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Created script to resolve phylorefs using the Open Tree of Life APIs #51

Merged
merged 27 commits into from
Nov 9, 2020
Merged

Created script to resolve phylorefs using the Open Tree of Life APIs #51

merged 27 commits into from
Nov 9, 2020

Commits on Oct 22, 2020

  1. Created script to resolve phylorefs using the Open Tree of Life APIs. 

    Also updated package-lock.json.
    @gaurav
    gaurav committed Oct 22, 2020
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  2. Added error messages to the output.

    @gaurav
    gaurav committed Oct 22, 2020
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  3. Filtered out "(originally X)" text from input names.

    @gaurav
    gaurav committed Oct 22, 2020
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  4. Improved errors when no input given.

    @gaurav
    gaurav committed Oct 22, 2020
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  5. Wrote basic test for running resolve.js.

    @gaurav
    gaurav committed Oct 22, 2020
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  6. Modified resolve.js to return results as JSON.

    @gaurav
    gaurav committed Oct 22, 2020
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  7. Updated resolve.js to produce a table of output.

    @gaurav
    gaurav committed Oct 22, 2020
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  8. Improved error message.

    @gaurav
    gaurav committed Oct 22, 2020
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  9. Fixed bug that caused program to exit before stdout had been flushed.

    @gaurav
    gaurav committed Oct 22, 2020
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  10. Added test for validating the included brochu_2003.json.

    @gaurav
    gaurav committed Oct 22, 2020
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  11. Change test to recursive so it can find out new test.

    @gaurav
    gaurav committed Oct 22, 2020
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  12. Updated Node JS versions to current and LTS versions on Travis.

    @gaurav
    gaurav committed Oct 22, 2020
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  13. Improved help text 

    Co-authored-by: Hilmar Lapp <[email protected]>
    @gaurav @hlapp
    gaurav and hlapp committed Oct 22, 2020
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  14. Fixed trailing space in URI.

    @gaurav
    gaurav committed Oct 22, 2020
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  15. Added check for error codes other than 200, 400 and 404.

    @gaurav
    gaurav committed Oct 22, 2020
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  16. Ran npm upgrade to upgrade all packages.

    @gaurav
    gaurav committed Oct 22, 2020
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  17. Attempt to fix NPM issue on Travis.

    @gaurav
    gaurav committed Oct 22, 2020
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  18. Checking NPM cache on Travis CI.

    @gaurav
    gaurav committed Oct 22, 2020
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  19. Upgraded npm to v6.

    @gaurav
    gaurav committed Oct 22, 2020
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  20. Removed NPM version setting, removed deprecated Node versions.

    @gaurav
    gaurav committed Oct 22, 2020
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  21. Adjusted versions, fixed path to NPM cache.

    @gaurav
    gaurav committed Oct 22, 2020
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  22. Added 'Diplocynodontinae' to brochu_2003.json. 

    This is so that we can test for the not-found error from the Open Tree
of Life.
    @gaurav
    gaurav committed Oct 22, 2020
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  23. Updated brochu_2003.jsonld/nq from new brochu_2003.json.

    @gaurav
    gaurav committed Oct 22, 2020
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  24. Added test for a 404 error from the Open Tree of Life.

    @gaurav
    gaurav committed Oct 22, 2020
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  25. Fixed bugs in OTL taxon ID resolution, added to tests.

    @gaurav
    gaurav committed Oct 22, 2020
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  26. Tweaked a test to prevent specifier from resolving to two OTT IDs.

    @gaurav
    gaurav committed Oct 22, 2020
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Commits on Nov 9, 2020

  1. Replaced local Phyx context with v0.2.0 from website.

    @gaurav
    gaurav committed Nov 9, 2020
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