Enable the exploration of bib entries' relations (cited by and citing) by HoussemNasri · Pull Request #10324 · JabRef/jabref

HoussemNasri · 2023-09-04T21:46:59Z

A continuation to #7160.

Known Limitations

Related entries cached in-memory; should be on disk.
Relations are fetched exclusively based on the entry's DOI (SemantciScholar allows the usage of other types of ids .e.g. URL, ARXIV, PMID, etc.
No pagination

Screenshots

Mandatory checks

Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

Co-authored-by: Tim Bachmann <58782027+timbachmann@users.noreply.github.com> Co-authored-by: Raphael Kreft <r.kreft@unibas.ch> Co-authored-by: Marcel Luethi <marcel.luethi@unibas.ch> Co-authored-by: olivierM <olivier.mattmann@stud.unibas.ch> Co-authored-by: matiascg <matiascargon@hotmail.com>

- Until we implement pagination, fetching 1000 citations/references seems fine.

github-actions · 2023-09-04T21:50:44Z

Your code currently does not meet JabRef's code guidelines. The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR. Please carefully follow the setup guide for the codestyle. Afterwards, please run checkstyle locally and fix the issues.

More information on code quality in JabRef is available at https://devdocs.jabref.org/getting-into-the-code/development-strategy.html.

ghost · 2023-09-04T21:58:00Z

Can I ask: is this the same as this request I made some time ago?
#10200

HoussemNasri · 2023-09-04T22:26:09Z

@the-dino-girl It's similar to that, but the references we get from a public web API (similar to how fetchers work). It's also possible to get bib entries that cites the selected entry. It's under the "cited by" section.

ghost · 2023-09-04T23:37:01Z

Can't wait for this feature!
I will extensively test it and report bugs (if any)

(Please add new translation strings if they are missing. I'm a jabref translator)

😍😍😍

koppor · 2023-09-05T19:50:07Z

Can't wait for this feature! I will extensively test it and report bugs (if any)

You can download the current build at https://builds.jabref.org/pull/10324/merge and report issues here.

(This is what the comment #10324 (comment) means -- grab the binary and play around with it)

github-actions · 2023-09-06T18:56:59Z

The build for this PR is no longer available. Please visit https://builds.jabref.org/main/ for the latest build.

Siedlerchr · 2023-09-07T16:10:13Z

+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.identifier.DOI;
+
+public class BibEntryRelationsCache {


For the moment this is okay, but we could store it in MV files as well or use something like caffeeine https://medium.com/outbrain-engineering/oh-my-guava-we-are-moving-to-caffeine-99387819fdbb

We already have a dependency on h2 MVStore, we could use that.

Yes, like the journal abbreviation stuff. Write the stuff to a db int he user's app data dir

Siedlerchr · 2023-09-07T16:13:40Z

Cool feature! Need to try this!

calixtus · 2023-09-10T15:40:35Z

+    /**
+     * Method to start search for relations and display them in the associated ListView
+     *
+     * @param entry         BibEntry currently selected in Jabref Database
+     * @param listView      ListView to use
+     * @param abortButton         Button to stop the search
+     * @param refreshButton refresh Button to use
+     * @param searchType    type of search (CITING / CITEDBY)
+     */
+    private void searchForRelations(BibEntry entry, CheckListView<CitationRelationItem> listView, Button abortButton,
+                                    Button refreshButton, CitationFetcher.SearchType searchType, Button importButton,
+                                    ProgressIndicator progress, boolean shouldRefresh) {
+        if (entry.getDOI().isEmpty()) {
+            hideNodes(abortButton, progress);
+            showNodes(refreshButton);
+            listView.getItems().clear();
+            listView.setPlaceholder(
+                    new Label(Localization.lang("The selected entry doesn't have a DOI linked to it. Lookup a DOI and try again.")));
+            return;
+        }
+
+        ObservableList<CitationRelationItem> observableList = FXCollections.observableArrayList();
+
+        listView.setItems(observableList);
+
+        if (citingTask != null && !citingTask.isCanceled() && searchType.equals(CitationFetcher.SearchType.CITING)) {
+            citingTask.cancel();
+        } else if (citedByTask != null && !citedByTask.isCanceled() && searchType.equals(CitationFetcher.SearchType.CITED_BY)) {
+            citedByTask.cancel();
+        }
+
+        BackgroundTask<List<BibEntry>> task;
+
+        if (searchType.equals(CitationFetcher.SearchType.CITING)) {
+            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))
+                .onFailure(exception -> {
+                    LOGGER.error("Error while fetching citing Articles", exception);
+                    hideNodes(abortButton, progress, importButton);
+                    listView.setPlaceholder(new Label(Localization.lang("Error while fetching citing entries: %0",
+                            exception.getMessage())));
+
+                    refreshButton.setVisible(true);
+                    dialogService.notify(exception.getMessage());
+                })
+                .executeWith(Globals.TASK_EXECUTOR);
+    }
+
+    private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationRelationItem> listView,
+                                             Button abortButton, Button refreshButton,
+                                             CitationFetcher.SearchType searchType, Button importButton,
+                                             ProgressIndicator progress, List<BibEntry> fetchedList,
+                                             ObservableList<CitationRelationItem> observableList) {
+        hideNodes(abortButton, progress);
+
+        observableList.setAll(fetchedList.stream().map(entr -> new CitationRelationItem(entr, false))
+                .collect(Collectors.toList()));
+
+        if (!observableList.isEmpty()) {
+            listView.refresh();
+        } else {
+            Label placeholder = new Label(Localization.lang("No articles found"));
+            listView.setPlaceholder(placeholder);
+        }
+        BooleanBinding booleanBind = Bindings.isEmpty(listView.getCheckModel().getCheckedItems());
+        importButton.disableProperty().bind(booleanBind);
+        importButton.setOnMouseClicked(event -> importEntries(listView.getCheckModel().getCheckedItems(), searchType, entry));
+        showNodes(refreshButton, importButton);
+    }
+
+    private void prepareToSearchForRelations(Button abortButton, Button refreshButton, Button importButton,
+                                             ProgressIndicator progress, BackgroundTask<List<BibEntry>> task) {
+        showNodes(abortButton, progress);
+        hideNodes(refreshButton, importButton);
+
+        abortButton.setOnAction(event -> {
+            hideNodes(abortButton, progress, importButton);
+            showNodes(refreshButton);
+            task.cancel();
+            dialogService.notify(Localization.lang("Search aborted!"));
+        });
+    }
+
+    private void hideNodes(Node... nodes) {
+        Arrays.stream(nodes).forEach(node -> node.setVisible(false));
+    }
+
+    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
+     *
+     * @param entriesToImport entries to import
+     */
+    private void importEntries(List<CitationRelationItem> entriesToImport, CitationFetcher.SearchType searchType, BibEntry entry) {
+        citingTask.cancel();
+        citedByTask.cancel();
+        List<BibEntry> entries = entriesToImport.stream().map(CitationRelationItem::getEntry).collect(Collectors.toList());
+        ImportHandler importHandler = new ImportHandler(
+                databaseContext,
+                preferencesService,
+                fileUpdateMonitor,
+                undoManager,
+                stateManager,
+                dialogService,
+                Globals.TASK_EXECUTOR);
+        importHandler.importEntries(entries);
+
+        dialogService.notify(Localization.lang("Number of entries successfully imported") + ": " + entriesToImport.size());
+    }


I have the strong suspicion, that some of this code belongs into a ViewModel

It surely does, but I thought we release the feature now letting users try it out and do some refactoring while working on the known limitations in later PRs.

ok, im fine with that. let ua just not forget about this, maybe an issue in the maintainers focus or sthg

koppor

Thank you for working on this!

We fixed the openrewrite complains by running ./gradlew rewriteRun (at 14ecf06 (#10324)).

Will merge as soon as tests are green.

Follow-up issues created (in the melting pot).

Lets see, what the users will tell!

HoussemNasri and others added 5 commits September 4, 2023 00:46

Improve package structure

24be417

Set a higher citations/references results limit per request

64641e8

- Until we implement pagination, fetching 1000 citations/references seems fine.

Cleanup code formatting

de209ab

Remove dead code

96c2d42

github-actions Bot reviewed Sep 4, 2023

View reviewed changes

HoussemNasri changed the title ~~Enable the exploration bib entries' relations (cited by and citing)~~ Enable the exploration of bib entries' relations (cited by and citing) Sep 4, 2023

koppor marked this pull request as draft September 5, 2023 19:50

HoussemNasri added 6 commits September 6, 2023 18:13

Avoid NPE when api returns a null year

9c58159

Display the authors of references and citations

867edd7

Rename package citationrelation to citationrelationtab

8fa2c5a

Add the ability to refresh citations and references

d6507a6

Checkstyle

9f4e5e1

l10n

52b2f0e

HoussemNasri marked this pull request as ready for review September 6, 2023 18:18

HoussemNasri added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Sep 6, 2023

HoussemNasri requested a review from koppor September 6, 2023 18:18

HoussemNasri and others added 2 commits September 6, 2023 19:19

Update CHANGELOG

8f7a334

Merge branch 'main' into citation-relation

3b77ca6

Siedlerchr reviewed Sep 7, 2023

View reviewed changes

Siedlerchr previously approved these changes Sep 7, 2023

View reviewed changes

calixtus reviewed Sep 10, 2023

View reviewed changes

Merge branch 'main' into citation-relation

6d000d4

koppor dismissed Siedlerchr’s stale review via 6d000d4 September 11, 2023 20:44

koppor added 3 commits September 11, 2023 20:58

Result of rewriteRun

14ecf06

Update CHANGELOG.md

86508a0

Merge branch 'main' into citation-relation

140b806

koppor approved these changes Sep 11, 2023

View reviewed changes

koppor merged commit 0c6c0a9 into main Sep 11, 2023

koppor deleted the citation-relation branch September 11, 2023 21:17

koppor mentioned this pull request Jan 9, 2024

Add support to explore citation relation JabRef/jabref-koppor#643

Closed

koppor added the component: citation-relations label Jul 31, 2025

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Known Limitations

Screenshots

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