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Refactor Citations Relations Service Layer (#11189)
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* Move logic from repository to service
* Refactor repositories
* Update tab configuration
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@alexandre-cremieux
alexandre-cremieux committed Sep 28, 2024
1 parent f603c78 commit 9fe8522
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Showing 11 changed files with 499 additions and 330 deletions.
89 changes: 57 additions & 32 deletions src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java
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Expand Up @@ -30,8 +30,9 @@
import org.jabref.gui.StateManager;
import org.jabref.gui.desktop.os.NativeDesktop;
import org.jabref.gui.entryeditor.EntryEditorTab;
import org.jabref.logic.citation.repository.BibEntryRelationsCache;
import org.jabref.logic.citation.repository.BibEntryRelationsRepository;
import org.jabref.logic.citation.repository.LRUBibEntryRelationsCache;
import org.jabref.logic.citation.repository.LRUBibEntryRelationsRepository;
import org.jabref.logic.citation.service.SearchCitationsRelationsService;
import org.jabref.logic.importer.fetcher.CitationFetcher;
import org.jabref.logic.importer.fetcher.SemanticScholarCitationFetcher;
import org.jabref.gui.icon.IconTheme;
Expand Down Expand Up @@ -73,7 +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;
private final CitationsRelationsTabViewModel citationsRelationsTabViewModel;
private final DuplicateCheck duplicateCheck;

Expand All @@ -94,11 +95,22 @@ public CitationRelationsTab(DialogService dialogService,
setTooltip(new Tooltip(Localization.lang("Show articles related by citation")));

this.duplicateCheck = new DuplicateCheck(new BibEntryTypesManager());
this.bibEntryRelationsRepository = new BibEntryRelationsRepository(
var bibEntryRelationsRepository = new LRUBibEntryRelationsRepository(
new LRUBibEntryRelationsCache()
);
this.searchCitationsRelationsService = new SearchCitationsRelationsService(
new SemanticScholarCitationFetcher(preferences.getImporterPreferences()),
new BibEntryRelationsCache()
bibEntryRelationsRepository
);
citationsRelationsTabViewModel = new CitationsRelationsTabViewModel(
databaseContext,
preferences,
undoManager,
stateManager,
dialogService,
fileUpdateMonitor,
taskExecutor
);
citationsRelationsTabViewModel = new CitationsRelationsTabViewModel(databaseContext, preferences, undoManager, stateManager, dialogService, fileUpdateMonitor, taskExecutor);
}

/**
Expand Down Expand Up @@ -347,41 +359,54 @@ private void searchForRelations(BibEntry entry, CheckListView<CitationRelationIt
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, shouldRefresh)
.consumeOnRunning(task -> 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())));

listView.setPlaceholder(
new Label(Localization.lang(
"Error while fetching citing entries: %0", exception.getMessage())
)
);
refreshButton.setVisible(true);
dialogService.notify(exception.getMessage());
})
.executeWith(taskExecutor);
}

private BackgroundTask<List<BibEntry>> createBackGroundTask(
BibEntry entry, CitationFetcher.SearchType searchType, boolean shouldRefresh
) {
return switch(searchType) {
case CitationFetcher.SearchType.CITES -> {
citingTask = BackgroundTask.wrap(
() -> this.searchCitationsRelationsService.searchReferences(entry, shouldRefresh)
);
yield citingTask;
}
case CitationFetcher.SearchType.CITED_BY -> {
citedByTask = BackgroundTask.wrap(
() -> this.searchCitationsRelationsService.searchCitations(entry, shouldRefresh)
);
yield citedByTask;
}
};
}

private void onSearchForRelationsSucceed(BibEntry entry, CheckListView<CitationRelationItem> listView,
Button abortButton, Button refreshButton,
CitationFetcher.SearchType searchType, Button importButton,
Expand Down
23 changes: 8 additions & 15 deletions src/main/java/org/jabref/logic/citation/repository/BibEntryRelationsRepository.java
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Expand Up @@ -4,23 +4,16 @@
import org.jabref.model.entry.BibEntry;

public interface BibEntryRelationsRepository {

void insertCitations(BibEntry entry, List<BibEntry> citations);

List<BibEntry> readCitations(BibEntry entry);

boolean containsCitations(BibEntry entry);

void insertReferences(BibEntry entry, List<BibEntry> citations);

List<BibEntry> readReferences(BibEntry entry);

/**
* Fetch citations for a bib entry and update local database.
* @param entry should not be null
* @deprecated fetching citations should be done by the service layer (calling code)
*/
@Deprecated
void forceRefreshCitations(BibEntry entry);

/**
* Fetch references made by a bib entry and update local database.
* @param entry should not be null
* @deprecated fetching references should be done by the service layer (calling code)
*/
@Deprecated
void forceRefreshReferences(BibEntry entry);
boolean containsReferences(BibEntry entry);
}
35 changes: 26 additions & 9 deletions src/main/java/org/jabref/logic/citation/repository/LRUBibEntryRelationsCache.java
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@@ -1,38 +1,55 @@
package org.jabref.logic.citation.repository;

import java.util.Collections;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.eclipse.jgit.util.LRUMap;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.identifier.DOI;

public class LRUBibEntryRelationsCache {
private static final Integer MAX_CACHED_ENTRIES = 100;
private static final Map<String, List<BibEntry>> CITATIONS_MAP = new LRUMap<>(MAX_CACHED_ENTRIES, MAX_CACHED_ENTRIES);
private static final Map<String, List<BibEntry>> REFERENCES_MAP = new LRUMap<>(MAX_CACHED_ENTRIES, MAX_CACHED_ENTRIES);
private static final Map<DOI, Set<BibEntry>> CITATIONS_MAP = new LRUMap<>(MAX_CACHED_ENTRIES, MAX_CACHED_ENTRIES);
private static final Map<DOI, Set<BibEntry>> REFERENCES_MAP = new LRUMap<>(MAX_CACHED_ENTRIES, MAX_CACHED_ENTRIES);

public List<BibEntry> getCitations(BibEntry entry) {
return CITATIONS_MAP.getOrDefault(entry.getDOI().map(DOI::getDOI).orElse(""), Collections.emptyList());
return entry
.getDOI()
.stream()
.flatMap(doi -> CITATIONS_MAP.getOrDefault(doi, Set.of()).stream())
.toList();
}

public List<BibEntry> getReferences(BibEntry entry) {
return REFERENCES_MAP.getOrDefault(entry.getDOI().map(DOI::getDOI).orElse(""), Collections.emptyList());
return entry
.getDOI()
.stream()
.flatMap(doi -> REFERENCES_MAP.getOrDefault(doi, Set.of()).stream())
.toList();
}

public void cacheOrMergeCitations(BibEntry entry, List<BibEntry> citations) {
entry.getDOI().ifPresent(doi -> CITATIONS_MAP.put(doi.getDOI(), citations));
entry.getDOI().ifPresent(doi -> {
var cachedRelations = CITATIONS_MAP.getOrDefault(doi, new LinkedHashSet<>());
cachedRelations.addAll(citations);
CITATIONS_MAP.put(doi, cachedRelations);
});
}

public void cacheOrMergeReferences(BibEntry entry, List<BibEntry> references) {
entry.getDOI().ifPresent(doi -> REFERENCES_MAP.putIfAbsent(doi.getDOI(), references));
entry.getDOI().ifPresent(doi -> {
var cachedRelations = REFERENCES_MAP.getOrDefault(doi, new LinkedHashSet<>());
cachedRelations.addAll(references);
REFERENCES_MAP.put(doi, cachedRelations);
});
}

public boolean citationsCached(BibEntry entry) {
return CITATIONS_MAP.containsKey(entry.getDOI().map(DOI::getDOI).orElse(""));
return entry.getDOI().map(CITATIONS_MAP::containsKey).orElse(false);
}

public boolean referencesCached(BibEntry entry) {
return REFERENCES_MAP.containsKey(entry.getDOI().map(DOI::getDOI).orElse(""));
return entry.getDOI().map(REFERENCES_MAP::containsKey).orElse(false);
}
}
69 changes: 20 additions & 49 deletions src/main/java/org/jabref/logic/citation/repository/LRUBibEntryRelationsRepository.java
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Expand Up @@ -2,77 +2,48 @@

import java.util.List;

import org.jabref.logic.importer.fetcher.CitationFetcher;
import org.jabref.logic.importer.FetcherException;
import java.util.Objects;
import org.jabref.model.entry.BibEntry;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class LRUBibEntryRelationsRepository implements BibEntryRelationsRepository {
private static final Logger LOGGER = LoggerFactory
.getLogger(LRUBibEntryRelationsRepository.class);

private final CitationFetcher fetcher;
private final LRUBibEntryRelationsCache cache;

public LRUBibEntryRelationsRepository(CitationFetcher fetcher, LRUBibEntryRelationsCache cache) {
this.fetcher = fetcher;
public LRUBibEntryRelationsRepository(LRUBibEntryRelationsCache cache) {
this.cache = cache;
}

@Override
public List<BibEntry> readCitations(BibEntry entry) {
if (needToRefreshCitations(entry)) {
forceRefreshCitations(entry);
}

return cache.getCitations(entry);
public void insertCitations(BibEntry entry, List<BibEntry> citations) {
cache.cacheOrMergeCitations(
entry, Objects.requireNonNullElseGet(citations, List::of)
);
}

@Override
public List<BibEntry> readReferences(BibEntry entry) {
if (needToRefreshReferences(entry)) {
List<BibEntry> references;
try {
references = fetcher.searchCiting(entry);
} catch (FetcherException e) {
LOGGER.error("Error while fetching references", e);
references = List.of();
}
cache.cacheOrMergeReferences(entry, references);
}

return cache.getReferences(entry);
public List<BibEntry> readCitations(BibEntry entry) {
return cache.getCitations(entry);
}

@Override
public void forceRefreshCitations(BibEntry entry) {
try {
List<BibEntry> citations = fetcher.searchCitedBy(entry);
cache.cacheOrMergeCitations(entry, citations);
} catch (FetcherException e) {
LOGGER.error("Error while fetching citations", e);
}
public boolean containsCitations(BibEntry entry) {
return cache.citationsCached(entry);
}

private boolean needToRefreshCitations(BibEntry entry) {
return !cache.citationsCached(entry);
@Override
public void insertReferences(BibEntry entry, List<BibEntry> references) {
cache.cacheOrMergeReferences(
entry, Objects.requireNonNullElseGet(references, List::of)
);
}

private boolean needToRefreshReferences(BibEntry entry) {
return !cache.referencesCached(entry);
@Override
public List<BibEntry> readReferences(BibEntry entry) {
return cache.getReferences(entry);
}

@Override
public void forceRefreshReferences(BibEntry entry) {
List<BibEntry> references;
try {
references = fetcher.searchCiting(entry);
} catch (FetcherException e) {
LOGGER.error("Error while fetching references", e);
references = List.of();
}
cache.cacheOrMergeReferences(entry, references);
public boolean containsReferences(BibEntry entry) {
return cache.referencesCached(entry);
}
}
54 changes: 38 additions & 16 deletions src/main/java/org/jabref/logic/citation/service/SearchCitationsRelationsService.java
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Expand Up @@ -2,35 +2,57 @@

import java.util.List;
import org.jabref.logic.citation.repository.BibEntryRelationsRepository;
import org.jabref.logic.importer.fetcher.CitationFetcher;
import org.jabref.model.entry.BibEntry;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class SearchCitationsRelationsService {

BibEntryRelationsRepository relationsRepository;
private static final Logger LOGGER = LoggerFactory
.getLogger(SearchCitationsRelationsService.class);

public SearchCitationsRelationsService(BibEntryRelationsRepository repository) {
this.relationsRepository = repository;
}
private final CitationFetcher citationFetcher;
private final BibEntryRelationsRepository relationsRepository;

public List<BibEntry> searchReferences(BibEntry referencer) {
return this.relationsRepository.readReferences(referencer);
public SearchCitationsRelationsService(
CitationFetcher citationFetcher, BibEntryRelationsRepository repository
) {
this.citationFetcher = citationFetcher;
this.relationsRepository = repository;
}

public List<BibEntry> searchReferences(BibEntry referencer, boolean forceUpdate) {
if (forceUpdate) {
this.relationsRepository.forceRefreshReferences(referencer);
if (forceUpdate || !this.relationsRepository.containsReferences(referencer)) {
try {
var references = this.citationFetcher.searchCiting(referencer);
if (!references.isEmpty()) {
this.relationsRepository.insertReferences(referencer, references);
}
} catch (Exception e) {
var errMsg = "Error while fetching references for entry %s".formatted(
referencer.getTitle()
);
LOGGER.error(errMsg);
}
}
return this.searchReferences(referencer);
}

public List<BibEntry> searchCitations(BibEntry cited) {
return this.relationsRepository.readCitations(cited);
return this.relationsRepository.readReferences(referencer);
}

public List<BibEntry> searchCitations(BibEntry cited, boolean forceUpdate) {
if (forceUpdate) {
this.relationsRepository.forceRefreshCitations(cited);
if (forceUpdate || !this.relationsRepository.containsCitations(cited)) {
try {
var citations = this.citationFetcher.searchCitedBy(cited);
if (!citations.isEmpty()) {
this.relationsRepository.insertCitations(cited, citations);
}
} catch (Exception e) {
var errMsg = "Error while fetching citations for entry %s".formatted(
cited.getTitle()
);
LOGGER.error(errMsg);
}
}
return this.searchCitations(cited);
return this.relationsRepository.readCitations(cited);
}
}
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