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| author | Peter Amstutz | 2020-07-16 12:32:43 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-16 12:33:07 -0400 |
| commit | 6bfefe984a84fb215d61e045c49a4ab123bb7339 (patch) | |
| tree | 86609a1d6b57dfac7ccbeb3ef3bcf6b36f677853 /scripts/cleanup.py | |
| parent | 0e84b18cb134855d572d1f94d5d3c43571afe7e9 (diff) | |
| download | bh20-seq-resource-6bfefe984a84fb215d61e045c49a4ab123bb7339.tar.gz bh20-seq-resource-6bfefe984a84fb215d61e045c49a4ab123bb7339.tar.lz bh20-seq-resource-6bfefe984a84fb215d61e045c49a4ab123bb7339.zip | |
Catch exceptions
Add script to cleanup bad uploads.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'scripts/cleanup.py')
| -rw-r--r-- | scripts/cleanup.py | 20 |
1 files changed, 20 insertions, 0 deletions
diff --git a/scripts/cleanup.py b/scripts/cleanup.py new file mode 100644 index 0000000..f4bd0b4 --- /dev/null +++ b/scripts/cleanup.py @@ -0,0 +1,20 @@ +import arvados +import arvados.util + +api = arvados.api() + +patterns = [ + "%missing%`collection_location`%", + "%missing%`technology`%", + "%missing%`host_species`%", + "%QC fail: alignment%", + "%does not look like a valid URI%", + ] + +for p in 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() |