diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/cleanup.py | 23 |
1 files changed, 21 insertions, 2 deletions
diff --git a/scripts/cleanup.py b/scripts/cleanup.py index 78f34c8..6919305 100644 --- a/scripts/cleanup.py +++ b/scripts/cleanup.py @@ -1,7 +1,13 @@ import arvados import arvados.util +import arvados.keep +import ruamel.yaml api = arvados.api() +keepclient = arvados.keep.KeepClient(api_client=api) + +UPLOADER_PROJECT = 'lugli-j7d0g-n5clictpuvwk8aa' +VALIDATED_PROJECT = 'lugli-j7d0g-5ct8p1i1wrgyjvp' delete_patterns = [ "%missing%`collection_location`%", @@ -21,7 +27,7 @@ revalidate_patterns = [ for p in delete_patterns: c = arvados.util.list_all(api.collections().list, filters=[ - ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["owner_uuid", "=", UPLOADER_PROJECT], ["properties.errors", "like", p]]) for i in c: print("trashing %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) @@ -29,7 +35,7 @@ for p in delete_patterns: for p in revalidate_patterns: c = arvados.util.list_all(api.collections().list, filters=[ - ["owner_uuid", "=", "lugli-j7d0g-n5clictpuvwk8aa"], + ["owner_uuid", "=", UPLOADER_PROJECT], ["properties.errors", "like", p]]) for i in c: print("clearing status %s %s" % (i["uuid"], i["properties"].get("sequence_label"))) @@ -39,3 +45,16 @@ for p in revalidate_patterns: if "errors" in pr: del pr["errors"] api.collections().update(uuid=i["uuid"], body={"properties": pr}).execute() + +c = arvados.util.list_all(api.collections().list, filters=[ + ["owner_uuid", "=", VALIDATED_PROJECT], + ["properties.sequence_label", "exists", False]]) +for i in c: + col = arvados.collection.Collection(i["uuid"], api_client=api, keep_client=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"] + + print("fixing sequence label %s %s" % (i["uuid"], colprop.get("sequence_label"))) + api.collections().update(uuid=i["uuid"], body={"properties": colprop}).execute() |