commit ee6ee144d7dd86bbbe578be3b9072e11c73f41ef
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Tue Jun 11 13:55:34 2019 -0300

    15350: Adds PySDK recipe to get a container request's state.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/doc/sdk/python/cookbook.html.textile.liquid b/doc/sdk/python/cookbook.html.textile.liquid
index c8ac5d103..1c0f4500d 100644
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -64,6 +64,40 @@ 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':
+        if c['exit_code'] == 0:
+            return c['state']
+        else:
+            return 'Failed'
+    elif c['state'] == 'Running':
+        if c['runtime_status'].get('error', None):
+            return 'Failing'
+        elif c['runtime_status'].get('warning', None):
+            return 'Warning'
+        else:
+            return c['state']
+    return c['state']
+container_request_uuid = 'qr1hi-xvhdp-zzzzzzzzzzzzzzz'
+print(get_cr_state(container_request_uuid))
+{% endcodeblock %}
+
 h2. List input of child requests
 
 {% codeblock as python %}

commit eb3fa630e4119363363e20ce00dbb4ff3635fe0b
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Tue Jun 11 13:49:16 2019 -0300

    15350: Fixes unnecessary api client instantiations on examples.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/doc/sdk/python/cookbook.html.textile.liquid b/doc/sdk/python/cookbook.html.textile.liquid
index 4a6c453ca..c8ac5d103 100644
--- a/doc/sdk/python/cookbook.html.textile.liquid
+++ b/doc/sdk/python/cookbook.html.textile.liquid
@@ -48,7 +48,7 @@ h2. Get input of a CWL workflow
 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 = api.container_requests().get(uuid=container_request_uuid).execute()
 print(container_request["mounts"]["/var/lib/cwl/cwl.input.json"])
 {% endcodeblock %}
 
@@ -59,7 +59,7 @@ 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 = 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 %}
@@ -71,9 +71,9 @@ import arvados
 api = arvados.api()
 parent_request_uuid = "qr1hi-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"]:
@@ -90,13 +90,13 @@ import arvados
 api = arvados.api()
 parent_request_uuid = "qr1hi-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"]]))
@@ -108,12 +108,12 @@ h2. List failed child requests
 import arvados
 api = arvados.api()
 parent_request_uuid = "qr1hi-xvhdp-zzzzzzzzzzzzzzz"
-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]], 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()
 for c in cancelled_child_containers["items"]:
@@ -127,7 +127,7 @@ 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 = 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())

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hooks/post-receive
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