Improve citation relations (#11016)

* Collect DOI and publication type from semantich scholar to be able to expand the information of the new entries later by search through DOI * Include abstract in the request. This lets the GUI show the abstract since that was implemented already. Refactor api request string since most of it is shared * Add button to open the relation paper's DOI URL. Fix DOI for some ArXiv entries. * Don't show the open link button if there is no link to open. * Make field value null error a bit more useful * Include SemanticScholar url in the request and use it as the URL field. * Add changes to changelog * Change tooltip text to an existing, more informative one * Run rewriter to fix pull request * improve url optional handling --------- Co-authored-by: Siedlerchr <[email protected]>
JabRef · Mar 18, 2024 · 2ac5335 · 2ac5335
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
 - We store the citation relations in an LRU cache to avoid bloating the memory and out-of-memory exceptions. [#10958](https://github.com/JabRef/jabref/issues/10958)
 - Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
+- Citation relations now get more information, and have quick access to view the articles in a browser without adding them to the library [#10869](https://github.com/JabRef/jabref/issues/10869)
 
 ### Fixed
 

diff --git a/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java b/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java
@@ -1,5 +1,7 @@
 package org.jabref.gui.entryeditor.citationrelationtab;
 
+import java.io.IOException;
+import java.net.URI;
 import java.util.Arrays;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -28,6 +30,7 @@
 import org.jabref.gui.Globals;
 import org.jabref.gui.LibraryTab;
 import org.jabref.gui.StateManager;
+import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.gui.entryeditor.EntryEditorPreferences;
 import org.jabref.gui.entryeditor.EntryEditorTab;
 import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
@@ -40,6 +43,9 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.identifier.DOI;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
 
@@ -201,6 +207,8 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
                     HBox hContainer = new HBox();
                     hContainer.prefWidthProperty().bind(listView.widthProperty().subtract(25));
 
+                    VBox vContainer = new VBox();
+
                     if (entry.isLocal()) {
                         Button jumpTo = IconTheme.JabRefIcons.LINK.asButton();
                         jumpTo.setTooltip(new Tooltip(Localization.lang("Jump to entry in library")));
@@ -211,7 +219,7 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
                             citingTask.cancel();
                             citedByTask.cancel();
                         });
-                        hContainer.getChildren().addAll(entryNode, separator, jumpTo);
+                        vContainer.getChildren().add(jumpTo);
                     } else {
                         ToggleButton addToggle = IconTheme.JabRefIcons.ADD.asToggleButton();
                         addToggle.setTooltip(new Tooltip(Localization.lang("Select entry")));
@@ -224,8 +232,28 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
                         });
                         addToggle.getStyleClass().add("addEntryButton");
                         addToggle.selectedProperty().bindBidirectional(listView.getItemBooleanProperty(entry));
-                        hContainer.getChildren().addAll(entryNode, separator, addToggle);
+                        vContainer.getChildren().add(addToggle);
+                    }
+
+                    if (entry.entry().getDOI().isPresent() || entry.entry().getField(StandardField.URL).isPresent()) {
+                        Button openWeb = IconTheme.JabRefIcons.OPEN_LINK.asButton();
+                        openWeb.setTooltip(new Tooltip(Localization.lang("Open URL or DOI")));
+                        openWeb.setOnMouseClicked(event -> {
+                            String url = entry.entry().getDOI().flatMap(DOI::getExternalURI).map(URI::toString)
+                                              .or(() -> entry.entry().getField(StandardField.URL)).orElse("");
+                            if (StringUtil.isNullOrEmpty(url)) {
+                                return;
+                            }
+                            try {
+                                JabRefDesktop.openBrowser(url, preferencesService.getFilePreferences());
+                            } catch (IOException ex) {
+                                dialogService.notify(Localization.lang("Unable to open link."));
+                            }
+                        });
+                        vContainer.getChildren().addLast(openWeb);
                     }
+
+                    hContainer.getChildren().addAll(entryNode, separator, vContainer);
                     hContainer.getStyleClass().add("entry-container");
 
                     return hContainer;
@@ -392,8 +420,6 @@ private void showNodes(Node... nodes) {
         Arrays.stream(nodes).forEach(node -> node.setVisible(true));
     }
 
-    // Absolute-phase phenomena in photoionization with few-cycle laser pulses
-
     /**
      * Function to import selected entries to the database. Also writes the entries to import to the CITING/CITED field
      *

diff --git a/...ain/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/PaperDetails.java b/...ain/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/PaperDetails.java
@@ -1,18 +1,28 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
 import java.util.List;
+import java.util.Map;
 import java.util.stream.Collectors;
 
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.types.StandardEntryType;
+
+import com.google.gson.annotations.SerializedName;
 
 public class PaperDetails {
     private String paperId;
     private String title;
     private String year;
+
+    @SerializedName("abstract")
+    private String abstr;
+    private String url;
     private int citationCount;
     private int referenceCount;
     private List<AuthorResponse> authors;
+    private List<String> publicationTypes;
+    private Map<String, String> externalIds;
 
     public String getPaperId() {
         return paperId;
@@ -38,6 +48,22 @@ public void setYear(String year) {
         this.year = year;
     }
 
+    public String getAbstract() {
+        return abstr;
+    }
+
+    public void setAbstract(String abstr) {
+        this.abstr = abstr;
+    }
+
+    public String getURL() {
+        return url;
+    }
+
+    public void setURL(String url) {
+        this.url = url;
+    }
+
     public int getCitationCount() {
         return citationCount;
     }
@@ -58,6 +84,56 @@ public List<AuthorResponse> getAuthors() {
         return authors;
     }
 
+    public String getPublicationType() {
+        if (publicationTypes == null || publicationTypes.isEmpty()) {
+            return "Misc";
+        }
+        if (publicationTypes.contains("Conference")) {
+            return "InProceedings";
+        } else if (publicationTypes.contains("JournalArticle")) {
+            return "Article";
+        } else {
+            return switch (publicationTypes.getFirst()) {
+                case "Review" ->
+                        "Misc";
+                case "CaseReport" ->
+                        "Report";
+                case "ClinicalTrial" ->
+                        "Report";
+                case "Dataset" ->
+                        "Dataset";
+                case "Editorial" ->
+                        "Misc";
+                case "LettersAndComments" ->
+                        "Misc";
+                case "MetaAnalysis" ->
+                        "Article";
+                case "News" ->
+                        "Misc";
+                case "Study" ->
+                        "Article";
+                case "Book" ->
+                        "Book";
+                case "BookSection" ->
+                        "InBook";
+                default ->
+                        "Misc";
+            };
+        }
+    }
+
+    public String getDOI() {
+        if (externalIds != null) {
+            if (externalIds.containsKey("DOI")) {
+                return externalIds.get("DOI");
+            } else if (externalIds.containsKey("ArXiv")) {
+                // Some ArXiv articles don't return the DOI, even though it's easy to obtain from the ArXiv ID
+                return "10.48550/arXiv." + externalIds.get("ArXiv");
+            }
+        }
+        return "";
+    }
+
     public BibEntry toBibEntry() {
         BibEntry bibEntry = new BibEntry();
         bibEntry.setField(StandardField.TITLE, getTitle());
@@ -70,6 +146,20 @@ public BibEntry toBibEntry() {
                                      .collect(Collectors.joining(" and "));
         bibEntry.setField(StandardField.AUTHOR, authors);
 
+        bibEntry.setType(StandardEntryType.valueOf(getPublicationType()));
+
+        if (getDOI() != null) {
+            bibEntry.setField(StandardField.DOI, getDOI());
+        }
+
+        if (getURL() != null) {
+            bibEntry.setField(StandardField.URL, getURL());
+        }
+
+        if (getAbstract() != null) {
+            bibEntry.setField(StandardField.ABSTRACT, getAbstract());
+        }
+
         return bibEntry;
     }
 

diff --git a/...rg/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java b/...rg/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java
@@ -25,17 +25,17 @@ public SemanticScholarFetcher(ImporterPreferences importerPreferences) {
         this.importerPreferences = importerPreferences;
     }
 
+    public String getAPIUrl(String entry_point, BibEntry entry) {
+        return SEMANTIC_SCHOLAR_API + "paper/" + "DOI:" + entry.getDOI().orElseThrow().getDOI() + "/" + entry_point
+                + "?fields=" + "title,authors,year,citationCount,referenceCount,externalIds,publicationTypes,abstract,url"
+                + "&limit=1000";
+    }
+
     @Override
     public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
         if (entry.getDOI().isPresent()) {
-            StringBuilder urlBuilder = new StringBuilder(SEMANTIC_SCHOLAR_API)
-                    .append("paper/")
-                    .append("DOI:").append(entry.getDOI().get().getDOI())
-                    .append("/citations")
-                    .append("?fields=").append("title,authors,year,citationCount,referenceCount")
-                    .append("&limit=1000");
             try {
-                URL citationsUrl = URI.create(urlBuilder.toString()).toURL();
+                URL citationsUrl = URI.create(getAPIUrl("citations", entry)).toURL();
                 URLDownload urlDownload = new URLDownload(citationsUrl);
 
                 String apiKey = getApiKey();
@@ -58,15 +58,8 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
     @Override
     public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
         if (entry.getDOI().isPresent()) {
-            StringBuilder urlBuilder = new StringBuilder(SEMANTIC_SCHOLAR_API)
-                    .append("paper/")
-                    .append("DOI:").append(entry.getDOI().get().getDOI())
-                    .append("/references")
-                    .append("?fields=")
-                    .append("title,authors,year,citationCount,referenceCount")
-                    .append("&limit=1000");
             try {
-                URL referencesUrl = URI.create(urlBuilder.toString()).toURL();
+                URL referencesUrl = URI.create(getAPIUrl("references", entry)).toURL();
                 URLDownload urlDownload = new URLDownload(referencesUrl);
                 String apiKey = getApiKey();
                 if (!apiKey.isEmpty()) {

diff --git a/src/main/java/org/jabref/model/entry/BibEntry.java b/src/main/java/org/jabref/model/entry/BibEntry.java
@@ -602,7 +602,7 @@ public void setField(Map<Field, String> fields) {
      */
     public Optional<FieldChange> setField(Field field, String value, EntriesEventSource eventSource) {
         Objects.requireNonNull(field, "field name must not be null");
-        Objects.requireNonNull(value, "field value must not be null");
+        Objects.requireNonNull(value, "field value for field " + field.getName() + " must not be null");
         Objects.requireNonNull(eventSource, "field eventSource must not be null");
 
         if (value.isEmpty()) {