Add features (HPO) is not working (local install)

[bnouyou]

Hello,

I have a local installation, and I just noticed that adding features (HPO) is currently not working for individuals.
See, I have "no result":

Thank you in advance for your help.

[hanars]

Can you provide the seqr application logs from the time period of this error?

[bnouyou]

These are the logs when I write an HPO term:

seqr-1  | {"timestamp": "2025-02-19 07:41:44,116", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "http://lx245/api/awesomebar?q=H&categories=hpo_terms", "status": 200, "responseSize": 21, "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/133.0.0.0 Safari/537.36", "remoteIp": "192.168.247.181", "referer": "http://lx245/project/R0001_iop/family_page/F000006_18_10890_a2", "protocol": "HTTP/1.1"}, "user": "benedicte.nouyou@chu-rennes.fr"}
seqr-1  | {"timestamp": "2025-02-19 07:41:44,398", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "http://lx245/api/awesomebar?q=HP&categories=hpo_terms", "status": 200, "responseSize": 21, "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/133.0.0.0 Safari/537.36", "remoteIp": "192.168.247.181", "referer": "http://lx245/project/R0001_iop/family_page/F000006_18_10890_a2", "protocol": "HTTP/1.1"}, "user": "benedicte.nouyou@chu-rennes.fr"}

[hanars]

So those logs do not reflect that you are using the typeahead to search for HPO terms at all - every time you type a letter into the search box for hpo terms it should be making a server request. Unless you can provide me with the logs for those requests, I can not help you

[bnouyou]

I have written something. See after the 'q=' , there is 'H' and then 'HP' on the other row.

[hanars]

Can you confirm that you have HPO terms in your database? They should be populated when you originally set up seqr but if you have done any funky database work they may have been removed, and you would need to re-populate them with the manage.py update_human_phenotype_ontology command

[bnouyou]

You are right, trhere is 0 record in the HPO table in database.
I did the command manage.py update_human_phenotype_ontology but there is still nothing in database.
See logs:

docker compose exec seqr python manage.py update_human_phenotype_ontology
WARN[0000] /home/cytogen/SEQR/docker-compose.yml: `version` is obsolete
{"timestamp": "2025-02-20 20:36:56,426", "severity": "INFO", "message": "Updating HPO"}
{"timestamp": "2025-02-20 20:36:56,452", "severity": "INFO", "message": "Re-using /tmp/hp.obo previously downloaded from http://purl.obolibrary.org/obo/hp.obo"}
Parsing http://purl.obolibrary.org/obo/hp.obo
38 lines [00:00, 335544.32 lines/s]
{"timestamp": "2025-02-20 20:36:56,463", "severity": "INFO", "message": "Deleting HumanPhenotypeOntology table with 0 records and creating new table with 0 records"}
0 records [00:00, ? records/s]
{"timestamp": "2025-02-20 20:36:56,468", "severity": "INFO", "message": "Done"}

[hanars]

You appear to have a temp file /tmp/hp.obo that seems to have been corrupted. Delete that file and try again

[bnouyou]

I just did that and I still have nothing:

WARN[0000] /home/cytogen/SEQR/docker-compose.yml: `version` is obsolete
{"timestamp": "2025-02-20 20:59:50,689", "severity": "INFO", "message": "Updating HPO"}
{"timestamp": "2025-02-20 20:59:50,737", "severity": "INFO", "message": "Downloading http://purl.obolibrary.org/obo/hp.obo to /tmp/hp.obo"}
1026 lines [00:00, 1429211.53 lines/s]
Parsing http://purl.obolibrary.org/obo/hp.obo
38 lines [00:00, 381300.36 lines/s]
{"timestamp": "2025-02-20 20:59:50,749", "severity": "INFO", "message": "Deleting HumanPhenotypeOntology table with 0 records and creating new table with 0 records"}
0 records [00:00, ? records/s]
{"timestamp": "2025-02-20 20:59:50,755", "severity": "INFO", "message": "Done"}

[hanars]

Hmm it looks like HPO has moved where they atopre the data. I will update seqr to fix this, but as a workaround you can downlload https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/hp.obo and save it to /tmp/hp.obo and then if you run that command again it should use the real data. Thank you for your patience!

[bnouyou]

Thank you for your help. I have done what you explained and the HPO database is nor correctly populated.

[hanars]

As an update, the latest seqr release includes the correct HPO download URL