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Predatory journal checker (JabRef#10592)
* add PredatoryJournalRepository class * Refactor PredatoryJournalRepository to match JournalAbbreviationRepository design * Add PredatoryJournalChecker and PredatoryJournalLoader classes * Add Integrity Message for en Resources * Integrate PredatoryJournalChecker into IntegrityCheck * Initialize PredatoryJournalRepository on Launch * Add PredatoryJournalCheckerTest and more logging * Refactor PredatoryJournalLoader to switch from temp dir to user's app data * Add MV file generation for predatory journal lists * update CHANGELOG.md * Refactor and create own record class for journal information move to own gradle task and file * checkstyle, rename methods in gradle * run rewrite * fix test * fix duplicate handling * fix gradle task fix zwsp in name * more exception handling * Make serializable to fix mvstore Just use simpler levenstein distance should be enough add javadoc * checkstyle * fuck you checkstyle * checkstyle * refactor test * use same copy behavior as for journal abbrevs * make link elemens non static fix checkstyle * fix static vars * Split loader into crawler and "real" loader * Checkstyle * Fix variable type --------- Co-authored-by: Siedlerchr <[email protected]> Co-authored-by: Oliver Kopp <[email protected]>
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47 changes: 47 additions & 0 deletions
47
src/main/java/org/jabref/cli/PredatoryJournalsMvGenerator.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,47 @@ | ||
| package org.jabref.cli; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.Set; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
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| import org.jabref.logic.journals.predatory.PredatoryJournalInformation; | ||
| import org.jabref.logic.journals.predatory.PredatoryJournalListCrawler; | ||
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| import org.h2.mvstore.MVMap; | ||
| import org.h2.mvstore.MVStore; | ||
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| public class PredatoryJournalsMvGenerator { | ||
| public static void main(String[] args) throws IOException { | ||
| boolean verbose = (args.length == 1) && ("--verbose".equals(args[0])); | ||
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| Path predatoryJournalsMvFile = Path.of("build", "resources", "main", "journals", "predatory-journals.mv"); | ||
| Files.createDirectories(predatoryJournalsMvFile.getParent()); | ||
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| try (MVStore store = new MVStore.Builder() | ||
| .fileName(predatoryJournalsMvFile.toString()) | ||
| .compressHigh() | ||
| .backgroundExceptionHandler((t, e) -> { | ||
| System.err.println("Exception occurred in Thread " + t + "with exception " + e); | ||
| e.printStackTrace(); | ||
| }) | ||
| .open()) { | ||
| MVMap<String, PredatoryJournalInformation> predatoryJournalsMap = store.openMap("PredatoryJournals"); | ||
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| PredatoryJournalListCrawler loader = new PredatoryJournalListCrawler(); | ||
| Set<PredatoryJournalInformation> predatoryJournals = loader.loadFromOnlineSources(); | ||
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| var resultMap = predatoryJournals.stream().collect(Collectors.toMap(PredatoryJournalInformation::name, Function.identity(), | ||
| (predatoryJournalInformation, predatoryJournalInformation2) -> { | ||
| if (verbose) { | ||
| System.out.println("Double entry " + predatoryJournalInformation.name()); | ||
| } | ||
| return predatoryJournalInformation2; | ||
| })); | ||
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| predatoryJournalsMap.putAll(resultMap); | ||
| } | ||
| } | ||
| } |
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29 changes: 29 additions & 0 deletions
29
src/main/java/org/jabref/logic/integrity/PredatoryJournalChecker.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,29 @@ | ||
| package org.jabref.logic.integrity; | ||
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| import java.util.List; | ||
| import java.util.Objects; | ||
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| import org.jabref.logic.journals.predatory.PredatoryJournalRepository; | ||
| import org.jabref.logic.l10n.Localization; | ||
| import org.jabref.model.entry.BibEntry; | ||
| import org.jabref.model.entry.field.Field; | ||
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| public class PredatoryJournalChecker implements EntryChecker { | ||
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| private final PredatoryJournalRepository predatoryJournalRepository; | ||
| private final List<Field> fieldNames; | ||
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| public PredatoryJournalChecker(PredatoryJournalRepository predatoryJournalRepository, List<Field> fieldsToCheck) { | ||
| this.predatoryJournalRepository = Objects.requireNonNull(predatoryJournalRepository); | ||
| this.fieldNames = fieldsToCheck; | ||
| } | ||
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| @Override | ||
| public List<IntegrityMessage> check(BibEntry entry) { | ||
| return entry.getFieldMap().entrySet().stream() | ||
| .filter(field -> fieldNames.contains(field.getKey())) | ||
| .filter(field -> predatoryJournalRepository.isKnownName(field.getValue())) | ||
| .map(field -> new IntegrityMessage(Localization.lang("Predatory journal %0 found", field.getValue()), entry, field.getKey())) | ||
| .toList(); | ||
| } | ||
| } |
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src/main/java/org/jabref/logic/journals/predatory/PredatoryJournalInformation.java
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| Original file line number | Diff line number | Diff line change |
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| package org.jabref.logic.journals.predatory; | ||
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| import java.io.Serializable; | ||
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| /** | ||
| * Represents predatory journal information | ||
| * | ||
| * @param name The full journal name | ||
| * @param abbr Abbreviation, if any | ||
| * @param url Url of the journal | ||
| */ | ||
| public record PredatoryJournalInformation( | ||
| String name, | ||
| String abbr, | ||
| String url) implements Serializable { // must implement @Serializable otherwise MVStore fails | ||
| } |
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