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Extract references from related work section (Part 1) (#15316)
* Extract text about papers from "related work" sections * Update comments Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * small refactor * small refactor of comments * Support more citation format * Modify logic for UI * Add UI * make `RelatedWorkAction` inline * add empty check before getting optional value * add javadoc and example to RelatedWorkSnippet.java * Update jabgui/src/main/java/org/jabref/gui/relatedwork/RelatedWorkResultDialogView.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Fix comment style * Add backticks around `comment-{username}`` * Add @NullMarked * Change parameter order * Change variable order * remove copyOf * remove copyOf * remove `skipped` * change comment style * add comment * Add backticks around `comment-{username}` * Add more explanation in the comment * Add "undefined" to `getCitationKey` * get owner from preference * Add action helper to check if PDF file is present * Hihglight non-editabel fileds differently * Update CHANGELOG.md * Fix failed test * Focus related work text field, auto insert clipboard content * Use sealed interface instead of enum * Fix failed tests * Add logger * Trigger CI * Replace all page separators to "-" * Split RelatedWorkService to matcher and inserter * Replace "[^a-z0-9]" as a constant NON_ALPHANUMERIC * use switch to replace ifelse * use mock to create filepreference * Normalize linebreak * Add requirement * Add requirement * Fix md format fail --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
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‎CHANGELOG.md‎

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@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
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### Added
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- We added a related work text extractor, which finds and inserts the related work text into bib entries from references in the texts. [#9840](https://github.com/JabRef/jabref/issues/9840)
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- We added a hover button on group rows to quickly add a new group or subgroup. [#12289](https://github.com/JabRef/jabref/issues/12289)
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- We added a shorthand for protecting terms in the fields: user can now select a text and type a opening curling brace to quickly wrap the selection in braces. [#15442](https://github.com/JabRef/jabref/pull/15442)
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- We added fallback search for `[DATE]` patterns in the file finder, so that if an exact date match is not found, progressively less specific dates (year-month, then year) are tried. [#8152](https://github.com/JabRef/jabref/issues/8152)

‎docs/requirements/dialog-with-text-input.md‎

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---
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parent: Requirements
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---
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# Dialog with text input
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## Automatic clipboard content detection and focus for text input
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`req~textinput.clipboard.autofocus~1`
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When a dialog with text input is opened:
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- Text field should be focused.
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- If the clipboard contains contents, it should be in the field and be marked.
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Needs: impl
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<!-- markdownlint-disable-file MD022 -->

‎jabgui/src/main/java/org/jabref/gui/actions/ActionHelper.java‎

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@@ -111,6 +111,28 @@ public static BooleanExpression isFilePresentForSelectedEntry(StateManager state
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return BooleanExpression.booleanExpression(fileIsPresent);
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}
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public static BooleanExpression isPdfFilePresentForSelectedEntry(StateManager stateManager, CliPreferences preferences) {
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ObservableList<BibEntry> selectedEntries = stateManager.getSelectedEntries();
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Binding<Boolean> pdfFileIsPresent = EasyBind.valueAt(selectedEntries, 0).mapOpt(entry -> {
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if (stateManager.getActiveDatabase().isEmpty()) {
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return false;
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}
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return entry.getFiles().stream()
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.filter(linkedFile -> linkedFile.getFileName()
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.map(Path::of)
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.map(FileUtil::isPDFFile)
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.orElse(false))
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.anyMatch(linkedFile -> FileUtil.find(
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stateManager.getActiveDatabase().get(),
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linkedFile.getLink(),
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preferences.getFilePreferences())
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.isPresent());
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}).orElseOpt(false);
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return BooleanExpression.booleanExpression(pdfFileIsPresent);
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}
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/// Check if at least one of the selected entries has linked files
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/// <br>
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/// Used in {@link org.jabref.gui.maintable.OpenSelectedEntriesFilesAction} when multiple entries selected

‎jabgui/src/main/java/org/jabref/gui/actions/StandardActions.java‎

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OPEN_EXTERNAL_FILE(Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),
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EXTRACT_FILE_REFERENCES_ONLINE(Localization.lang("Extract references from file (online)"), IconTheme.JabRefIcons.FILE_STAR),
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EXTRACT_FILE_REFERENCES_OFFLINE(Localization.lang("Extract references from file (offline)"), IconTheme.JabRefIcons.FILE_STAR),
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EXTRACT_RELATED_WORK_COMMENTS(Localization.lang("Extract related work comments"), IconTheme.JabRefIcons.COMMENT),
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OPEN_URL(Localization.lang("Open URL or DOI"), IconTheme.JabRefIcons.WWW, KeyBinding.OPEN_URL_OR_DOI),
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SEARCH(Localization.lang("Search...")),
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SEARCH_GOOGLE_SCHOLAR(Localization.lang("Search Google Scholar")),

‎jabgui/src/main/java/org/jabref/gui/frame/MainMenu.java‎

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import org.jabref.gui.preview.PreviewControls;
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import org.jabref.gui.pseudonymize.PseudonymizeAction;
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import org.jabref.gui.push.GuiPushToApplicationCommand;
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import org.jabref.gui.relatedwork.RelatedWorkAction;
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import org.jabref.gui.search.RebuildFulltextSearchIndexAction;
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import org.jabref.gui.shared.ConnectToSharedDatabaseCommand;
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import org.jabref.gui.shared.PullChangesFromSharedAction;
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factory.createMenuItem(StandardActions.NEW_SUB_LIBRARY_FROM_AUX, new NewSubLibraryAction(frame, stateManager, dialogService)),
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factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_ONLINE, new NewLibraryFromPdfActionOnline(frame, stateManager, dialogService, preferences, taskExecutor)),
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factory.createMenuItem(StandardActions.NEW_LIBRARY_FROM_PDF_OFFLINE, new NewLibraryFromPdfActionOffline(frame, stateManager, dialogService, preferences, taskExecutor)),
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factory.createMenuItem(StandardActions.EXTRACT_RELATED_WORK_COMMENTS, new RelatedWorkAction(dialogService, stateManager, preferences)),
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factory.createMenuItem(StandardActions.PSEUDONYMIZE_LIBRARY, new PseudonymizeAction(stateManager, dialogService, preferences)),
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new SeparatorMenuItem(),

‎jabgui/src/main/java/org/jabref/gui/maintable/RightClickMenu.java‎

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import org.jabref.gui.preferences.GuiPreferences;
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import org.jabref.gui.preview.CopyCitationAction;
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import org.jabref.gui.preview.PreviewPreferences;
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import org.jabref.gui.relatedwork.RelatedWorkAction;
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import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
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import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
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import org.jabref.logic.importer.WebFetchers;
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factory.createMenuItem(StandardActions.OPEN_EXTERNAL_FILE, new OpenSelectedEntriesFilesAction(dialogService, stateManager, preferences, taskExecutor)),
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extractFileReferencesOnline,
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extractFileReferencesOffline,
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factory.createMenuItem(StandardActions.EXTRACT_RELATED_WORK_COMMENTS, new RelatedWorkAction(dialogService, stateManager, preferences)),
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factory.createMenuItem(StandardActions.OPEN_URL, new OpenUrlAction(dialogService, stateManager, preferences)),
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‎jabgui/src/main/java/org/jabref/gui/newentry/NewEntryView.java‎

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@@ -370,6 +370,7 @@ private void initializeLookupIdentifier() {
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}
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private void initializeInterpretCitations() {
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// [impl->req~textinput.clipboard.autofocus~1]
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interpretText.textProperty().bindBidirectional(viewModel.interpretTextProperty());
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final String clipboardText = ClipBoardManager.getContents().trim();
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if (!StringUtil.isBlank(clipboardText)) {
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currentApproach = NewEntryDialogTab.INTERPRET_CITATIONS;
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newEntryPreferences.setLatestApproach(NewEntryDialogTab.INTERPRET_CITATIONS);
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// [impl->req~textinput.clipboard.autofocus~1]
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if (interpretText != null) {
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Platform.runLater(() -> interpretText.requestFocus());
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}

‎jabgui/src/main/java/org/jabref/gui/relatedwork/RelatedWorkAction.java‎

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package org.jabref.gui.relatedwork;
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import java.nio.file.Path;
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import java.util.Optional;
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import org.jabref.gui.DialogService;
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import org.jabref.gui.StateManager;
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import org.jabref.gui.actions.ActionHelper;
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import org.jabref.gui.actions.SimpleCommand;
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import org.jabref.logic.l10n.Localization;
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import org.jabref.logic.preferences.CliPreferences;
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import org.jabref.logic.util.io.FileUtil;
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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.LinkedFile;
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public class RelatedWorkAction extends SimpleCommand {
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private final DialogService dialogService;
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private final StateManager stateManager;
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public RelatedWorkAction(DialogService dialogService, StateManager stateManager, CliPreferences preferences) {
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this.dialogService = dialogService;
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this.stateManager = stateManager;
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executable.bind(ActionHelper.needsDatabase(stateManager)
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.and(ActionHelper.needsEntriesSelected(1, stateManager))
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.and(ActionHelper.isPdfFilePresentForSelectedEntry(stateManager, preferences)));
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}
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@Override
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public void execute() {
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BibDatabaseContext databaseContext = stateManager.getActiveDatabase().orElseThrow();
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BibEntry sourceEntry = stateManager.getSelectedEntries().getFirst();
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Optional<LinkedFile> linkedPDFFile = sourceEntry.getFiles().stream()
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.filter(this::isPDFLinkedFile)
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.findFirst();
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if (linkedPDFFile.isEmpty()) {
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dialogService.showWarningDialogAndWait(
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Localization.lang("No PDF files available"),
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Localization.lang("Please attach PDF files")
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);
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return;
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}
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Optional<String> citationKey = sourceEntry.getCitationKey();
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if (citationKey.isEmpty()) {
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dialogService.showWarningDialogAndWait(
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Localization.lang("Insert related work text"),
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Localization.lang("Selected entry does not have an associated citation key.")
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);
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return;
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}
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dialogService.showCustomDialogAndWait(new RelatedWorkDialogView(
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databaseContext,
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sourceEntry,
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linkedPDFFile.get(),
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citationKey.get()
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));
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}
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private boolean isPDFLinkedFile(LinkedFile linkedFile) {
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return linkedFile.getFileName()
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.map(Path::of)
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.map(FileUtil::isPDFFile)
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.orElse(false);
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}
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}

‎jabgui/src/main/java/org/jabref/gui/relatedwork/RelatedWorkDialogView.java‎

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package org.jabref.gui.relatedwork;
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import java.util.List;
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import javafx.application.Platform;
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import javafx.fxml.FXML;
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import javafx.scene.control.Button;
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import javafx.scene.control.ButtonType;
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import javafx.scene.control.TextArea;
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import javafx.scene.control.TextField;
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import org.jabref.gui.DialogService;
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import org.jabref.gui.clipboard.ClipBoardManager;
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import org.jabref.gui.util.BaseDialog;
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import org.jabref.gui.util.ControlHelper;
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import org.jabref.logic.l10n.Localization;
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import org.jabref.logic.preferences.CliPreferences;
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import org.jabref.logic.relatedwork.RelatedWorkMatchResult;
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import org.jabref.logic.util.strings.StringUtil;
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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.BibEntryTypesManager;
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import org.jabref.model.entry.LinkedFile;
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import com.airhacks.afterburner.views.ViewLoader;
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import jakarta.inject.Inject;
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public class RelatedWorkDialogView extends BaseDialog<Void> {
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private final BibDatabaseContext databaseContext;
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private final BibEntry sourceEntry;
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private final LinkedFile linkedFile;
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private final String sourceEntryCitationKey;
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@FXML private TextField entryField;
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@FXML private TextField linkedFileField;
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@FXML private TextField userNameField;
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@FXML private TextArea relatedWorkTextArea;
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@FXML private ButtonType parseButtonType;
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@Inject private DialogService dialogService;
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@Inject private CliPreferences preferences;
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@Inject private BibEntryTypesManager entryTypesManager;
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private RelatedWorkDialogViewModel viewModel;
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public RelatedWorkDialogView(BibDatabaseContext databaseContext,
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BibEntry sourceEntry,
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LinkedFile linkedPdfFile,
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String sourceEntryCitationKey) {
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this.databaseContext = databaseContext;
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this.sourceEntry = sourceEntry;
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this.linkedFile = linkedPdfFile;
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this.sourceEntryCitationKey = sourceEntryCitationKey;
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setTitle(Localization.lang("Insert related work text"));
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ViewLoader.view(this).load().setAsDialogPane(this);
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ControlHelper.setAction(parseButtonType, getDialogPane(), event -> viewModel.matchRelatedWork().ifPresent(this::openResultDialog));
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Button parseButton = (Button) getDialogPane().lookupButton(parseButtonType);
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parseButton.disableProperty().bind(viewModel.parseDisabledProperty());
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}
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@FXML
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private void initialize() {
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this.viewModel = new RelatedWorkDialogViewModel(
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databaseContext,
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sourceEntry,
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linkedFile,
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sourceEntryCitationKey,
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dialogService,
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preferences,
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entryTypesManager
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);
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this.entryField.textProperty().bind(viewModel.sourceEntryCitationKeyProperty());
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this.linkedFileField.textProperty().bind(viewModel.linkedPDFFileProperty());
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this.userNameField.textProperty().bind(viewModel.userNameProperty());
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this.relatedWorkTextArea.textProperty().bindBidirectional(viewModel.relatedWorkTextProperty());
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// [impl->req~textinput.clipboard.autofocus~1]
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String clipboardText = ClipBoardManager.getContents().trim();
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if (!StringUtil.isBlank(clipboardText)) {
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relatedWorkTextArea.setText(clipboardText);
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relatedWorkTextArea.selectAll();
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}
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Platform.runLater(relatedWorkTextArea::requestFocus);
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}
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private void openResultDialog(List<RelatedWorkMatchResult> matchedResults) {
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dialogService.showCustomDialogAndWait(new RelatedWorkResultDialogView(sourceEntry, matchedResults, viewModel.userNameProperty().get()));
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}
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}

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