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AAO: physical files missing from production parsing box #137

Closed jvendetti closed 4 years ago

jvendetti commented 4 years ago

Currently unable to browse classes for the Amphibian Gross Anatomy ontology (AAO) in the BioPortal UI. The REST endpoint reports 8 submission objects in the triplestore (http://data.bioontology.org/ontologies/AAO/submissions). Tried to troubleshoot, but discovered that the production parsing box is missing all physical files for current and previous submissions. The only thing we have left is a directory for the latest submission with parsing.log and metrics.csv files:

[ncbo-deployer@ncbo-prd-app-31 AAO]$ pwd
/srv/ncbo/repository/AAO
[ncbo-deployer@ncbo-prd-app-31 AAO]$ ls -l
total 4
drwxrwsr-x. 2 ncbo-deployer ncbo-deployer 4096 Oct  1 15:02 8
[ncbo-deployer@ncbo-prd-app-31 AAO]$ ls -l 8
total 44
-rw-rw-r--. 1 ncbo-deployer ncbo-deployer    50 Sep 19 09:40 metrics.csv
-rw-rw-r--. 1 ncbo-deployer ncbo-deployer 40486 Oct  2 14:33 parsing.log

@maseda reports that "it doesn't look like the missing files/dirs were deleted - since root dir timestamps don't indicate that":

[root@ncbo-prd-app-31 AAO]# ll -rtha
total 100K
drwxrwsr-x.    3 ncbo-deployer ncbo-deployer 4.0K May  2 01:16 .
drwsrwsr-x. 1141 ncbo-deployer ncbo-deployer  88K Sep 30 23:19 ..
drwxrwsr-x.    2 ncbo-deployer ncbo-deployer 4.0K Oct  1 15:02 8
[root@ncbo-prd-app-31 AAO]# ll -rthd
drwxrwsr-x. 3 ncbo-deployer ncbo-deployer 4.0K May  2 01:16 .

This ontology was originally part of the OBO Foundry, but is marked by them as deprecated. I wasn't able to retrieve a copy of the ontology source file from the OBO Foundry, OntoBee, AberOWL, OLS, or the author's GitHub page.

It's unclear what happened to our physical files/directories for AAO. Since the ontology is deprecated and unavailable in any of the other ontology repositories, I recommend we delete it from the triplestore and remove ontology directory from the production parsing box.

jvendetti commented 4 years ago

Contacted ontology maintainer David Blackburn who confirmed that he would like AAO to be removed from BioPortal.

Manually deleted ontology and submission objects from the triplestore, as well as confirmed that all physical files were removed from the production parsing box.