ontobio

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I am trying to run the Phenotype_Enrichment notebook. The AssociationSetFactory function enrichment_test is not returning anything. I have tried using different p-values as well as printing out messages from within...

kcortes133

fix header emitted from gpad writer to match 2.0 specifications

2

Note: I did not update the header in the tests that specifically request GPAD 1.2. This PR should not be merged yet.

sierra-moxon

File "...\Anaconda3\envs\torch_nlp\lib\site-packages\diskcache\core.py", line 661, in _con settings = con.execute(select).fetchall() sqlite3.DatabaseError: file is not a database

AITCM

Go site 676 gorule 0000022 check for retracted publications

4

mugitty

ontobio pull request failing workflow actions due to Monarch

1

https://scigraph-data.monarchinitiative.org/ is no longer returning results. There maybe other links that are also not working

mugitty

Go site 2210 gorule 0000027 must check dbs are in the db xref file

7

mugitty

update relation map in relations.py to match expectations

1

related to: https://github.com/geneontology/pipeline/issues/397

sierra-moxon

Current version of ontobio, in some cases, has trouble parsing GAF(?)

1

In the pipeline output, we are seeing the error: ``` 17:08:35 temp_output_gaf_path: /opt/go-site/pipeline/target/groups/cgd/cgd_temp.gaf 17:08:35 2024-08-21 00:08:35 [INFO] [PID:5250 TID:140489894875136] [assocparser.py:888 in `_ensure_file`] Ensure file: None 17:08:35 Traceback (most recent call...

kltm

ontobio is not HTTPS-safe

1

We recently discovered, while working on Cloudflare for GO public access points (https://github.com/geneontology/operations/issues/70) that we got errors in ontobio. ``` [2024-08-20T06:50:13.986Z] Traceback (most recent call last): [2024-08-20T06:50:13.986Z] File "/usr/local/bin/validate.py", line...

kltm