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Bibliography API and listing functionality #320

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@stschiff stschiff commented Nov 19, 2024

This PR finally adds a new Server API /bibliography as well as a new command-line option trident list --bibliography to gather bibliography information.

The feature is straight-forward in terms of usability.

In terms of implementation, I have made some additional changes to the Aeson interface specifically for the Server Communication. Specifically I looked a bit closer how Aeson encodes for Nothings in Maybe types, and found out that by default these get encoded as null in objects. This is slightly wasteful, as null-fields can also simply be omitted in a given object. When decoding into Haskell types again, we anyway use the operator .:?, which takes care of interpreting missing keys in objects as Nothings. I have therefore added a small function called removeNulls in ServerClient.hs to remove null-fields from objects. Not sure how big the effect is, but it was simple enough and I'm glad I now understand Maybe-encoding in Aeson better. The newest version of Aeson (>2.2.2.0) actually adds an encoding operator to remove null-values, which will eventually make my function redundant, but that latest version isn't even in the latest LTS, so it'll be some time.

Running the new bibliography function on the Community-Archive reveals some gaps in our bibliography records, which we can easily fix with a bit of curation work.

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codecov bot commented Nov 20, 2024

Codecov Report

Attention: Patch coverage is 42.17687% with 85 lines in your changes missing coverage. Please review.

Project coverage is 59.53%. Comparing base (46b0043) to head (45f5982).

Files with missing lines Patch % Lines
src/Poseidon/CLI/List.hs 36.17% 26 Missing and 4 partials ⚠️
src/Poseidon/ServerClient.hs 50.00% 26 Missing ⚠️
src/Poseidon/CLI/OptparseApplicativeParsers.hs 0.00% 14 Missing ⚠️
src/Poseidon/CLI/Serve.hs 21.42% 10 Missing and 1 partial ⚠️
src/Poseidon/Package.hs 80.00% 2 Missing and 2 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #320      +/-   ##
==========================================
- Coverage   60.29%   59.53%   -0.76%     
==========================================
  Files          29       29              
  Lines        4181     4298     +117     
  Branches      491      497       +6     
==========================================
+ Hits         2521     2559      +38     
- Misses       1169     1242      +73     
- Partials      491      497       +6     

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@stschiff stschiff marked this pull request as ready for review November 20, 2024 22:13
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I bumped the version to 1.5.9.0, so I expect this to be merged in after #318.

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The code looks great and trident list --bibliography behaves as expected. I think, though, that the default table output is too wide. Maybe some columns can be omitted here (Journal? Author?).

I'll later test the server-client interaction with this new API feature.

@@ -1,5 +1,5 @@
name: poseidon-hs
version: 1.5.7.4
version: 1.5.9.0
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Probably 1.6.1.0 as things stand right now on the master branch.

"Bibliography field " ++ bibFieldKey ++ "is not present in any bibliography entry"
_ -> return ()

let tableH = ["BibKey", "Title", "Author", "Year", "Journal", "Doi",
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Doi -> DOI

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