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Enable automated cross library search using a cross library query lan… (
#7124) * Enable automated cross library search using a cross library query language. Signed-off-by: Dominik Voigt <dominik.ingo.voigt@gmail.com> * Pull Global upward through constructor. * Pull Globals and ImportFormatPreferences up through constructor Signed-off-by: Dominik Voigt <dominik.ingo.voigt@gmail.com> * Integrate requested changes and fix architecture tests by correcting test classes Signed-off-by: Dominik Voigt <dominik.ingo.voigt@gmail.com> * Remove unused imports Signed-off-by: Dominik Voigt <dominik.ingo.voigt@gmail.com>
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81 changes: 81 additions & 0 deletions
81
src/main/java/org/jabref/gui/StartLiteratureReviewAction.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| package org.jabref.gui; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.util.Optional; | ||
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| import org.jabref.gui.actions.SimpleCommand; | ||
| import org.jabref.gui.importer.actions.OpenDatabaseAction; | ||
| import org.jabref.gui.util.BackgroundTask; | ||
| import org.jabref.gui.util.FileDialogConfiguration; | ||
| import org.jabref.gui.util.TaskExecutor; | ||
| import org.jabref.logic.crawler.Crawler; | ||
| import org.jabref.logic.importer.ParseException; | ||
| import org.jabref.logic.l10n.Localization; | ||
| import org.jabref.model.entry.BibEntryTypesManager; | ||
| import org.jabref.model.util.FileUpdateMonitor; | ||
| import org.jabref.preferences.JabRefPreferences; | ||
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| import org.eclipse.jgit.api.errors.GitAPIException; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| public class StartLiteratureReviewAction extends SimpleCommand { | ||
| private static final Logger LOGGER = LoggerFactory.getLogger(StartLiteratureReviewAction.class); | ||
| private final JabRefFrame frame; | ||
| private final DialogService dialogService; | ||
| private final FileUpdateMonitor fileUpdateMonitor; | ||
| private final Path workingDirectory; | ||
| private final TaskExecutor taskExecutor; | ||
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| public StartLiteratureReviewAction(JabRefFrame frame, FileUpdateMonitor fileUpdateMonitor, Path standardWorkingDirectory, TaskExecutor taskExecutor) { | ||
| this.frame = frame; | ||
| this.dialogService = frame.getDialogService(); | ||
| this.fileUpdateMonitor = fileUpdateMonitor; | ||
| this.workingDirectory = getInitialDirectory(standardWorkingDirectory); | ||
| this.taskExecutor = taskExecutor; | ||
| } | ||
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| @Override | ||
| public void execute() { | ||
| FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder() | ||
| .withInitialDirectory(workingDirectory) | ||
| .build(); | ||
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| Optional<Path> studyDefinitionFile = dialogService.showFileOpenDialog(fileDialogConfiguration); | ||
| if (studyDefinitionFile.isEmpty()) { | ||
| // Do nothing if selection was canceled | ||
| return; | ||
| } | ||
| final Crawler crawler; | ||
| try { | ||
| crawler = new Crawler(studyDefinitionFile.get(), fileUpdateMonitor, JabRefPreferences.getInstance().getImportFormatPreferences(), JabRefPreferences.getInstance().getSavePreferences(), new BibEntryTypesManager()); | ||
| } catch (IOException | ParseException | GitAPIException e) { | ||
| LOGGER.error("Error during reading of study definition file.", e); | ||
| dialogService.showErrorDialogAndWait(Localization.lang("Error during reading of study definition file."), e); | ||
| return; | ||
| } | ||
| BackgroundTask.wrap(() -> { | ||
| crawler.performCrawl(); | ||
| return 0; // Return any value to make this a callable instead of a runnable. This allows throwing exceptions. | ||
| }) | ||
| .onFailure(e -> { | ||
| LOGGER.error("Error during persistence of crawling results."); | ||
| dialogService.showErrorDialogAndWait(Localization.lang("Error during persistence of crawling results."), e); | ||
| }) | ||
| .onSuccess(unused -> new OpenDatabaseAction(frame).openFile(Path.of(studyDefinitionFile.get().getParent().toString(), "studyResult.bib"), true)) | ||
| .executeWith(taskExecutor); | ||
| } | ||
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| /** | ||
| * @return Path of current panel database directory or the standard working directory | ||
| */ | ||
| private Path getInitialDirectory(Path standardWorkingDirectory) { | ||
| if (frame.getBasePanelCount() == 0) { | ||
| return standardWorkingDirectory; | ||
| } else { | ||
| Optional<Path> databasePath = frame.getCurrentLibraryTab().getBibDatabaseContext().getDatabasePath(); | ||
| return databasePath.map(Path::getParent).orElse(standardWorkingDirectory); | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| package org.jabref.logic.crawler; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.util.List; | ||
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| import org.jabref.logic.crawler.git.GitHandler; | ||
| import org.jabref.logic.exporter.SavePreferences; | ||
| import org.jabref.logic.importer.ImportFormatPreferences; | ||
| import org.jabref.logic.importer.ParseException; | ||
| import org.jabref.model.entry.BibEntryTypesManager; | ||
| import org.jabref.model.study.QueryResult; | ||
| import org.jabref.model.study.Study; | ||
| import org.jabref.model.util.FileUpdateMonitor; | ||
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| import org.eclipse.jgit.api.errors.GitAPIException; | ||
|
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| /** | ||
| * This class provides a service for SLR support by conducting an automated search and persistance | ||
| * of studies using the queries and E-Libraries specified in the provided study definition file. | ||
| * | ||
| * It composes a StudyRepository for repository management, | ||
| * and a StudyFetcher that manages the crawling over the selected E-Libraries. | ||
| */ | ||
| public class Crawler { | ||
| private final StudyRepository studyRepository; | ||
| private final StudyFetcher studyFetcher; | ||
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| /** | ||
| * Creates a crawler for retrieving studies from E-Libraries | ||
| * | ||
| * @param studyDefinitionFile The path to the study definition file that contains the list of targeted E-Libraries and used cross-library queries | ||
| */ | ||
| public Crawler(Path studyDefinitionFile, FileUpdateMonitor fileUpdateMonitor, ImportFormatPreferences importFormatPreferences, SavePreferences savePreferences, BibEntryTypesManager bibEntryTypesManager) throws IllegalArgumentException, IOException, ParseException, GitAPIException { | ||
| Path studyRepositoryRoot = studyDefinitionFile.getParent(); | ||
| studyRepository = new StudyRepository(studyRepositoryRoot, new GitHandler(studyRepositoryRoot), importFormatPreferences, fileUpdateMonitor, savePreferences, bibEntryTypesManager); | ||
| Study study = studyRepository.getStudy(); | ||
| LibraryEntryToFetcherConverter libraryEntryToFetcherConverter = new LibraryEntryToFetcherConverter(study.getActiveLibraryEntries(), importFormatPreferences); | ||
| this.studyFetcher = new StudyFetcher(libraryEntryToFetcherConverter.getActiveFetchers(), study.getSearchQueryStrings()); | ||
| } | ||
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| /** | ||
| * This methods performs the crawling of the active libraries defined in the study definition file. | ||
| * This method also persists the results in the same folder the study definition file is stored in. | ||
| * | ||
| * @throws IOException Thrown if a problem occurred during the persistence of the result. | ||
| */ | ||
| public void performCrawl() throws IOException, GitAPIException { | ||
| List<QueryResult> results = studyFetcher.crawl(); | ||
| studyRepository.persist(results); | ||
| } | ||
| } |
67 changes: 67 additions & 0 deletions
67
src/main/java/org/jabref/logic/crawler/LibraryEntryToFetcherConverter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| package org.jabref.logic.crawler; | ||
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| import java.util.List; | ||
| import java.util.Objects; | ||
| import java.util.Set; | ||
| import java.util.stream.Collectors; | ||
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| import org.jabref.logic.importer.ImportFormatPreferences; | ||
| import org.jabref.logic.importer.SearchBasedFetcher; | ||
| import org.jabref.logic.importer.WebFetchers; | ||
| import org.jabref.model.entry.BibEntry; | ||
| import org.jabref.model.entry.field.UnknownField; | ||
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| import static org.jabref.model.entry.types.SystematicLiteratureReviewStudyEntryType.LIBRARY_ENTRY; | ||
|
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| /** | ||
| * Converts library entries from the given study into their corresponding fetchers. | ||
| */ | ||
| class LibraryEntryToFetcherConverter { | ||
| private final List<BibEntry> libraryEntries; | ||
| private final ImportFormatPreferences importFormatPreferences; | ||
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| public LibraryEntryToFetcherConverter(List<BibEntry> libraryEntries, ImportFormatPreferences importFormatPreferences) { | ||
| this.libraryEntries = libraryEntries; | ||
| this.importFormatPreferences = importFormatPreferences; | ||
| } | ||
|
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| /** | ||
| * Returns a list of instances of all active library fetchers. | ||
| * | ||
| * A fetcher is considered active if there exists an library entry of the library the fetcher is associated with that is enabled. | ||
| * | ||
| * @return Instances of all active fetchers defined in the study definition. | ||
| */ | ||
| public List<SearchBasedFetcher> getActiveFetchers() { | ||
| return getFetchersFromLibraryEntries(this.libraryEntries); | ||
| } | ||
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| /** | ||
| * Transforms a list of libraryEntries into a list of SearchBasedFetcher instances. | ||
| * | ||
| * @param libraryEntries List of entries | ||
| * @return List of fetcher instances | ||
| */ | ||
| private List<SearchBasedFetcher> getFetchersFromLibraryEntries(List<BibEntry> libraryEntries) { | ||
| return libraryEntries.parallelStream() | ||
| .filter(bibEntry -> bibEntry.getType().getName().equals(LIBRARY_ENTRY.getName())) | ||
| .map(this::createFetcherFromLibraryEntry) | ||
| .filter(Objects::nonNull) | ||
| .collect(Collectors.toList()); | ||
| } | ||
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| /** | ||
| * Transforms a library entry into a SearchBasedFetcher instance. This only works if the library entry specifies a supported fetcher. | ||
| * | ||
| * @param libraryEntry the entry that will be converted | ||
| * @return An instance of the fetcher defined by the library entry. | ||
| */ | ||
| private SearchBasedFetcher createFetcherFromLibraryEntry(BibEntry libraryEntry) { | ||
| Set<SearchBasedFetcher> searchBasedFetchers = WebFetchers.getSearchBasedFetchers(importFormatPreferences); | ||
| String libraryNameFromFetcher = libraryEntry.getField(new UnknownField("name")).orElse(""); | ||
| return searchBasedFetchers.stream() | ||
| .filter(searchBasedFetcher -> searchBasedFetcher.getName().toLowerCase().equals(libraryNameFromFetcher.toLowerCase())) | ||
| .findAny() | ||
| .orElse(null); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| package org.jabref.logic.crawler; | ||
|
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Objects; | ||
| import java.util.stream.Collectors; | ||
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| import org.jabref.logic.importer.FetcherException; | ||
| import org.jabref.logic.importer.PagedSearchBasedFetcher; | ||
| import org.jabref.logic.importer.SearchBasedFetcher; | ||
| import org.jabref.model.database.BibDatabase; | ||
| import org.jabref.model.entry.BibEntry; | ||
| import org.jabref.model.study.FetchResult; | ||
| import org.jabref.model.study.QueryResult; | ||
|
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
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| /** | ||
| * Delegates the search of the provided set of targeted E-Libraries with the provided queries to the E-Library specific fetchers, | ||
| * and aggregates the results returned by the fetchers by query and E-Library. | ||
| */ | ||
| class StudyFetcher { | ||
| private static final Logger LOGGER = LoggerFactory.getLogger(StudyFetcher.class); | ||
| private static final int MAX_AMOUNT_OF_RESULTS_PER_FETCHER = 100; | ||
|
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| private final List<SearchBasedFetcher> activeFetchers; | ||
| private final List<String> searchQueries; | ||
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| StudyFetcher(List<SearchBasedFetcher> activeFetchers, List<String> searchQueries) throws IllegalArgumentException { | ||
| this.searchQueries = searchQueries; | ||
| this.activeFetchers = activeFetchers; | ||
| } | ||
|
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| /** | ||
| * Each Map Entry contains the results for one search term for all libraries. | ||
| * Each entry of the internal map contains the results for a given library. | ||
| * If any library API is not available, its corresponding entry is missing from the internal map. | ||
| */ | ||
| public List<QueryResult> crawl() { | ||
| return searchQueries.parallelStream() | ||
| .map(this::getQueryResult) | ||
| .collect(Collectors.toList()); | ||
| } | ||
|
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| private QueryResult getQueryResult(String searchQuery) { | ||
| return new QueryResult(searchQuery, performSearchOnQuery(searchQuery)); | ||
| } | ||
|
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| /** | ||
| * Queries all Databases on the given searchQuery. | ||
| * | ||
| * @param searchQuery The query the search is performed for. | ||
| * @return Mapping of each fetcher by name and all their retrieved publications as a BibDatabase | ||
| */ | ||
| private List<FetchResult> performSearchOnQuery(String searchQuery) { | ||
| return activeFetchers.parallelStream() | ||
| .map(fetcher -> performSearchOnQueryForFetcher(searchQuery, fetcher)) | ||
| .filter(Objects::nonNull) | ||
| .collect(Collectors.toList()); | ||
| } | ||
|
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| private FetchResult performSearchOnQueryForFetcher(String searchQuery, SearchBasedFetcher fetcher) { | ||
| try { | ||
| List<BibEntry> fetchResult = new ArrayList<>(); | ||
| if (fetcher instanceof PagedSearchBasedFetcher) { | ||
| int pages = ((int) Math.ceil(((double) MAX_AMOUNT_OF_RESULTS_PER_FETCHER) / ((PagedSearchBasedFetcher) fetcher).getPageSize())); | ||
| for (int page = 0; page < pages; page++) { | ||
| fetchResult.addAll(((PagedSearchBasedFetcher) fetcher).performSearchPaged(searchQuery, page).getContent()); | ||
| } | ||
| } else { | ||
| fetchResult = fetcher.performSearch(searchQuery); | ||
| } | ||
| return new FetchResult(fetcher.getName(), new BibDatabase(fetchResult)); | ||
| } catch (FetcherException e) { | ||
| LOGGER.warn(String.format("%s API request failed", fetcher.getName()), e); | ||
| return null; | ||
| } | ||
| } | ||
| } |
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