-
Notifications
You must be signed in to change notification settings - Fork 18
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Changes from 2.0.0 + CI fix: * Explicitly define type in definitions * Change properties to snakes case and endpoints to camelcase * Move enum to its own definition * Incrementing version due to breaking changes * New endpoint and object definition to describe available files * For issues #21 and #22 * Renamed File definition to ToolFile due to swagger editor * Increment version in comment * Add more file types, better descriptions * Tool checker proposal (#26) From https://docs.google.com/document/d/1PTge27WBOKCiR2MkVSOvWKUwnFk0kx-bjq39aKRQxcY/edit?usp=sharing * Generalize the TRS to account for Singularity and Nextflow * Change toolversion's boolean indicator * Add terms of service placeholder * Install swagger2openapi * Adding operationIds (#33) See dockstore/dockstore#1210 * Moved checker to a property in Tool, also added a boolean * Specify unencoded paths are also allowed * Feature/search (#48) * Add option for search for checker workflows * For #37 , allow meta_version to be optional ga4gh/workflow-execution-service-schemas#6 ga4gh/workflow-execution-service-schemas@337cd42 * Add alias suggestion from #38 * Standardize file fields * Simplify standard (#49) * Feature/link check (#55) * Create CONTRIBUTING.md (#65) * Automatically generate docs for all branches and tags * TRS documentation update (#64) * Update openAPI3.sh * Update BasePath (#72) Updated base path to `basePath: `/ga4gh/trs/v2` * Update ga4gh-tool-discovery.yaml (#74) * Updated LICENCE Copyright (#76) * Include mention to Nextflow (#77) Mentioning nextflow as long the API is supporting workflows based on Nextflow language (NFL) https://github.com/pditommaso/tool-registry-service-schemas/blob/develop/src/main/resources/swagger/openapi.yaml#L741-L744 * Allow for more than one container image (#58) * fix type, update OpenAPI version * fix array examples * Update openapi.yaml * Rename metadata to match GA4GH PAP (#78) * Adding zenodo reference as recommended * Adding contact URL inspired by WES for PAP From security questionaire * More convention sync with cloud workstream APIs (#84) * Working on #82 also see ga4gh/workflow-execution-service-schemas#134 * Working on harmonizing with GA4GH Discovery https://github.com/ga4gh-discovery/service-info * Fix description for #85 * WS-2019-0032 WS-2019-0063 * Attempt to fix tooling (#89) * Update README.md for gitflow (#91) * Simple PRC feedback PR (#92) * Feedback from BOSC * Typo in example (#99) * Remove service-info to avoid breaking change (#101) * Move around a few fields (#97) * test gradle fix for site deployment (#105) * Optional auth (#102) * PRC feedback - strict tool versioning for reproducibility (#93) * Update to match discussion in DRS checksum object added and tweaked to match ga4gh/data-repository-service-schemas#282 * Corrects link to GA4GH . checksum hash algorithm registry (#106) * Correcting hash algorithm registry link * Correcting hash alg registry link * Fixing unrelated link * Glitchy badge (#112) * Update registry.json (#115) * Fix CI (#123) Co-authored-by: Denis Yuen <denis.yuen@oicr.on.ca> Co-authored-by: Yasset Perez-Riverol <ypriverol@gmail.com> Co-authored-by: Chris Llanwarne <cjllanwarne@users.noreply.github.com> Co-authored-by: Susheel Varma <susheel@users.noreply.github.com> Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Co-authored-by: dependabot-preview[bot] <27856297+dependabot-preview[bot]@users.noreply.github.com>
- Loading branch information
7 people
authored
Feb 6, 2020
1 parent
d894afe
commit 7ad7891
Showing
18 changed files
with
4,198 additions
and
15 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| .gradle/ | ||
| gradle/ | ||
| gradlew | ||
| gradlew.bat | ||
| node_modules/ | ||
| spec/ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| dist: xenial | ||
| language: java | ||
| jdk: openjdk8 | ||
|
|
||
| # looks like papa32 plugin 1.5.0 is no longer compatible with gradle 5, the other option is to try running without it | ||
| before_install: | ||
| - wget https://services.gradle.org/distributions/gradle-4.10.2-bin.zip | ||
| - unzip -qq gradle-4.10.2-bin.zip | ||
| - export GRADLE_HOME=$PWD/gradle-4.10.2 | ||
| - export PATH=$GRADLE_HOME/bin:$PATH | ||
| - gradle -v | ||
|
|
||
| jobs: | ||
| include: | ||
| - stage: check-links | ||
| install: npm i -g markdown-link-check | ||
| script: markdown-link-check ./README.md | ||
| - stage: commit-OpenAPI | ||
| install: npm i -g swagger2openapi | ||
| script: | ||
| - swagger2openapi openapi/ga4gh-tool-discovery.yaml -o openapi/openapi.yaml | ||
| after_success: | ||
| - git checkout -B ${TRAVIS_BRANCH} | ||
| - bash scripts/openAPI3.sh | ||
| - stage: build_pages | ||
| script: | ||
| - "gradle wrapper" | ||
| - "chmod +x gradlew" | ||
| - "./gradlew installSwagger buildSwagger asciidoctor" | ||
| after_success: | ||
| - bash scripts/update-ghpages.sh |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| # CONTRIBUTING | ||
|
|
||
| This schema is developed by the [Cloud Work Stream](https://ga4gh.cloud) of the [Global Alliance for Genomics and Health](https://ga4gh.org). | ||
|
|
||
| ## Semantic Versioning | ||
|
|
||
| We use [semantic versioning](https://semver.org/) for TRS, this will determine if your proposed changes impact a major or minor release. | ||
|
|
||
| ## Suggesting Changes | ||
|
|
||
| Suggested changes to this schema can be initiated as [**Issues**](https://github.com/ga4gh/tool-registry-service-schemas/issues) or [**Pull Requests**](https://github.com/ga4gh/workflow-execution-service-schemas/pulls) to allow for discussion and review. | ||
|
|
||
| Even those with write access to the main repository should in general create pull request branches within their own forks. This way when the main repository is forked again, the new fork is created with a minimum of extraneous volatile branches. | ||
|
|
||
| <!-- activate after https://github.com/ga4gh/tool-registry-service-schemas/issues/60 | ||
| > To facilitate review of external pull requests, users are encouraged to activate [**Travis CI**](https://travis-ci.org/) to monitor the build status (documentation, Swagger UI) of their fork. By following the documentation for [deployment to GitHub Pages](https://docs.travis-ci.com/user/deployment/pages/) and adding a `$GITHUB_TOKEN` environment variable to their repo configuration, pushes to the forked repo should be viewable relative to `https://[user-or-org].github.io/workflow-execution-service-schemas/preview/<branch>/`: | ||
| + https://[user-or-org].github.io/workflow-execution-service-schemas/preview/\<branch\>/docs/ | ||
| + https://[user-or-org].github.io/workflow-execution-service-schemas/preview/\<branch\>/swagger-ui/ | ||
| + https://[user-or-org].github.io/workflow-execution-service-schemas/preview/\<branch\>/swagger.json | ||
| + https://[user-or-org].github.io/workflow-execution-service-schemas/preview/\<branch\>/swagger.yaml | ||
| > Providing this base URL in the pull request comment is appreciated, but not required. | ||
| If a security vulnerability is identified with the specification please send an email to security-notification@ga4gh.org detailing your concerns. | ||
| ## Approving Changes | ||
| ### pre-WES v1.0.0 / Testbed Voting Procedure | ||
| Changes for the release are to be approved by four developers - Marcus Kinsella (HCA), Jeff Gentry (Broad Institute), James Eddy (Sage Bionetworks), Peter Amstutz (Veritas Genetics). In addition they must not be overridden by the Cloud Work Stream Leads, Brian O'Connor and David Glazer. | ||
| ### post WES v1.0.0 Voting Procedure | ||
| GA4GH has a number of Driver Projects. Each of those associated with the Cloud Work Stream will nominate a representative. None of these may vote against a proposed change for it to proceed. In addition they must not be overridden by the Cloud Work Stream Leads, Brian O'Connor and David Glazer. | ||
| --> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| buildscript { | ||
| repositories { | ||
| jcenter() | ||
| mavenCentral() | ||
| maven { url 'http://oss.jfrog.org/artifactory/oss-snapshot-local/' } | ||
| maven { | ||
| url "https://plugins.gradle.org/m2/" | ||
| } | ||
| //mavenLocal() | ||
| } | ||
| dependencies { | ||
| classpath 'org.asciidoctor:asciidoctor-gradle-plugin:1.5.3' | ||
| classpath 'io.github.swagger2markup:swagger2markup-gradle-plugin:1.3.1' | ||
| classpath "io.github.swagger2markup:swagger2markup:1.3.1" | ||
| classpath "io.github.swagger2markup:swagger2markup-import-files-ext:1.3.1" | ||
| classpath "com.bluepapa32:gradle-watch-plugin:0.1.5" | ||
| classpath "org.kordamp.gradle:livereload-gradle-plugin:0.2.1" | ||
| classpath "com.moowork.gradle:gradle-node-plugin:1.2.0" | ||
| } | ||
| } | ||
|
|
||
| apply plugin: 'org.asciidoctor.convert' | ||
| apply plugin: 'com.bluepapa32.watch' | ||
| apply plugin: 'org.kordamp.gradle.livereload' | ||
| apply plugin: 'io.github.swagger2markup' | ||
| apply plugin: 'com.moowork.node' | ||
| node { | ||
| version = '8.9.0' | ||
| download = true | ||
| } | ||
|
|
||
| group 'io.github.swagger2markup' | ||
| version '1.3.1' | ||
|
|
||
| repositories { | ||
| jcenter() | ||
| mavenCentral() | ||
| } | ||
|
|
||
| ext { | ||
| asciiDocDir = file("src/asciidoc") | ||
| asciiDocOutputDir = file("docs/asciidoc/swagger2markup") | ||
| } | ||
|
|
||
| convertSwagger2markup { | ||
| swaggerInput file("openapi/ga4gh-tool-discovery.yaml").getAbsolutePath() | ||
| outputDir asciiDocOutputDir | ||
| config = ['swagger2markup.markupLanguage' : 'ASCIIDOC', | ||
| 'swagger2markup.extensions.dynamicDefinitions.contentPath' : file('docs/asciidoc/swagger2markup/definitions').absolutePath, | ||
| 'swagger2markup.extensions.dynamicOverview.contentPath' : file('docs/asciidoc/swagger2markup/overview').absolutePath, | ||
| 'swagger2markup.extensions.dynamicPaths.contentPath' : file('docs/asciidoc/swagger2markup/paths').absolutePath, | ||
| 'swagger2markup.extensions.dynamicSecurity.contentPath' : file('docs/asciidoc/swagger2markup/security').absolutePath] | ||
| } | ||
|
|
||
| asciidoctorj { | ||
| version = '1.5.5' | ||
| } | ||
|
|
||
| asciidoctor { | ||
| dependsOn convertSwagger2markup | ||
| sourceDir asciiDocDir | ||
| outputDir file("docs") | ||
| sources { | ||
| include 'index.adoc' | ||
| } | ||
| backends = ['html5', 'pdf'] | ||
| attributes = [ | ||
| doctype: 'book', | ||
| toc: 'left', | ||
| toclevels: '3', | ||
| numbered: '', | ||
| sectlinks: '', | ||
| sectanchors: '', | ||
| hardbreaks: '', | ||
| generated: asciiDocOutputDir | ||
| ] | ||
| } | ||
|
|
||
| dependencies { | ||
| // add converters and extensions using `asciidoctor` configuration | ||
| asciidoctor 'org.asciidoctor:asciidoctorj-pdf:1.5.0-alpha.15' | ||
| } | ||
|
|
||
| watch { | ||
| asciidoc { | ||
| files fileTree('docs/asciidoc') | ||
| tasks 'asciidoctor' | ||
| } | ||
| } | ||
|
|
||
| liveReload { | ||
| docRoot asciidoctor.outputDir.canonicalPath | ||
| } | ||
|
|
||
|
|
||
| task wrapper(type: Wrapper) { | ||
| gradleVersion = '3.5' | ||
| } | ||
|
|
||
| task installSwagger(type: NpmTask) { | ||
| npmCommand = ["install"] | ||
| } | ||
|
|
||
| task buildSwagger(type: NpmTask) { | ||
| npmCommand = ["run", "build"] | ||
| } | ||
|
|
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| ## Instruction for modifying the TRS | ||
|
|
||
| To make changes to the TRS, join the GA4GH organization or ask to join this repository as a collaborator. Then in your branch, modify: | ||
| - The swagger yaml file (`ga4gh-tool-discovery.yaml`) with a Swagger 2 definition of the changes. | ||
| - This swagger yaml file will be used in the validation server. | ||
| - An OpenAPI yaml file (`openapi.yaml`) with an OpenAPI 3 definition of the changes will be auto-generated by swagger2openapi and checked in by an automated TravisCI build | ||
|
|
Oops, something went wrong.