Merge pull request #210 from ga4gh/release-1.1.0

RC-v1.1.0

.github/workflows/build.yml

@@ -0,0 +1,34 @@
+name: docs-build-publish
+on:
+  push:
+    branches:
+      - master
+      - develop
+      - "feature/issue-*"
+      - "fix/issue-*"
+      - "support/issue-*"
+  pull_request_target:
+    branches:
+      - master
+      - develop
+      - "feature/issue-*"
+      - "fix/issue-*"
+      - "support/issue-*"
+permissions:
+  contents: write
+jobs:
+  docs-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Docker Pull 🐳
+        run: |
+          docker pull ga4gh/gh-openapi-docs:0.2.3-rc1
+      - name: Build Docs 🔧
+        run: |
+          docker run --name docs-builder --rm -v `pwd`:/docs ga4gh/gh-openapi-docs:0.2.3-rc1
+      - name: Deploy 🚀
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: publish

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: Lint and validate OpenAPI specs
+on:
+  - push
+  - pull_request_target
+jobs:
+  lint:
+    name: Lint OpenAPI definition
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out head branch
+        uses: actions/checkout@v3
+      - name: Run OpenAPI Lint Action
+        uses: nwestfall/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          file: openapi/workflow_execution_service.openapi.yaml
+  diff:
+    name: Show OpenAPI differences relative to target branch
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'pull_request' }}
+    steps:
+      - name: Check out head branch
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.ref }}
+          path: head
+      - name: Check out base branch
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.base.ref }}
+          path: base
+      - name: Run OpenAPI Diff Action
+        uses: mvegter/[email protected]
+        with:
+          head-spec: head/openapi/workflow_execution_service.openapi.yaml
+          base-spec: base/openapi/workflow_execution_service.openapi.yaml
+
+  validate:
+    name: Validate OpenAPI definition
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out head branch
+        uses: actions/checkout@v3
+      - name: Run OpenAPI Validate Action
+        uses: char0n/swagger-editor-validate@v1
+        with:
+          definition-file: openapi/workflow_execution_service.openapi.yaml

.gitignore

@@ -134,3 +134,6 @@ node_modules
 # OS generated files #
 .DS_Store
 .DS_Store?
+
+# Documentation build system artifacts
+publish/

.spec-docs.json

@@ -1,4 +1,14 @@
 {
-    "apiSpecPath": "openapi/workflow_execution_service.openapi.yaml",
-    "redocTheme": "ga4gh"
-}
+    "docsRoot": "docs",
+    "defaultBranch": "master",
+    "branchPathBase": "preview",
+    "redocTheme": "ga4gh",
+    "buildPages": [
+        {
+            "apiSpecPath": "openapi/workflow_execution_service.openapi.yaml",
+            "htmlOutfile": "index.html",
+            "yamlOutfile": "openapi.yaml",
+            "jsonOutfile": "openapi.json"
+        }
+    ]
+}

README.md

@@ -1,20 +1,44 @@
-<img src="https://www.ga4gh.org/wp-content/themes/ga4gh-theme/gfx/GA-logo-horizontal-tag-RGB.svg" alt="GA4GH Logo" style="width: 400px;"/>
+![ga4gh logo](https://raw.githubusercontent.com/dockstore/dockstore-ui2/2.7.4/images/high-res/ga4gh.png)
+
+![release_badge](https://img.shields.io/github/v/tag/ga4gh/workflow-execution-service-schemas)
+
 
 Workflow Execution Service (WES) API
 ====================================
 
-<sup>`develop` branch status: </sup>[![Build Status](https://travis-ci.org/ga4gh/workflow-execution-service-schemas.svg?branch=develop)](https://travis-ci.org/ga4gh/workflow-execution-service-schemas?branch=develop)
-<a href="https://ga4gh.github.io/workflow-execution-service-schemas/preview/develop/swagger.yaml"><img src="http://online.swagger.io/validator?url=https://ga4gh.github.io/workflow-execution-service-schemas/preview/develop/swagger.yaml" alt="Swagger Validator" height="20em" width="72em"></A>
 
-The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international coalition, formed to enable the sharing of genomic and clinical data.
+This repository is the home for the schema for the GA4GH Workflow Execution Service API. The Goal of the API is to
+provide
+a standardized way to submit and manage workflows described in a workflow language (eg. WDL, CWL, Nextflow, Galaxy,
+Snakemake)
+against an execution backend.
+
+See the human-readable [Reference Documentation](https://ga4gh.github.io/workflow-execution-service-schemas/docs/)
+You can also explore the specification in
+the [Swagger Editor](https://editor.swagger.io/?url=https://ga4gh.github.io/workflow-execution-service-schemas/openapi.yaml)**
+*Manually load the JSON if working from a non-develop branch version.* Preview documentation from
+the [gh-openapi-docs](https://github.com/ga4gh/gh-openapi-docs) for the development
+branch [here](https://ga4gh.github.io/workflow-execution-service-schemas/preview/develop/docs/index.html)
+
+> All documentation and pages hosted at 'ga4gh.github.io/workflow-execution-service' reflect the latest API release from
+> the `master` branch. To monitor the latest development work, add 'preview/\<branch\>' to the URLs above (e.g., '
+> ga4gh.github.io/ga4gh.github.io/workflow-execution-service/preview/\<branch\>/docs'). To view the latest *stable*
+> development API specification, refer to the `develop` branch.
+
+
+The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international coalition, formed to
+enable the sharing of genomic and clinical data.
 
 Cloud Work Stream
 -----------------
 
-The [Cloud Work Stream](https://ga4gh.cloud) helps the genomics and health communities take full advantage of modern cloud environments.
-Our initial focus is on “bringing the algorithms to the data”, by creating standards for defining, sharing, and executing portable workflows.
+The [Cloud Work Stream](https://ga4gh.cloud) helps the genomics and health communities take full advantage of modern
+cloud environments.
+Our initial focus is on “bringing the algorithms to the data”, by creating standards for defining, sharing, and
+executing portable workflows.
 
-We work with platform development partners and industry leaders to develop standards that will facilitate interoperability.
+We work with platform development partners and industry leaders to develop standards that will facilitate
+interoperability.
 
 What is WES?
 ============
@@ -28,21 +52,23 @@ Key features include:
 * ability to parameterize that workflow using a JSON schema
 * ability to get information about running workflows
 
-API Definition
---------------
-
-See the human-readable [Reference Documentation](https://ga4gh.github.io/workflow-execution-service-schemas/docs/) 
-and the [OpenAPI YAML description](openapi/workflow_execution_service.swagger.yaml). You can also explore the specification in the [Swagger Editor](https://editor.swagger.io/?url=https://ga4gh.github.io/workflow-execution-service-schemas/openapi.yaml).
-
-> All documentation and pages hosted at 'ga4gh.github.io/workflow-execution-service' reflect the latest API release from the `master` branch. To monitor the latest development work, add 'preview/\<branch\>' to the URLs above (e.g., 'ga4gh.github.io/ga4gh.github.io/workflow-execution-service/preview/\<branch\>/docs'). To view the latest *stable* development API specification, refer to the `develop` branch.
 
 Use Cases
 ---------
 
 Use cases include:
 
-* "Bring your code to the data": a researcher who has built their own custom analysis can submit it to run on a dataset owned by an external organization, instead of having to make a copy of the data
-* Best-practices pipelines: a researcher who maintains their own controlled data environment can find useful workflows in a shared directory (e.g., [Dockstore.org](http://dockstore.org)), and run them over their data
+* "Bring your code to the data": a researcher who has built their own custom analysis can submit it to run on a dataset
+  owned by an external organization, instead of having to make a copy of the data
+* Best-practices pipelines: a researcher who maintains their own controlled data environment can find useful workflows
+  in a shared directory (e.g., [Dockstore.org](http://dockstore.org)), and run them over their data
+
+Starter Kit
+-----------
+If you are a future implementor or would like to start using a WES API locally you can try
+the [GA4GH WES Starter Kit](https://starterkit.ga4gh.org/docs/starter-kit-apis/wes/wes_overview/). This project provides
+a fully functioning WES API written in java and allows you to run workflows using the Nextflow workflow language.
+
 
 Possible Future Enhancements
 ----------------------------
@@ -58,7 +84,8 @@ How to Contribute Changes
 
 See [CONTRIBUTING.md](CONTRIBUTING.md).
 
-If a security issue is identified with the specification, please send an email to [email protected] detailing your concerns.
+If a security issue is identified with the specification, please send an email to [email protected]
+detailing your concerns.
 
 License
 -------