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Show fetch exception at citation relation #13549

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563b8ff
Show fetch exception at citation relation
koppor Jul 15, 2025
5165288
Add link
koppor Jul 15, 2025
7068b25
Fix typo
koppor Jul 15, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
- We added the field `monthfiled` to the default list of fields to resolve BibTeX-Strings for [#13375](https://github.com/JabRef/jabref/issues/13375)
- We added a new ID based fetcher for [EuropePMC](https://europepmc.org/). [#13389](https://github.com/JabRef/jabref/pull/13389)
- We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)
- In case no citation relation information can be fetched, we show the data providers reason. [#13549](https://github.com/JabRef/jabref/pull/13549)

### Changed

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2 changes: 1 addition & 1 deletion jabgui/src/main/java/org/jabref/gui/collab/groupchange/GroupChangeDetailsView.java
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Expand Up @@ -8,7 +8,7 @@
public final class GroupChangeDetailsView extends DatabaseChangeDetailsView {

public GroupChangeDetailsView(GroupChange groupChange) {
String labelValue = "";
String labelValue;
if (groupChange.getGroupDiff().getNewGroupRoot() == null) {
labelValue = groupChange.getName() + '.';
} else {
Expand Down
82 changes: 46 additions & 36 deletions ...ui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java
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Expand Up @@ -201,22 +201,22 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {

refreshCitingButton.setOnMouseClicked(_ -> {
searchForRelations(
entry,
citingListView,
entry,
citingListView,
abortCitingButton,
refreshCitingButton,
CitationFetcher.SearchType.CITES,
importCitingButton,
refreshCitingButton,
CitationFetcher.SearchType.CITES,
importCitingButton,
citingProgress);
});

refreshCitedByButton.setOnMouseClicked(_ -> searchForRelations(
entry,
citedByListView,
entry,
citedByListView,
abortCitedButton,
refreshCitedByButton,
CitationFetcher.SearchType.CITED_BY,
importCitedByButton,
refreshCitedByButton,
CitationFetcher.SearchType.CITED_BY,
importCitedByButton,
citedByProgress));

// Create SplitPane to hold all nodes above
Expand All @@ -225,21 +225,21 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {
styleFetchedListView(citingListView);

searchForRelations(
entry,
citingListView,
abortCitingButton,
entry,
citingListView,
abortCitingButton,
refreshCitingButton,
CitationFetcher.SearchType.CITES,
importCitingButton,
CitationFetcher.SearchType.CITES,
importCitingButton,
citingProgress);

searchForRelations(
entry,
citedByListView,
abortCitedButton,
entry,
citedByListView,
abortCitedButton,
refreshCitedByButton,
CitationFetcher.SearchType.CITED_BY,
importCitedByButton,
CitationFetcher.SearchType.CITED_BY,
importCitedByButton,
citedByProgress);

return container;
Expand Down Expand Up @@ -444,14 +444,13 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt
return;
}

ObservableList<CitationRelationItem> observableList = FXCollections.observableArrayList();

listView.setItems(observableList);
ObservableList<CitationRelationItem> resultList = FXCollections.observableArrayList();
listView.setItems(resultList);

// TODO: It should not be possible to cancel a search task that is already running for same tab
if (citingTask != null && !citingTask.isCancelled() && searchType == CitationFetcher.SearchType.CITES) {
if (searchType == CitationFetcher.SearchType.CITES && citingTask != null && !citingTask.isCancelled()) {
citingTask.cancel();
} else if (citedByTask != null && !citedByTask.isCancelled() && searchType == CitationFetcher.SearchType.CITED_BY) {
} else if (searchType == CitationFetcher.SearchType.CITED_BY && citedByTask != null && !citedByTask.isCancelled()) {
citedByTask.cancel();
}

Expand All @@ -468,13 +467,22 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt
importButton,
progress,
fetchedList,
observableList
resultList
))
.onFailure(exception -> {
LOGGER.error("Error while fetching citing Articles", exception);
LOGGER.error("Error while fetching {} papers",
searchType == CitationFetcher.SearchType.CITES ? "cited" : "citing",
exception);
hideNodes(abortButton, progress, importButton);
listView.setPlaceholder(new Label(Localization.lang("Error while fetching citing entries: %0",
exception.getMessage())));
String labelText;
if (searchType == CitationFetcher.SearchType.CITES) {
labelText = Localization.lang("Error while fetching cited entries: %0", exception.getMessage());
} else {
labelText = Localization.lang("Error while fetching citing entries: %0", exception.getMessage());
}
Label placeholder = new Label(labelText);
placeholder.setWrapText(true);
listView.setPlaceholder(placeholder);
refreshButton.setVisible(true);
dialogService.notify(exception.getMessage());
})
Expand All @@ -490,13 +498,13 @@ private BackgroundTask<List<BibEntry>> createBackgroundTask(
return switch (searchType) {
case CitationFetcher.SearchType.CITES -> {
citingTask = BackgroundTask.wrap(
() -> this.searchCitationsRelationsService.searchReferences(entry)
() -> this.searchCitationsRelationsService.searchCites(entry)
);
yield citingTask;
}
case CitationFetcher.SearchType.CITED_BY -> {
citedByTask = BackgroundTask.wrap(
() -> this.searchCitationsRelationsService.searchCitations(entry)
() -> this.searchCitationsRelationsService.searchCitedBy(entry)
);
yield citedByTask;
}
Expand All @@ -510,6 +518,8 @@ private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationR
ObservableList<CitationRelationItem> observableList) {
hideNodes(abortButton, progress);

// TODO: This could be a wrong database, because the user might have switched to another library
// If we were on fixing this, we would need to a) associate a BibEntry with a database or b) pass the database at "bindToEntry"
BibDatabase database = stateManager.getActiveDatabase().map(BibDatabaseContext::getDatabase)
.orElse(new BibDatabase());
observableList.setAll(
Expand All @@ -523,15 +533,15 @@ private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationR
.toList()
);

if (!observableList.isEmpty()) {
listView.refresh();
} else {
if (observableList.isEmpty()) {
Label placeholder = new Label(Localization.lang("No articles found"));
listView.setPlaceholder(placeholder);
} else {
listView.refresh();
}
BooleanBinding booleanBind = Bindings.isEmpty(listView.getCheckModel().getCheckedItems());
importButton.disableProperty().bind(booleanBind);
importButton.setOnMouseClicked(event -> importEntries(listView.getCheckModel().getCheckedItems(), searchType, entry));
importButton.setOnMouseClicked(_ -> importEntries(listView.getCheckModel().getCheckedItems(), searchType, entry));
showNodes(refreshButton, importButton);
}

Expand All @@ -540,7 +550,7 @@ private void prepareToSearchForRelations(Button abortButton, Button refreshButto
showNodes(abortButton, progress);
hideNodes(refreshButton, importButton);

abortButton.setOnAction(event -> {
abortButton.setOnAction(_ -> {
hideNodes(abortButton, progress, importButton);
showNodes(refreshButton);
task.cancel();
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2 changes: 2 additions & 0 deletions jablib/build.gradle.kts
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Expand Up @@ -106,6 +106,8 @@ dependencies {

implementation("com.fasterxml:aalto-xml")

implementation("org.hisp.dhis:json-tree")
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Why another json library?

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@Siedlerchr Siedlerchr Jul 16, 2025 •
edited
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For optionals use kongs unirest json

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Why another json library?

Because I know the author personally. And it is fast

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For optionals use kongs unirest json

Show me. 😅

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Because I know the author personally. And it is fast
Argument by authority is not a valid reason

see: eg.g
JSONObject result = item.getJSONObject("resultList").getJSONArray("result").getJSONObject(0);

jabref/jablib/src/main/java/org/jabref/logic/importer/fetcher/EuropePmcFetcher.java

Line 117 in e29044c

Optional.ofNullable(result.optString("pubModel")).ifPresent(pubModel -> entry.setField(StandardField.HOWPUBLISHED, pubModel));


implementation("org.postgresql:postgresql")

antlr("org.antlr:antlr4")
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1 change: 1 addition & 0 deletions jablib/src/main/java/module-info.java
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Expand Up @@ -145,6 +145,7 @@
requires com.fasterxml.jackson.databind;
requires com.fasterxml.jackson.dataformat.yaml;
requires com.fasterxml.jackson.datatype.jsr310;
requires org.hisp.dhis.jsontree;
// endregion

// region HTTP clients
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37 changes: 14 additions & 23 deletions jablib/src/main/java/org/jabref/logic/citation/SearchCitationsRelationsService.java
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Expand Up @@ -39,46 +39,37 @@ public SearchCitationsRelationsService(ImporterPreferences importerPreferences,
);
}

/**
* @implNote Typically, this would be a Shim in JavaFX
*/
@VisibleForTesting
public SearchCitationsRelationsService(CitationFetcher citationFetcher,
SearchCitationsRelationsService(CitationFetcher citationFetcher,
BibEntryCitationsAndReferencesRepository repository
) {
this.citationFetcher = citationFetcher;
this.relationsRepository = repository;
}

public List<BibEntry> searchReferences(BibEntry referenced) {
boolean isFetchingAllowed = relationsRepository.isReferencesUpdatable(referenced)
|| !relationsRepository.containsReferences(referenced);
public List<BibEntry> searchCites(BibEntry referencing) throws FetcherException {
boolean isFetchingAllowed =
!relationsRepository.containsReferences(referencing) ||
relationsRepository.isReferencesUpdatable(referencing);
if (isFetchingAllowed) {
try {
List<BibEntry> referencedBy = citationFetcher.searchCiting(referenced);
relationsRepository.insertReferences(referenced, referencedBy);
} catch (FetcherException e) {
LOGGER.error("Error while fetching references for entry {}", referenced.getTitle(), e);
}
List<BibEntry> referencedBy = citationFetcher.searchCiting(referencing);
relationsRepository.insertReferences(referencing, referencedBy);
}
return relationsRepository.readReferences(referenced);
return relationsRepository.readReferences(referencing);
}

/**
* If the store was empty and nothing was fetch in any case (empty fetch, or error) then yes => empty list
* If the store was not empty and nothing was fetched after a successful fetch => the store will be erased and the returned collection will be empty
* If the store was not empty and an error occurs while fetching => will return the content of the store
*/
public List<BibEntry> searchCitations(BibEntry cited) {
boolean isFetchingAllowed = relationsRepository.isCitationsUpdatable(cited)
|| !relationsRepository.containsCitations(cited);
public List<BibEntry> searchCitedBy(BibEntry cited) throws FetcherException {
boolean isFetchingAllowed =
!relationsRepository.containsCitations(cited) ||
relationsRepository.isCitationsUpdatable(cited);
if (isFetchingAllowed) {
try {
List<BibEntry> citedBy = citationFetcher.searchCitedBy(cited);
relationsRepository.insertCitations(cited, citedBy);
} catch (FetcherException e) {
LOGGER.error("Error while fetching citations for entry {}", cited.getTitle(), e);
}
List<BibEntry> citedBy = citationFetcher.searchCitedBy(cited);
relationsRepository.insertCitations(cited, citedBy);
}
return relationsRepository.readCitations(cited);
}
Expand Down
30 changes: 27 additions & 3 deletions ...abref/logic/importer/fetcher/citation/semanticscholar/SemanticScholarCitationFetcher.java
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Expand Up @@ -8,15 +8,23 @@
import org.jabref.logic.importer.ImporterPreferences;
import org.jabref.logic.importer.fetcher.CustomizableKeyFetcher;
import org.jabref.logic.importer.fetcher.citation.CitationFetcher;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.net.URLDownload;
import org.jabref.logic.util.URLUtil;
import org.jabref.model.entry.BibEntry;

import com.google.gson.Gson;
import org.hisp.dhis.jsontree.JsonMixed;
import org.hisp.dhis.jsontree.JsonNode;
import org.jspecify.annotations.NonNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class SemanticScholarCitationFetcher implements CitationFetcher, CustomizableKeyFetcher {
public static final String FETCHER_NAME = "Semantic Scholar Citations Fetcher";

private static final Logger LOGGER = LoggerFactory.getLogger(SemanticScholarCitationFetcher.class);

private static final String SEMANTIC_SCHOLAR_API = "https://api.semanticscholar.org/graph/v1/";

private static final Gson GSON = new Gson();
Expand All @@ -27,8 +35,8 @@ public SemanticScholarCitationFetcher(ImporterPreferences importerPreferences) {
this.importerPreferences = importerPreferences;
}

public String getAPIUrl(String entry_point, BibEntry entry) {
return SEMANTIC_SCHOLAR_API + "paper/" + "DOI:" + entry.getDOI().orElseThrow().asString() + "/" + entry_point
public String getAPIUrl(String entryPoint, BibEntry entry) {
return SEMANTIC_SCHOLAR_API + "paper/" + "DOI:" + entry.getDOI().orElseThrow().asString() + "/" + entryPoint
+ "?fields=" + "title,authors,year,citationCount,referenceCount,externalIds,publicationTypes,abstract,url"
+ "&limit=1000";
}
Expand All @@ -42,6 +50,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
URL citationsUrl;
try {
citationsUrl = URLUtil.create(getAPIUrl("citations", entry));
LOGGER.debug("Cited URL {} ", citationsUrl);
} catch (MalformedURLException e) {
throw new FetcherException("Malformed URL", e);
}
Expand All @@ -66,15 +75,30 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
URL referencesUrl;
try {
referencesUrl = URLUtil.create(getAPIUrl("references", entry));
LOGGER.debug("Citing URL {} ", referencesUrl);
} catch (MalformedURLException e) {
throw new FetcherException("Malformed URL", e);
}

URLDownload urlDownload = new URLDownload(referencesUrl);
importerPreferences.getApiKey(getName()).ifPresent(apiKey -> urlDownload.addHeader("x-api-key", apiKey));
ReferencesResponse referencesResponse = GSON.fromJson(urlDownload.asString(), ReferencesResponse.class);
String response = urlDownload.asString();
ReferencesResponse referencesResponse = GSON.fromJson(response, ReferencesResponse.class);

if (referencesResponse.getData() == null) {
JsonNode json = JsonNode.of(response);
JsonNode disclaimerJson = json.getOrNull("citingPaperInfo.openAccessPdf.disclaimer");
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@Siedlerchr Siedlerchr Jul 16, 2025 •
edited
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Use kong's unirest json that allows you to use optionals

            JSONObject response = JsonReader.toJsonObject(inputStream);


      JSONObject journal = journalInfo.getJSONObject("journal");
                    Optional.ofNullable(journal.optString("title")).ifPresent(title -> entry.setField(StandardField.JOURNAL, title));
                    ```

if (disclaimerJson != null) {
JsonMixed disclaimerNode = JsonMixed.of(disclaimerJson);
if (disclaimerNode.isString()) {
String disclaimer = disclaimerNode.string();
LOGGER.debug("Received a disclaimer from Semantic Scholar: {}", disclaimer);
if (disclaimer.contains("'references'")) {
throw new FetcherException(Localization.lang("Restricted access to references: %0", disclaimer));
}
}
}

return List.of();
}

Expand Down
10 changes: 7 additions & 3 deletions jablib/src/main/resources/l10n/JabRef_en.properties
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Expand Up @@ -1697,6 +1697,12 @@ Open\ one\ before\ citing.=Open one before citing.
Select\ one\ before\ citing.=Select one before citing.
Select\ some\ before\ citing.=Select some before citing.

Citation\ relations=Citation relations
Show\ articles\ related\ by\ citation=Show articles related by citation
Error\ while\ fetching\ cited\ entries\:\ %0=Error while fetching cited entries: %0
Error\ while\ fetching\ citing\ entries\:\ %0=Error while fetching citing entries: %0
Restricted\ access\ to\ references\:\ %0=Restricted access to references: %0

Found\ identical\ ranges=Found identical ranges
Found\ overlapping\ ranges=Found overlapping ranges
Found\ touching\ ranges=Found touching ranges
Expand Down Expand Up @@ -2809,9 +2815,7 @@ Restart\ search=Restart search
Cancel\ search=Cancel search
Select\ entry=Select entry
Search\ aborted!=Search aborted!
Citation\ relations=Citation relations
Show\ articles\ related\ by\ citation=Show articles related by citation
Error\ while\ fetching\ citing\ entries\:\ %0=Error while fetching citing entries: %0

Help\ on\ external\ applications=Help on external applications
Identifier-based\ Web\ Search=Identifier-based Web Search

Expand Down
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