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8bfbdb6
Compatibility matrix
aniewielska 07e79e1
Styling the table
aniewielska 9f2126d
Update the link to logo
aniewielska e6f61f8
And logo in openapi.yaml
aniewielska 739f3d6
Permalink
aniewielska a142c02
docs: add Snakemake to TES client implementers
uniqueg cafac9c
Merge pull request #153 from uniqueg/new-tes-client-snakemake
aniewielska a6328fe
Added "additional_properties" field to tesResources
MattMcL4475 de9e48a
Updated description
MattMcL4475 12ba268
draft changes
MattMcL4475 4724d30
updated description
MattMcL4475 560a14e
Changes from call with Ania and Kyle
MattMcL4475 738f205
Merge pull request #1 from MattMcL4475/develop-info-draft
MattMcL4475 c01054c
Add additional description regarding callers passing runtime parameters
MattMcL4475 a057229
fix minor typo in description
MattMcL4475 3de465e
Minor language change
MattMcL4475 9575021
Added backend_parameters_strict option to force TES to fail a task if…
MattMcL4475 e88e86f
Making file type an optional argument
kellrott d9086d9
Adding streamable flag to tesInput
kellrott 6a55857
Adding ignore_error flag
kellrott dbbca50
Porting code from #104
kellrott 8292fb5
Fixing tag filtering description
kellrott 5cbf2bd
Fixing state filtering variable
kellrott 9dad23d
Switch to Github Actions
aniewielska aee0e32
Delete .travis.yml
aniewielska 53627cb
Merge pull request #172 from ga4gh/gh-actions
kellrott 8d6e6ea
Merge pull request #150 from aniewielska/impl-matrix
kellrott 04a6abb
Merge pull request #147 from aniewielska/logo
kellrott 61558fd
Merge remote-tracking branch 'origin/develop' into develop-1.1
kellrott 36181ff
Merge pull request #173 from ga4gh/develop-1.1
kellrott 3772b39
Merge remote-tracking branch 'origin/develop' into issue/104
kellrott aaf4cfd
Merge remote-tracking branch 'origin/develop' into issue/158
kellrott 6c8d7c3
Merge remote-tracking branch 'origin/develop' into issue/156
kellrott 88c8b1b
Merge remote-tracking branch 'origin/develop' into issue/76
kellrott d79f2a5
Updating tag filtering structure to use a pair of arrays
kellrott aac56b3
Adding some code quotes
kellrott e551804
Changing int64 to int32 for page_size and cpu_count
kellrott d523f90
Update link for Azure TES implementation.
vsmalladi fa8d96f
Merge pull request #177 from vsmalladi/fix_azure_links
kellrott 3b6f0b9
ci: add OpenAPI linting and validation
uniqueg 90ba26d
Merge branch 'patch-2' of github.com:uniqueg/task-execution-schemas i…
kellrott b3b1028
Add in new tesState for preemted state.
vsmalladi 2f9579f
Fix spacing and spelling
vsmalladi 328fe1f
feat: allow wildcards in output paths
uniqueg 9c89664
Merge pull request #181 from ga4gh/issue/178
kellrott 5e42a7c
Merge pull request #184 from vsmalladi/preemted
kellrott 70b8270
Merge pull request #185 from uniqueg/issue/77
kellrott dfbda82
Merge pull request #155 from ga4gh/issue/76
kellrott 3657404
Merge pull request #175 from ga4gh/issue/174
kellrott dbe6ea6
Merge pull request #159 from ga4gh/issue/158
kellrott ca0e31e
Add CANCELLATION_REQUESTED state
MattMcL4475 4544067
Change state name to CANCELING to match WES
MattMcL4475 e541087
Minor edit to CANCELING state description
MattMcL4475 793aae8
Merge branch 'feature/AddCancellationRequestedState' of github.com:Ma…
kellrott 8f5f0ce
Adding link to TES license
kellrott 241ecef
Fixing typo
kellrott 9b29a79
Merge pull request #157 from ga4gh/issue/156
kellrott 95af30d
Clarifying some examples
9791e97
Merge pull request #170 from ga4gh/issue/104
kellrott 82103d7
Merge pull request #187 from ga4gh/develop-1.1
kellrott ffd9f0e
Update task_execution_service.openapi.yaml
kellrott 117cd92
Merge pull request #190 from ga4gh/version-1.1-numbering
kellrott cf21915
Update TES link for Azure
vsmalladi 1df37d3
Merge pull request #192 from vsmalladi/develop
kellrott 9acda2d
Update README.md
johanneskoester 4a56260
Update README.md
alextsaihi b8108f4
Update readme for projects
vsmalladi 0c95751
Fix build docs.
vsmalladi e4a5720
Merge pull request #212 from vsmalladi/211-readme
vsmalladi f495fae
Merge branch 'develop' into develop
vsmalladi ebde4bb
Update build.yml
vsmalladi 1de8ebe
Update ci.yml
vsmalladi d49bc65
Merge pull request #218 from vsmalladi/197-branch
vsmalladi 2082a8f
Merge pull request #201 from alextsaihi/ga4gh-logo-update
vsmalladi a5fb76e
Fix some of the description in readme and tags. (#1)
vsmalladi b0c08ee
Resolve issue with two sections
vsmalladi 4362315
Merge pull request #220 from vsmalladi/develop
vsmalladi b0eb2d5
Update logo
vsmalladi c157712
Merge pull request #221 from vsmalladi/develop
vsmalladi 42bb695
Update to be linked to the latest tag.
vsmalladi a0da756
Fix repo.
vsmalladi 93b1e3a
Add back build and spec badges.
vsmalladi 0c05b27
Check with develop.
vsmalladi d04eca1
Testing ci badge.
vsmalladi 6288dc4
Testing ci badge.
vsmalladi c4f8d98
check validtor.
vsmalladi 244a8b8
Make a table and visualize all on the status for both master and deve…
vsmalladi 4bf02c6
Change the develop branch name.
vsmalladi f6495ef
Reword description.
vsmalladi d9ebe9c
Fix formating and full stops.
vsmalladi c02bcb9
Add rewording.
vsmalladi a248cde
Update JSON.
vsmalladi b287476
Remove Possible future enhancemnts section.
vsmalladi 7f253a0
Add Governance.
vsmalladi 9b19cf7
Add in license.
vsmalladi 8614de7
Fix badges.
vsmalladi 07cbe93
Simplify build.
vsmalladi aab9eba
Build in PR.
vsmalladi a55038c
Change the plugin to be used so doesnt require secrets.
vsmalladi ab2f679
Fix security.
vsmalladi 7e0f90c
Fix spelling error.
vsmalladi 15c3088
update for security.
vsmalladi 31dbd36
Update links.
vsmalladi 6834190
Fix some wording.
vsmalladi 3d1733b
Fix build.
vsmalladi 6209a56
Fix build.
vsmalladi fc905dd
Fix build.
vsmalladi e482eac
Fix build syntax.
vsmalladi 04550ed
Add in push.
vsmalladi 4592b2a
Fix voting.
vsmalladi 639ca06
Merge pull request #222 from vsmalladi/develop
vsmalladi 2bafe3d
Update GOVERNANCE.md
uniqueg f43298b
Update build.yml
uniqueg e10cdb0
Update build.yml
uniqueg 9a3e78d
Update build.yml
uniqueg 00946b3
Update README.md
uniqueg 060d08a
Update README.md
uniqueg 9a38e48
Update README.md
uniqueg e6a5275
Update README.md
uniqueg 5fdc081
Update README.md
uniqueg e87ac17
Update README.md
uniqueg cf7b478
Update CONTRIBUTING.md
uniqueg 22d7ae7
Update CONTRIBUTING.md
uniqueg df497df
Merge pull request #223 from ga4gh/uniqueg-patch-1
vsmalladi 6f40e15
Merge pull request #224 from ga4gh/uniqueg-patch-2
vsmalladi e15a1aa
Merge pull request #225 from ga4gh/uniqueg-patch-3
vsmalladi 3ba6a09
Merge pull request #226 from ga4gh/uniqueg-patch-4
vsmalladi 8e7a7c9
Update ci.yml
uniqueg 63fb1e9
Merge pull request #1 from uniqueg/openapi-diff-pr-comment
uniqueg 04712c1
Update task_execution_service.openapi.yaml
uniqueg 2637b6b
Update ci.yml
uniqueg ec8683f
Update ci.yml
uniqueg 59dee75
Update ci.yml
uniqueg f34e3fa
Update ci.yml
uniqueg 20b23d4
Update ci.yml
uniqueg e97a969
Update ci.yml
uniqueg 6e221f4
Update ci.yml
uniqueg 8cd84fd
Create diff_comment.yml
uniqueg 8fed9ee
Create diff_comment.yml
uniqueg a73ca16
Delete .github/workflows/diff_comment.yml
uniqueg 607552f
Update task_execution_service.openapi.yaml
uniqueg 556b134
Update diff_comment.yml
uniqueg a0800f1
Update ci.yml
uniqueg ed4499b
Update diff_comment.yml
uniqueg e3fe649
Update task_execution_service.openapi.yaml
uniqueg 2f6a18a
Update diff_comment.yml
uniqueg cfe4f6c
Update task_execution_service.openapi.yaml
uniqueg 2ea05ea
Update diff_comment.yml
uniqueg 3a15e8b
Update task_execution_service.openapi.yaml
uniqueg 7cb1d0c
Update diff_comment.yml
uniqueg aeeed03
Update task_execution_service.openapi.yaml
uniqueg 8379c63
Update diff_comment.yml
uniqueg 8680ea3
Update task_execution_service.openapi.yaml
uniqueg 98143d2
Update diff_comment.yml
uniqueg 586fc59
Update task_execution_service.openapi.yaml
uniqueg e55af78
Update ci.yml
uniqueg dc099c8
Update diff_comment.yml
uniqueg ee771a5
Update ci.yml
uniqueg d41e922
Update diff_comment.yml
uniqueg 13e7b96
Update diff_comment.yml
uniqueg f099807
Delete .github/workflows/diff_comment.yml
uniqueg 7069773
Create diff_comment.yml
uniqueg 3e6cecc
Update task_execution_service.openapi.yaml
uniqueg 6364e19
Fix failure
vsmalladi 5ae7a84
Update ci.yml
vsmalladi 6569f4b
Log OpenAPI Diff errors to error.log
vsmalladi 382de99
Update error log path in CI workflow
vsmalladi 8d1a7f0
Update OpenAPI Diff to latest version
vsmalladi c7f948c
Fix OpenAPI Diff error handling in CI
vsmalladi 0b5271f
Fix typo and add checkout action in CI
vsmalladi 05676c2
Remove redundant checkout step in CI workflow
vsmalladi 79875f1
Fix indentation for GitHub token in CI script
vsmalladi 2f4dcf3
Add PR comment step to try comment
vsmalladi a36d910
Just testing
vsmalladi 9e9c17d
Add GitHub token to CI workflow
vsmalladi f3f3c28
Add GitHub context import in CI script
vsmalladi b6e8e75
Update GitHub token in CI workflow
vsmalladi a9c51e1
Reorder and update CI workflow steps
vsmalladi e5747c9
Add exit command on diff failure in CI
vsmalladi 6bd4c0d
Fix docker image
vsmalladi 185107c
Add Docker image pull step in CI
vsmalladi 39772ee
Fix ci build
vsmalladi aa61f70
Update CI workflow comments and permissions
vsmalladi d2a79a7
Update CI workflow for OpenAPI validation
vsmalladi 1b4f9fb
Update ci.yml
vsmalladi b52443b
Update OpenAPI Validate Action usage
vsmalladi 91c5064
Merge pull request #227 from uniqueg/develop
vsmalladi cf3e6d1
Update ci.yml to reverse head and base for old and new
vsmalladi 5b07fab
Delete diff comment now in ci.yml.
vsmalladi 0bc05dd
Merge pull request #234 from vsmalladi/develop
vsmalladi 7c05551
Fix markdown link formatting in README.md
vsmalladi 371f1b9
Update CI workflow triggers for push and pull_request_target
vsmalladi c7c57c8
Update compatibility status for TESK and TES Azure
vsmalladi c4c17c9
Merge pull request #196 from johanneskoester/develop
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| name: Build OpenAPI docs | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - develop | ||
| - 'release*' | ||
| pull_request: | ||
| types: [opened, reopened, sychronize] | ||
| jobs: | ||
| docs-build: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Setup Node.js environment | ||
| uses: actions/setup-node@v4 | ||
| with: | ||
| node-version: 14.x | ||
| # Comes with npm 6. For newer Node, encountered: https://github.com/npm/cli/issues/3359 | ||
| - run: npm install -g @redocly/openapi-cli && npm install -g redoc-cli | ||
| - run: npm install -g gh-openapi-docs | ||
| - name: Check out repository code | ||
| uses: actions/checkout@v4 | ||
| - run: gh-openapi-docs | ||
| - name: Deploy 🚀 | ||
| uses: JamesIves/github-pages-deploy-action@v4 | ||
| with: | ||
| branch: gh-pages | ||
| folder: . | ||
| target-folder: ${{ github.ref == 'refs/heads/main' && 'docs/index.html' || '' }} # Deploy to docs/index.html only if on main | ||
| clean: ${{ github.ref == 'refs/heads/main' }} # Clean only if on the main branch |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| 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@v4 | ||
| - name: Run OpenAPI Lint Action | ||
| uses: mhiew/redoc-lint-github-action@v4 | ||
| with: | ||
| args: 'openapi/task_execution_service.openapi.yaml' | ||
| validate: | ||
| name: Validate OpenAPI definition | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out head branch | ||
| uses: actions/checkout@v4 | ||
| - name: Run OpenAPI Validate Action | ||
| uses: swaggerexpert/swagger-editor-validate@v1 | ||
| with: | ||
| definition-file: openapi/task_execution_service.openapi.yaml | ||
|
|
||
| diff: | ||
| name: Show OpenAPI differences relative to target branch | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| diff_generated: ${{ steps.upload-log.outputs.artifact_id }} | ||
| steps: | ||
| - name: Check out head branch | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ref: ${{ github.ref }} | ||
| path: head | ||
| - name: Check out base branch | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| ref: ${{ github.event.pull_request.base.ref }} | ||
| path: base | ||
| - name: Create output directory | ||
| run: mkdir -p diff-artifacts/ | ||
| - name: Pull Docker Image | ||
| run: docker pull openapitools/openapi-diff:2.0.1 | ||
| - name: Run openapi-diff tool | ||
| run: | | ||
| docker run --rm \ | ||
| -v $(pwd)/head:/head:ro \ | ||
| -v $(pwd)/base:/base:ro \ | ||
| -v $(pwd)/diff-artifacts:/local \ | ||
| openapitools/openapi-diff:2.0.1 \ | ||
| /base/openapi/task_execution_service.openapi.yaml \ | ||
| /head/openapi/task_execution_service.openapi.yaml \ | ||
| --markdown /local/diff.md 2> diff-artifacts/error.log | ||
| - name: Get PR number | ||
| id: get-pr-number | ||
| run: | | ||
| echo "${{ github.event.pull_request.number }}" > diff-artifacts/pr_number | ||
| - name: Upload artifacts | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: diff-artifacts | ||
| path: diff-artifacts/ | ||
| if-no-files-found: ignore | ||
| - name: Check if OpenAPI Diff failed | ||
| id: check-diff | ||
| run: | | ||
| if [ -s diff-artifacts/error.log ]; then | ||
| echo "The diff failed. Please see artifact error.log." | ||
| exit 1 | ||
| fi | ||
|
|
||
| permissions: | ||
| contents: read | ||
| pull-requests: write | ||
| issues: write | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,47 @@ | ||
|
|
||
| # CONTRIBUTING | ||
|
|
||
| This schema is developed by the [Cloud Work Stream](https://ga4gh.cloud) of the [Global Alliance for Genomics and Health](https://ga4gh.org). | ||
| This schema is developed by the [Cloud Work | ||
| Stream]([https://ga4gh.cloud](https://www.ga4gh.org/work_stream/cloud/)) of the | ||
| [Global Alliance for Genomics and Health](https://ga4gh.org). | ||
|
|
||
| ## Semantic Versioning | ||
|
|
||
| We use [semantic versioning](https://semver.org/) for TES, this will determine if your proposed changes impact a major or minor release. | ||
| The Task Execution Service (TES) API uses [semantic | ||
| versioning](https://semver.org/) for TES. Please consider that breaking changes | ||
| imply a new major version release, which is associated with considerable | ||
| administrative work and therefore happen only rarely. | ||
|
|
||
| ## Suggesting Changes | ||
|
|
||
| Suggested changes to this schema can be initiated as [**Issues**](https://github.com/ga4gh/task-execution-schemas/issues) or [**Pull Requests**](https://github.com/ga4gh/task-execution-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. | ||
|
|
||
| > 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/task-execution-schemas/preview/\<branch\>/docs/ | ||
| + https://[user-or-org].github.io/task-execution-schemas/preview/\<branch\>/swagger-ui/ | ||
| + https://[user-or-org].github.io/task-execution-schemas/preview/\<branch\>/swagger.json | ||
| + https://[user-or-org].github.io/task-execution-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-TES v1.0.0 / Testbed Voting Procedure | ||
| Changes for the release are to be approved by 2 TES specification leads. | ||
|
|
||
| ### post TES v1.0.0 Voting Procedure | ||
| The post v1.0.0 voting group include stakeholders, such as server and client implementors. | ||
| The membership of this group will be established as part of the v1.0.0 release. | ||
| Changes to TES can be initiated as | ||
| [**issues**](https://github.com/ga4gh/task-execution-schemas/issues) or | ||
| [**pull requests**](https://github.com/ga4gh/task-execution-schemas/pulls) to | ||
| allow for discussion and review. For considerable changes, we generally | ||
| recommend opening issues first in order to discuss scope and feasibility. | ||
|
|
||
| When creating pull requests, please do so from your own fork - even if you have | ||
| write access to the repository. In this way, when the main repository is forked | ||
| again, the new fork is created with a minimum of extraneous, volatile branches. | ||
|
|
||
| > To facilitate the review of external pull requests, users are encouraged to | ||
| > activate [**GitHub Actions**](https://github.com/features/actions) to monitor | ||
| > the build status of their fork. By following the documentation for [deployment | ||
| > to GitHub | ||
| > Pages](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site), | ||
| > pushes to the forked repository will be viewable at | ||
| > `https://[user-or-org].github.io/task-execution-service/preview/<branch>/`, | ||
| > e.g.,: | ||
| > - `https://[user-or-org].github.io/task-execution-schemas/preview/\<branch\>/docs/` | ||
| > - `https://[user-or-org].github.io/task-execution-schemas/preview/\<branch\>/swagger-ui/` | ||
| > - `https://[user-or-org].github.io/task-execution-schemas/preview/\<branch\>/swagger.json` | ||
| > - `https://[user-or-org].github.io/task-execution-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 <mailto:security-notification@ga4gh.org> detailing your concerns. | ||
|
|
||
| For more information please refer to the [**governance | ||
| documentation**](GOVERNANCE.md). |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| TES Governance and Process | ||
| ============================== | ||
|
|
||
| The Task Execution Service (TES) operates under a community-driven development model, where advancements to the specification occur exclusively through community contributions. The standard is governed by a core team of Product Leads that fosters collaboration and consensus among contributors. This team is tasked with overseeing the design and development processes, setting priorities, managing the release schedule, and making decisions in instances where consensus cannot be reached. | ||
|
|
||
| Current TES Product Leads are: | ||
|
|
||
| | Name | Organization | github | | ||
| |:-------------------|:-------------|:------------------ | ||
| | Kyle Ellrot | [Oregon Health and Science University](https://www.ohsu.edu/) | [kellrott](https://github.com/kellrott) | | ||
| | Venkat Malladi | [Microsoft](https://www.microsoft.com/en-us/genomics/) | [vsmalladi](https://github.com/vsmalladi) | | ||
| | Alex Kanitz | [Swiss Institute of Bioinformatics / ELIXIR Switzerland](https://www.sib.swiss/) | [uniqueg](https://github.com/uniqueg) | | ||
|
|
||
|
|
||
| ## Voting Procedure | ||
|
|
||
| Proposed changes and releases are voted on by Driver Project champions and other key stakeholders, such as product implementers (client- and sever-side). Product Leads review proposed changes on a regular product-specific call, then solicit community feedback during regular Cloud Work Stream calls and through the [product-specific](mailto:ga4gh-cloud-tes+subscribe@ga4gh.org) mailing list for a specified time period. Proposed releases are further shared through official GA4GH channels (Slack board and mailing list with wider scope) and with a longer feedback period. Product Leads, in close connection with the Cloud Work Stream leadership, will always strive to reach broad consensus, but may accept simple majority decisions if broad consensus cannot be reached. | ||
|
|
||
| Sign up for the [**GA4GH TES API mailing list**](mailto:ga4gh-cloud-tes+subscribe@ga4gh.org) to stay updated about the latest news and developments around the TES API, in particular for soliciting comments on proposed specification changes and for notifications about TES subgroup meetings. |
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