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Feature/prioritise X over Y #5

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Feature/prioritise X over Y #5

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Commits on Aug 10, 2023

  1. First attempt at API hosting hgvs conversion

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 10, 2023
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  2. Add dockerfile

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 10, 2023
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  3. Create QuickStart.md

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 10, 2023
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  4. Update QuickStart.md

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 10, 2023
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  5. Update QuickStart.md

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 10, 2023
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Commits on Aug 11, 2023

  1. Refactoring

    @h-joshi
    h-joshi committed Aug 11, 2023
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  2. Testing framework WIP

    @h-joshi
    h-joshi committed Aug 11, 2023
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Commits on Aug 13, 2023

  1. Added tests and valid, invalid scenarios

    @h-joshi
    h-joshi committed Aug 13, 2023
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  2. Merge pull request #2 from kidsneuro-lab/test_data_prep

    @h-joshi
    h-joshi authored Aug 13, 2023
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  3. API and Docker build fixes

    @h-joshi
    h-joshi committed Aug 13, 2023
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Commits on Aug 14, 2023

  1. Create docker-image.yml

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 14, 2023
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  2. Setup basic docker action

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  3. Add env

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  4. Use var for username

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  5. Apply docker tags

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  6. Add download_refGene.sh -hg38

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  7. Add notes on pulling images

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  8. Break on first error and dont run in interactive mode

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  9. Break on first error and dont run in interactive mode

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  10. Isolate error conditions - missing env var vs missing file

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  11. Add env vars to devcontainer environment

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  12. No longer ignore files that are downloaded

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  13. Use the files copied in at build time rather than those mounted

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  14. add notes

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  15. Updated python version, packaging and cli

    @h-joshi
    h-joshi committed Aug 14, 2023
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  16. Removing file accidentally added

    @h-joshi
    h-joshi committed Aug 14, 2023
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  17. Add command to run via docker run

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  18. Fix paths to assemblies and reference in docker compose

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  19. Add graceful shutdown timeout

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  20. Reduced error verbosity in CLI

    @h-joshi
    h-joshi committed Aug 14, 2023
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  21. Execute tests on the PR, deploy on merge to master

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  22. Merge branch 'master' of github.com:kidsneuro-lab/hgvs

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  23. Always push on master

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  24. Rename actions

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Aug 14, 2023
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  25. tests (#5) 

    * Make tests runnable locally and on agent
    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 14, 2023
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  26. Fixed use of tests fixtures (#7)

    @h-joshi
    h-joshi authored Aug 14, 2023
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  27. Fixed hgvs2vcf header (#8)

    @h-joshi
    h-joshi authored Aug 14, 2023
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Commits on Aug 15, 2023

  1. Updated assembly and refgene to use non "chr" (#9)

    @h-joshi
    h-joshi authored Aug 15, 2023
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Commits on Aug 16, 2023

  1. Update QuickStart.md (#10)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 16, 2023
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  2. Update QuickStart.md (#13)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 16, 2023
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  3. Log file names (#12)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Aug 16, 2023
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Commits on Sep 20, 2023

  1. Publish under new dockerhub username: kidsneurolab (#14)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Sep 20, 2023
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Commits on Sep 21, 2023

  1. update docker file to port 8002 (#15) 

    * Update docker container definition to operate on port 8002

* Update to port 8002

* Update examples to work with the sample data
    @PeterKnealeCMRI
    PeterKnealeCMRI authored Sep 21, 2023
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  2. Update docker repository name again (#16)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Sep 21, 2023
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  3. Add alive and ready endpoints (#17)

    @PeterKnealeCMRI
    PeterKnealeCMRI authored Sep 21, 2023
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Commits on Nov 27, 2023

  1. Update pull_request.yml

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Nov 27, 2023
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  2. Issue #18. Add pre-computed outputs for the valid files (#19) 

    * Issue #18. Add pre-computed outputs for the valid files

* Add readme

* Add readme

* Handle lookup failures

* Update to use two sources

* Update to use two sources

* Add tests that use the ensembl and variant validator files as inputs for comparison

* Refactor tests

* Add commend to execute tests

* Perform comparison tests

* Add instructions for diff

* add http retries

* Add resiliency

* Add complete comparison files
    @PeterKnealeCMRI
    PeterKnealeCMRI authored Nov 27, 2023
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  3. Add BCF Tools to dev container

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Nov 27, 2023
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  4. ignore bcf tools folder

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. normalise and report (#23) 

    * Install validaotor
* Add normalise script
* Process both sources
* Added report
    @PeterKnealeCMRI
    PeterKnealeCMRI authored Nov 28, 2023
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  2. Support returning 400 bad request for invalid HGVS input

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Nov 28, 2023
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Commits on Dec 1, 2023

  1. Setup dev container better

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Dec 1, 2023
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Commits on Dec 3, 2023

  1. Switch from get to post to mitigate the url encoding issue with +'s 

    Resolves issue #78
    @PeterKnealeCMRI
    PeterKnealeCMRI committed Dec 3, 2023
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  2. Fix logging issue when running integration tests

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Dec 3, 2023
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  3. Remove the chr for consistancy

    @PeterKnealeCMRI
    PeterKnealeCMRI committed Dec 3, 2023
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Commits on Jan 23, 2024

  1. Updated API, error handling and tests (#29) 

    - Clearly defined API request and response models
- Exposed additional parameters within the API
- Moved testing to pytest-bdd
- Added error handling
    @h-joshi
    h-joshi authored Jan 23, 2024
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  2. hotfix/removed-pytest-env-override (#30)

    @h-joshi
    h-joshi authored Jan 23, 2024
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  3. Update .dockerignore (#31) 

    Exclude pyc files during build
    @h-joshi
    h-joshi authored Jan 23, 2024
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  4. Ensuring test fixtures are avail during publish (#32)

    @h-joshi
    h-joshi authored Jan 23, 2024
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  5. Update README.md (#33) 

    Added examples based on updated API spec
    @h-joshi
    h-joshi authored Jan 23, 2024
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Commits on Mar 19, 2024

  1. Handling of multiple loci for given transcript

    @h-joshi
    h-joshi committed Mar 19, 2024
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