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| author | Peter Amstutz | 2020-07-16 16:41:33 -0400 |
|---|---|---|
| committer | GitHub | 2020-07-16 16:41:33 -0400 |
| commit | eb3bdab1109959deb5b11fd74310832bdaa50899 (patch) | |
| tree | a79ace1119a78401c9383b0e107da4f9c1734ba1 /scripts | |
| parent | 8d995b271f20d15b2b6a7845ade22c396a383da3 (diff) | |
| parent | d49f6b5e11a41a51cb257bbafdcba410544f8486 (diff) | |
| download | bh20-seq-resource-eb3bdab1109959deb5b11fd74310832bdaa50899.tar.gz bh20-seq-resource-eb3bdab1109959deb5b11fd74310832bdaa50899.tar.lz bh20-seq-resource-eb3bdab1109959deb5b11fd74310832bdaa50899.zip | |
Merge pull request #98 from arvados/analysis-refactor
Analysis refactor
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/cleanup.py | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/scripts/cleanup.py b/scripts/cleanup.py new file mode 100644 index 0000000..6a82659 --- /dev/null +++ b/scripts/cleanup.py @@ -0,0 +1,38 @@ +import arvados +import arvados.util + +api = arvados.api() + +delete_patterns = [ + "%missing%`collection_location`%", + "%missing%`technology`%", + "%missing%`host_species`%", + "%QC fail: alignment%", + "%does not look like a valid URI%", + "%Duplicate of%" + ] + +revalidate_patterns = [ + "%missing%`license`%" +] + +for p in delete_patterns: + c = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["properties.errors", "like", p]]) + for i in c: + print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) + api.collections().delete(uuid=i["uuid"]).execute() + +for p in revalidate_patterns: + c = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["properties.errors", "like", p]]) + for i in c: + print("clearing status %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) + pr = i["properties"] + if "status" in pr: + del pr["status"] + if "errors" in pr: + del pr["errors"] + api.collections().update(uuid=i["uuid"], body={"properties": pr}).execute() |