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

alexandre-cremieux · 2024-09-28T20:38:04Z

This contributions aims to simplify the citations/references fetching and caching logic by introducing two layers:

service
repository

This should help to make this feature more extendable without modifying orchestration logic following open/close principle.

Also, this PR will allow to introduce a new caching logic in coming PR.

Missing requirements for merging will come after draft review.

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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.

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We use OpenRewrite to ensure "modern" Java coding practices.
The issues found can be automatically fixed.
Please execute the gradle task rewriteRun, check the results, commit, and push.

You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".

alexandre-cremieux

Add code explanations to the PR

alexandre-cremieux · 2024-09-29T10:36:10Z

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/BibEntryRelationsCache.java

-
-import org.eclipse.jgit.util.LRUMap;
-
-public class BibEntryRelationsCache {


Renamed and tested. Also, we were not merging the relations but overwriting them when cacheOrMerge... was called (see code and fix).

alexandre-cremieux · 2024-09-29T10:36:42Z

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/BibEntryRelationsRepository.java

-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class BibEntryRelationsRepository {


Renamed and tested.

alexandre-cremieux · 2024-09-29T10:38:23Z

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

@@ -71,7 +74,7 @@ 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;


Introduces a service layer that segregates the fetching and repository logic definitions.

alexandre-cremieux · 2024-09-29T10:45:01Z

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

-            .onSuccess(fetchedList -> onSearchForRelationsSucceed(entry, listView, abortButton, refreshButton,
-                    searchType, importButton, progress, fetchedList, observableList))
+        this.createBackGroundTask(entry, searchType, shouldRefresh)
+            .consumeOnRunning(task -> prepareToSearchForRelations(


Could probably be renamed applyOnRunning(Consumer<Task> consumer).

alexandre-cremieux · 2024-09-29T13:28:36Z

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

+    ) {
+        return switch (searchType) {
+            case CitationFetcher.SearchType.CITES -> {
+                citingTask = BackgroundTask.wrap(


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.

alexandre-cremieux · 2024-09-29T13:30:22Z

src/main/java/org/jabref/logic/citation/repository/LRUBibEntryRelationsCache.java

+    private static final Map<DOI, Set<BibEntry>> REFERENCES_MAP = new LRUMap<>(MAX_CACHED_ENTRIES, MAX_CACHED_ENTRIES);
+
+    public List<BibEntry> getCitations(BibEntry entry) {
+        return entry


Returns a copy now.

alexandre-cremieux · 2024-09-29T13:31:38Z

src/main/java/org/jabref/logic/citation/repository/LRUBibEntryRelationsCache.java

+            .toList();
+    }
+
+    public void cacheOrMergeCitations(BibEntry entry, List<BibEntry> citations) {


Method used to rewrite data, now it does merge inputs according the method name.

alexandre-cremieux · 2024-09-29T13:32:19Z

src/main/java/org/jabref/logic/citation/repository/LRUBibEntryRelationsRepository.java

+
+import org.jabref.model.entry.BibEntry;
+
+public class LRUBibEntryRelationsRepository implements BibEntryRelationsRepository {


Removed the fetcher logic from previous implementation.

alexandre-cremieux · 2024-09-29T13:35:21Z

src/main/java/org/jabref/logic/importer/fetcher/CitationFetcher.java

@@ -1,4 +1,4 @@
-package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
+package org.jabref.logic.importer.fetcher;


Move this to the logic package, Fecthing is more like a back-end process - should belong to an adapter layer.

alexandre-cremieux · 2024-09-29T13:40:03Z

src/main/java/org/jabref/logic/citation/service/SearchCitationsRelationsService.java

+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class SearchCitationsRelationsService {


Fetching and Repository logic can now be injected in orchestration logic that should not vary in next PR.

This should also make it possible to configure a citation search service based on the execution context. This approach can also enable new features like offering the user the possibility to choose between multiple fetchers targeting another online search engine.

Siedlerchr · 2024-09-29T14:19:32Z

Please no force push if not needed. All commits will be squashed when merged

* Move repository, cache, and fetcher to logic package * Move citations model to model/citations/semanticscholar package

* Introduce service layer * Rename LRU cache implementation * Add tests helpers for repository

* Move logic from repository to service * Refactor repositories * Update tab configuration

alexandre-cremieux · 2024-09-29T15:02:44Z

Please no force push if not needed. All commits will be squashed when merged

Sorry, just re-based main branch locally.

alexandre-cremieux marked this pull request as draft September 28, 2024 20:38

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alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 9fe8522 to cbe9e96 Compare September 28, 2024 21:15

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alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from cbe9e96 to 8231340 Compare September 28, 2024 21:51

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alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 8231340 to 33967c2 Compare September 28, 2024 22:20

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alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 33967c2 to 592d4d7 Compare September 28, 2024 22:47

koppor changed the title ~~Fix issue 11189 part 00 refactor citation relation tab logic~~ Fix issue #11189 part 00 refactor citation relation tab logic Sep 29, 2024

alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch 2 times, most recently from d94f4d3 to 3155242 Compare September 29, 2024 13:24

alexandre-cremieux commented Sep 29, 2024

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alexandre-cremieux mentioned this pull request Sep 29, 2024

Implement caching for citation relations #11189

Open

alexandre-cremieux added 3 commits September 29, 2024 17:00

Refactor Citations Relations Tab (JabRef#11189)

3785cb1

* Move repository, cache, and fetcher to logic package * Move citations model to model/citations/semanticscholar package

Refactor Citations Relations Tab (JabRef#11189)

8048da8

* Introduce service layer * Rename LRU cache implementation * Add tests helpers for repository

Refactor Citations Relations Service Layer (JabRef#11189)

18db75e

* Move logic from repository to service * Refactor repositories * Update tab configuration

alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 3155242 to 18db75e Compare September 29, 2024 15:01

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

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

alexandre-cremieux commented Sep 28, 2024 •

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Siedlerchr commented Sep 29, 2024

alexandre-cremieux commented Sep 29, 2024


		import org.eclipse.jgit.util.LRUMap;

		public class BibEntryRelationsCache {


		import org.jabref.model.entry.BibEntry;

		public class LRUBibEntryRelationsRepository implements BibEntryRelationsRepository {

		@@ -1,4 +1,4 @@
		package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
		package org.jabref.logic.importer.fetcher;

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

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alexandre-cremieux commented Sep 28, 2024 • edited Loading

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Siedlerchr commented Sep 29, 2024

alexandre-cremieux commented Sep 29, 2024

alexandre-cremieux commented Sep 28, 2024 •

edited

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