Refactor EprintCleanup to handle institution, version, and EID fields #11627

18bce133 · 2024-08-14T21:32:51Z

What

This PR refactors the EprintCleanup class to handle additional fields: INSTITUTION, VERSION, and EID. It also includes new tests to ensure the correct functionality of these changes.

Why

The changes are necessary to improve the handling of e-print entries by including more comprehensive cleanup logic. This ensures that entries with INSTITUTION, VERSION, and EID fields are properly normalized and cleaned up.

Changes

Updated EprintCleanup to handle INSTITUTION, VERSION, and EID fields.
Added logic to append the version to the EPRINT field if it is not already present.
Cleared the VERSION and INSTITUTION fields after processing.
Added a new test case in EprintCleanupTest to verify the cleanup of entries with VERSION, INSTITUTION, and EID fields.

Issue
Closes #11306

Mandatory checks

Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
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.

koppor

Small comment.

Moreover, please add the link to the documentation of the identifier, Tobias provided. That knowledge should be persistet in the code!

koppor · 2024-08-18T22:40:52Z

src/test/java/org/jabref/logic/cleanup/EprintCleanupTest.java

+    @Test
+    void cleanupEntryWithVersionAndInstitutionAndEid() {
+        BibEntry input = new BibEntry()
+                .withField(StandardField.NOTE, "arXiv: 1503.05173")
+                .withField(StandardField.VERSION, "1")
+                .withField(StandardField.INSTITUTION, "arXiv")
+                .withField(StandardField.EID, "arXiv:1503.05173");
+
+        BibEntry expected = new BibEntry()
+                .withField(StandardField.EPRINT, "1503.05173v1")
+                .withField(StandardField.EPRINTTYPE, "arxiv");
+
+        EprintCleanup cleanup = new EprintCleanup();
+        cleanup.cleanup(input);
+
+        assertEquals(expected, input);
+    }


Please add another test with INSTITUTION tbd. That field value should be kept IMHO. --> JabRef should not destory data.

@koppor I have made the suggested changes and pushed it to this PR , please review.

I think, I was not clear with another

This means: A second test case. This means: Keep the original test as is.

I did not also not "unzip" my comment, sorry!

This will require changes in the code. The code needs to check if the institution is arXiv. Then, the field can be cleared. Otherwise, the field needs to be kept.

…ix-11306

koppor · 2024-08-21T02:49:12Z

src/test/java/org/jabref/logic/cleanup/EprintCleanupTest.java

+    @Test
+    void cleanupEntryWithVersionAndInstitutionAndEid() {
+        BibEntry input = new BibEntry()
+                .withField(StandardField.NOTE, "arXiv: 1503.05173")
+                .withField(StandardField.VERSION, "1")
+                .withField(StandardField.INSTITUTION, "arXiv")
+                .withField(StandardField.EID, "arXiv:1503.05173");
+
+        BibEntry expected = new BibEntry()
+                .withField(StandardField.EPRINT, "1503.05173v1")
+                .withField(StandardField.EPRINTTYPE, "arxiv");
+
+        EprintCleanup cleanup = new EprintCleanup();
+        cleanup.cleanup(input);
+
+        assertEquals(expected, input);
+    }


I think, I was not clear with another

This means: A second test case. This means: Keep the original test as is.

I did not also not "unzip" my comment, sorry!

This will require changes in the code. The code needs to check if the institution is arXiv. Then, the field can be cleared. Otherwise, the field needs to be kept.

koppor · 2024-08-21T02:51:21Z

src/test/java/org/jabref/logic/cleanup/EprintCleanupTest.java

+        BibEntry expected = new BibEntry()
+                .withField(StandardField.EPRINT, "1503.05173v1")
+                .withField(StandardField.EPRINTTYPE, "arxiv")
+                .withField(StandardField.INSTITUTION, "tbd");


Lets use other-institution as example for the new test.

@koppor I have done the necessary changes, updated the EprintCleanup class to clear the institution field if it is "arXiv" else keep it otherInstitution as it is.

subhramit · 2024-08-27T09:53:58Z

@18bce133 Hey, how is it going? Are you still working on this PR?
Let us know if you need any help finishing it.

18bce133 · 2024-08-29T21:00:36Z

Hey @subhramit ! I'm still on the PR. I've been quite busy lately with some interviews lined up, which slowed me down a bit. I'll make sure to wrap up this PR in the next few days. Thanks for checking in!

github-actions

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We use OpenRewrite to ensure "modern" Java coding practices.
The issues found can be automatically fixed.
Please execute the gradle task rewriteRun, check the results, commit, and push.

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koppor · 2024-09-13T12:30:56Z

CHANGELOG.md was not modified. I add the entry by myself to get this merged.

18bce133 and others added 4 commits August 13, 2024 14:57

Refactor EprintCleanup to handle institution, version, and EID fields

453345e

Add test for cleanup with VERSION, INSTITUTION, and EID

6a8960e

Add version to EPRINT if not present

80d49d9

Merge branch 'JabRef:main' into fix-11306

18b43b3

koppor requested changes Aug 18, 2024

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18bce133 and others added 3 commits August 20, 2024 19:01

Modify test to retain INSTITUTION as "tbd"; include documentation link

6d6e037

Merge branch 'JabRef:main' into fix-11306

beeeb69

Merge branch 'JabRef:main' into fix-11306

b46e8e9

koppor marked this pull request as draft August 21, 2024 02:27

Merge branch 'fix-11306' of https://github.com/18bce133/jabref into f…

2c48bcb

…ix-11306

18bce133 marked this pull request as ready for review August 21, 2024 02:38

koppor requested changes Aug 21, 2024

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Merge branch 'main' into fix-11306

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18bce133 and others added 3 commits September 3, 2024 18:45

Merge branch 'JabRef:main' into fix-11306

9e06282

Merge branch 'refs/heads/main' into fix-11306

728a79d

clear institution field if it is "arXiv" else keep it as it is.

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github-actions bot reviewed Sep 7, 2024

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Complied to OpenRewrite to ensure "modern" Java coding practices.

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18bce133 requested a review from koppor September 7, 2024 22:49

subhramit requested a review from Siedlerchr September 9, 2024 16:59

koppor previously approved these changes Sep 13, 2024

View reviewed changes

Update CHANGELOG.md

ebe0a94

koppor dismissed their stale review via ebe0a94 September 13, 2024 12:33

Add "real" hyperlink

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koppor previously approved these changes Sep 13, 2024

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Merge branch 'main' into fix-11306

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koppor dismissed their stale review via 91aad7d September 13, 2024 12:34

koppor enabled auto-merge September 13, 2024 12:34

koppor approved these changes Sep 13, 2024

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koppor added this pull request to the merge queue Sep 13, 2024

Merged via the queue into JabRef:main with commit f7fde15 Sep 13, 2024
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koppor mentioned this pull request Oct 25, 2024

Fix issue #12000: Parsing arXiv Id when importing a PDF with arXiv Id #12079

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Refactor EprintCleanup to handle institution, version, and EID fields #11627

Refactor EprintCleanup to handle institution, version, and EID fields #11627

18bce133 commented Aug 14, 2024 •

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koppor commented Sep 13, 2024

Refactor EprintCleanup to handle institution, version, and EID fields #11627

Refactor EprintCleanup to handle institution, version, and EID fields #11627

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