From 3b0b1d00fb6212a4dd38054a84df5dfc476fc61c Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Wed, 5 Oct 2022 22:00:58 +0200 Subject: [PATCH 1/5] Add new metadata field for pull request added This PR adds the ability to encode the pull request when an ontology was added to the OBO Foundry GitHub repository. It's true that this repository does not well-reflect ontologies that were pulled over from SVN, and therefore the oldest ontologies will not have good entries for this. Please do not let this deter the acceptance of this PR. This PR will allow an alternate venue of identifying the date added for new repositories. It can be made a requirement for new ontologies later. It can also be a nice curation task as a "good first issue" --- _layouts/ontology_detail.html | 7 +++++++ ontology/clao.md | 1 + ontology/clyh.md | 1 + util/schema/registry_schema.json | 5 +++++ 4 files changed, 14 insertions(+) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 15685e204..29f73f45b 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -277,6 +277,13 @@

Usages

>{{page.exampleClass}} + {% endif %} {% if page.pull_request_added %} +
PR Added
+
+ + {{ page.pull_request_added }} + +
{% endif %} {% if page.dependencies %}
Dependencies
{% for x in page.dependencies %} diff --git a/ontology/clao.md b/ontology/clao.md index 2fc2479ab..c096ef9c1 100644 --- a/ontology/clao.md +++ b/ontology/clao.md @@ -23,6 +23,7 @@ preferredPrefix: CLAO products: - id: clao.owl - id: clao.obo +pull_request_added: 1337 repository: https://github.com/luis-gonzalez-m/Collembola tracker: https://github.com/luis-gonzalez-m/Collembola/issues activity_status: active diff --git a/ontology/clyh.md b/ontology/clyh.md index 83d35165b..c658d9b67 100644 --- a/ontology/clyh.md +++ b/ontology/clyh.md @@ -25,6 +25,7 @@ preferredPrefix: CLYH products: - id: clyh.owl - id: clyh.obo +pull_request_added: 1205 repository: https://github.com/EBISPOT/clyh_ontology tracker: https://github.com/EBISPOT/clyh_ontology/issues activity_status: active diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 734126734..e5b88adb6 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -370,6 +370,11 @@ ] } }, + "pull_request_added": { + "suggest": false, + "type": "integer", + "description": "This encodes the number of the pull request on the OBO Foundry GitHub repository that was originally used to add this ontology. You can curate additional ones by going to the ontology page (e.g., https://github.com/OBOFoundry/OBOFoundry.github.io/commits/master/ontology/clyh.md) and looking the whole way down the list for the first commit. Click on the title for the commit then you will see if there's a PR associated with it." + }, "releases": { "suggest": false }, From a281a733142f10f4f793c422aa4a9533d09dd05d Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 15 Nov 2022 14:03:39 +0100 Subject: [PATCH 2/5] Add NOR field --- _layouts/ontology_detail.html | 7 +++++++ util/schema/registry_schema.json | 5 +++++ 2 files changed, 12 insertions(+) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 29f73f45b..8ee860b4d 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -277,6 +277,13 @@

Usages

>{{page.exampleClass}} + {% endif %} {% if page.issue_requested %} +
New Ontology Request
+
+ + {{ page.issue_requested }} + +
{% endif %} {% if page.pull_request_added %}
PR Added
diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index e5b88adb6..f7b8104b5 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -370,6 +370,11 @@ ] } }, + "issue_requested": { + "suggest": false, + "type": "integer", + "description": "This encodes the number of the issue on the OBO Foundry GitHub repository that was originally used to request this ontology." + }, "pull_request_added": { "suggest": false, "type": "integer", From 8e5fd542b20d9af469e591e213f11302d05fbb80 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 15 Nov 2022 14:04:46 +0100 Subject: [PATCH 3/5] Update t4fs.md --- ontology/t4fs.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ontology/t4fs.md b/ontology/t4fs.md index 954810656..1758a9764 100644 --- a/ontology/t4fs.md +++ b/ontology/t4fs.md @@ -10,6 +10,7 @@ contact: description: A terminology for the skills necessary to make data FAIR and to keep it FAIR. domain: information homepage: https://github.com/terms4fairskills/FAIRterminology +issue_requested: 1520 license: label: CC BY 4.0 url: https://creativecommons.org/licenses/by/4.0/ @@ -27,6 +28,7 @@ products: publications: - id: https://doi.org/10.5281/zenodo.4705219 title: 'EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report' +pull_request_added: 2140 repository: https://github.com/terms4fairskills/FAIRterminology tracker: https://github.com/terms4fairskills/FAIRterminology/issues usages: From b0080e2e70e1556893a2f672d85e609243b2a839 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 15 Nov 2022 14:12:52 +0100 Subject: [PATCH 4/5] Update ontology_detail.html --- _layouts/ontology_detail.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 4c9920c5b..867d9531d 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -281,15 +281,15 @@

{% endif %} {% if page.issue_requested %}
New Ontology Request
- - {{ page.issue_requested }} + + #{{ page.issue_requested }}
{% endif %} {% if page.pull_request_added %}
PR Added
- {{ page.pull_request_added }} + #{{ page.pull_request_added }}
{% endif %} {% if page.dependencies %} From 3fb923e7022dc18430b84b7ed07ee861d145c378 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 15 Nov 2022 16:45:02 +0200 Subject: [PATCH 5/5] Update ontology_detail.html --- _layouts/ontology_detail.html | 7 ------- 1 file changed, 7 deletions(-) diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index 867d9531d..6b455f4d4 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -285,13 +285,6 @@

#{{ page.issue_requested }}

- {% endif %} {% if page.pull_request_added %} -
PR Added
-
- - #{{ page.pull_request_added }} - -
{% endif %} {% if page.dependencies %}
Dependencies
{% for x in page.dependencies %}