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authorPeter Amstutz2020-07-16 16:27:32 -0400
committerPeter Amstutz2020-07-16 16:27:48 -0400
commitd49f6b5e11a41a51cb257bbafdcba410544f8486 (patch)
treea79ace1119a78401c9383b0e107da4f9c1734ba1 /bh20seqanalyzer
parentd34374f0e822edd1539ea5de6f8522f2b761de3f (diff)
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Add "validated" and "running workflows" tables to statusanalysis-refactor
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20seqanalyzer')
-rw-r--r--bh20seqanalyzer/main.py12
1 files changed, 7 insertions, 5 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index f18a93a..b3a439d 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -240,24 +240,26 @@ class SeqAnalyzer:
def move_fastq_to_fasta_results(self):
projects = self.api.groups().list(filters=[['owner_uuid', '=', self.fastq_project],
["properties.moved_output", "!=", True]],
- order="created_at desc",).execute()
+ order="created_at asc",).execute()
for p in projects["items"]:
wf = self.get_workflow_output_from_project(p["uuid"])
if not wf:
continue
logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"])
- self.api.collections().update(uuid=wf["output_uuid"],
- body={"owner_uuid": self.uploader_project}).execute()
col = arvados.collection.Collection(wf["output_uuid"], api_client=self.api, keep_client=self.keepclient)
with col.open("metadata.yaml") as md:
metadata_content = ruamel.yaml.round_trip_load(md)
+ colprop = col.get_properties()
+ colprop["sequence_label"] = metadata_content["sample"]["sample_id"]
+ self.api.collections().update(uuid=wf["output_uuid"],
+ body={"owner_uuid": self.uploader_project,
+ "properties": colprop}).execute()
+
p["properties"]["moved_output"] = True
- p["properties"]["sequence_label"] = metadata_content["sample"]["sample_id"]
self.api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
- break
def upload_schema(self):