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ror3dSiedlerchr
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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 <siedlerkiller@gmail.com>
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‎CHANGELOG.md‎

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@@ -49,6 +49,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
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- 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)
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- 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)
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- Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
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- 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)
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### Fixed
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‎src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java‎

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

‎src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/PaperDetails.java‎

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

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@@ -25,17 +25,17 @@ public SemanticScholarFetcher(ImporterPreferences importerPreferences) {
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this.importerPreferences = importerPreferences;
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}
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public String getAPIUrl(String entry_point, BibEntry entry) {
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return SEMANTIC_SCHOLAR_API + "paper/" + "DOI:" + entry.getDOI().orElseThrow().getDOI() + "/" + entry_point
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+ "?fields=" + "title,authors,year,citationCount,referenceCount,externalIds,publicationTypes,abstract,url"
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+ "&limit=1000";
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}
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@Override
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public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
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if (entry.getDOI().isPresent()) {
31-
StringBuilder urlBuilder = new StringBuilder(SEMANTIC_SCHOLAR_API)
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.append("paper/")
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.append("DOI:").append(entry.getDOI().get().getDOI())
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.append("/citations")
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.append("?fields=").append("title,authors,year,citationCount,referenceCount")
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.append("&limit=1000");
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try {
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URL citationsUrl = URI.create(urlBuilder.toString()).toURL();
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URL citationsUrl = URI.create(getAPIUrl("citations", entry)).toURL();
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URLDownload urlDownload = new URLDownload(citationsUrl);
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4141
String apiKey = getApiKey();
@@ -58,15 +58,8 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
5858
@Override
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public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
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if (entry.getDOI().isPresent()) {
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StringBuilder urlBuilder = new StringBuilder(SEMANTIC_SCHOLAR_API)
62-
.append("paper/")
63-
.append("DOI:").append(entry.getDOI().get().getDOI())
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.append("/references")
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.append("?fields=")
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.append("title,authors,year,citationCount,referenceCount")
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.append("&limit=1000");
6861
try {
69-
URL referencesUrl = URI.create(urlBuilder.toString()).toURL();
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URL referencesUrl = URI.create(getAPIUrl("references", entry)).toURL();
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URLDownload urlDownload = new URLDownload(referencesUrl);
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String apiKey = getApiKey();
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if (!apiKey.isEmpty()) {

‎src/main/java/org/jabref/model/entry/BibEntry.java‎

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@@ -602,7 +602,7 @@ public void setField(Map<Field, String> fields) {
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*/
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public Optional<FieldChange> setField(Field field, String value, EntriesEventSource eventSource) {
604604
Objects.requireNonNull(field, "field name must not be null");
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Objects.requireNonNull(value, "field value must not be null");
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Objects.requireNonNull(value, "field value for field " + field.getName() + " must not be null");
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Objects.requireNonNull(eventSource, "field eventSource must not be null");
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if (value.isEmpty()) {

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