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Add phyloreferences curated by Rebecca Stubbs over summer 2018 #45

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Add phyloreferences curated by Rebecca Stubbs over summer 2018 #45

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Commits on Jan 17, 2019

  1. First attempt at writing out phyloref details during testing.

    @gaurav
    gaurav committed Jan 17, 2019
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  2. Added support for parsing the TAP output from JPhyloRef.

    @gaurav
    gaurav committed Jan 17, 2019
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  3. Add internal/external specifier count to phyloref name.

    @gaurav
    gaurav committed Jan 17, 2019
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  4. Replaced index-based lookups w/ name-based lookups 

    Using index-based lookups relies on JPhyloRef returning phylorefs in a
particular order, which it doesn't.
    @gaurav
    gaurav committed Jan 17, 2019
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  5. Fixed indentation, added a check for a regex failure.

    @gaurav
    gaurav committed Jan 17, 2019
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  6. Improve debugging output.

    @gaurav
    gaurav committed Jan 17, 2019
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  7. Moved command line synthesis closer to where it is used.

    @gaurav
    gaurav committed Jan 17, 2019
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  8. Removed testing code that should not have been committed.

    @gaurav
    gaurav committed Jan 17, 2019
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  9. Write out STDOUT/STDERR from JPhyloRef if failures occur.

    @gaurav
    gaurav committed Jan 17, 2019
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  10. Write out STDOUT/STDERR unless successes reported.

    @gaurav
    gaurav committed Jan 17, 2019
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  11. Added two new curated phyloreferences.

    @gaurav
    gaurav committed Jan 17, 2019
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  12. Minor fix for Newick, added verbatim apomorphy-based specifier

    @gaurav
    gaurav committed Jan 17, 2019
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  13. Fixed phylogeny, deleted duplicate specifier

    @gaurav
    gaurav committed Jan 17, 2019
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  14. Added two new phylorefs from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  15. Fixed internal node label.

    @gaurav
    gaurav committed Jan 17, 2019
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  16. Added Asteridae, curated by RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  17. Updated Amorphea from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  18. Removed "@context" from PHYX file so we can insert our own as needed.

    @gaurav
    gaurav committed Jan 17, 2019
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  19. Added Basidiomycota from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  20. Added a phyloreference from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  21. Added phyloreference for Discicristata from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  22. Fixed a typo in the phylogeny.

    @gaurav
    gaurav committed Jan 17, 2019
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  23. Added Bignoniaceae from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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  24. Added new phyloreferences from RS.

    @gaurav
    gaurav committed Jan 17, 2019
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Commits on Jan 18, 2019

  1. Fixed code for naming '_as_owl.json' file.

    @gaurav
    gaurav committed Jan 18, 2019
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  2. Added first attempt at complete test results.

    @gaurav
    gaurav committed Jan 18, 2019
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Commits on Dec 21, 2019

  1. Add 1 git-crypt collaborator 

    New collaborators:

	2B41C898 Gaurav Vaidya <[email protected]>
    @gaurav
    gaurav committed Dec 21, 2019
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