From b2aa81123107eed2cf6a067dafd5e91ea5ce45ef Mon Sep 17 00:00:00 2001 From: matentzn Date: Sun, 5 Apr 2026 05:17:25 +0000 Subject: [PATCH 1/2] Add .claude/ to gitignore https://claude.ai/code/session_01ChK2mm7BcsKrL7Hwjksw4f --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index f8cfb6a0..f180f098 100644 --- a/.gitignore +++ b/.gitignore @@ -67,6 +67,8 @@ src/patterns/pattern_owl_seed.txt src/patterns/all_pattern_terms.txt # End of ODK-managed rules +.claude/ + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] From 6f9f1fa575c9693c04b7b013e4ee59853d6399f2 Mon Sep 17 00:00:00 2001 From: matentzn Date: Sun, 5 Apr 2026 05:18:19 +0000 Subject: [PATCH 2/2] Fix broken S3 links in pattern overview script (#1008) https://claude.ai/code/session_01ChK2mm7BcsKrL7Hwjksw4f --- src/scripts/patterns_create_overview.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/scripts/patterns_create_overview.py b/src/scripts/patterns_create_overview.py index e3e07519..36231a7e 100644 --- a/src/scripts/patterns_create_overview.py +++ b/src/scripts/patterns_create_overview.py @@ -25,8 +25,8 @@ #pattern_dir="/ws/upheno/src/patterns/dosdp-dev" #md_file=pattern_dir+"/README.md" config_file = "https://raw.githubusercontent.com/obophenotype/upheno-dev/master/src/curation/upheno-config.yaml" -pattern_matches_location = "https://bbop-ontologies.s3.amazonaws.com/upheno/current/pattern-matches" -pattern_matches_location_gh = "https://bbop-ontologies.s3.amazonaws.com/upheno/current/pattern-matches" +pattern_matches_location = "https://raw.githubusercontent.com/obophenotype/upheno/master/src/curation/pattern-matches" +pattern_matches_location_gh = "https://github.com/obophenotype/upheno/blob/master/src/curation/pattern-matches" config = yaml.load(urllib.request.urlopen(config_file), Loader=yaml.FullLoader) phenotype_ontologies = config.get("species_modules")