Add doi-to-bibtex to examples and JabKit by koppor · Pull Request #14244 · JabRef/jabref

koppor · 2025-11-06T22:54:13Z

Strongly demanded by the community. Was available inside JabRef; now we can offer as CLI.

Kind of follow-up to #14233.

We use CrossRef

Steps to test

Create and modify debug configuration for org.jabref.JabKit#main

Mandatory checks

I own the copyright of the code submitted and I license it under the MIT license
I manually tested my changes in running JabRef (always required)
[/] I added JUnit tests for changes (if applicable)
[/] I added screenshots in the PR description (if change is visible to the user)
I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
[/] I checked the user 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 updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

palukku · 2025-11-07T10:58:12Z

I tried running it with a valid and an completely invalid doi 1234test as two arguments and it threw an error:

Unmatched argument at index 2: '1abref'
Usage: jabkit doi-to-bibtex DOI...
Converts a DOI to BibTeX
      DOI...   one or more DOIs to fetch

But I would say it should not completely "crash" but print out the valid one and for the second the Could not fetch DOI from BibTeX.

subhramit

Micro comments - I am committed to not letting vars enter again - so keeping them only in the example file

palukku · 2025-11-07T18:16:57Z

And maybe also a option which disables the error messages but still returns exit code 1, so if you want to work with the output and ignore errors for example. Can't name a case for that, but i can imagine that it could be helpful.

But one could probably just read the out and ignore err output and achieve it without the extra option

…mple

koppor · 2025-11-09T15:07:35Z

Micro comments - I am committed to not letting vars enter again - so keeping them only in the example file

We should create an architecture test for that ^^

Co-authored-by: Subhramit Basu <subhramit.bb@live.in>

…into add-doi-to-bibtex-example

koppor · 2025-11-09T15:15:21Z

It's far from perfect... Even with --porcelain we get some error output.

Needs to be more thought how we deal with --porcelain

I tried with

doi-to-bibtex --porcelain abc 10:333 10.47397/tb/44-3/tb138kopp-jabref

Result:

2025-11-09 16:12:37 [main] org.jabref.logic.preferences.JabRefCliPreferences.getFetcherKeysFromKeyring()
WARN: JabRef could not open the key store
2025-11-09 16:12:39 [main] org.jabref.logic.journals.JournalAbbreviationLoader.loadRepository()
INFO: Loaded journal abbreviations from C:\Users\olive\AppData\Local\Temp\jabref-journal831676151345966999\journal-list.mv
2025-11-09 16:12:39 [main] org.jabref.cli.DoiToBibtex.call()
WARN: Skipped DOI abc, because it is not a valid DOI string
2025-11-09 16:12:40 [main] org.jabref.logic.net.URLDownload.openConnection()
INFO: https://api.crossref.org/works/10:333: SimpleHttpResponse{statusCode=404, responseMessage='Not Found', responseBody='Resource not found.'}
2025-11-09 16:12:40 [main] org.jabref.cli.DoiToBibtex.call()
ERROR: Could not fetch DOI from BibTeX: org.jabref.logic.importer.FetcherClientException: 
	at org.jabref.jablib/org.jabref.logic.net.URLDownload.openConnection(URLDownload.java:389)
	at org.jabref.jablib/org.jabref.logic.net.URLDownload.asInputStream(URLDownload.java:279)
	at org.jabref.jablib/org.jabref.logic.importer.IdBasedParserFetcher.performSearchById(IdBasedParserFetcher.java:50)
	at org.jabref.jabkit/org.jabref.cli.DoiToBibtex.call(DoiToBibtex.java:49)
	at org.jabref.jabkit/org.jabref.cli.DoiToBibtex.call(DoiToBibtex.java:25)
	at info.picocli@4.7.7/picocli.CommandLine.executeUserObject(CommandLine.java:2031)
	at info.picocli@4.7.7/picocli.CommandLine.access$1500(CommandLine.java:148)
	at info.picocli@4.7.7/picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2469)
	at info.picocli@4.7.7/picocli.CommandLine$RunLast.handle(CommandLine.java:2461)
	at info.picocli@4.7.7/picocli.CommandLine$RunLast.handle(CommandLine.java:2423)
	at info.picocli@4.7.7/picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2277)
	at info.picocli@4.7.7/picocli.CommandLine$RunLast.execute(CommandLine.java:2425)
	at info.picocli@4.7.7/picocli.CommandLine.execute(CommandLine.java:2174)
	at org.jabref.jabkit/org.jabref.JabKit.main(JabKit.java:99)
ERROR: Could not fetch DOI from BibTeX: org.jabref.logic.importer.FetcherClientException: 

@Article{,
  author    = {Oliver Kopp and Carl Christian Snethlage and Christoph Schwentker},
  title     = {JabRef: BibTeX-based literature management software},
  doi       = {10.47397/tb/44-3/tb138kopp-jabref},
  issn      = {0896-3207},
  number    = {3},
  pages     = {441-447},
  volume    = {44},
  journal   = {TUGboat},
  publisher = {TeX Users Group},
  year      = {2023},
}

koppor · 2025-11-09T15:16:48Z

And maybe also a option which disables the error messages but still returns exit code 1, so if you want to work with the output and ignore errors for example. Can't name a case for that, but i can imagine that it could be helpful.

This is what --porcelain is useful for.

But one could probably just read the out and ignore err output and achieve it without the extra option

This is the intention of this PR ^^

koppor · 2025-11-09T19:51:04Z

OK, --porcelain also fixed. Did not want to add new localization, re-used as much as possible.

DOI abc is invalid

No data was found for the identifier - 10:333
URL: https://api.crossref.org/works/10:333
HTTP 404 Not Found
Resource not found.

@Article{,
  author    = {Oliver Kopp and Carl Christian Snethlage and Christoph Schwentker},
  title     = {JabRef: BibTeX-based literature management software},
  doi       = {10.47397/tb/44-3/tb138kopp-jabref},
  issn      = {0896-3207},
  number    = {3},
  pages     = {441-447},
  volume    = {44},
  journal   = {TUGboat},
  publisher = {TeX Users Group},
  year      = {2023},
}

subhramit · 2025-11-09T19:58:23Z

ah some ci checks

koppor · 2025-11-09T19:59:29Z

ah some ci checks

 > Compilation failed; see the compiler output below.
  /home/runner/work/jabref/jabref/jabsrv/src/main/java/module-info.java:63: error: module not found: tools.jackson.databind
      requires tools.jackson.databind;
                            ^

Refs #14259 maybe

koppor · 2025-11-09T20:14:03Z

Somehow jackson was updated in main - and jabsrv does not compile any more.

koppor · 2025-11-09T20:19:51Z

Commit breaking main 32ce0b9

* main: Fix calling JBang command (#14282) .jbang scripts should not be included inside themselves (#14278) Fix typos (#14277) Refactor importDatabase for better readability (#14274) fix jbang (#14276) Feat: Add definition links for TeX Files (#14260) Update preventing module commits (#14273) Fix JabKitLuancher Rename packages in jabkit to start with org.jabref.toolkit to avoid split packages between jabkit and jabgui (#14052). (#14271) Add doi-to-bibtex to examples and JabKit (#14244)

* Simplyfy code * Fix step ignore * Add doi_to_bibtex.java * Add doi-to-bibtex to JabKit * Add CHANGELOG.md entry * Add some debug code (again) * Fix formatting * Fix logger * Also deal with jabkit * Remove debug * Fix casing * Fix condition * Continue on wrong DOI * Apply suggestions from code review Co-authored-by: Subhramit Basu <subhramit.bb@live.in> * Fix checkstyle * Fix space * Disable JUL output at JabKit * --porcelain does not output any logs to the console any more * Fix logger config * Have --porcelain working * Improve strings * Update CHANGELOG.md * Update jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java * Workaround for tests * Compilefix --------- Co-authored-by: Subhramit Basu <subhramit.bb@live.in>

koppor added 4 commits November 6, 2025 23:14

Simplyfy code

dafaeba

Fix step ignore

5e85c5d

Add doi_to_bibtex.java

5b1ffaf

Add doi-to-bibtex to JabKit

3f66895

koppor added the component: JabKit [cli] label Nov 6, 2025

koppor added 8 commits November 6, 2025 23:54

Add CHANGELOG.md entry

242436d

Add some debug code (again)

5ed9435

Fix formatting

f765241

Fix logger

c803beb

Also deal with jabkit

df625ab

Remove debug

d3dcc6b

Fix casing

3455a03

Fix condition

7ea1a65

koppor requested a review from subhramit November 6, 2025 23:20

subhramit reviewed Nov 7, 2025

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Comment thread jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java Outdated

Comment thread jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java Outdated

koppor added 3 commits November 9, 2025 15:47

Merge remote-tracking branch 'origin/main' into add-doi-to-bibtex-exa…

f19675b

…mple

Continue on wrong DOI

d2aca73

Merge remote-tracking branch 'origin/main' into add-doi-to-bibtex-exa…

6ebc93c

…mple

koppor and others added 3 commits November 9, 2025 16:09

Apply suggestions from code review

b68c6e0

Co-authored-by: Subhramit Basu <subhramit.bb@live.in>

Fix checkstyle

05c4a8b

Merge branch 'add-doi-to-bibtex-example' of github.com:JabRef/jabref …

7ebb00b

…into add-doi-to-bibtex-example

Fix space

1f88fb3

koppor requested a review from palukku November 9, 2025 15:16

koppor removed the request for review from palukku November 9, 2025 15:16

Disable JUL output at JabKit

19e0ded

subhramit reviewed Nov 9, 2025

View reviewed changes

Comment thread CHANGELOG.md Outdated

subhramit reviewed Nov 9, 2025

View reviewed changes

Comment thread jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java Outdated

Improve strings

43b4b87

koppor requested a review from subhramit November 9, 2025 19:53

subhramit reviewed Nov 9, 2025

View reviewed changes

Comment thread jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java Outdated

subhramit added 2 commits November 10, 2025 01:25

Update CHANGELOG.md

b439fdf

Update jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java

bea7fc5

subhramit previously approved these changes Nov 9, 2025

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koppor and others added 2 commits November 9, 2025 20:59

Merge branch 'main' into add-doi-to-bibtex-example

8faed65

Merge branch 'main' into add-doi-to-bibtex-example

d4b287d

subhramit dismissed their stale review via d4b287d November 9, 2025 20:10

koppor added 3 commits November 9, 2025 21:20

Merge branch 'main' into add-doi-to-bibtex-example

fd63a0d

Workaround for tests

06b5c48

Compilefix

1644f8b

koppor requested a review from subhramit November 9, 2025 20:56

koppor enabled auto-merge November 9, 2025 20:56

subhramit approved these changes Nov 9, 2025

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koppor mentioned this pull request Nov 9, 2025

Rename packages in jabkit to start with org.jabref.toolkit to avoid split packages between jabkit and jabgui (#14052). #14271

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koppor added this pull request to the merge queue Nov 9, 2025

Merged via the queue into main with commit 59355d2 Nov 9, 2025
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koppor deleted the add-doi-to-bibtex-example branch November 9, 2025 21:27

koppor mentioned this pull request Nov 13, 2025

Prepare maven3 example project #14294

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