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Fixed ZBMathTest and extracted keyWordSeparator (#9485)
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* Cleanup tests, removed getKeywordSeparator from ImportFormatPreferences and made it a record, applied simple ide suggestions

* Fixed MathSciNetTest

* Fixed checkstyle

* Fixed AstrophysicsDataSystemTest
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@calixtus
calixtus authored Dec 20, 2022
1 parent cfc8c94 commit ec08afe
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Showing 48 changed files with 155 additions and 254 deletions.
2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/crawler/StudyRepository.java
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Expand Up @@ -385,7 +385,7 @@ private String computeIDForQuery(String query) {
* @param crawlResults The results that shall be persisted.
*/
private void persistResults(List<QueryResult> crawlResults) throws IOException, SaveException {
DatabaseMerger merger = new DatabaseMerger(importFormatPreferences.getKeywordSeparator());
DatabaseMerger merger = new DatabaseMerger(importFormatPreferences.bibEntryPreferences().getKeywordSeparator());
BibDatabase newStudyResultEntries = new BibDatabase();

for (QueryResult result : crawlResults) {
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68 changes: 7 additions & 61 deletions src/main/java/org/jabref/logic/importer/ImportFormatPreferences.java
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@@ -1,71 +1,17 @@
package org.jabref.logic.importer;

import javafx.beans.property.ReadOnlyObjectProperty;
import javafx.beans.property.SimpleObjectProperty;

import org.jabref.logic.bibtex.FieldContentFormatterPreferences;
import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
import org.jabref.logic.importer.fetcher.GrobidPreferences;
import org.jabref.logic.preferences.DOIPreferences;
import org.jabref.logic.xmp.XmpPreferences;
import org.jabref.preferences.BibEntryPreferences;

public class ImportFormatPreferences {

private final ReadOnlyObjectProperty<BibEntryPreferences> bibEntryPreferences;
private final CitationKeyPatternPreferences citationKeyPatternPreferences;
private final FieldContentFormatterPreferences fieldContentFormatterPreferences;
private final XmpPreferences xmpPreferences;
private final DOIPreferences doiPreferences;
private final GrobidPreferences grobidPreferences;

public ImportFormatPreferences(BibEntryPreferences bibEntryPreferences,
CitationKeyPatternPreferences citationKeyPatternPreferences,
FieldContentFormatterPreferences fieldContentFormatterPreferences,
XmpPreferences xmpPreferences,
DOIPreferences doiPreferences,
GrobidPreferences grobidPreferences) {
this.bibEntryPreferences = new SimpleObjectProperty<>(bibEntryPreferences);
this.citationKeyPatternPreferences = citationKeyPatternPreferences;
this.fieldContentFormatterPreferences = fieldContentFormatterPreferences;
this.xmpPreferences = xmpPreferences;
this.doiPreferences = doiPreferences;
this.grobidPreferences = grobidPreferences;
}

public DOIPreferences getDoiPreferences() {
return doiPreferences;
}

public ReadOnlyObjectProperty<BibEntryPreferences> bibEntryPreferencesProperty() {
return bibEntryPreferences;
}

public BibEntryPreferences getBibEntryPreferences() {
return bibEntryPreferences.getValue();
}

/**
* @deprecated use {@link BibEntryPreferences#getKeywordSeparator} instead.
*/
@Deprecated
public Character getKeywordSeparator() {
return bibEntryPreferencesProperty().getValue().getKeywordSeparator();
}

public CitationKeyPatternPreferences getCitationKeyPatternPreferences() {
return citationKeyPatternPreferences;
}

public FieldContentFormatterPreferences getFieldContentFormatterPreferences() {
return fieldContentFormatterPreferences;
}

public XmpPreferences getXmpPreferences() {
return xmpPreferences;
}

public GrobidPreferences getGrobidPreferences() {
return grobidPreferences;
}
public record ImportFormatPreferences(
BibEntryPreferences bibEntryPreferences,
CitationKeyPatternPreferences citationKeyPatternPreferences,
FieldContentFormatterPreferences fieldContentFormatterPreferences,
XmpPreferences xmpPreferences,
DOIPreferences doiPreferences,
GrobidPreferences grobidPreferences) {
}
4 changes: 2 additions & 2 deletions src/main/java/org/jabref/logic/importer/ImportFormatReader.java
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Expand Up @@ -73,10 +73,10 @@ public void resetImportFormats(ImporterPreferences importerPreferences,
formats.add(new PdfVerbatimBibTextImporter(importFormatPreferences));
formats.add(new PdfContentImporter(importFormatPreferences));
formats.add(new PdfEmbeddedBibFileImporter(importFormatPreferences));
if (importFormatPreferences.getGrobidPreferences().isGrobidEnabled()) {
if (importFormatPreferences.grobidPreferences().isGrobidEnabled()) {
formats.add(new PdfGrobidImporter(importFormatPreferences));
}
formats.add(new PdfXmpImporter(importFormatPreferences.getXmpPreferences()));
formats.add(new PdfXmpImporter(importFormatPreferences.xmpPreferences()));
formats.add(new RepecNepImporter(importFormatPreferences));
formats.add(new RisImporter());
formats.add(new SilverPlatterImporter());
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7 changes: 1 addition & 6 deletions src/main/java/org/jabref/logic/importer/OpenDatabase.java
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Expand Up @@ -12,13 +12,8 @@
import org.jabref.migrations.SpecialFieldsToSeparateFields;
import org.jabref.model.util.FileUpdateMonitor;

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

public class OpenDatabase {

private static final Logger LOGGER = LoggerFactory.getLogger(OpenDatabase.class);

private OpenDatabase() {
}

Expand All @@ -32,7 +27,7 @@ public static ParserResult loadDatabase(Path fileToOpen, ImportFormatPreferences
throws IOException {
ParserResult result = new BibtexImporter(importFormatPreferences, fileMonitor).importDatabase(fileToOpen);

performLoadDatabaseMigrations(result, importFormatPreferences.getKeywordSeparator());
performLoadDatabaseMigrations(result, importFormatPreferences.bibEntryPreferences().getKeywordSeparator());

return result;
}
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2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/importer/WebFetchers.java
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Expand Up @@ -186,7 +186,7 @@ public static Set<FulltextFetcher> getFullTextFetchers(ImportFormatPreferences i
Set<FulltextFetcher> fetchers = new HashSet<>();

// Original
fetchers.add(new DoiResolution(importFormatPreferences.getDoiPreferences()));
fetchers.add(new DoiResolution(importFormatPreferences.doiPreferences()));

// Publishers
fetchers.add(new ScienceDirect(importerPreferences));
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14 changes: 9 additions & 5 deletions src/main/java/org/jabref/logic/importer/fetcher/ArXivFetcher.java
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Expand Up @@ -148,7 +148,10 @@ private void adaptKeywordsFrom(BibEntry bibEntry) {
allKeywords = Optional.of(allKeywords.get().replaceAll(entry.getKey(), entry.getValue()));
}

String filteredKeywords = KeywordList.merge(allKeywords.get(), "", importFormatPreferences.getKeywordSeparator()).toString();
String filteredKeywords = KeywordList.merge(
allKeywords.get(),
"",
importFormatPreferences.bibEntryPreferences().getKeywordSeparator()).toString();
bibEntry.setField(StandardField.KEYWORDS, filteredKeywords);
}
}
Expand Down Expand Up @@ -596,9 +599,10 @@ public Optional<HelpFile> getHelpPage() {
public Page<BibEntry> performSearchPaged(QueryNode luceneQuery, int pageNumber) throws FetcherException {
ArXivQueryTransformer transformer = new ArXivQueryTransformer();
String transformedQuery = transformer.transformLuceneQuery(luceneQuery).orElse("");
List<BibEntry> searchResult = searchForEntries(transformedQuery, pageNumber).stream()
.map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.getKeywordSeparator()))
.collect(Collectors.toList());
List<BibEntry> searchResult = searchForEntries(transformedQuery, pageNumber)
.stream()
.map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.bibEntryPreferences().getKeywordSeparator()))
.collect(Collectors.toList());
return new Page<>(transformedQuery, pageNumber, filterYears(searchResult, transformer));
}

Expand All @@ -624,7 +628,7 @@ protected CompletableFuture<Optional<BibEntry>> asyncPerformSearchById(String id
@Override
public Optional<BibEntry> performSearchById(String identifier) throws FetcherException {
return searchForEntryById(identifier)
.map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.getKeywordSeparator()));
.map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.bibEntryPreferences().getKeywordSeparator()));
}

@Override
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2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java
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Expand Up @@ -211,7 +211,7 @@ public Parser getParser() {
JSONArray results = jsonObject.getJSONArray("results");
for (int i = 0; i < results.length(); i++) {
JSONObject bibJsonEntry = results.getJSONObject(i).getJSONObject("bibjson");
BibEntry entry = parseBibJSONtoBibtex(bibJsonEntry, preferences.getKeywordSeparator());
BibEntry entry = parseBibJSONtoBibtex(bibJsonEntry, preferences.bibEntryPreferences().getKeywordSeparator());
entries.add(entry);
}
}
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2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/importer/fetcher/IEEE.java
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Expand Up @@ -214,7 +214,7 @@ public Parser getParser() {
JSONArray results = jsonObject.getJSONArray("articles");
for (int i = 0; i < results.length(); i++) {
JSONObject jsonEntry = results.getJSONObject(i);
BibEntry entry = parseJsonResponse(jsonEntry, importFormatPreferences.getKeywordSeparator());
BibEntry entry = parseJsonResponse(jsonEntry, importFormatPreferences.bibEntryPreferences().getKeywordSeparator());
boolean addEntry;
// In case entry has no year, add it
// In case an entry has a year, check if its in the year range
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6 changes: 3 additions & 3 deletions src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
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Expand Up @@ -83,7 +83,7 @@ public class BibtexParser implements Parser {

public BibtexParser(ImportFormatPreferences importFormatPreferences, FileUpdateMonitor fileMonitor) {
this.importFormatPreferences = Objects.requireNonNull(importFormatPreferences);
fieldContentFormatter = new FieldContentFormatter(importFormatPreferences.getFieldContentFormatterPreferences());
fieldContentFormatter = new FieldContentFormatter(importFormatPreferences.fieldContentFormatterPreferences());
metaDataParser = new MetaDataParser(fileMonitor);
}

Expand Down Expand Up @@ -228,7 +228,7 @@ private ParserResult parseFileContent() throws IOException {

// Instantiate meta data
try {
parserResult.setMetaData(metaDataParser.parse(meta, importFormatPreferences.getBibEntryPreferences().getKeywordSeparator()));
parserResult.setMetaData(metaDataParser.parse(meta, importFormatPreferences.bibEntryPreferences().getKeywordSeparator()));
} catch (ParseException exception) {
parserResult.addException(exception);
}
Expand Down Expand Up @@ -611,7 +611,7 @@ private void parseField(BibEntry entry) throws IOException {
entry.setField(field, entry.getField(field).get() + " and " + content);
} else if (StandardField.KEYWORDS.equals(field)) {
// multiple keywords fields should be combined to one
entry.addKeyword(content, importFormatPreferences.getBibEntryPreferences().getKeywordSeparator());
entry.addKeyword(content, importFormatPreferences.bibEntryPreferences().getKeywordSeparator());
}
} else {
entry.setField(field, content);
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7 changes: 4 additions & 3 deletions src/main/java/org/jabref/logic/importer/fileformat/EndnoteXmlImporter.java
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Expand Up @@ -28,6 +28,7 @@
import org.jabref.logic.importer.fileformat.endnote.Dates;
import org.jabref.logic.importer.fileformat.endnote.ElectronicResourceNum;
import org.jabref.logic.importer.fileformat.endnote.Isbn;
import org.jabref.logic.importer.fileformat.endnote.Keyword;
import org.jabref.logic.importer.fileformat.endnote.Keywords;
import org.jabref.logic.importer.fileformat.endnote.Label;
import org.jabref.logic.importer.fileformat.endnote.Notes;
Expand Down Expand Up @@ -212,7 +213,7 @@ private BibEntry parseRecord(Record endNoteRecord) {
.ifPresent(value -> entry.setField(StandardField.NOTE, value.trim()));
getUrl(endNoteRecord)
.ifPresent(value -> entry.setField(StandardField.URL, value));
entry.putKeywords(getKeywords(endNoteRecord), preferences.getKeywordSeparator());
entry.putKeywords(getKeywords(endNoteRecord), preferences.bibEntryPreferences().getKeywordSeparator());
Optional.ofNullable(endNoteRecord.getAbstract())
.map(Abstract::getStyle)
.map(Style::getContent)
Expand Down Expand Up @@ -307,9 +308,9 @@ private List<String> getKeywords(Record endNoteRecord) {
if (keywords != null) {
return keywords.getKeyword()
.stream()
.map(keyword -> keyword.getStyle())
.map(Keyword::getStyle)
.filter(Objects::nonNull)
.map(style -> style.getContent())
.map(Style::getContent)
.collect(Collectors.toList());
} else {
return Collections.emptyList();
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10 changes: 5 additions & 5 deletions src/main/java/org/jabref/logic/importer/fileformat/ModsImporter.java
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Expand Up @@ -81,7 +81,7 @@ public class ModsImporter extends Importer implements Parser {
private JAXBContext context;

public ModsImporter(ImportFormatPreferences importFormatPreferences) {
keywordSeparator = importFormatPreferences.getKeywordSeparator() + " ";
keywordSeparator = importFormatPreferences.bibEntryPreferences().getKeywordSeparator() + " ";
}

@Override
Expand Down Expand Up @@ -179,7 +179,7 @@ private void parseModsGroup(Map<Field, String> fields, List<Object> modsGroup, B
nameDefinition.ifPresent(name -> handleAuthorsInNamePart(name, authors, fields));

originInfoDefinition.ifPresent(originInfo -> originInfo
.getPlaceOrPublisherOrDateIssued().stream()
.getPlaceOrPublisherOrDateIssued()
.forEach(element -> putPlaceOrPublisherOrDate(fields, element.getName().getLocalPart(),
element.getValue())));

Expand Down Expand Up @@ -229,7 +229,7 @@ private void parseTitle(Map<Field, String> fields, List<Object> titleOrSubTitleO

private void parseIdentifier(Map<Field, String> fields, IdentifierDefinition identifier, BibEntry entry) {
String type = identifier.getType();
if ("citekey".equals(type) && !entry.getCitationKey().isPresent()) {
if ("citekey".equals(type) && entry.getCitationKey().isEmpty()) {
entry.setCitationKey(identifier.getValue());
} else if (!"local".equals(type) && !"citekey".equals(type)) {
// put all identifiers (doi, issn, isbn,...) except of local and citekey
Expand Down Expand Up @@ -381,8 +381,8 @@ private void putPlaceOrPublisherOrDate(Map<Field, String> fields, String element

List<String> places = new ArrayList<>();
placeDefinition
.ifPresent(place -> place.getPlaceTerm().stream().filter(placeTerm -> placeTerm.getValue() != null)
.map(PlaceTermDefinition::getValue).forEach(element -> places.add(element)));
.ifPresent(place -> place.getPlaceTerm().stream().map(PlaceTermDefinition::getValue)
.filter(Objects::nonNull).forEach(places::add));
putIfListIsNotEmpty(fields, places, StandardField.ADDRESS, ", ");

dateDefinition.ifPresent(date -> putDate(fields, elementName, date));
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2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/PdfGrobidImporter.java
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Expand Up @@ -25,7 +25,7 @@ public class PdfGrobidImporter extends Importer {
private final ImportFormatPreferences importFormatPreferences;

public PdfGrobidImporter(ImportFormatPreferences importFormatPreferences) {
this.grobidService = new GrobidService(importFormatPreferences.getGrobidPreferences());
this.grobidService = new GrobidService(importFormatPreferences.grobidPreferences());
this.importFormatPreferences = importFormatPreferences;
}

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4 changes: 2 additions & 2 deletions src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java
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Expand Up @@ -46,10 +46,10 @@ public PdfMergeMetadataImporter(ImportFormatPreferences importFormatPreferences)
this.metadataImporters = new ArrayList<>();
this.metadataImporters.add(new PdfVerbatimBibTextImporter(importFormatPreferences));
this.metadataImporters.add(new PdfEmbeddedBibFileImporter(importFormatPreferences));
if (importFormatPreferences.getGrobidPreferences().isGrobidEnabled()) {
if (importFormatPreferences.grobidPreferences().isGrobidEnabled()) {
this.metadataImporters.add(new PdfGrobidImporter(importFormatPreferences));
}
this.metadataImporters.add(new PdfXmpImporter(importFormatPreferences.getXmpPreferences()));
this.metadataImporters.add(new PdfXmpImporter(importFormatPreferences.xmpPreferences()));
this.metadataImporters.add(new PdfContentImporter(importFormatPreferences));
}

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2 changes: 1 addition & 1 deletion src/main/java/org/jabref/logic/importer/fileformat/RepecNepImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,7 @@ private void parseAdditionalFields(BibEntry be, boolean multilineUrlFieldAllowed
String content = readMultipleLines(in);
String[] keywords = content.split("[,;]");
be.addKeywords(Arrays.asList(keywords),
importFormatPreferences.getKeywordSeparator());
importFormatPreferences.bibEntryPreferences().getKeywordSeparator());
} else if ("JEL".equals(keyword)) {
// parse JEL field
be.setField(new UnknownField("jel"), readMultipleLines(in));
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10 changes: 3 additions & 7 deletions src/test/java/org/jabref/gui/entryeditor/SourceTabTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,12 @@
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.util.DummyFileUpdateMonitor;
import org.jabref.preferences.BibEntryPreferences;
import org.jabref.testutils.category.GUITest;

import org.fxmisc.richtext.CodeArea;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Answers;
import org.testfx.api.FxRobot;
import org.testfx.framework.junit5.ApplicationExtension;
import org.testfx.framework.junit5.Start;
Expand All @@ -52,12 +52,8 @@ public void onStart(Stage stage) {
StateManager stateManager = mock(StateManager.class);
when(stateManager.activeSearchQueryProperty()).thenReturn(OptionalObjectProperty.empty());
KeyBindingRepository keyBindingRepository = new KeyBindingRepository(Collections.emptyList(), Collections.emptyList());
BibEntryPreferences bibEntryPreferences = mock(BibEntryPreferences.class);
when(bibEntryPreferences.getKeywordSeparator()).thenReturn(',');
ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class);
when(importFormatPreferences.getFieldContentFormatterPreferences())
.thenReturn(mock(FieldContentFormatterPreferences.class));
when(importFormatPreferences.getBibEntryPreferences()).thenReturn(bibEntryPreferences);
ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
when(importFormatPreferences.bibEntryPreferences().getKeywordSeparator()).thenReturn(',');
FieldWriterPreferences fieldWriterPreferences = new FieldWriterPreferences(true, List.of(StandardField.MONTH), new FieldContentFormatterPreferences());

sourceTab = new SourceTab(new BibDatabaseContext(), new CountingUndoManager(), fieldWriterPreferences, importFormatPreferences, new DummyFileUpdateMonitor(), mock(DialogService.class), stateManager, keyBindingRepository);
Expand Down
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