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Changes to definitions.yaml #66

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laserson opened this Issue Nov 30, 2017 · 10 comments

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laserson commented Nov 30, 2017

Would it be ok to change definitions.yaml to be called airr-standards.yaml (or something similar)?

Also, could we change it from 3 space tabs to 4 space tabs (or 2 space tabs)? It's messing with my editor.

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schristley commented Dec 13, 2017

How about airr-definitions or airr-schema? I don't like standards in the filename exactly because it isn't the standard per se. I called the file definitions to match the OpenAPI which calls these definitions and/or schema objects.

Only if you promise to use actual tab characters instead of spaces, I'm running on disk space ;-D j/k, feel free to change the spacing, I'm fine with it.

@schristley schristley added the DataRep label Dec 21, 2017

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javh commented Apr 4, 2018

+1 for 4 space character "tabs".

javh added a commit that referenced this issue Apr 13, 2018

Rearrangement spec updates from discussions
1. Removed `*_score` fields from required list.
2. Removed `vdj_score`, `vdj_identity`, `vdj_evalue`, and `vdj_cigar` from the spec.
3. Renamed `*_evalue` to `*_support` and generalized description to E-value, p-value, probability, likelihood, etc.
4. Added note about indexing scheme to `*_start` and `*_end` fields.
5. Reindented definitions.yaml to 4 space "tabs" per #66.
6. Sync'd Alignments spec.
7. Minor description fixes.
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javh commented Apr 13, 2018

Indentation fixed in #106.

Decision on renaming the file?

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javh commented Apr 16, 2018

schema.yaml?

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schristley commented Apr 16, 2018

schema.yaml is okay, airr-schema.yaml might be better, avoids being too generic just in case services have to drop multiple yamls into the same directory, which tends to happen.

javh added a commit that referenced this issue Apr 18, 2018

Rearrangement definition tweaks. (#106)
Rearrangement definition tweaks.

1. Removed `c_call`, `c_score` and `c_cigar` from `required`.
2. Removed `*_score` fields from required list.
3. Removed `vdj_score`, `vdj_identity`, `vdj_evalue`, and `vdj_cigar` from the spec.
4. Renamed `*_evalue` to `*_support` and generalized description to E-value, p-value, probability, likelihood, etc.
5. Added note about indexing scheme to `*_start` and `*_end` fields.
6. Re-indented definitions.yaml to 4 space "tabs" per #66.
7. Sync'd Alignments spec.
8. Minor description fixes.
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javh commented Apr 18, 2018

All right, airr-schema.yaml, going once? Any other opinions?

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schristley commented Apr 20, 2018

going twice...

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bcorrie commented Apr 20, 2018

Got my vote...

@bcorrie bcorrie closed this Apr 20, 2018

@bcorrie bcorrie reopened this Apr 20, 2018

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bcorrie commented Apr 20, 2018

Opps, hit close and comment not comment 8-)

javh added a commit that referenced this issue Apr 20, 2018

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javh commented Apr 20, 2018

Done in #124.

@javh javh closed this Apr 20, 2018

javh added a commit that referenced this issue Apr 20, 2018

Rename definitions.yaml to airr-schema.yaml per #66. (#124)
* Rename definitions.yaml to airr-schema.yaml per #66.
* Updated docs to denoted Alignment spec as experimental, removed metadata information, and some xrefs.
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