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authorPeter Amstutz2020-07-08 14:02:11 -0400
committerPeter Amstutz2020-07-08 15:18:00 -0400
commitcbb191cb23f4e40b1a1d3024401960939fda9bc3 (patch)
tree3cf9259067b1fcacfaf9d9488629eb390596f657 /bh20seqanalyzer/main.py
parent44e3c21ba89aa19c066148fdd18745f45e168d50 (diff)
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Get count from arvados
Separate pending/rejected tables "Lastest results" is latest successful run. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20seqanalyzer/main.py')
-rw-r--r--bh20seqanalyzer/main.py10
1 files changed, 6 insertions, 4 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 1746587..ce9a723 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -187,14 +187,15 @@ def get_workflow_output_from_project(api, uuid):
cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid],
["requesting_container_uuid", "=", None]]).execute()
if cr["items"] and cr["items"][0]["output_uuid"]:
- return cr["items"][0]
- else:
- return None
+ container = api.containers().get(uuid=cr["items"][0]["container_uuid"]).execute()
+ if container["state"] == "Complete" and container["exit_code"] == 0:
+ return cr["items"][0]
+ return None
def copy_most_recent_result(api, analysis_project, latest_result_uuid):
most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]],
- order="created_at desc", limit=1).execute()
+ order="created_at desc").execute()
for m in most_recent_analysis["items"]:
wf = get_workflow_output_from_project(api, m["uuid"])
if wf:
@@ -220,6 +221,7 @@ def move_fastq_to_fasta_results(api, analysis_project, uploader_project):
body={"owner_uuid": uploader_project}).execute()
p["properties"]["moved_output"] = True
api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
+ break
def upload_schema(api, workflow_def_project):