Merge branch 'main' into schema-urgent-fixes

ga4gh-beacon · Jan 16, 2024 · f4f8264 · f4f8264
2 parents 11312cd + 7c64fdf
commit f4f8264
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diff --git a/.github/workflows/github-actions-demo-yml b/.github/workflows/github-actions-demo-yml
@@ -0,0 +1,18 @@
+name: GitHub Actions Demo
+run-name: ${{ github.actor }} is testing out GitHub Actions 🚀
+on: [push]
+jobs:
+  Explore-GitHub-Actions:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
+      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
+      - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
+      - run: echo "🖥️ The workflow is now ready to test your code on the runner."
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
+      - run: echo "🍏 This job's status is ${{ job.status }}."
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,7 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
  * Updated `docs`:
     - `filters.md`
     - `variant-queries.md`
-    - `bugs-changes-log.md` 
+    - `changes-todo.md` 
     - `ComplexValue.md`
     - `README.md`
     - Added missing descriptions to models properties (see issue #42)

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ This repository is a unified repository representing the different parts of the
 * [models](models)
 * Beacon v2 Documentation
     - authoritive source already in this repository [`/docs`](docs)
-    - rendered version through [here](https://beacon-project.io/beacon-v2/) (alternative address is [docs.genomebeacons.org](http://docs.genomebeacons.org))
+    - rendered version through [here](https://beacon-project.io/beacon-v2/) (alternative address is [docs.genomebeacons.org](https://docs.genomebeacons.org))
 
 As with other schema projects, here we separate between the schema source files (in `src`; JSON-Schema written in YAML) and the generated versions for referencing. The current setup allows already the direct referencing of the generated JSON schemas. Examples:
 
@@ -30,10 +30,10 @@ There is a set of tools in [`/bin`](./bin/) to facilitate the conversion. ATM, a
 
 ### Changes
 
-* change notes with respect to the repository & documentation are now in [docs.genomebeacons.org](http://docs.genomebeacons.org/bugs-changes-log/)
+* change notes with respect to the repository & documentation are now in [docs.genomebeacons.org](https://docs.genomebeacons.org/changes-todo/)
 * NOTE: on 2022-06-20 the previous development repositories have been archived:
     - ARCHIVE - [beacon-framework-v2](https://github.com/ga4gh-beacon/beacon-framework-v2)
-    - ARCHIVE - [[beacon-v2-Models](https://github.com/ga4gh-beacon/beacon-v2-Models)
+    - ARCHIVE - [beacon-v2-Models](https://github.com/ga4gh-beacon/beacon-v2-Models)
 
 
 ## Directory structure

diff --git a/bin/SCHEMAS2MD.md b/bin/SCHEMAS2MD.md
@@ -32,11 +32,11 @@ YAMLs schemas. Each time the original MS Word document was edited, someone had t
 
 This script inverts the process, i.e., **it enforces modifying the schema specification directly at the YAML/JSON level**.
 
-Editing the schemas directly at the YAML/JSON level has two advantages, the first is that because we follow [OpenAPI](https://swagger.io/specification/) specification (along with JSON schema), _a priori_ we could use [SWAGGER UI](https://swagger.io/docs/open-source-tools/swagger-ui/usage/installation). The second is that the YAML/JSON files can be converted to Markdown tables in order to create [Markdown based documentation](http://docs.genomebeacons.org) documentation. This script **transforms YAML/JSON to Markdown tables**, including their nested objects **up to a third degree of hierarchy**.
+Editing the schemas directly at the YAML/JSON level has two advantages, the first is that because we follow [OpenAPI](https://swagger.io/specification/) specification (along with JSON schema), _a priori_ we could use [SWAGGER UI](https://swagger.io/docs/open-source-tools/swagger-ui/usage/installation). The second is that the YAML/JSON files can be converted to Markdown tables in order to create [Markdown based documentation](https://docs.genomebeacons.org) documentation. This script **transforms YAML/JSON to Markdown tables**, including their nested objects **up to a third degree of hierarchy**.
 
-The **Markdown** format can be directly rendered as tables at the GitHub repository, and it can be used with [MkDocs](https://www.mkdocs.org/) to create [HTML](http://docs.genomebeacons.org) documentation. 
+The **Markdown** format can be directly rendered as tables at the GitHub repository, and it can be used with [MkDocs](https://www.mkdocs.org/) to create [HTML](https://docs.genomebeacons.org) documentation. 
 
-Everytime a `git push` is performed to the [repo](https://github.com/ga4gh-beacon/beacon-v2) the documentation at [Github Pages](http://docs.genomebeacons.org) gets updated. Note that only content under directory `docs/` will make it to [Github Pages](http://docs.genomebeacons.org).
+Everytime a `git push` is performed to the [repo](https://github.com/ga4gh-beacon/beacon-v2) the documentation at [Github Pages](https://docs.genomebeacons.org) gets updated. Note that only content under directory `docs/` will make it to [Github Pages](https://docs.genomebeacons.org).
 
 Before creating this tool, the author made an exhaustive search on what had been dveloped by the _community_ to automatically convert YAML/JSON to Markdown tables and found that there were many ways to go from YAML/JSON to HTML (e.g., CPAN, Python, Node.js), but not much from YAML/JSON to Markdown. Obviously, even in the case we had found something, some major tweaking will be needed in order to display things the way we want.
 

diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl
@@ -582,7 +582,7 @@ sub create_str_yaml {
   description: References to the tool
   examples:
     - bio.toolsId: https://bio.tools/vep
-    - url: http://www.ensembl.org/vep
+    - url: https://www.ensembl.org/vep
   type: object
 EOF
 
@@ -769,11 +769,11 @@ =head1 MOTIVATION
 
 This script inverts the process, i.e., B<it enforces modifying the schema specification directly at the YAML/JSON level>.
 
-Editing the schemas directly at the YAML/JSON level has two advantages, the first is that because we follow L<OpenAPI|https://swagger.io/specification/> specification (along with JSON schema), I<a priori> we could use L<SWAGGER UI|https://swagger.io/docs/open-source-tools/swagger-ui/usage/installation>. The second is that the YAML/JSON files can be converted to Markdown tables in order to create L<Markdown based documentation|http://docs.genomebeacons.org> documentation. This script B<transforms YAML/JSON to Markdown tables>, including their nested objects B<up to a third degree of hierarchy>.
+Editing the schemas directly at the YAML/JSON level has two advantages, the first is that because we follow L<OpenAPI|https://swagger.io/specification/> specification (along with JSON schema), I<a priori> we could use L<SWAGGER UI|https://swagger.io/docs/open-source-tools/swagger-ui/usage/installation>. The second is that the YAML/JSON files can be converted to Markdown tables in order to create L<Markdown based documentation|https://docs.genomebeacons.org> documentation. This script B<transforms YAML/JSON to Markdown tables>, including their nested objects B<up to a third degree of hierarchy>.
 
-The B<Markdown> format can be directly rendered as tables at the GitHub repository, and it can be used with L<MkDocs|https://www.mkdocs.org/> to create L<HTML|http://docs.genomebeacons.org> documentation. 
+The B<Markdown> format can be directly rendered as tables at the GitHub repository, and it can be used with L<MkDocs|https://www.mkdocs.org/> to create L<HTML|https://docs.genomebeacons.org> documentation. 
 
-Everytime a C<git push> is performed to the L<repo|https://github.com/ga4gh-beacon/beacon-v2> the documentation at L<Github Pages|http://docs.genomebeacons.org> gets updated. Note that only content under directory C<docs/> will make it to L<Github Pages|http://docs.genomebeacons.org>.
+Everytime a C<git push> is performed to the L<repo|https://github.com/ga4gh-beacon/beacon-v2> the documentation at L<Github Pages|https://docs.genomebeacons.org> gets updated. Note that only content under directory C<docs/> will make it to L<Github Pages|https://docs.genomebeacons.org>.
 
 Before creating this tool, the author made an exhaustive search on what had been dveloped by the I<community> to automatically convert YAML/JSON to Markdown tables and found that there were many ways to go from YAML/JSON to HTML (e.g., CPAN, Python, Node.js), but not much from YAML/JSON to Markdown. Obviously, even in the case we had found something, some major tweaking will be needed in order to display things the way we want.
 

diff --git a/bin/deref_schemas/datasets/defaultSchema.json b/bin/deref_schemas/datasets/defaultSchema.json
@@ -247,7 +247,7 @@
         "externalUrl": {
             "description": "URL to an external system providing more dataset information (RFC 3986 format).",
             "examples": [
-                "http://example.org/wiki/Main_Page"
+                "https://example.org/wiki/Main_Page"
             ],
             "type": "string"
         },

diff --git a/bin/deref_schemas/datasets/defaultSchema.yaml b/bin/deref_schemas/datasets/defaultSchema.yaml
@@ -165,7 +165,7 @@ properties:
   externalUrl:
     description: URL to an external system providing more dataset information (RFC 3986 format).
     examples:
-      - http://example.org/wiki/Main_Page
+      - https://example.org/wiki/Main_Page
     type: string
   id:
     description: Unique identifier of the dataset

diff --git a/bin/deref_schemas/genomicVariations/defaultSchema.json b/bin/deref_schemas/genomicVariations/defaultSchema.json
@@ -98,7 +98,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,
@@ -295,7 +295,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,
@@ -706,7 +706,7 @@
                             {
                                 "id": "ClinGen:CA152954",
                                 "notes": "ClinGen Allele Registry id",
-                                "reference": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954"
+                                "reference": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954"
                             },
                             {
                                 "id": "UniProtKB:P35557#VAR_003699",
@@ -1563,7 +1563,7 @@
                                     "bio.toolsId": "https://bio.tools/vep"
                                 },
                                 {
-                                    "url": "http://www.ensembl.org/vep"
+                                    "url": "https://www.ensembl.org/vep"
                                 }
                             ],
                             "minProperties": 1,
@@ -1766,7 +1766,7 @@
                             "bio.toolsId": "https://bio.tools/vep"
                         },
                         {
-                            "url": "http://www.ensembl.org/vep"
+                            "url": "https://www.ensembl.org/vep"
                         }
                     ],
                     "minProperties": 1,
@@ -1811,7 +1811,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,
@@ -1994,7 +1994,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,
@@ -2259,7 +2259,7 @@
                                                     "bio.toolsId": "https://bio.tools/vep"
                                                 },
                                                 {
-                                                    "url": "http://www.ensembl.org/vep"
+                                                    "url": "https://www.ensembl.org/vep"
                                                 }
                                             ],
                                             "minProperties": 1,
@@ -2456,7 +2456,7 @@
                                                     "bio.toolsId": "https://bio.tools/vep"
                                                 },
                                                 {
-                                                    "url": "http://www.ensembl.org/vep"
+                                                    "url": "https://www.ensembl.org/vep"
                                                 }
                                             ],
                                             "minProperties": 1,
@@ -2797,7 +2797,7 @@
                             {
                                 "id": "ClinGen:CA152954",
                                 "notes": "ClinGen Allele Registry id",
-                                "reference": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954"
+                                "reference": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA152954"
                             },
                             {
                                 "id": "UniProtKB:P35557#VAR_003699",
@@ -3022,7 +3022,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,
@@ -3205,7 +3205,7 @@
                                                 "bio.toolsId": "https://bio.tools/vep"
                                             },
                                             {
-                                                "url": "http://www.ensembl.org/vep"
+                                                "url": "https://www.ensembl.org/vep"
                                             }
                                         ],
                                         "minProperties": 1,