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poseidon-framework / poseidon-hs

A toolset to work with modular genotype databases in the Poseidon format
https://poseidon-framework.github.io/#/trident
MIT License
7 stars 2 forks source link

Refactoring `list --individuals -j ...` #226

Closed nevrome closed 1 year ago

nevrome commented 1 year ago

I'm either a fool or I had a stroke of genius. Difficult to judge with this one.

As suggested in #225 I replaced the unsatisfying extractAdditionalField with a much simpler, much more flexible solution, that relies on the hashmap in Data.CSV. JannoRow already is an instance of Csv.ToNamedRecord, because that's the mechanism we use to write .janno files. I think we can abuse this fact to transform JannoRows to hashmaps and read their content as strings for arbitrary keys (so: .janno column names). What do you think?

A big problem is, that we can not really test this with the remote server at the moment. My changes in 1.1.8.4 (#221) changed the way janno data is encoded in JSON, so server and client can not speak to each other any more. --remote triggers an error, when I try to read from the old server with the new client:

[Error]   Error in parsing JSON: "Error in $[0][1][0].jGenotypePloidy: Genotype_Ploidy \"Haploid\" not in [diploid, haploid]"

This is a separate issue from this PR, but it affects how I can test it. See #228 for an attempt to fix that.

nevrome commented 1 year ago
  1. Yes, that is true. I thought it's not important to print a warning here, actually. If a user requests a non-existent column, then they get an empty column. But alright - I think it should be possible to add one.
  2. I thought that is fine, because we treat empty strings and "n/a" equally in the .janno file. But I guess I can change that as well.
stschiff commented 1 year ago

OK, for 1) yes, I think a warning would be good, at least if a column is requested that is present nowhere. For 2) OK, that's fine then.

codecov-commenter commented 1 year ago

Codecov Report

Base: 64.91% // Head: 70.96% // Increases project coverage by +6.04% :tada:

Coverage data is based on head (34ead2a) compared to base (c76e0e2). Patch coverage: 68.90% of modified lines in pull request are covered.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #226 +/- ## ========================================== + Coverage 64.91% 70.96% +6.04% ========================================== Files 18 18 Lines 2289 2211 -78 Branches 253 245 -8 ========================================== + Hits 1486 1569 +83 + Misses 550 397 -153 + Partials 253 245 -8 ``` | [Impacted Files](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework) | Coverage Δ | | |---|---|---| | [src/Poseidon/Janno.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0phbm5vLmhz) | `82.32% <67.34%> (+16.56%)` | :arrow_up: | | [src/Poseidon/CLI/List.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9MaXN0Lmhz) | `80.88% <77.77%> (+39.07%)` | :arrow_up: | | [src/Poseidon/CLI/Forge.hs](https://codecov.io/gh/poseidon-framework/poseidon-hs/pull/226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework#diff-c3JjL1Bvc2VpZG9uL0NMSS9Gb3JnZS5ocw==) | `61.60% <87.50%> (+1.76%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=poseidon-framework)

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