From 9697a5879884c6703ac5785b3b8e541cf2e12549 Mon Sep 17 00:00:00 2001 From: kltm Date: Mon, 9 Sep 2024 10:59:05 -0700 Subject: [PATCH 1/9] Update requirements.txt to known working version Temporary reversion to support https://github.com/geneontology/pipeline/issues/385 --- pipeline/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/requirements.txt b/pipeline/requirements.txt index 236910fe..87087d7d 100644 --- a/pipeline/requirements.txt +++ b/pipeline/requirements.txt @@ -1,5 +1,5 @@ PyYAML -ontobio==2.9.8 +ontobio==2.9.2 click pyparsing==2.4.7 antlr4-python3-runtime==4.9.3 From ead5ae15f3bd9bd0d5f55aa601b0283ab8d44c4a Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 18:53:23 +0200 Subject: [PATCH 2/9] Update gorule-0000058.md --- metadata/rules/gorule-0000058.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata/rules/gorule-0000058.md b/metadata/rules/gorule-0000058.md index 840f8661..6d4e36fb 100644 --- a/metadata/rules/gorule-0000058.md +++ b/metadata/rules/gorule-0000058.md @@ -8,7 +8,7 @@ status: proposed tags: [context-import] contact: "go-quality@lists.stanford.edu" --- -In the go-site/metadata directory there is a file `extensions-constraints.yaml`. This is +Rules are in the `extensions-constraints.yaml` file. This is a list of allowed extension Relation, Filler (the ID inside the parentheses), and the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. From 70f76a51196fd64db5b59b78ca9a64503f507891 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 16:53:40 +0000 Subject: [PATCH 3/9] refreshing rules README.md file --- metadata/rules/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index 26f3d12d..beeb9861 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -993,7 +993,7 @@ For the MOD Imports Project into Noctua, it was proposed that group-specific ann * status: proposed -In the go-site/metadata directory there is a file `extensions-constraints.yaml`. This is +Rules are in the `extensions-constraints.yaml` file. This is a list of allowed extension Relation, Filler (the ID inside the parentheses), and the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. From 612e1decd49fea99f5884c5d3bba1a7bbf1055a0 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 18:54:08 +0200 Subject: [PATCH 4/9] Update gorule-0000058.md --- metadata/rules/gorule-0000058.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata/rules/gorule-0000058.md b/metadata/rules/gorule-0000058.md index 6d4e36fb..ba93286a 100644 --- a/metadata/rules/gorule-0000058.md +++ b/metadata/rules/gorule-0000058.md @@ -8,7 +8,7 @@ status: proposed tags: [context-import] contact: "go-quality@lists.stanford.edu" --- -Rules are in the `extensions-constraints.yaml` file. This is +Rules are in the `extensions-constraints.yaml` file (https://github.com/geneontology/go-site/blob/master/metadata/extensions-constraints.yaml). This is a list of allowed extension Relation, Filler (the ID inside the parentheses), and the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. From ec794e8874a55ce3c903798839e6c3c94e434f21 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 16:54:26 +0000 Subject: [PATCH 5/9] refreshing rules README.md file --- metadata/rules/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index beeb9861..3a9bf6c3 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -993,7 +993,7 @@ For the MOD Imports Project into Noctua, it was proposed that group-specific ann * status: proposed -Rules are in the `extensions-constraints.yaml` file. This is +Rules are in the `extensions-constraints.yaml` file (https://github.com/geneontology/go-site/blob/master/metadata/extensions-constraints.yaml). This is a list of allowed extension Relation, Filler (the ID inside the parentheses), and the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. From e686dcdee3ff7bbdbc760c1aff6a6faa912ce95c Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 18:55:25 +0200 Subject: [PATCH 6/9] Update gorule-0000058.md --- metadata/rules/gorule-0000058.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/metadata/rules/gorule-0000058.md b/metadata/rules/gorule-0000058.md index ba93286a..b26a237c 100644 --- a/metadata/rules/gorule-0000058.md +++ b/metadata/rules/gorule-0000058.md @@ -4,7 +4,7 @@ id: GORULE:0000058 title: "Object extensions should conform to the extensions-patterns.yaml file in metadata" type: repair fail_mode: hard -status: proposed +status: implemented tags: [context-import] contact: "go-quality@lists.stanford.edu" --- @@ -16,3 +16,5 @@ applied. Extensions in annotations should conform to these constraints. If an element of a disjunction in the extensions does not follow one of the constraints as listed in the above file, that element should be dropped from the extensions. + +Note that in the GO Central pipeline, this is only implmented upon imports of external annotations into Noctua. From 64bf74e2eb4b6a268d426ed5dc48d4122f50b301 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 16:55:43 +0000 Subject: [PATCH 7/9] refreshing rules README.md file --- metadata/rules/README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index 3a9bf6c3..c48dfe8c 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -990,7 +990,7 @@ For the MOD Imports Project into Noctua, it was proposed that group-specific ann ## Object extensions should conform to the extensions-patterns.yaml file in metadata * id: [GORULE:0000058](https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000058.md) - * status: proposed + * status: implemented Rules are in the `extensions-constraints.yaml` file (https://github.com/geneontology/go-site/blob/master/metadata/extensions-constraints.yaml). This is @@ -1002,6 +1002,8 @@ Extensions in annotations should conform to these constraints. If an element of disjunction in the extensions does not follow one of the constraints as listed in the above file, that element should be dropped from the extensions. +Note that in the GO Central pipeline, this is only implmented upon imports of external annotations into Noctua. + ## GAF Version 2.0 and 2.1 are converted into GAF Version 2.2 From 82e21535ee8b8e98a79782a96e79736547b2b7a2 Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 18:57:53 +0200 Subject: [PATCH 8/9] Update gorule-0000058.md --- metadata/rules/gorule-0000058.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metadata/rules/gorule-0000058.md b/metadata/rules/gorule-0000058.md index b26a237c..199e7196 100644 --- a/metadata/rules/gorule-0000058.md +++ b/metadata/rules/gorule-0000058.md @@ -13,8 +13,8 @@ a list of allowed extension Relation, Filler (the ID inside the parentheses), an the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. -Extensions in annotations should conform to these constraints. If an element of a +Extensions in annotations should conform to these constraints. If an element of a disjunction in the extensions does not follow one of the constraints as listed in -the above file, that element should be dropped from the extensions. +the above file, that element is dropped from the extensions with a warning, and the remaining annotation is kept. Note that in the GO Central pipeline, this is only implmented upon imports of external annotations into Noctua. From 133deb62e0f84e7bf18cfeb4cbbe3f9147e9aeeb Mon Sep 17 00:00:00 2001 From: pgaudet Date: Wed, 11 Sep 2024 16:58:09 +0000 Subject: [PATCH 9/9] refreshing rules README.md file --- metadata/rules/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metadata/rules/README.md b/metadata/rules/README.md index c48dfe8c..0eb5da48 100644 --- a/metadata/rules/README.md +++ b/metadata/rules/README.md @@ -998,9 +998,9 @@ a list of allowed extension Relation, Filler (the ID inside the parentheses), an the acceptable GO Term roots used with this relation. A cardinality constraint may also be applied. -Extensions in annotations should conform to these constraints. If an element of a +Extensions in annotations should conform to these constraints. If an element of a disjunction in the extensions does not follow one of the constraints as listed in -the above file, that element should be dropped from the extensions. +the above file, that element is dropped from the extensions with a warning, and the remaining annotation is kept. Note that in the GO Central pipeline, this is only implmented upon imports of external annotations into Noctua.