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| author | Peter Amstutz | 2020-04-07 14:27:10 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-07 14:27:30 -0400 |
| commit | 102a3663123292375440eeb04276d22a5b4645e0 (patch) | |
| tree | bcaed1baaf57fc5b2e6e4436f695c989c10d51a6 | |
| parent | a2f33ff68810a99bc28ea33bb6a745e59795cfb9 (diff) | |
| download | bh20-seq-resource-102a3663123292375440eeb04276d22a5b4645e0.tar.gz bh20-seq-resource-102a3663123292375440eeb04276d22a5b4645e0.tar.lz bh20-seq-resource-102a3663123292375440eeb04276d22a5b4645e0.zip | |
Copy recent results to a set destination
| -rw-r--r-- | bh20seqanalyzer/main.py | 24 |
1 files changed, 23 insertions, 1 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index dae8eca..2db97f6 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -11,7 +11,7 @@ logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="% level=logging.INFO) logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) -def validate_upload(api, collection, validated_project): +def validate_upload(api, collection, validated_project, latest_result_uuid): col = arvados.collection.Collection(collection["uuid"]) # validate the collection here. Check metadata, etc. @@ -79,12 +79,31 @@ def start_analysis(api, logging.error(comp.stderr.decode('utf-8')) +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").execute() + for m in most_recent_analysis["items"]: + cr = api.container_requests().list(filters=[['owner_uuid', '=', m["uuid"]], + ["requesting_container_uuid", "=", None]]).execute() + if cr["items"] and cr["items"][0]["output_uuid"]: + wf = cr["items"][0] + src = api.collections().get(uuid=wf["output_uuid"]).execute() + dst = api.collections().get(uuid=latest_result_uuid).execute() + if src["portable_data_hash"] != dst["portable_data_hash"]: + logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid) + api.collections().update(uuid=latest_result_uuid, + body={"manifest_text": src["manifest_text"], + "description": "latest result from %s %s" % (m["name"], wf["uuid"])}).execute() + break + + def main(): parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='') parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='') parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') + parser.add_argument('--latest-result-uuid', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') args = parser.parse_args() api = arvados.api() @@ -101,4 +120,7 @@ def main(): start_analysis(api, args.analysis_project, args.workflow_uuid, args.validated_project) + + copy_most_recent_result(api, args.analysis_project, args.latest_result_uuid) + time.sleep(10) |