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Fix handling of DOIs #14704

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Merged
koppor merged 2 commits into from
Dec 23, 2025
Merged

Fix handling of DOIs #14704

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9db28c7
Fix handling of DOIs
koppor Dec 23, 2025
289d41b
-add link
koppor Dec 23, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -65,6 +65,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
- We fixed the fallback window height (786 → 768) in JabRefGUI. [#14295](https://github.com/JabRef/jabref/pull/14295)
- We fixed localization of the "New Entries" dialog. [#14455](https://github.com/JabRef/jabref/pull/14455)
- We fixed an issue where keybindings could not be edited and saved. [#14237](https://github.com/JabRef/jabref/issues/14237)
- We fixed an issue of cleaning of wrongly encoded DOIs. [#14704](https://github.com/JabRef/jabref/pull/14704)
- We readded the missing gui commands for importing and exporting preferences. [#14492](https://github.com/JabRef/jabref/pull/14492)
- We fixed the keyboard navigation in the entry editor: pressing <kbd>Shift</kbd> + <kbd>Tab</kbd> on the first field now correctly focuses the last field of the previous tab. [#14513](https://github.com/JabRef/jabref/issues/14513)
- We fixed a crash when importing preferences from older JabRef versions. [#14497](https://github.com/JabRef/jabref/issues/14497)
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108 changes: 58 additions & 50 deletions jablib/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java
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Expand Up @@ -3,9 +3,9 @@
import java.net.URLDecoder;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.atomic.AtomicBoolean;

import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
import org.jabref.model.FieldChange;
Expand All @@ -16,70 +16,78 @@
import org.jabref.model.entry.identifier.ArXivIdentifier;
import org.jabref.model.entry.identifier.DOI;

/**
* Formats the DOI (e.g. removes http part) and also infers DOIs from the note, url, eprint or ee fields.
*/
/// Formats the DOI (e.g. removes http part) and also infers DOIs from the note, url, eprint or ee fields.
public class DoiCleanup implements CleanupJob {

/**
* Fields to check for DOIs.
*/
private static final List<Field> FIELDS = Arrays.asList(StandardField.NOTE, StandardField.URL, StandardField.EPRINT,
new UnknownField("ee"));
/// Fields to check for DOIs.
private static final List<Field> FIELDS = List.of(
StandardField.NOTE,
StandardField.URL,
StandardField.EPRINT,
new UnknownField("ee")
);

@Override
public List<FieldChange> cleanup(BibEntry entry) {
List<FieldChange> changes = new ArrayList<>();

// First check if the Doi Field is empty
if (entry.hasField(StandardField.DOI)) {
String doiFieldValue = entry.getField(StandardField.DOI).orElse(null);
AtomicBoolean validDoiExistsInDoiField = new AtomicBoolean(false);

String decodeDoiFieldValue = "";
decodeDoiFieldValue = URLDecoder.decode(doiFieldValue, StandardCharsets.UTF_8);
doiFieldValue = decodeDoiFieldValue;
entry.getField(StandardField.DOI)
.ifPresent(currentlyStoredDoi -> {
String decodedDoiFieldValue;
try {
decodedDoiFieldValue = URLDecoder.decode(currentlyStoredDoi, StandardCharsets.UTF_8);
} catch (IllegalArgumentException e) {
// If decoding fails, we keep the original value
decodedDoiFieldValue = currentlyStoredDoi;
}

Optional<DOI> doi = DOI.parse(doiFieldValue);
String cleanCurrentlyStoredDoi = decodedDoiFieldValue;

if (doi.isPresent()) {
String newValue = doi.get().asString();
if (!doiFieldValue.equals(newValue)) {
entry.setField(StandardField.DOI, newValue);
DOI.parse(cleanCurrentlyStoredDoi)
.map(DOI::asString)
.ifPresent(parsedDoi -> {
validDoiExistsInDoiField.set(true);
if (!parsedDoi.equals(cleanCurrentlyStoredDoi)) {
entry.setField(StandardField.DOI, parsedDoi);

FieldChange change = new FieldChange(entry, StandardField.DOI, doiFieldValue, newValue);
changes.add(change);
}
FieldChange change = new FieldChange(entry, StandardField.DOI, currentlyStoredDoi, parsedDoi);
changes.add(change);
}

// Doi field seems to contain Doi -> cleanup note, url, ee field
for (Field field : FIELDS) {
entry.getField(field).flatMap(DOI::parse)
.ifPresent(unused -> removeFieldValue(entry, field, changes));
}
}
} else {
// As the Doi field is empty we now check if note, url, or ee field contains a Doi
for (Field field : FIELDS) {
Optional<String> fieldContentOpt = entry.getField(field);
// Doi field seems to contain Doi -> cleanup note, url, ee field
for (Field field : FIELDS) {
entry.getField(field)
.flatMap(DOI::parse) // only returns something if **complete** field is a DOI
.ifPresent(_ -> removeFieldValue(entry, field, changes));
}
});
});

Optional<DOI> doi = fieldContentOpt.flatMap(DOI::parse);

if (doi.isPresent()) {
// Update Doi
Optional<FieldChange> change = entry.setField(StandardField.DOI, doi.get().asString());
change.ifPresent(changes::add);
removeFieldValue(entry, field, changes);
}
for (Field field : FIELDS) {
entry.getField(field)
.flatMap(DOI::parse) // covers a full DOI only
.ifPresent(doi -> {
if (!validDoiExistsInDoiField.get()) {
Optional<FieldChange> change = entry.setField(StandardField.DOI, doi.asString());
change.ifPresent(changes::add);
}
removeFieldValue(entry, field, changes);
});
}

if (StandardField.EPRINT == field) {
fieldContentOpt.flatMap(ArXivIdentifier::parse)
.flatMap(ArXivIdentifier::inferDOI)
.ifPresent(inferredDoi -> {
Optional<FieldChange> change = entry.setField(StandardField.DOI, inferredDoi.asString());
change.ifPresent(changes::add);
});
}
}
if (!validDoiExistsInDoiField.get()) {
// Try to infer DOI from arXiv ID in eprint field and set it if DOI field is empty
entry.getField(StandardField.EPRINT)
.flatMap(ArXivIdentifier::parse)
.flatMap(ArXivIdentifier::inferDOI)
.ifPresent(inferredDoi -> {
Optional<FieldChange> change = entry.setField(StandardField.DOI, inferredDoi.asString());
change.ifPresent(changes::add);
});
}

return changes;
}

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24 changes: 21 additions & 3 deletions jablib/src/test/java/org/jabref/logic/cleanup/DoiCleanupTest.java
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Expand Up @@ -15,15 +15,15 @@
class DoiCleanupTest {

@ParameterizedTest
@MethodSource("provideDoiForAllLowers")
@MethodSource
void changeDoi(BibEntry expected, BibEntry doiInfoField) {
DoiCleanup cleanUp = new DoiCleanup();
cleanUp.cleanup(doiInfoField);

assertEquals(expected, doiInfoField);
}

private static Stream<Arguments> provideDoiForAllLowers() {
private static Stream<Arguments> changeDoi() {
UnknownField unknownField = new UnknownField("ee");
BibEntry doiResult = new BibEntry().withField(StandardField.DOI, "10.1145/2594455");

Expand Down Expand Up @@ -66,6 +66,24 @@ private static Stream<Arguments> provideDoiForAllLowers() {
Arguments.of(new BibEntry()
.withField(StandardField.DOI, "10.18726/2018_3"),
new BibEntry()
.withField(unknownField, "https://doi.org/10.18726/2018%7B%5Ctextunderscore%7D3")));
.withField(unknownField, "https://doi.org/10.18726/2018%7B%5Ctextunderscore%7D3")),

// cleanup of wrong percent encoded chars
Arguments.of(new BibEntry()
.withField(StandardField.NOTE, "Some strange %% LaTeX %% text"),
new BibEntry()
.withField(StandardField.NOTE, "Some strange %% LaTeX %% text")),

// cleanup of correct percent encoded chars
Arguments.of(new BibEntry()
.withField(StandardField.DOI, "10.18726/2018_3"),
new BibEntry()
.withField(StandardField.NOTE, "10.18726/2018%7B%5Ctextunderscore%7D3")),

// cleanup of wrong percent encoded chars in DOI field
Arguments.of(new BibEntry()
.withField(StandardField.NOTE, "10.18726/2018%7B%%5Ctextunderscore%7D3"),
new BibEntry()
.withField(StandardField.NOTE, "10.18726/2018%7B%%5Ctextunderscore%7D3")));
}
}
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