Add OpenCitations

CHANGELOG.md

@@ -18,6 +18,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for selecting citation fetcher in Citations Tab. [#14430](https://github.com/JabRef/jabref/issues/14430)
 - In the "New Entry" dialog the identifier type is now automatically updated on typing. [#14660](https://github.com/JabRef/jabref/issues/14660)
 - Consistency check is now aware of custom entry types, custom fields, and reports missing required fields. [#14257](https://github.com/JabRef/jabref/pull/14257)
+- We added support for [OpenCitations](https://opencitations.net/) both in the GUI (tab "Citations") and JabKit (`--get-cited-works`, `--get-citing-works`). [#14996](https://github.com/JabRef/jabref/pull/14996)
 - We added the ability to copy selected text from AI chat interface. [#14655](https://github.com/JabRef/jabref/issues/14655)
 - We added cover images for books, which will display in entry previews if available, and can be automatically downloaded when adding an entry via ISBN. [#10120](https://github.com/JabRef/jabref/issues/10120)
 - REST-API: Added more commands (`selectentries`, `open`, `focus`). [#14855](https://github.com/JabRef/jabref/pull/14855)
@@ -44,6 +45,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue when importing an entry to a library without groups, but group "Imported Entries" was automatically created.
 - We fixed an issue where journal abbreviations chose the wrong abbreviation when fuzzy matching. [#14850](https://github.com/JabRef/jabref/pull/14850)
 - We fixed an issue where JaRef would not correctly remember the opened side panels in the preferences [#14818](https://github.com/JabRef/jabref/issues/14818)
+- We fixed an issue fetching DOI information when DOIs included URL-invalid characters (e.g., `10.1002/1098-108x(198905)8:3<343::aid-eat2260080310>3.0.co;2-c`). [#14996](https://github.com/JabRef/jabref/pull/14996)
 - Updates of the pre-selected fetchers are now followed at the Web fetchers. [#14768](https://github.com/JabRef/jabref/pull/14768)
 - Restart search button in citation-relation panel now refreshes using external services. [#14757](https://github.com/JabRef/jabref/issues/14757)
 - Fixed groups sidebar not refreshing after importing a library. [#13684](https://github.com/JabRef/jabref/issues/13684)

docs/glossary/references.md

@@ -9,7 +9,8 @@ parent: Glossary
 ## Meaning
 
 **References** is a structured list of works cited in a scientific work.
-collection of bibliographic records describing scholarly works such as articles, books, or reports.
+
+It is usually described as the outgoing references to other cited works appearing in the reference list.
 
 In JabRef, a bibliography usually corresponds to a **.bib file** (BibTeX or BibLaTeX format) that stores all entries used for citation and reference management.
 

jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

@@ -394,7 +394,7 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {
                 .withText(CitationFetcherType::getName)
                 .install(fetcherCombo);
         styleTopBarNode(fetcherCombo, 75.0);
-        fetcherCombo.setValue(entryEditorPreferences.getCitationFetcherType());
+        fetcherCombo.valueProperty().bindBidirectional(entryEditorPreferences.citationFetcherTypeProperty());
 
         // Create abort buttons for both sides
         Button abortCitingButton = IconTheme.JabRefIcons.CLOSE.asButton();
@@ -457,16 +457,9 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {
                 return;
             }
 
-            // Fetcher can only be changed for the citing search.
-            // Therefore, we handle this part only.
-
-            // Cancel any running searches so they don't continue with the old fetcher
-            if (citingTask != null && !citingTask.isCancelled()) {
-                citingTask.cancel();
-            }
-            entryEditorPreferences.setCitationFetcherType(newValue);
-            // switch the fetcher will not trigger refresh from the remote
+            // switch the fetcher will not trigger refresh from the remote, therefore we trigger it explicitly.
             searchForRelations(citingComponents, citedByComponents, false);
+            searchForRelations(citedByComponents, citingComponents, false);
         });
 
         // Create SplitPane to hold all nodes above
@@ -650,6 +643,16 @@ public boolean shouldShow(BibEntry entry) {
     protected void bindToEntry(BibEntry entry) {
         citationsRelationsTabViewModel.bindToEntry(entry);
 
+        // TODO: All this should go to ViewModel
+        if (citingTask != null && !citingTask.isCancelled()) {
+            citingTask.cancel();
+            citingTask = null;
+        }
+        if (citedByTask != null && !citedByTask.isCancelled()) {
+            citedByTask.cancel();
+            citedByTask = null;
+        }
+
         SplitPane splitPane = getPaneAndStartSearch(entry);
         splitPane.setMaxSize(Double.MAX_VALUE, Double.MAX_VALUE);
         splitPane.setMinSize(0, 0);
@@ -728,7 +731,6 @@ private void executeSearch(CitationComponents citationComponents, boolean bypass
         ObservableList<CitationRelationItem> observableList = FXCollections.observableArrayList();
         citationComponents.listView().setItems(observableList);
 
-        // TODO: It should not be possible to cancel a search task that is already running for same tab
         if (citationComponents.searchType() == CitationFetcher.SearchType.CITES && citingTask != null && !citingTask.isCancelled()) {
             citingTask.cancel();
         } else if (citationComponents.searchType() == CitationFetcher.SearchType.CITED_BY && citedByTask != null && !citedByTask.isCancelled()) {
@@ -765,13 +767,13 @@ private BackgroundTask<List<BibEntry>> createBackgroundTask(
     ) {
         return switch (searchType) {
             case CitationFetcher.SearchType.CITES -> {
-                citingTask = BackgroundTask.wrap(
+                this.citingTask = BackgroundTask.wrap(
                         () -> this.searchCitationsRelationsService.searchCites(entry, bypassCache)
                 );
                 yield citingTask;
             }
             case CitationFetcher.SearchType.CITED_BY -> {
-                citedByTask = BackgroundTask.wrap(
+                this.citedByTask = BackgroundTask.wrap(
                         () -> this.searchCitationsRelationsService.searchCitedBy(entry, bypassCache)
                 );
                 yield citedByTask;

jabkit/src/main/java/org/jabref/toolkit/commands/GetCitedWorks.java

@@ -35,7 +35,7 @@ class GetCitedWorks implements Callable<Integer> {
             converter = CitationFetcherTypeConverter.class,
             description = "Metadata provider: ${COMPLETION-CANDIDATES}"
     )
-    private CitationFetcherType citationFetcherType = CitationFetcherType.CROSSREF;
+    private CitationFetcherType citationFetcherType = CitationFetcherType.OPEN_CITATIONS;
 
     @CommandLine.Parameters(description = "DOI to check")
     private String doi;
@@ -50,15 +50,14 @@ public Integer call() {
                 LOGGER::info,
                 new CurrentThreadTaskExecutor());
 
-        CitationFetcher citationFetcher = CitationFetcherType
-                .getCitationFetcher(
-                        citationFetcherType,
-                        preferences.getImporterPreferences(),
-                        preferences.getImportFormatPreferences(),
-                        preferences.getCitationKeyPatternPreferences(),
-                        preferences.getGrobidPreferences(),
-                        aiService
-                );
+        CitationFetcher citationFetcher = CitationFetcherType.getCitationFetcher(
+                citationFetcherType,
+                preferences.getImporterPreferences(),
+                preferences.getImportFormatPreferences(),
+                preferences.getCitationKeyPatternPreferences(),
+                preferences.getGrobidPreferences(),
+                aiService
+        );
 
         List<BibEntry> entries;
 

jabkit/src/main/java/org/jabref/toolkit/commands/GetCitingWorks.java

@@ -3,12 +3,16 @@
 import java.util.List;
 import java.util.concurrent.Callable;
 
+import org.jabref.logic.ai.AiService;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.fetcher.citation.CitationFetcher;
-import org.jabref.logic.importer.fetcher.citation.semanticscholar.SemanticScholarCitationFetcher;
+import org.jabref.logic.importer.fetcher.citation.CitationFetcherType;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.util.CurrentThreadTaskExecutor;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
+import org.jabref.toolkit.converter.CitationFetcherTypeConverter;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -26,12 +30,34 @@ class GetCitingWorks implements Callable<Integer> {
     @CommandLine.Mixin
     private JabKit.SharedOptions sharedOptions = new JabKit.SharedOptions();
 
+    @CommandLine.Option(
+            names = "--provider",
+            converter = CitationFetcherTypeConverter.class,
+            description = "Metadata provider: ${COMPLETION-CANDIDATES}"
+    )
+    private CitationFetcherType citationFetcherType = CitationFetcherType.OPEN_CITATIONS;
+
     @CommandLine.Parameters(description = "DOI to check")
     private String doi;
 
     @Override
     public Integer call() {
-        CitationFetcher citationFetcher = new SemanticScholarCitationFetcher(argumentProcessor.cliPreferences.getImporterPreferences());
+        CliPreferences preferences = argumentProcessor.cliPreferences;
+        AiService aiService = new AiService(
+                preferences.getAiPreferences(),
+                preferences.getFilePreferences(),
+                preferences.getCitationKeyPatternPreferences(),
+                LOGGER::info,
+                new CurrentThreadTaskExecutor());
+
+        CitationFetcher citationFetcher = CitationFetcherType.getCitationFetcher(
+                citationFetcherType,
+                preferences.getImporterPreferences(),
+                preferences.getImportFormatPreferences(),
+                preferences.getCitationKeyPatternPreferences(),
+                preferences.getGrobidPreferences(),
+                aiService
+        );
 
         List<BibEntry> entries;
 

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

@@ -3,6 +3,8 @@
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
@@ -63,8 +65,8 @@ public URL getURLForEntry(BibEntry entry) throws URISyntaxException, MalformedUR
         entry.getFieldLatexFree(StandardField.YEAR).ifPresent(year ->
                 uriBuilder.addParameter("filter", "from-pub-date:" + year)
         );
-        uriBuilder.addParameter("rows", "20"); // = API default
-        uriBuilder.addParameter("offset", "0"); // start at beginning
+        uriBuilder.addParameter("rows", "20");  // = API default
+        uriBuilder.addParameter("offset", "0"); // start at the beginning
         return uriBuilder.build().toURL();
     }
 
@@ -77,7 +79,7 @@ public URL getURLForQuery(BaseQueryNode queryNode) throws URISyntaxException, Ma
 
     @Override
     public URL getUrlForIdentifier(String identifier) throws URISyntaxException, MalformedURLException {
-        URIBuilder uriBuilder = new URIBuilder(API_URL + "/" + identifier);
+        URIBuilder uriBuilder = new URIBuilder(API_URL + "/" + URLEncoder.encode(identifier, StandardCharsets.UTF_8));
         return uriBuilder.build().toURL();
     }
 

jablib/src/main/java/org/jabref/logic/importer/fetcher/citation/CitationFetcherType.java

@@ -5,12 +5,14 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.fetcher.citation.crossref.CrossRefCitationFetcher;
+import org.jabref.logic.importer.fetcher.citation.opencitations.OpenCitationsFetcher;
 import org.jabref.logic.importer.fetcher.citation.semanticscholar.SemanticScholarCitationFetcher;
 import org.jabref.logic.importer.util.GrobidPreferences;
 
 public enum CitationFetcherType {
-    CROSSREF("CrossRef"),
-    SEMANTIC_SCHOLAR("Semantic Scholar");
+    CROSSREF(CrossRefCitationFetcher.FETCHER_NAME),
+    OPEN_CITATIONS(OpenCitationsFetcher.FETCHER_NAME),
+    SEMANTIC_SCHOLAR(SemanticScholarCitationFetcher.FETCHER_NAME);
 
     private final String name;
 
@@ -37,6 +39,8 @@ public static CitationFetcher getCitationFetcher(CitationFetcherType citationFet
             case CROSSREF ->
                     new CrossRefCitationFetcher(importerPreferences, importFormatPreferences,
                             citationKeyPatternPreferences, grobidPreferences, aiService);
+            case OPEN_CITATIONS ->
+                    new OpenCitationsFetcher(importerPreferences);
             case SEMANTIC_SCHOLAR ->
                     new SemanticScholarCitationFetcher(importerPreferences);
         };

jablib/src/main/java/org/jabref/logic/importer/fetcher/citation/opencitations/CitationItem.java

@@ -0,0 +1,60 @@
+package org.jabref.logic.importer.fetcher.citation.opencitations;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.jabref.model.entry.field.Field;
+import org.jabref.model.entry.field.FieldFactory;
+import org.jabref.model.entry.field.StandardField;
+
+import com.google.gson.annotations.SerializedName;
+import org.jspecify.annotations.NullMarked;
+import org.jspecify.annotations.Nullable;
+
+@NullMarked
+class CitationItem {
+    @Nullable String oci;
+    @Nullable String citing;
+    @Nullable String cited;
+    @Nullable String creation;
+    @Nullable String timespan;
+
+    @SerializedName("journal_sc")
+    @Nullable String journalSelfCitation;
+
+    @SerializedName("author_sc")
+    @Nullable String authorSelfCitation;
+
+    record IdentifierWithField(Field field, String value) {
+    }
+
+    List<IdentifierWithField> extractIdentifiers(@Nullable String pidString) {
+        if (pidString == null || pidString.isEmpty()) {
+            return List.of();
+        }
+
+        String[] pids = pidString.split("\\s+");
+        List<IdentifierWithField> identifiers = new ArrayList<>();
+        for (String pid : pids) {
+            int colonIndex = pid.indexOf(':');
+            if (colonIndex > 0) {
+                String prefix = pid.substring(0, colonIndex);
+                String value = pid.substring(colonIndex + 1);
+                Field field = FieldFactory.parseField(prefix);
+                identifiers.add(new IdentifierWithField(field, value));
+            } else {
+                identifiers.add(new IdentifierWithField(StandardField.NOTE, pid));
+            }
+        }
+
+        return identifiers;
+    }
+
+    List<IdentifierWithField> citingIdentifiers() {
+        return extractIdentifiers(citing);
+    }
+
+    List<IdentifierWithField> citedIdentifiers() {
+        return extractIdentifiers(cited);
+    }
+}

jablib/src/main/java/org/jabref/logic/importer/fetcher/citation/opencitations/CountResponse.java

@@ -0,0 +1,20 @@
+package org.jabref.logic.importer.fetcher.citation.opencitations;
+
+import org.jspecify.annotations.NullMarked;
+import org.jspecify.annotations.Nullable;
+
+@NullMarked
+class CountResponse {
+    @Nullable String count;
+
+    int countAsInt() {
+        if (count == null) {
+            return 0;
+        }
+        try {
+            return Integer.parseInt(count);
+        } catch (NumberFormatException e) {
+            return 0;
+        }
+    }
+}