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Add support for scite.ai (JabRef#10617)
* task: first cut of Scite tab and associated preference * task: comments and minor refactoring * task: Updated readme.md for issue #375 * fix: Import ordering and markdown space * fix: imports and whitespace (checkstyle) * fix: imports and whitespace (checkstyle) * fix: imports and whitespace (checkstyle) * fix: Removed unnecessary parentheses (OpenRewrite) * fix: Unit tests and localisation keys * fix: Removed unnecessary heading in CHANGELOG.md * fix: Made SciteTallyDTO a record type and moved it to new file * fix: Made the scite.ai base url a constant * fix: Exception handling now catches most specific exceptions, and rethrows them as FetcherException * fix: style for scite message box * fix: Catch specific exception and display error message rather than throwing a generic unchecked exception * fix: Localization for SciteTab error messages, and "Scite" name is no longer localized * some small refactoring * checkstyle and rename * Update CHANGELOG.md * Update EntryEditorTab.java * move and checkstyle * fix l10n and rename --------- Co-authored-by: Siedlerchr <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| package org.jabref.gui.entryeditor; | ||
|
|
||
| import java.io.IOException; | ||
| import java.net.URLEncoder; | ||
| import java.nio.charset.StandardCharsets; | ||
|
|
||
| import javafx.geometry.HPos; | ||
| import javafx.scene.control.Hyperlink; | ||
| import javafx.scene.control.Label; | ||
| import javafx.scene.control.ProgressIndicator; | ||
| import javafx.scene.control.Tooltip; | ||
| import javafx.scene.layout.ColumnConstraints; | ||
| import javafx.scene.layout.GridPane; | ||
| import javafx.scene.layout.VBox; | ||
| import javafx.scene.text.Text; | ||
|
|
||
| import org.jabref.gui.DialogService; | ||
| import org.jabref.gui.desktop.JabRefDesktop; | ||
| import org.jabref.gui.util.TaskExecutor; | ||
| import org.jabref.logic.l10n.Localization; | ||
| import org.jabref.model.entry.BibEntry; | ||
| import org.jabref.preferences.PreferencesService; | ||
|
|
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| import com.tobiasdiez.easybind.EasyBind; | ||
| import org.controlsfx.control.HyperlinkLabel; | ||
|
|
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| public class SciteTab extends EntryEditorTab { | ||
|
|
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| public static final String NAME = "Scite"; | ||
| public static final String SCITE_REPORTS_URL_BASE = "https://scite.ai/reports/"; | ||
|
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| private final GridPane sciteResultsPane; | ||
| private final ProgressIndicator progressIndicator; | ||
| private final SciteTabViewModel viewModel; | ||
| private final PreferencesService preferencesService; | ||
| private final DialogService dialogService; | ||
|
|
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| public SciteTab(PreferencesService preferencesService, TaskExecutor taskExecutor, DialogService dialogService) { | ||
| this.preferencesService = preferencesService; | ||
| this.viewModel = new SciteTabViewModel(preferencesService, taskExecutor); | ||
| this.dialogService = dialogService; | ||
| this.sciteResultsPane = new GridPane(); | ||
| this.progressIndicator = new ProgressIndicator(); | ||
| setText(NAME); | ||
| setTooltip(new Tooltip(Localization.lang("Search scite.ai for Smart Citations"))); | ||
| setSciteResultsPane(); | ||
| } | ||
|
|
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| private void setSciteResultsPane() { | ||
| progressIndicator.setMaxSize(100, 100); | ||
| sciteResultsPane.add(progressIndicator, 0, 0); | ||
|
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| ColumnConstraints column = new ColumnConstraints(); | ||
| column.setPercentWidth(100); | ||
| column.setHalignment(HPos.CENTER); | ||
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| sciteResultsPane.getColumnConstraints().setAll(column); | ||
| sciteResultsPane.setId("scitePane"); | ||
| setContent(sciteResultsPane); | ||
|
|
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| EasyBind.subscribe(viewModel.statusProperty(), status -> { | ||
| sciteResultsPane.getChildren().clear(); | ||
| switch (status) { | ||
| case IN_PROGRESS -> | ||
| sciteResultsPane.add(progressIndicator, 0, 0); | ||
| case FOUND -> | ||
| viewModel.getCurrentResult().ifPresent(result -> sciteResultsPane.add(getTalliesPane(result), 0, 0)); | ||
| case ERROR -> | ||
| sciteResultsPane.add(getErrorPane(), 0, 0); | ||
| } | ||
| }); | ||
| } | ||
|
|
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| @Override | ||
| public boolean shouldShow(BibEntry entry) { | ||
| return viewModel.shouldShow(); | ||
| } | ||
|
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| @Override | ||
| protected void bindToEntry(BibEntry entry) { | ||
| viewModel.bindToEntry(entry); | ||
| } | ||
|
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| private VBox getErrorPane() { | ||
| Label titleLabel = new Label(Localization.lang("Error")); | ||
| titleLabel.getStyleClass().add("scite-error-label"); | ||
| Text errorMessageText = new Text(viewModel.searchErrorProperty().get()); | ||
| VBox errorMessageBox = new VBox(30, titleLabel, errorMessageText); | ||
| errorMessageBox.getStyleClass().add("scite-error-box"); | ||
| return errorMessageBox; | ||
| } | ||
|
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| private VBox getTalliesPane(SciteTallyModel tallModel) { | ||
| Label titleLabel = new Label(Localization.lang("Tallies for %0", tallModel.doi())); | ||
| titleLabel.getStyleClass().add("scite-tallies-label"); | ||
| Text message = new Text(String.format("Total Citations: %d\nSupporting: %d\nContradicting: %d\nMentioning: %d\nUnclassified: %d\nCiting Publications: %d", | ||
| tallModel.total(), | ||
| tallModel.supporting(), | ||
| tallModel.contradicting(), | ||
| tallModel.mentioning(), | ||
| tallModel.unclassified(), | ||
| tallModel.citingPublications() | ||
| )); | ||
|
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| String url = SCITE_REPORTS_URL_BASE + URLEncoder.encode(tallModel.doi(), StandardCharsets.UTF_8); | ||
| VBox messageBox = getMessageBox(url, titleLabel, message); | ||
| messageBox.getStyleClass().add("scite-message-box"); | ||
| return messageBox; | ||
| } | ||
|
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| private VBox getMessageBox(String url, Label titleLabel, Text message) { | ||
| HyperlinkLabel link = new HyperlinkLabel(Localization.lang("See full report at [%0]", url)); | ||
| link.setOnAction(event -> { | ||
| if (event.getSource() instanceof Hyperlink) { | ||
| var filePreferences = preferencesService.getFilePreferences(); | ||
| try { | ||
| JabRefDesktop.openBrowser(url, filePreferences); | ||
| } catch (IOException ioex) { | ||
| // Can't throw a checked exception from here, so display a message to the user instead. | ||
| dialogService.showErrorDialogAndWait( | ||
| "An error occurred opening web browser", | ||
| "JabRef was unable to open a web browser for link:\n\n" + url + "\n\nError Message:\n\n" + ioex.getMessage(), | ||
| ioex | ||
| ); | ||
| } | ||
| } | ||
| }); | ||
|
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||
| return new VBox(30, titleLabel, message, link); | ||
| } | ||
| } |
131 changes: 131 additions & 0 deletions
131
src/main/java/org/jabref/gui/entryeditor/SciteTabViewModel.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,131 @@ | ||
| package org.jabref.gui.entryeditor; | ||
|
|
||
| import java.io.IOException; | ||
| import java.net.MalformedURLException; | ||
| import java.net.URI; | ||
| import java.net.URISyntaxException; | ||
| import java.net.URL; | ||
| import java.util.Optional; | ||
| import java.util.concurrent.Future; | ||
|
|
||
| import javafx.beans.property.ObjectProperty; | ||
| import javafx.beans.property.SimpleObjectProperty; | ||
| import javafx.beans.property.SimpleStringProperty; | ||
| import javafx.beans.property.StringProperty; | ||
|
|
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| import org.jabref.gui.AbstractViewModel; | ||
| import org.jabref.gui.util.BackgroundTask; | ||
| import org.jabref.gui.util.TaskExecutor; | ||
| import org.jabref.logic.importer.FetcherException; | ||
| import org.jabref.logic.l10n.Localization; | ||
| import org.jabref.logic.net.URLDownload; | ||
| import org.jabref.model.entry.BibEntry; | ||
| import org.jabref.model.entry.identifier.DOI; | ||
| import org.jabref.preferences.PreferencesService; | ||
|
|
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| import kong.unirest.json.JSONObject; | ||
| import org.tinylog.Logger; | ||
|
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| public class SciteTabViewModel extends AbstractViewModel { | ||
|
|
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| /** | ||
| * Status enum for Scite tab | ||
| */ | ||
| public enum SciteStatus { | ||
| IN_PROGRESS, | ||
| FOUND, | ||
| ERROR | ||
| } | ||
|
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| private static final String BASE_URL = "https://api.scite.ai/"; | ||
| private final PreferencesService preferencesService; | ||
| private final TaskExecutor taskExecutor; | ||
| private final ObjectProperty<SciteStatus> status; | ||
| private final StringProperty searchError; | ||
| private Optional<SciteTallyModel> currentResult = Optional.empty(); | ||
|
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| private Future<?> searchTask; | ||
|
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| public SciteTabViewModel(PreferencesService preferencesService, TaskExecutor taskExecutor) { | ||
| this.preferencesService = preferencesService; | ||
| this.taskExecutor = taskExecutor; | ||
| this.status = new SimpleObjectProperty<>(SciteStatus.IN_PROGRESS); | ||
| this.searchError = new SimpleStringProperty(""); | ||
| } | ||
|
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| public boolean shouldShow() { | ||
| return preferencesService.getEntryEditorPreferences().shouldShowSciteTab(); | ||
| } | ||
|
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| public void bindToEntry(BibEntry entry) { | ||
| // If a search is already running, cancel it | ||
| cancelSearch(); | ||
|
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| if (entry == null) { | ||
| searchError.set(Localization.lang("No active entry")); | ||
| status.set(SciteStatus.ERROR); | ||
| return; | ||
| } | ||
|
|
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| // The scite.ai api requires a DOI | ||
| if (entry.getDOI().isEmpty()) { | ||
| searchError.set(Localization.lang("This entry does not have a DOI")); | ||
| status.set(SciteStatus.ERROR); | ||
| return; | ||
| } | ||
|
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| searchTask = BackgroundTask.wrap(() -> fetchTallies(entry.getDOI().get())) | ||
| .onRunning(() -> status.set(SciteStatus.IN_PROGRESS)) | ||
| .onSuccess(result -> { | ||
| currentResult = Optional.of(result); | ||
| status.set(SciteStatus.FOUND); | ||
| }) | ||
| .onFailure(error -> { | ||
| searchError.set(error.getMessage()); | ||
| status.set(SciteStatus.ERROR); | ||
| }) | ||
| .executeWith(taskExecutor); | ||
| } | ||
|
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| private void cancelSearch() { | ||
| if (searchTask == null || searchTask.isCancelled() || searchTask.isDone()) { | ||
| return; | ||
| } | ||
|
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| status.set(SciteStatus.IN_PROGRESS); | ||
| searchTask.cancel(true); | ||
| } | ||
|
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| public SciteTallyModel fetchTallies(DOI doi) throws FetcherException { | ||
| try { | ||
| URL url = new URI(BASE_URL + "tallies/" + doi.getDOI()).toURL(); | ||
| URLDownload download = new URLDownload(url); | ||
| String response = download.asString(); | ||
| Logger.debug("Response {}", response); | ||
| JSONObject tallies = new JSONObject(response); | ||
| if (tallies.has("detail")) { | ||
| String message = tallies.getString("detail"); | ||
| throw new FetcherException(message); | ||
| } else if (!tallies.has("total")) { | ||
| throw new FetcherException("Unexpected result data!"); | ||
| } | ||
| return SciteTallyModel.fromJSONObject(tallies); | ||
| } catch (MalformedURLException | URISyntaxException ex) { | ||
| throw new FetcherException("Malformed url for DOs", ex); | ||
| } catch (IOException ioex) { | ||
| throw new FetcherException("Failed to retrieve tallies for DOI - IO Exception", ioex); | ||
| } | ||
| } | ||
|
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| public ObjectProperty<SciteStatus> statusProperty() { | ||
| return status; | ||
| } | ||
|
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| public StringProperty searchErrorProperty() { | ||
| return searchError; | ||
| } | ||
|
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| public Optional<SciteTallyModel> getCurrentResult() { | ||
| return currentResult; | ||
| } | ||
| } |
34 changes: 34 additions & 0 deletions
34
src/main/java/org/jabref/gui/entryeditor/SciteTallyModel.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| package org.jabref.gui.entryeditor; | ||
|
|
||
| import kong.unirest.json.JSONObject; | ||
|
|
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| /** | ||
| * Simple model object to hold the scite.ai tallies data for a given DOI | ||
| */ | ||
| public record SciteTallyModel( | ||
| String doi, | ||
| int total, | ||
| int supporting, | ||
| int contradicting, | ||
| int mentioning, | ||
| int unclassified, | ||
| int citingPublications) { | ||
|
|
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| /** | ||
| * Creates a {@link SciteTallyModel} from a JSONObject (dictionary/map) | ||
| * | ||
| * @param jsonObject The JSON object holding the tally values | ||
| * @return a new {@link SciteTallyModel} | ||
| */ | ||
| public static SciteTallyModel fromJSONObject(JSONObject jsonObject) { | ||
| return new SciteTallyModel( | ||
| jsonObject.getString("doi"), | ||
| jsonObject.getInt("total"), | ||
| jsonObject.getInt("supporting"), | ||
| jsonObject.getInt("contradicting"), | ||
| jsonObject.getInt("mentioning"), | ||
| jsonObject.getInt("unclassified"), | ||
| jsonObject.getInt("citingPublications") | ||
| ); | ||
| } | ||
| } |
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