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Fix predatory journal loading resoures (JabRef#10693)
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* Fix resource does not exist

* Fix journal loading and resource opening

* Use MVStore directly (an experiment)

* Add comments

---------

Co-authored-by: Oliver Kopp <[email protected]>
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@Siedlerchr @koppor
Siedlerchr and koppor authored Dec 6, 2023
1 parent 2a7fc1a commit 43a4393
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Showing 5 changed files with 91 additions and 54 deletions.
10 changes: 10 additions & 0 deletions src/main/java/org/jabref/gui/MainApplication.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,15 @@
import org.jabref.model.util.FileUpdateMonitor;
import org.jabref.preferences.JabRefPreferences;

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

/**
* JabRef's main class to process command line options and to start the UI
*/
public class MainApplication extends Application {
private static final Logger LOGGER = LoggerFactory.getLogger(MainApplication.class);

private static List<ParserResult> parserResults;
private static boolean isBlank;
private static JabRefPreferences preferences;
Expand Down Expand Up @@ -43,5 +48,10 @@ public void stop() {
OOBibBaseConnect.closeOfficeConnection();
Globals.stopBackgroundTasks();
Globals.shutdownThreadPools();
try {
Globals.predatoryJournalRepository.close();
} catch (Exception e) {
LOGGER.warn("Cloud not shut down predatoryJournalRepository", e);
}
}
}
35 changes: 20 additions & 15 deletions src/main/java/org/jabref/logic/journals/predatory/PredatoryJournalListLoader.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
package org.jabref.logic.journals.predatory;

import java.net.URISyntaxException;
import java.net.URL;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;

import org.slf4j.Logger;
Expand All @@ -13,20 +14,24 @@ public class PredatoryJournalListLoader {

public static PredatoryJournalRepository loadRepository() {
PredatoryJournalRepository repository = new PredatoryJournalRepository();

Path path;
try {
URL resource = PredatoryJournalRepository.class.getResource("/journals/predatory-journals.mv");
if (resource == null) {
LOGGER.error("predatoryJournal-list.mv not found. Using demo list.");
return new PredatoryJournalRepository();
// Initialize with built-in list
// We cannot use PredatoryJournalRepository.class.getResource, because this is null in JPackage, thus we need "getResourceAsStream"
try (InputStream resourceAsStream = PredatoryJournalListLoader.class.getResourceAsStream("/journals/predatory-journals.mv")) {
if (resourceAsStream == null) {
LOGGER.warn("There is no predatory-journal.mv. We use a default predatory dummy list");
repository = new PredatoryJournalRepository();
} else {
// MVStore does not support loading from stream. Thus, we need to have a file copy of the stream.
Path tempDir = Files.createTempDirectory("jabref-journal");
Path tempJournalList = tempDir.resolve("predatory-journals.mv");
Files.copy(resourceAsStream, tempJournalList);
repository = new PredatoryJournalRepository(tempJournalList);
tempDir.toFile().deleteOnExit();
tempJournalList.toFile().deleteOnExit();
}
path = Path.of(resource.toURI());
} catch (URISyntaxException e) {
LOGGER.error("Could not determine path to predatoryJournal-list.mv. Using demo list.");
return new PredatoryJournalRepository();
} catch (IOException e) {
LOGGER.error("Error while copying journal list", e);
}

return new PredatoryJournalRepository(path);
return repository;
}
}
22 changes: 14 additions & 8 deletions src/main/java/org/jabref/logic/journals/predatory/PredatoryJournalRepository.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package org.jabref.logic.journals.predatory;

import java.nio.file.Path;
import java.util.HashMap;
import java.util.Locale;
import java.util.Map;
import java.util.regex.Matcher;
Expand All @@ -17,27 +16,27 @@
/**
* A repository for all predatory journals and publishers, including add and find methods.
*/
public class PredatoryJournalRepository {
public class PredatoryJournalRepository implements AutoCloseable {
private final Logger LOGGER = LoggerFactory.getLogger(PredatoryJournalRepository.class);
private final Map<String, PredatoryJournalInformation> predatoryJournals = new HashMap<>();
private final Map<String, PredatoryJournalInformation> predatoryJournals;
private final StringSimilarity match = new StringSimilarity();
private final MVStore store;

/**
* Initializes the internal data based on the predatory journals found in the given MV file
*/
public PredatoryJournalRepository(Path mvStore) {
MVMap<String, PredatoryJournalInformation> predatoryJournalsMap;
try (MVStore store = new MVStore.Builder().readOnly().fileName(mvStore.toAbsolutePath().toString()).open()) {
predatoryJournalsMap = store.openMap("PredatoryJournals");
predatoryJournals.putAll(predatoryJournalsMap);
}
store = new MVStore.Builder().readOnly().fileName(mvStore.toAbsolutePath().toString()).open();
predatoryJournals = store.openMap("PredatoryJournals");
}

/**
* Initializes the repository with demonstration data. Used if no abbreviation file is found.
*/
public PredatoryJournalRepository() {
predatoryJournals.put("Demo", new PredatoryJournalInformation("Demo", "Demo", ""));
store = null;
predatoryJournals = Map.of("Demo", new PredatoryJournalInformation("Demo", "Demo", ""));
}

/**
Expand All @@ -58,4 +57,11 @@ public boolean isKnownName(String journalName) {
LOGGER.info("Found multiple possible predatory journals {}", String.join(", ", matches));
return !matches.isEmpty();
}

@Override
public void close() throws Exception {
if (store != null) {
store.close();
}
}
}
68 changes: 38 additions & 30 deletions src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package org.jabref.logic.integrity;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Collections;
Expand All @@ -14,6 +13,7 @@
import org.jabref.logic.citationkeypattern.GlobalCitationKeyPattern;
import org.jabref.logic.journals.JournalAbbreviationLoader;
import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseMode;
Expand Down Expand Up @@ -47,36 +47,36 @@
class IntegrityCheckTest {

@Test
void bibTexAcceptsStandardEntryType() {
void bibTexAcceptsStandardEntryType() throws Exception {
assertCorrect(withMode(createContext(StandardField.TITLE, "sometitle", StandardEntryType.Article), BibDatabaseMode.BIBTEX));
}

@Test
void bibTexDoesNotAcceptIEEETranEntryType() {
void bibTexDoesNotAcceptIEEETranEntryType() throws Exception {
assertWrong(withMode(createContext(StandardField.TITLE, "sometitle", IEEETranEntryType.Patent), BibDatabaseMode.BIBTEX));
}

@Test
void bibLaTexAcceptsIEEETranEntryType() {
void bibLaTexAcceptsIEEETranEntryType() throws Exception {
assertCorrect((withMode(createContext(StandardField.TITLE, "sometitle", IEEETranEntryType.Patent), BibDatabaseMode.BIBLATEX)));
}

@Test
void bibLaTexAcceptsStandardEntryType() {
void bibLaTexAcceptsStandardEntryType() throws Exception {
assertCorrect(withMode(createContext(StandardField.TITLE, "sometitle", StandardEntryType.Article), BibDatabaseMode.BIBLATEX));
}

@ParameterizedTest
@MethodSource("provideCorrectFormat")
void authorNameChecksCorrectFormat(String input) {
void authorNameChecksCorrectFormat(String input) throws Exception {
for (Field field : FieldFactory.getPersonNameFields()) {
assertCorrect(withMode(createContext(field, input), BibDatabaseMode.BIBLATEX));
}
}

@ParameterizedTest
@MethodSource("provideIncorrectFormat")
void authorNameChecksIncorrectFormat(String input) {
void authorNameChecksIncorrectFormat(String input) throws Exception {
for (Field field : FieldFactory.getPersonNameFields()) {
assertWrong(withMode(createContext(field, input), BibDatabaseMode.BIBLATEX));
}
Expand All @@ -94,7 +94,7 @@ private static Stream<String> provideIncorrectFormat() {
}

@Test
void testFileChecks() {
void testFileChecks() throws Exception {
MetaData metaData = mock(MetaData.class);
Mockito.when(metaData.getDefaultFileDirectory()).thenReturn(Optional.of("."));
Mockito.when(metaData.getUserFileDirectory(any(String.class))).thenReturn(Optional.empty());
Expand All @@ -107,7 +107,7 @@ void testFileChecks() {
}

@Test
void fileCheckFindsFilesRelativeToBibFile(@TempDir Path testFolder) throws IOException {
void fileCheckFindsFilesRelativeToBibFile(@TempDir Path testFolder) throws Exception {
Path bibFile = testFolder.resolve("lit.bib");
Files.createFile(bibFile);
Path pdfFile = testFolder.resolve("file.pdf");
Expand All @@ -120,7 +120,7 @@ void fileCheckFindsFilesRelativeToBibFile(@TempDir Path testFolder) throws IOExc
}

@Test
void testEntryIsUnchangedAfterChecks() {
void testEntryIsUnchangedAfterChecks() throws Exception {
BibEntry entry = new BibEntry();

// populate with all known fields
Expand All @@ -137,12 +137,14 @@ void testEntryIsUnchangedAfterChecks() {
bibDatabase.insertEntry(entry);
BibDatabaseContext context = new BibDatabaseContext(bibDatabase);

new IntegrityCheck(context,
mock(FilePreferences.class),
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
PredatoryJournalListLoader.loadRepository(), false)
.check();
try (PredatoryJournalRepository predatoryJournalRepository = PredatoryJournalListLoader.loadRepository()) {
new IntegrityCheck(context,
mock(FilePreferences.class),
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
predatoryJournalRepository, false)
.check();
}

assertEquals(clonedEntry, entry);
}
Expand All @@ -169,25 +171,31 @@ private BibDatabaseContext createContext(Field field, String value) {
return createContext(field, value, metaData);
}

private void assertWrong(BibDatabaseContext context) {
List<IntegrityMessage> messages = new IntegrityCheck(context,
mock(FilePreferences.class),
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
PredatoryJournalListLoader.loadRepository(), false)
.check();
private void assertWrong(BibDatabaseContext context) throws Exception {
List<IntegrityMessage> messages;
try (PredatoryJournalRepository predatoryJournalRepository = PredatoryJournalListLoader.loadRepository()) {
messages = new IntegrityCheck(context,
mock(FilePreferences.class),
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
predatoryJournalRepository, false)
.check();
}
assertNotEquals(Collections.emptyList(), messages);
}

private void assertCorrect(BibDatabaseContext context) {
private void assertCorrect(BibDatabaseContext context) throws Exception {
FilePreferences filePreferencesMock = mock(FilePreferences.class);
when(filePreferencesMock.shouldStoreFilesRelativeToBibFile()).thenReturn(true);
List<IntegrityMessage> messages = new IntegrityCheck(context,
filePreferencesMock,
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
PredatoryJournalListLoader.loadRepository(), false)
.check();
List<IntegrityMessage> messages;
try (PredatoryJournalRepository predatoryJournalRepository = PredatoryJournalListLoader.loadRepository()) {
messages = new IntegrityCheck(context,
filePreferencesMock,
createCitationKeyPatternPreferences(),
JournalAbbreviationLoader.loadBuiltInRepository(),
predatoryJournalRepository, false)
.check();
}
assertEquals(Collections.emptyList(), messages);
}

Expand Down
10 changes: 9 additions & 1 deletion src/test/java/org/jabref/logic/integrity/PredatoryJournalCheckerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,11 @@
import java.util.List;

import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;

import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;

Expand All @@ -15,13 +17,19 @@
class PredatoryJournalCheckerTest {

static PredatoryJournalChecker checker;
static PredatoryJournalRepository predatoryJournalRepository = PredatoryJournalListLoader.loadRepository();

@BeforeAll
static void initChecker() {
checker = new PredatoryJournalChecker(PredatoryJournalListLoader.loadRepository(),
checker = new PredatoryJournalChecker(predatoryJournalRepository,
List.of(StandardField.JOURNAL, StandardField.PUBLISHER, StandardField.BOOKTITLE));
}

@AfterAll
static void close() throws Exception {
predatoryJournalRepository.close();
}

@Test
void journalIsNotPredatory() {
BibEntry entry = new BibEntry().withField(StandardField.JOURNAL, "IEEE Software");
Expand Down

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