Revert "New study.yml format"

jabgui/src/main/java/org/jabref/gui/slr/EditExistingStudyAction.java

@@ -8,7 +8,7 @@
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.logic.crawler.StudyRepository;
-import org.jabref.logic.crawler.StudyYamlService;
+import org.jabref.logic.crawler.StudyYamlParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.study.Study;
@@ -51,7 +51,7 @@ public void execute() {
 
  Study study;
  try {
- study = new StudyYamlService().parseStudyYamlFile(studyDirectory.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME));
+ study = new StudyYamlParser().parseStudyYamlFile(studyDirectory.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME));
  } catch (IOException e) {
  dialogService.showErrorDialogAndWait(Localization.lang("Error opening file"), e);
  return;

jabgui/src/main/java/org/jabref/gui/slr/ManageStudyDefinitionViewModel.java

@@ -17,7 +17,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.WorkspacePreferences;
 import org.jabref.logic.crawler.StudyRepository;
-import org.jabref.logic.crawler.StudyYamlService;
+import org.jabref.logic.crawler.StudyYamlParser;
 import org.jabref.logic.git.GitHandler;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImporterPreferences;
@@ -30,7 +30,7 @@
 import org.jabref.logic.importer.fetcher.SpringerNatureWebFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.study.Study;
-import org.jabref.model.study.StudyCatalog;
+import org.jabref.model.study.StudyDatabase;
 import org.jabref.model.study.StudyQuery;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -103,15 +103,15 @@ public ManageStudyDefinitionViewModel(@NonNull Study study,
  title.setValue(study.getTitle());
  researchQuestions.addAll(study.getResearchQuestions());
  queries.addAll(study.getQueries().stream().map(StudyQuery::getQuery).toList());
- List<StudyCatalog> studyCatalogs = study.getCatalogs();
+ List<StudyDatabase> studyDatabases = study.getDatabases();
  databases.addAll(WebFetchers.getSearchBasedFetchers(importFormatPreferences, importerPreferences)
  .stream()
  .map(SearchBasedFetcher::getName)
  // The user wants to select specific fetchers
  // The fetcher summarizing ALL fetchers can be emulated by selecting ALL fetchers (which happens rarely when doing an SLR)
  .filter(name -> !CompositeSearchBasedFetcher.FETCHER_NAME.equals(name))
  .map(name -> {
- boolean enabled = studyCatalogs.contains(new StudyCatalog(name, true));
+ boolean enabled = studyDatabases.contains(new StudyDatabase(name, true));
  return new StudyCatalogItem(name, enabled);
  })
  .toList());
@@ -172,7 +172,7 @@ public SlrStudyAndDirectory saveStudy() {
  title.getValueSafe(),
  researchQuestions,
  queries.stream().map(StudyQuery::new).collect(Collectors.toList()),
- databases.stream().map(studyDatabaseItem -> new StudyCatalog(studyDatabaseItem.getName(), studyDatabaseItem.isEnabled())).filter(StudyCatalog::isEnabled).collect(Collectors.toList()));
+ databases.stream().map(studyDatabaseItem -> new StudyDatabase(studyDatabaseItem.getName(), studyDatabaseItem.isEnabled())).filter(StudyDatabase::isEnabled).collect(Collectors.toList()));
  Path studyDirectory;
  final String studyDirectoryAsString = directory.getValueSafe();
  try {
@@ -185,7 +185,7 @@ public SlrStudyAndDirectory saveStudy() {
  }
  Path studyDefinitionFile = studyDirectory.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME);
  try {
- new StudyYamlService().writeStudyYamlFile(study, studyDefinitionFile);
+ new StudyYamlParser().writeStudyYamlFile(study, studyDefinitionFile);
  } catch (IOException e) {
  LOGGER.error("Could not write study file {}", studyDefinitionFile, e);
  dialogService.notify(Localization.lang("Please enter a valid file path.") +

jabgui/src/main/java/org/jabref/gui/slr/StartNewStudyAction.java

@@ -10,7 +10,7 @@
 import org.jabref.gui.StateManager;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.logic.crawler.StudyRepository;
-import org.jabref.logic.crawler.StudyYamlService;
+import org.jabref.logic.crawler.StudyYamlParser;
 import org.jabref.logic.git.GitHandler;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
@@ -57,8 +57,8 @@ public StartNewStudyAction(LibraryTabContainer tabContainer,
 
  @Override
  protected void crawlPreparation(Path studyRepositoryRoot) throws IOException, GitAPIException {
- StudyYamlService studyYamlService = new StudyYamlService();
- studyYamlService.writeStudyYamlFile(newStudy, studyRepositoryRoot.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME));
+ StudyYamlParser studyYAMLParser = new StudyYamlParser();
+ studyYAMLParser.writeStudyYamlFile(newStudy, studyRepositoryRoot.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME));
 
  // When execution reaches this point, the user created a new study.
  // The GitHandler is already called to initialize the repository with one single commit "Initial commit".

jabgui/src/main/java/org/jabref/gui/slr/StudyCatalogItem.java

@@ -7,12 +7,12 @@
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
 
-import org.jabref.model.study.StudyCatalog;
+import org.jabref.model.study.StudyDatabase;
 
 import org.jspecify.annotations.NonNull;
 
 /**
- * View representation of {@link StudyCatalog}
+ * View representation of {@link StudyDatabase}
  */
 public class StudyCatalogItem {
  private final StringProperty name;

jabgui/src/test/java/org/jabref/gui/slr/ManageStudyDefinitionViewModelTest.java

@@ -8,7 +8,7 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.model.study.Study;
-import org.jabref.model.study.StudyCatalog;
+import org.jabref.model.study.StudyDatabase;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -34,7 +34,7 @@ void setUp() {
  }
 
  @Test
- void emptyStudyConstructorFillsCatalogsCorrectly() {
+ void emptyStudyConstructorFillsDatabasesCorrectly() {
  ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = new ManageStudyDefinitionViewModel(importFormatPreferences, importerPreferences, workspacePreferences, dialogService);
  assertEquals(List.of(
  new StudyCatalogItem("ACM Portal", true),
@@ -65,7 +65,7 @@ void emptyStudyConstructorFillsCatalogsCorrectly() {
  }
 
  @Test
- void studyConstructorFillsCatalogsCorrectly(@TempDir Path tempDir) {
+ void studyConstructorFillsDatabasesCorrectly(@TempDir Path tempDir) {
  ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = getManageStudyDefinitionViewModel(tempDir);
  assertEquals(List.of(
  new StudyCatalogItem("ACM Portal", true),
@@ -96,14 +96,14 @@ void studyConstructorFillsCatalogsCorrectly(@TempDir Path tempDir) {
  }
 
  private ManageStudyDefinitionViewModel getManageStudyDefinitionViewModel(Path tempDir) {
- List<StudyCatalog> catalogs = List.of(
- new StudyCatalog("ACM Portal", true));
+ List<StudyDatabase> databases = List.of(
+ new StudyDatabase("ACM Portal", true));
  Study study = new Study(
  List.of("Name"),
  "title",
  List.of("Q1"),
  List.of(),
- catalogs
+ databases
  );
  return new ManageStudyDefinitionViewModel(
  study,

jablib/build.gradle.kts

@@ -107,7 +107,6 @@ dependencies {
  implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310")
  // TODO: Somwewhere we get a warning: unknown enum constant Id.CLASS reason: class file for com.fasterxml.jackson.annotation.JsonTypeInfo$Id not found
  // implementation("com.fasterxml.jackson.core:jackson-annotations:2.19.1")
- implementation("com.fasterxml.jackson.datatype:jackson-datatype-jdk8")
 
  implementation("com.fasterxml:aalto-xml")
 

jablib/src/main/java/module-info.java

@@ -261,6 +261,5 @@
  requires org.jooq.jool;
  requires org.libreoffice.uno;
  requires transitive org.jspecify;
- requires com.fasterxml.jackson.datatype.jdk8;
  // endregion
 }

jablib/src/main/java/org/jabref/logic/crawler/StudyCatalogToFetcherConverter.java

@@ -9,17 +9,17 @@
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.SearchBasedFetcher;
 import org.jabref.logic.importer.WebFetchers;
-import org.jabref.model.study.StudyCatalog;
+import org.jabref.model.study.StudyDatabase;
 
 /**
  * Converts library entries from the given study into their corresponding fetchers.
  */
 class StudyCatalogToFetcherConverter {
- private final List<StudyCatalog> libraryEntries;
+ private final List<StudyDatabase> libraryEntries;
  private final ImportFormatPreferences importFormatPreferences;
  private final ImporterPreferences importerPreferences;
 
- public StudyCatalogToFetcherConverter(List<StudyCatalog> libraryEntries,
+ public StudyCatalogToFetcherConverter(List<StudyDatabase> libraryEntries,
  ImportFormatPreferences importFormatPreferences,
  ImporterPreferences importerPreferences) {
  this.libraryEntries = libraryEntries;
@@ -44,7 +44,7 @@ public List<SearchBasedFetcher> getActiveFetchers() {
  * @param libraryEntries List of entries
  * @return List of fetcher instances
  */
- private List<SearchBasedFetcher> getFetchersFromLibraryEntries(List<StudyCatalog> libraryEntries) {
+ private List<SearchBasedFetcher> getFetchersFromLibraryEntries(List<StudyDatabase> libraryEntries) {
  return libraryEntries.parallelStream()
  .map(this::createFetcherFromLibraryEntry)
  .filter(Objects::nonNull)
@@ -54,12 +54,12 @@ private List<SearchBasedFetcher> getFetchersFromLibraryEntries(List<StudyCatalog
  /**
  * Transforms a library entry into a SearchBasedFetcher instance. This only works if the library entry specifies a supported fetcher.
  *
- * @param studyCatalog the entry that will be converted
+ * @param studyDatabase the entry that will be converted
  * @return An instance of the fetcher defined by the library entry.
  */
- private SearchBasedFetcher createFetcherFromLibraryEntry(StudyCatalog studyCatalog) {
+ private SearchBasedFetcher createFetcherFromLibraryEntry(StudyDatabase studyDatabase) {
  Set<SearchBasedFetcher> searchBasedFetchers = WebFetchers.getSearchBasedFetchers(importFormatPreferences, importerPreferences);
- String libraryNameFromFetcher = studyCatalog.getName();
+ String libraryNameFromFetcher = studyDatabase.getName();
  return searchBasedFetchers.stream()
  .filter(searchBasedFetcher -> searchBasedFetcher.getName().equalsIgnoreCase(libraryNameFromFetcher))
  .findAny()

jablib/src/main/java/org/jabref/logic/crawler/StudyRepository.java

@@ -34,7 +34,7 @@
 import org.jabref.model.study.FetchResult;
 import org.jabref.model.study.QueryResult;
 import org.jabref.model.study.Study;
-import org.jabref.model.study.StudyCatalog;
+import org.jabref.model.study.StudyDatabase;
 import org.jabref.model.study.StudyQuery;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -116,9 +116,9 @@ public StudyRepository(Path pathToRepository,
 
  gitHandler.checkoutBranch(SEARCH_BRANCH);
  // If study definition does not exist on this branch or was changed on work branch, copy it from work
- boolean studyDefinitionDoesNotExistOrChanged = !(Files.exists(studyDefinitionFile) && new StudyYamlService().parseStudyYamlFile(studyDefinitionFile).equals(study));
+ boolean studyDefinitionDoesNotExistOrChanged = !(Files.exists(studyDefinitionFile) && new StudyYamlParser().parseStudyYamlFile(studyDefinitionFile).equals(study));
  if (studyDefinitionDoesNotExistOrChanged) {
- new StudyYamlService().writeStudyYamlFile(study, studyDefinitionFile);
+ new StudyYamlParser().writeStudyYamlFile(study, studyDefinitionFile);
  }
  setUpRepositoryStructureForQueriesAndFetchers();
  gitHandler.createCommitOnCurrentBranch(updateRepositoryStructureMessage, false);
@@ -175,7 +175,7 @@ public BibDatabaseContext getStudyResultEntries() throws IOException {
  * @throws IOException Problem opening the input stream.
  */
  private Study parseStudyFile() throws IOException {
- return new StudyYamlService().parseStudyYamlFile(studyDefinitionFile);
+ return new StudyYamlParser().parseStudyYamlFile(studyDefinitionFile);
  }
 
  /**
@@ -196,10 +196,10 @@ public List<String> getSearchQueryStrings() {
  * @return List of BibEntries of type Library
  * @throws IllegalArgumentException If a transformation from Library entry to LibraryDefinition fails
  */
- public List<StudyCatalog> getActiveLibraryEntries() throws IllegalArgumentException {
- return study.getCatalogs()
+ public List<StudyDatabase> getActiveLibraryEntries() throws IllegalArgumentException {
+ return study.getDatabases()
  .parallelStream()
- .filter(StudyCatalog::isEnabled)
+ .filter(StudyDatabase::isEnabled)
  .collect(Collectors.toList());
  }
 

jablib/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java

@@ -10,7 +10,6 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import com.fasterxml.jackson.dataformat.yaml.YAMLGenerator;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
 
 /**
  * Example use: <code>new StudyYamlParser().parseStudyYamlFile(studyDefinitionFile);</code>
@@ -22,7 +21,6 @@ public class StudyYamlParser {
  */
  public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
  ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory());
- yamlMapper.registerModule(new Jdk8Module());
  try (InputStream fileInputStream = Files.newInputStream(studyYamlFile)) {
  return yamlMapper.readValue(fileInputStream, Study.class);
  }
@@ -34,7 +32,6 @@ public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
  public void writeStudyYamlFile(Study study, Path studyYamlFile) throws IOException {
  ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory().disable(YAMLGenerator.Feature.WRITE_DOC_START_MARKER)
  .enable(YAMLGenerator.Feature.MINIMIZE_QUOTES));
- yamlMapper.registerModule(new Jdk8Module());
  yamlMapper.writeValue(studyYamlFile.toFile(), study);
  }
 }