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Fix issue #11189 part 00 refactor citation relation tab logic #11845

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3785cb1
Refactor Citations Relations Tab (#11189)
alexandre-cremieux Sep 19, 2024
8048da8
Refactor Citations Relations Tab (#11189)
alexandre-cremieux Sep 24, 2024
18db75e
Refactor Citations Relations Service Layer (#11189)
alexandre-cremieux Sep 28, 2024
0e9de3c
Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…
koppor Oct 10, 2024
9a31735
Address PR comments (#11901)
alexandre-cremieux Nov 6, 2024
b1133d0
MVStore implementation for citations: first approach (wip for open di…
alexandre-cremieux Nov 11, 2024
6a8b21b
Introduce the DAO layer for relations (#11189):
alexandre-cremieux Nov 17, 2024
01f6da4
MVStoreDAO implementation for citations relations (#11189):
alexandre-cremieux Nov 17, 2024
337780d
Implement a search lock mechanism for citations relations (#11189):
alexandre-cremieux Nov 24, 2024
7c2e32d
Avoid user to force update citation relations even the fetcher return…
alexandre-cremieux Nov 27, 2024
187b5d4
Make the citation relations update automatic after the guard delay is…
alexandre-cremieux Dec 8, 2024
b71d9fc
SearchCitationsRelationsService as singleton
Jan 11, 2025
dda21ed
Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…
Jan 20, 2025
077e9ca
Update failing tests after merge
Jan 20, 2025
0bff913
Clean code style according to checkstyle
Jan 20, 2025
ea36f1a
Clean code style according to checkstyle
Jan 20, 2025
d7f9c2d
Fix pending PR comments
Jan 20, 2025
97b38c6
Fix null pointer exception in CitationsRelationsTab
Jan 22, 2025
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6 changes: 6 additions & 0 deletions src/main/java/org/jabref/gui/JabRefGUI.java
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
import org.jabref.gui.util.UiTaskExecutor;
import org.jabref.logic.UiCommand;
import org.jabref.logic.ai.AiService;
import org.jabref.logic.citation.SearchCitationsRelationsService;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.net.ProxyRegisterer;
import org.jabref.logic.os.OS;
Expand Down Expand Up @@ -175,6 +176,11 @@ public void initialize() {
dialogService,
taskExecutor);
Injector.setModelOrService(AiService.class, aiService);

Injector.setModelOrService(
SearchCitationsRelationsService.class,
new SearchCitationsRelationsService(preferences.getImporterPreferences())
);
}

private void setupProxy() {
Expand Down
11 changes: 9 additions & 2 deletions src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@
import org.jabref.gui.util.UiTaskExecutor;
import org.jabref.logic.ai.AiService;
import org.jabref.logic.bibtex.TypedBibEntry;
import org.jabref.logic.citation.SearchCitationsRelationsService;
import org.jabref.logic.help.HelpFile;
import org.jabref.logic.importer.EntryBasedFetcher;
import org.jabref.logic.importer.WebFetchers;
Expand Down Expand Up @@ -123,6 +124,7 @@ public class EntryEditor extends BorderPane {
@Inject private KeyBindingRepository keyBindingRepository;
@Inject private JournalAbbreviationRepository journalAbbreviationRepository;
@Inject private AiService aiService;
@Inject private SearchCitationsRelationsService searchCitationsRelationsService;

private final List<EntryEditorTab> allPossibleTabs;

Expand Down Expand Up @@ -305,8 +307,13 @@ private List<EntryEditorTab> createTabs() {
tabs.add(new MathSciNetTab());
tabs.add(new FileAnnotationTab(libraryTab.getAnnotationCache()));
tabs.add(new SciteTab(preferences, taskExecutor, dialogService));
tabs.add(new CitationRelationsTab(dialogService, databaseContext,
undoManager, stateManager, fileMonitor, preferences, libraryTab, taskExecutor, bibEntryTypesManager));
tabs.add(new CitationRelationsTab(
dialogService, databaseContext,
undoManager, stateManager,
fileMonitor, preferences,
libraryTab, taskExecutor,
bibEntryTypesManager, searchCitationsRelationsService
));
tabs.add(new RelatedArticlesTab(buildInfo, databaseContext, preferences, dialogService, taskExecutor));
sourceTab = new SourceTab(
databaseContext,
Expand Down

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This file was deleted.

Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,6 @@
import org.jabref.gui.collab.entrychange.PreviewWithSourceTab;
import org.jabref.gui.desktop.os.NativeDesktop;
import org.jabref.gui.entryeditor.EntryEditorTab;
import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.SemanticScholarFetcher;
import org.jabref.gui.icon.IconTheme;
import org.jabref.gui.mergeentries.EntriesMergeResult;
import org.jabref.gui.mergeentries.MergeEntriesDialog;
Expand All @@ -51,8 +49,10 @@
import org.jabref.logic.bibtex.BibEntryWriter;
import org.jabref.logic.bibtex.FieldPreferences;
import org.jabref.logic.bibtex.FieldWriter;
import org.jabref.logic.citation.SearchCitationsRelationsService;
import org.jabref.logic.database.DuplicateCheck;
import org.jabref.logic.exporter.BibWriter;
import org.jabref.logic.importer.fetcher.CitationFetcher;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.os.OS;
import org.jabref.logic.util.BackgroundTask;
Expand Down Expand Up @@ -92,7 +92,7 @@ public class CitationRelationsTab extends EntryEditorTab {
private final GuiPreferences preferences;
private final LibraryTab libraryTab;
private final TaskExecutor taskExecutor;
private final BibEntryRelationsRepository bibEntryRelationsRepository;
private final SearchCitationsRelationsService searchCitationsRelationsService;
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Introduces a service layer that segregates the fetching and repository logic definitions.

private final CitationsRelationsTabViewModel citationsRelationsTabViewModel;
private final DuplicateCheck duplicateCheck;
private final BibEntryTypesManager entryTypesManager;
Expand All @@ -107,7 +107,8 @@ public CitationRelationsTab(DialogService dialogService,
GuiPreferences preferences,
LibraryTab libraryTab,
TaskExecutor taskExecutor,
BibEntryTypesManager bibEntryTypesManager) {
BibEntryTypesManager bibEntryTypesManager,
SearchCitationsRelationsService searchCitationsRelationsService) {
this.dialogService = dialogService;
this.databaseContext = databaseContext;
this.preferences = preferences;
Expand All @@ -121,9 +122,17 @@ public CitationRelationsTab(DialogService dialogService,

this.entryTypesManager = bibEntryTypesManager;
this.duplicateCheck = new DuplicateCheck(entryTypesManager);
this.bibEntryRelationsRepository = new BibEntryRelationsRepository(new SemanticScholarFetcher(preferences.getImporterPreferences()),
new BibEntryRelationsCache());
citationsRelationsTabViewModel = new CitationsRelationsTabViewModel(databaseContext, preferences, undoManager, stateManager, dialogService, fileUpdateMonitor, taskExecutor);
this.searchCitationsRelationsService = searchCitationsRelationsService;

citationsRelationsTabViewModel = new CitationsRelationsTabViewModel(
databaseContext,
preferences,
undoManager,
stateManager,
dialogService,
fileUpdateMonitor,
taskExecutor
);
}

/**
Expand Down Expand Up @@ -199,22 +208,22 @@ private SplitPane getPaneAndStartSearch(BibEntry entry) {

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

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

// Create SplitPane to hold all nodes above
SplitPane container = new SplitPane(citingVBox, citedByVBox);
styleFetchedListView(citedByListView);
styleFetchedListView(citingListView);

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

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

return container;
}
Expand Down Expand Up @@ -410,7 +419,7 @@ protected void bindToEntry(BibEntry entry) {
*/
private void searchForRelations(BibEntry entry, CheckListView<CitationRelationItem> listView, Button abortButton,
Button refreshButton, CitationFetcher.SearchType searchType, Button importButton,
ProgressIndicator progress, boolean shouldRefresh) {
ProgressIndicator progress) {
if (entry.getDOI().isEmpty()) {
hideNodes(abortButton, progress);
showNodes(refreshButton);
Expand All @@ -424,47 +433,59 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt

listView.setItems(observableList);

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

BackgroundTask<List<BibEntry>> task;

if (searchType == CitationFetcher.SearchType.CITES) {
task = BackgroundTask.wrap(() -> {
if (shouldRefresh) {
bibEntryRelationsRepository.forceRefreshReferences(entry);
}
return bibEntryRelationsRepository.getReferences(entry);
});
citingTask = task;
} else {
task = BackgroundTask.wrap(() -> {
if (shouldRefresh) {
bibEntryRelationsRepository.forceRefreshCitations(entry);
}
return bibEntryRelationsRepository.getCitations(entry);
});
citedByTask = task;
}

task.onRunning(() -> prepareToSearchForRelations(abortButton, refreshButton, importButton, progress, task))
.onSuccess(fetchedList -> onSearchForRelationsSucceed(entry, listView, abortButton, refreshButton,
searchType, importButton, progress, fetchedList, observableList))
this.createBackGroundTask(entry, searchType)
.consumeOnRunning(task -> prepareToSearchForRelations(
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Could probably be renamed applyOnRunning(Consumer<Task> consumer).

abortButton, refreshButton, importButton, progress, task
))
.onSuccess(fetchedList -> onSearchForRelationsSucceed(
entry,
listView,
abortButton,
refreshButton,
searchType,
importButton,
progress,
fetchedList,
observableList
))
.onFailure(exception -> {
LOGGER.error("Error while fetching citing Articles", exception);
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citing Articles -> citing articles

just a typo 😃

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@InAnYan This was here before I touched this code. I am leaving this for now in this PR as this out of the scope.

hideNodes(abortButton, progress, importButton);
listView.setPlaceholder(new Label(Localization.lang("Error while fetching citing entries: %0",
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articles or entries? 😅

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@InAnYan This was here before I touched this code. I am leaving this for now in this PR as this out of the scope.

exception.getMessage())));

refreshButton.setVisible(true);
dialogService.notify(exception.getMessage());
})
.executeWith(taskExecutor);
}

/**
* TODO: Make the method return a callable and let the calling method create the background task.
*/
private BackgroundTask<List<BibEntry>> createBackGroundTask(
BibEntry entry, CitationFetcher.SearchType searchType
) {
return switch (searchType) {
case CitationFetcher.SearchType.CITES -> {
citingTask = BackgroundTask.wrap(
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I do not really appreciate this solution. The method should return a Callable instead of BackGroundTask and it should not be possible to restart a search if one is already running for same tab. I propose to refactor this in a next PR but lets focus on the cache refactoring first. For now logic is same as before.

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OK for me.

You can add a TODO comment if you want.

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TODO added. Will see how to enhance the task management after this PR merge.

() -> this.searchCitationsRelationsService.searchReferences(entry)
);
yield citingTask;
}
case CitationFetcher.SearchType.CITED_BY -> {
citedByTask = BackgroundTask.wrap(
() -> this.searchCitationsRelationsService.searchCitations(entry)
);
yield citedByTask;
}
};
}

private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationRelationItem> listView,
Button abortButton, Button refreshButton,
CitationFetcher.SearchType searchType, Button importButton,
Expand All @@ -481,7 +502,7 @@ private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationR
.map(localEntry -> new CitationRelationItem(entr, localEntry, true))
.orElseGet(() -> new CitationRelationItem(entr, false)))
.toList()
);
);

if (!observableList.isEmpty()) {
listView.refresh();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@

import org.jabref.gui.DialogService;
import org.jabref.gui.StateManager;
import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
import org.jabref.gui.externalfiles.ImportHandler;
import org.jabref.gui.preferences.GuiPreferences;
import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
import org.jabref.logic.importer.fetcher.CitationFetcher;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.util.TaskExecutor;
import org.jabref.model.database.BibDatabaseContext;
Expand Down
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