Add Pseudonymization to CLI #13158

paudelritij · 2025-05-24T15:41:56Z

This PR adds a new jabkit CLI command 'pseudonymize'.

jabkit pseudonymize  
--input /path/to/library.bib 
[--output /path/to/pseudonymized-library.bib] 
[--key /path/to/pseudonymized-keys.csv] 
[-f | --force]

Parameters:

--input <file> : (required) Path to the input BibTeX file to pseudonymize.
--output <file> : Path to save the pseudonymized BibTex file. (Default: <input-filename>.pseudo.bib)
--key <file> : Path to save the entries key mapping CSV file. (Default: <input-filename>.pseudo.csv)
-f, --force : Overwrite output file(s) if they already exist.

Example

jabkit pseudonymize --input myLib.bib --output myLib.pseudo.bib  --key myLib.pseudo.csv --force

Mandatory checks

I own the copyright of the code submitted and I license it under the MIT license
Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
[/] Screenshots added in PR description (if change is visible to the user)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

- A new pseudonymize command has been created. - Test cases has been added. - The display of commands has been sorted for ease of use. - An entry has been added to CHANGELOG.md.

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

jablib/src/main/java/module-info.java

koppor

Quick check while on the road. Maybe you can address this before a full review?

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

jabkit/src/test/java/org/jabref/cli/ArgumentProcessorTest.java

jabkit/src/test/resources/org/jabref/cli/Chocolate.bib

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

paudelritij · 2025-05-25T15:47:51Z

@calixtus for the output file shall I add check (of it's existence while output option is not passed) before parsing result or at the end where the new database is saved... and shall I ask the user to overwrite or not or define numerical formate automatically (origin_pseudo_1.bib, origin_pseudo_2.bib ...) ?

calixtus · 2025-05-25T17:03:26Z

Test the logic you implement, not the logic, you imported by dependencies. If you feel that this is a not-trivial test, then do it. If you are just testing already tested logic its superfluous.

calixtus · 2025-05-25T17:04:34Z

This might not be real TDD, but real TDD is too much noise anyway imho.

CHANGELOG.md

jabkit/src/test/resources/org/jabref/cli/Chocolate.bib

jabkit/src/test/java/org/jabref/cli/ArgumentProcessorTest.java

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

koppor · 2025-05-27T21:34:42Z

@paudelritij It would be nice if you wrote the new command on the PR description - then it is easier for non-programmers to follow...

@calixtus for the output file shall I add check (of it's existence while output option is not passed) before parsing result or at the end where the new database is saved... and shall I ask the user to overwrite or not or define numerical formate automatically (origin_pseudo_1.bib, origin_pseudo_2.bib ...) ?

I answered in-line, but I repeat:

error on file existance
Offer flag --force (short: -f) for overwrite.

paudelritij · 2025-05-27T21:47:41Z

Thank you for the comprehensive review. I have already implemented some of the suggestions yesterday and will make the necessary changes asap

calixtus · 2025-05-28T05:30:57Z

Don't forget to push after commiting, so we can follow

- Implement ADR 0045 - Add -f / --force flag to overwrite if file exist - Reformat saving of database to save meta-data as well - Add methods from FileUtil - Reformat CHANGELOG.md entry - Add JabRef_en.properties entry - A Comment added - Remove duplicate file Chocolate.bib - Improve logger and localization lang - Remove trivial test case - Rename all occurrence of word anon. to pseudo

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

jablib/src/main/resources/l10n/JabRef_en.properties

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

koppor · 2025-05-29T22:56:09Z

For ADR one needs to add this as dependency to build.gradle.kts - just copy and paste from another build.gradle.kts with this dependency.

koppor

Overwrite output file(s) if it exist reads strange. replace by

Overwrite output file(s) if any exist(s)

The path is not resolved correctly.

If no output file names are given, the output should be stored next to the input file.

./gradlew :jabkit:run --args="pseudonymize --input=C:\git-repositories\jabref-all\jabref-demo-libraries\chocolate\Chocolate.bib"

Results in output in jabkit folder - very strange

- Default output file path is now the same as input file location if not specified. - Created a single method to check for file existence.

koppor

On CLI output:

... is progress...

intead of

Pseudonymizing library 'Chocolate'.
Saving: C:\git-repositories\jabref-all\jabref-demo-libraries\chocolate\Chocolate.pseudo.bib.
Saving: C:\git-repositories\jabref-all\jabref-demo-libraries\chocolate\Chocolate.pseudo.csv.

Please

Pseudonymizing library 'Chocolate'...
Saved C:\git-repositories\jabref-all\jabref-demo-libraries\chocolate\Chocolate.pseudo.bib.
Saved C:\git-repositories\jabref-all\jabref-demo-libraries\chocolate\Chocolate.pseudo.csv.
`´`

Saving does not take long time, thus it can be the output oafer successful save

.jbang/JabKitLauncher.java

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

trag-bot · 2025-06-02T12:36:30Z

@trag-bot didn't find any issues in the code! ✅✨

trag-bot · 2025-06-02T12:38:27Z

@trag-bot didn't find any issues in the code! ✅✨

…or-test * upstream/main: (102 commits) Try to fix output Improve AI preferences UI and templates (JabRef#13202) Bump jablib/src/main/abbrv.jabref.org from `6926b83` to `333c2f1` (JabRef#13216) Bump jablib/src/main/resources/csl-styles from `8a2317a` to `c3df987` (JabRef#13215) Fixed search result focus handling (JabRef#13174) New Crowdin updates (JabRef#13214) Add Pseudonymization to CLI (JabRef#13158) Try parallel gource build Update gource.yml Fix position of checkout Preapre: Enable gradle configuration cache (JabRef#13212) Add yml as YAML extension (JabRef#13213) Fix wrong detection of issue numbers (JabRef#13211) Miscellaneous refactoring - II (JabRef#13197) Run Windows tests only on main (and on demand) (JabRef#13210) Fix porcelain for consistency check (JabRef#13209) Use setup-jbang action (instead of custom call of .sh script) (JabRef#13208) Add link to JabRef guru (JabRef#13207) Switch to gradlex for modularity (JabRef#13112) feat(ci-cd): change issue URL pattern (JabRef#13206) ...

Add Pseudonymization to CLI

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- A new pseudonymize command has been created. - Test cases has been added. - The display of commands has been sorted for ease of use. - An entry has been added to CHANGELOG.md.

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calixtus mentioned this pull request May 25, 2025

Remove --input= for consistency check #13128

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koppor mentioned this pull request May 26, 2025

Create ADR 0045 for --input #13164

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paudelritij added 2 commits May 30, 2025 07:08

Remove exclamation(!) sign

8ba58e2

Rename BibTex to BibTeX

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paudelritij marked this pull request as draft May 29, 2025 22:46

paudelritij added 2 commits May 30, 2025 09:09

Add implementation dependency for ADR

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paudelritij requested a review from koppor June 1, 2025 15:27

Merge branch 'main' into fix-for-issue-13109

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Improve output file path handling and consolidate file existence check

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- Default output file path is now the same as input file location if not specified. - Created a single method to check for file existence.

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Add new class to JabKitLauncher

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Enhance CLI output messages

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Refactor methods to display success message after successful save

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Adapt Command Line Docs to new PicoCLI verbs JabRef/user-documentation#562

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Merged via the queue into JabRef:main with commit 7d9815c Jun 2, 2025
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Add Pseudonymization to CLI #13109

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Add Pseudonymization to CLI #13158

Add Pseudonymization to CLI #13158

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paudelritij commented May 24, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Parameters:

Example

Mandatory checks

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paudelritij commented May 24, 2025 •

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