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

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XYZ567AB
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Describe the changes you have made here: what, why, ...
Link the issue that will be closed, e.g., "Closes #333". If your PR closes a koppor issue, link it using its URL, e.g., "Closes JabRef#47".

Add 'ARXIVID' field to 'StandardField' enum class
Add 'getArxivId' method to 'PdfContentImporter' class
Add logic to handle arxivId in 'getEntryFromPDFContent' method
Add 'extractArxivIdFromPage1' test method to 'PdfContentImporterTest' class

Closes #12000
Closes #12000

Mandatory checks

  • I own the copyright of the code submitted and I licence it under the MIT license
  • 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.

Simon7878912 and others added 3 commits October 25, 2024 12:08
2. Add 'getArxivId' method to 'PdfContentImporter' class
3. Add logic to handle arxivId in 'getEntryFromPDFContent' method
4. Add 'extractArxivIdFromPage1' test method to 'PdfContentImporterTest' class
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Arxiv is not a Standard field

@@ -25,6 +25,7 @@ public enum StandardField implements Field {
ARCHIVEPREFIX("archiveprefix"),
ASSIGNEE("assignee", FieldProperty.PERSON_NAMES),
AUTHOR("author", FieldProperty.PERSON_NAMES),
ARXIVID("arXivId", FieldProperty.VERBATIM),
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Arxiv is no StandardField, you need to use eprint for this
see chapter 3.14.7 Electronic Publishing Information of the biblatex spec
http://mirrors.ctan.org/macros/latex/contrib/biblatex/doc/biblatex.pdf

.withField(StandardField.AUTHOR, "Review Article")
.withField(StandardField.TITLE, "British Journal of Nutrition (2008), 99, 1–11 doi: 10.1017/S0007114507795296 arXiv:2408.06224v1 q The Authors")
.withField(StandardField.YEAR, "2024")
.withField(StandardField.ARXIVID, "2408.06224v1");
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Needs to be eprint

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Thanks for your feedback! I see, I will change it.

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You then should also add the correpsonding eprinttype field to arxiv

@koppor koppor added the status: changes required Pull requests that are not yet complete label Oct 25, 2024
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koppor commented Oct 25, 2024

@XYZ567AB You can add a code comment into StandardField.java to guide someone also working here. Saying how the arXiv ID is stored and also add a link to the Java class handling arXiv Ids and the functionality introduced at #11627.

CHANGELOG.md Outdated
@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv

### Added

- We added functionality to handle arXiv ID in `PdfContentImporter` and implemented related test case. [#12000](https://github.com/JabRef/jabref/issues/12000)
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These comments are user facing. A user does not see PdfContentImporter in the UI. We are updating the docs at JabRef/user-documentation#537 - and the updated section should be linked.

Comment on lines +493 to +506
private String getArxivId(String arxivId) {
int pos;
if (arxivId == null) {
pos = curString.indexOf("arxiv");
if (pos < 0) {
pos = curString.indexOf("arXiv");
}
if (pos >= 0) {
String arxivText = curString.substring(pos);
return ArXivIdentifier.parse(arxivText).map(ArXivIdentifier::asString).orElse(null);
}
}
return arxivId;
}
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No! We have the class org.jabref.model.entry.identifier.ArXivIdentifier use this.

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This is still unfixed.

Comment on lines 48 to 54
Pattern oldIdentifierPattern = Pattern.compile("(" + ARXIV_PREFIX + ")?\\s?:?\\s?(?<id>(?<classification>[a-z\\-]+(\\.[A-Z]{2})?)/\\d{7})(v(?<version>\\d+))?");
Matcher oldIdentifierMatcher = oldIdentifierPattern.matcher(identifier);
if (oldIdentifierMatcher.matches()) {
return getArXivIdentifier(oldIdentifierMatcher);
}
Pattern oldIdentifierPattern = Pattern.compile("(" + ARXIV_PREFIX + ")?\\s?:?\\s?(?<id>(?<classification>[a-z\\-]+(\\.[A-Z]{2})?)/\\d{7})(v(?<version>\\d+))?");
Matcher oldIdentifierMatcher = oldIdentifierPattern.matcher(identifier);
if (oldIdentifierMatcher.matches()) {
return getArXivIdentifier(oldIdentifierMatcher);
}

return Optional.empty();
return Optional.empty();
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Wrong indent. Please revert.

@@ -123,4 +123,38 @@ British Journal of Nutrition (2008), 99, 1–11 doi: 10.1017/S0007114507795296

assertEquals(Optional.of(entry), importer.getEntryFromPDFContent(firstPageContent, "\n"));
}

@Test
void extractArxivIdFromPage1() {
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Please also use a real arXiv PDF. I think, there is a link to one in the issue?

Comment on lines +468 to +470
if (arxivId != null) {
year = "20" + arxivId.substring(0, 2);
}
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This should go to the else branch. - If there is no year then one can check for arxivId and guess a year out of it.

Comment on lines +493 to +506
private String getArxivId(String arxivId) {
int pos;
if (arxivId == null) {
pos = curString.indexOf("arxiv");
if (pos < 0) {
pos = curString.indexOf("arXiv");
}
if (pos >= 0) {
String arxivText = curString.substring(pos);
return ArXivIdentifier.parse(arxivText).map(ArXivIdentifier::asString).orElse(null);
}
}
return arxivId;
}
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This is still unfixed.

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koppor commented Dec 9, 2024

Closing this issue due to inactivity 💤

@koppor koppor closed this Dec 9, 2024
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