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

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

High level description

This contributions aims to provide a local temporary local storage for citations relations using MVStore. Please see #11189 for more information.

Implementation details

No new dependency added.

Caching strategy

The implemented caching logic is following a 2 levels side-caching strategy with:

an in memory caching level powered by an LRU MAP
a local storage powered by a an h2.mvstore.MVStore

The interaction between the two levels of cache is backed by a responsibility chain pattern. This helps to:

avoid searching on file if the citations/references are already available from RAM
avoid purely technical code to leak into the service layer that should only orchestrate fetching, storing, reading
ease future optimization for each of the levels of caching
should ease change of technologies for this use case in the future

Search high level logic

Check if the fetch is possible: if the cache does not contain anything or if the local storage TTL ran out
If the fetch is possible: fetch and insert into cache (in memory and locally
Read from cache: if the in-memory cache is empty then load from local storage and update update in-memory cache

Serialization

MVStoreDAO uses the canonical representation to serialize a BibEntry and the BibtexParser to deserialize it.

Configuration

the search service is a singleton injected in each new Citations Relations tab using the JabRef IoC provider
the store path is configured to target the citations folder under JabRef's app directory

Setting translation

The the local storage TTL setting message has been traduced in:

DE
FR
EN
PL
IT
BR

Refactoring

This contributions simplifies 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.

Screen shots

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.

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alexandre-cremieux

Add code explanations to the PR

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

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

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

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

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

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

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

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.

…lation-tab-logic # Conflicts: # src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

koppor

In general looks good. Some minor comments.

Sorry for delay. Please go ahead with everything.

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

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

src/test/java/org/jabref/logic/citation/service/SearchCitationsRelationsServiceTest.java

koppor · 2024-10-10T20:31:12Z

Small other comments - IntelliJ proposed to extract a method

private static SearchCitationsRelationsService getSearchCitationsRelationsService(BibEntry cited, List<BibEntry> citationsToReturn, BibEntryRelationsRepository citationsToReturn1) {

in the tests - maybe you can also include that.

koppor · 2024-10-10T20:31:37Z

@alexandre-cremieux Please pull before you continue working on it - I merged main for you (and resolved conflicts).

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

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

alexandre-cremieux · 2024-10-11T21:24:42Z

@alexandre-cremieux Please pull before you continue working on it - I merged main for you (and resolved conflicts).

Thanks for the review and the merge. I will resume the work on this branch and apply the changes.

koppor · 2024-11-08T09:19:45Z

@alexandre-cremieux Sorry for the merge conflicts - can you handle them? I was always happy with IntelliJ's "resolve merge conflicts" dialog. Hope, it works in this case, too.

alexandre-cremieux · 2024-11-08T21:03:04Z

@alexandre-cremieux Sorry for the merge conflicts - can you handle them? I was always happy with IntelliJ's "resolve merge conflicts" dialog. Hope, it works in this case, too.

Hello @koppor . Seems that we have new conflicts to resolve to be able to merge main. But I will do that when the feature will be fully developed. Was quite busy last month, I resumed the work this week. PR comments were addressed.

… exhausted * Remove the isForceUpdate boolean * User is still able to trigger the fetch if an error occurs

alexandre-cremieux · 2024-12-08T21:57:39Z

Code update:

The update will be done automatically after the guard delay of the repo is exhausted
The user is still able to re-trigger the fetch if on error occurs (UX improvement will be done later: Improve "Refresh button" of CSL Preview #12247)

* Instantiate service in JabRefGui * Inject service in EntryEditor

alexandre-cremieux · 2025-01-11T21:26:30Z

Hello @koppor.

Now, only preference for the MV store TTL time is missing. I thought about adding it under Web search preferences like this:

Citation relations search cache time-to-live (in days): [value-here]

Default value would be 7.

It would be added under a new category: Citation relations web search

alexandre-cremieux · 2025-01-20T19:47:33Z

I assume, you are working on "Task 1" of the issue. Thus, I need to file "Task 2" as separate issue?
Task 2 is included here. Just a question: do you want Jabref to automatically fetch citations relations after 7 days since last search even if citations are referenced in the store ? (I guess you are asking that because of the cited by list).

Think, we need this configurable. With a higher default value. Maybe 30 days? - And also disable the feature by default.

Hello @koppor

Could you please help me a bit here ?

The single missing part is the configuration that you asked for in December. Could you please explain me how to implement this: new tab in Preferences or adding it into existing one (like Web search), naming of the parameter for the user, what about the localization, etc ?

Otherwise, could you please let me know if I misunderstood something ?

Thank in advance

…lation-tab-logic

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alexandre-cremieux

Answered comments.

alexandre-cremieux · 2025-01-20T21:44:10Z

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

+                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",


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

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

alexandre-cremieux · 2025-01-20T21:54:47Z

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

+                LOGGER.error("Error while fetching citations for entry {}", cited.getTitle(), e);
+            }
+        }
+        return this.relationsRepository.readCitations(cited);


It depends. Normally:

If the store was empty and nothing was fetch in any case (empty fetch, or error) then yes => empty list

If the store was not empty and nothing was fetch after a successful fetch => the store will be erased and the returned collection will be empty

If the store was not empty and an error occurs while fetching => will return the content of the store

alexandre-cremieux · 2025-01-20T22:01:57Z

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

+    MVStoreBibEntryRelationDAO(Path path, String mapName) {
+        this.mapName = mapName;
+        this.insertionTimeStampMapName = mapName + "-insertion-timestamp";
+        this.storeConfiguration = new MVStore.Builder().autoCommitDisabled().fileName(path.toAbsolutePath().toString());


Thank, me also usually. Hopefully, it is a proof that I am not yet a machine 🤖 😄 🌹

alexandre-cremieux · 2025-01-20T22:02:07Z

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

+
+    MVStoreBibEntryRelationDAO(Path path, String mapName) {
+        this.mapName = mapName;
+        this.insertionTimeStampMapName = mapName + "-insertion-timestamp";


alexandre-cremieux · 2025-01-20T22:30:00Z

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

+            .orElse(true);
+    }
+
+    private static class BibEntrySerializer extends BasicDataType<BibEntry> {


Hello @InAnYan,

Please do not take this comment in account. You were right, ad-hoc serialization does not seem to be necessary. It should possible to apply existing logic provided by BibDatabaseWriter' and 'BibTexParser classes.

~~This is the complicated part:~~

The BibEntry is used here in fact not to represent BibEntry but something else, a citation/reference fetched from SemanticsScholar's API. The output of the API is not a BibEntry, but a Citation or a Reference and the fetcher (JabRef) convert it to BibEntry. A BibEntry is larger in memory than a citation/reference. So to avoid using more space than needed the serializer is adapted to this use case.

~~Also, until the Citation/Reference is inserted into the bib, the user does not have access to as much information than for a BibEntry accessible from a bib, or even cannot edit it.~~

I had this discussion with @koppor. I proposed to change the type of the Citation/Reference to something else and only transform it into a BibEntry when necessary (search or insertion into the bib). I thought it would simplify the code but it seems that this is not really needed.

~~Why did I propose those changes: (all the discussion is in the PR)~~

* Managing citations/references in this context is another domain than managing a BibEntry
* Interpreting DDD here (sorry, sometimes I am dogmatic), as it is not the same domain then it seems normal to not use the same model (as we are not representing the same thing)
* Avoiding mixing the concerns between citation/relation could (maybe should) reduce the ramp-up for the developer on this use case in the future
* Managing duplicates in the citations/relations stores would be easier from my point of view because it would only rely on the DOI for equality tests (I am saying this but maybe it is already the case with BibEntry ?!?) - with another model you can decide to switch to a more suitable ID (as DDD encourage it).

I let you see with @koppor. I am still willing to do those changes: create a specific model for citations/references and use this one for fetching, storage, and view in citations tabs. But convert it to BibEntry only when needed (search/insertion from/into the bib).

~~However, if you have a plan that implies to store it as a full BibEntry then please let me know and please indicate me where to find the proper serializer (so I do not re-invent the wheel).~~

alexandre-cremieux · 2025-01-20T22:30:48Z

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

+        private static String toString(BibEntry entry) {
+            return String.join(
+                FIELD_SEPARATOR,
+                entry.getTitle().orElse("null"),


Than "null" would be serialized (and deserialized).

alexandre-cremieux · 2025-01-20T22:31:31Z

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

+        private static BibEntry fromString(String serializedString) {
+            var fields = serializedString.split(FIELD_SEPARATOR);
+            BibEntry entry = new BibEntry();
+            extractFieldValue(fields[0]).ifPresent(title -> entry.setField(StandardField.TITLE, title));


Because there are the only ones available for a citations or reference.

alexandre-cremieux · 2025-01-20T22:48:27Z

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

+                progress,
+                fetchedList,
+                observableList
+            ))
            .onFailure(exception -> {
                LOGGER.error("Error while fetching citing Articles", exception);


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

alexandre-cremieux · 2025-01-25T18:53:34Z

Still missing:

Correcting the MVStore serialization using serialization tool already implemented by JabRef
Describe code addition in CHANGELOG.MD

alexandre-cremieux · 2025-01-25T20:42:57Z

TODO here:

add description in CHANGELOG.MD
update PR description

After this, the PR should be ready for last review.

…#11189)

…lation-tab-logic

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Please carefully follow the setup guide for the codestyle.
Afterwards, please run checkstyle locally and fix the issues.

In case of issues with the import order, double check that you activated Auto Import.
You can trigger fixing imports by pressing Ctrl+Alt+O to trigger Optimize Imports.

…arsing error (JabRef#11189)

…erialization error (JabRef#11189)

alexandre-cremieux · 2025-01-27T18:08:39Z

Ready for review. Normally everything should be there.

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 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

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Implement caching for citation relations #11189

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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

Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…

0e9de3c

…lation-tab-logic # Conflicts: # src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

koppor requested changes Oct 10, 2024

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koppor marked this pull request as ready for review October 10, 2024 20:29

InAnYan requested changes Oct 11, 2024

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Address PR comments (JabRef#11901)

9a31735

Make the citation relations update automatic after the guard delay is…

187b5d4

… exhausted * Remove the isForceUpdate boolean * User is still able to trigger the fetch if an error occurs

SearchCitationsRelationsService as singleton

b71d9fc

* Instantiate service in JabRefGui * Inject service in EntryEditor

Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…

dda21ed

…lation-tab-logic

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Update failing tests after merge

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Clean code style according to checkstyle

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alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 32aa56a to 4956095 Compare January 20, 2025 21:20

Clean code style according to checkstyle

ea36f1a

alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from 4956095 to ea36f1a Compare January 20, 2025 21:24

Fix pending PR comments

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Alexandre CREMIEUX added 2 commits January 22, 2025 20:52

Fix null pointer exception in CitationsRelationsTab

97b38c6

Add settings for Citations relations store TTL

54e7e21

Update MVStoreBibEntryRelationDAO serializer/deserializer

6415b1b

Alexandre CREMIEUX added 2 commits January 26, 2025 21:25

Update CHANGELOG-MD for Citations relations tab caching logic (JabRef…

e18d557

…#11189)

Merge branch 'main' into fix-issue-11189-part-00-refactor-citation-re…

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…lation-tab-logic

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alexandre-cremieux requested review from koppor and InAnYan January 26, 2025 21:30

Return an empty BibEntry from MVStoreBibEntryRelationDAO in case of p…

16cfd2c

…arsing error (JabRef#11189)

alexandre-cremieux force-pushed the fix-issue-11189-part-00-refactor-citation-relation-tab-logic branch from e56497e to 16cfd2c Compare January 26, 2025 21:32

Add a test to ensure that an empty list is returned from in case of s…

33f5cdf

…erialization error (JabRef#11189)

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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

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

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High level description

Implementation details

Caching strategy

Search high level logic

Serialization

Configuration

Setting translation

Refactoring

Screen shots

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