diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1bf428b8b64..08445740dd0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -11,9 +11,12 @@ The title of the PR must not reference an issue, because GitHub does not support - [x] done; [ ] not done / not applicable --> +```[tasklist] +### Compulsory checks - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable) - [ ] Tests created for changes (if applicable) - [ ] Manually tested changed features in running JabRef (always required) - [ ] Screenshots added in PR description (for UI changes) - [ ] [Checked developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request. - [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at or, even better, I submitted a pull request to the documentation repository. +``` diff --git a/CHANGELOG.md b/CHANGELOG.md index 6bb5077ebe8..71be86913a7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,10 +23,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve ### Changed - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568) +- We modified the `Add Group` dialog to use the most recently selected group hierarchical context. [#9141](https://github.com/JabRef/jabref/issues/9141) - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625) +- JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679) +- Backups of libraries are not stored per JabRef version, but collected together. +- We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`. - `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678) - `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678) -- We modified the `Add Group` dialog to use the most recently selected group hierarchical context [#9141](https://github.com/JabRef/jabref/issues/9141) +- We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536) diff --git a/build.gradle b/build.gradle index 5fc07a2252b..101993dce22 100644 --- a/build.gradle +++ b/build.gradle @@ -259,7 +259,6 @@ processResources { task generateSource(dependsOn: ["generateBstGrammarSource", "generateSearchGrammarSource", - "generateMedlineSource", "generateBibtexmlSource", "generateEndnoteSource", "generateModsSource", @@ -290,15 +289,6 @@ tasks.register("generateSearchGrammarSource", JavaExec) { args = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"] } -task generateMedlineSource(type: XjcTask) { - group = 'JabRef' - description = "Generates java files for the medline importer." - - schemaFile = "src/main/resources/xjc/medline/medline.xsd" - outputDirectory = "src-gen/main/java" - javaPackage = "org.jabref.logic.importer.fileformat.medline" -} - task generateBibtexmlSource(type: XjcTask) { group = 'JabRef' description = "Generates java files for the bibtexml importer." diff --git a/docs/Gemfile b/docs/Gemfile index 4c00e14eb36..3056e5acfb5 100644 --- a/docs/Gemfile +++ b/docs/Gemfile @@ -5,7 +5,7 @@ gem "jekyll", "~> 4.3" # installed by `gem jekyll` # Homepage: https://github.com/paulrobertlloyd/jekyll-figure#jekyll-figure gem 'jekyll-figure' -gem "just-the-docs", "0.4.0.rc3" +gem "just-the-docs", "0.4.2" gem "jekyll-remote-theme" diff --git a/src/main/java/org/jabref/cli/Launcher.java b/src/main/java/org/jabref/cli/Launcher.java index 70e4042e6ac..bc9dd85d26e 100644 --- a/src/main/java/org/jabref/cli/Launcher.java +++ b/src/main/java/org/jabref/cli/Launcher.java @@ -22,6 +22,7 @@ import org.jabref.logic.remote.RemotePreferences; import org.jabref.logic.remote.client.RemoteClient; import org.jabref.logic.util.BuildInfo; +import org.jabref.logic.util.OS; import org.jabref.migrations.PreferencesMigrations; import org.jabref.model.database.BibDatabaseContext; import org.jabref.model.database.BibDatabaseMode; @@ -90,10 +91,12 @@ public static void main(String[] args) { * the log configuration programmatically anymore. */ private static void addLogToDisk() { - Path directory = Path.of(AppDirsFactory.getInstance().getUserLogDir( - "jabref", - new BuildInfo().version.toString(), - "org.jabref")); + Path directory = Path.of(AppDirsFactory.getInstance() + .getUserDataDir( + OS.APP_DIR_APP_NAME, + "logs", + OS.APP_DIR_APP_AUTHOR)) + .resolve(new BuildInfo().version.toString()); try { Files.createDirectories(directory); } catch (IOException e) { diff --git a/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java b/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java index 64f24662ecf..bdd2fbd2d16 100644 --- a/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java +++ b/src/main/java/org/jabref/gui/backup/BackupResolverDialog.java @@ -32,7 +32,7 @@ public BackupResolverDialog(Path originalPath) { getDialogPane().setMinHeight(180); getDialogPane().getButtonTypes().setAll(RESTORE_FROM_BACKUP, REVIEW_BACKUP, IGNORE_BACKUP); - Optional backupPathOpt = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP); + Optional backupPathOpt = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP); String backupFilename = backupPathOpt.map(Path::getFileName).map(Path::toString).orElse(Localization.lang("File not found")); String content = new StringBuilder() .append(Localization.lang("A backup file for '%0' was found at [%1]", diff --git a/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java b/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java index 3c0536bf4af..ceba43dd088 100644 --- a/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java +++ b/src/main/java/org/jabref/gui/dialogs/BackupUIManager.java @@ -63,7 +63,7 @@ private static Optional showReviewBackupDialog(DialogService dialo // This will be modified by using the `DatabaseChangesResolverDialog`. BibDatabaseContext originalDatabase = originalParserResult.getDatabaseContext(); - Path backupPath = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow(); + Path backupPath = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow(); BibDatabaseContext backupDatabase = OpenDatabase.loadDatabase(backupPath, importFormatPreferences, new DummyFileUpdateMonitor()).getDatabaseContext(); DatabaseChangeResolverFactory changeResolverFactory = new DatabaseChangeResolverFactory(dialogService, originalDatabase, preferencesService.getBibEntryPreferences()); diff --git a/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java b/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java index c88930619dd..789671c0b14 100644 --- a/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java +++ b/src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java @@ -64,7 +64,7 @@ public class BackupManager { // During a write, the less recent backup file is deleted private final Queue backupFilesQueue = new LinkedBlockingQueue<>(); - private boolean needsBackup = true; + private boolean needsBackup = false; BackupManager(BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) { this.bibDatabaseContext = bibDatabaseContext; @@ -87,7 +87,7 @@ static Path getBackupPathForNewBackup(Path originalPath) { * Determines the most recent existing backup file name */ static Optional getLatestBackupPath(Path originalPath) { - return BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP); + return BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP); } /** diff --git a/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java index b9e9eac39d4..4522c34429f 100644 --- a/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java +++ b/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java @@ -4,7 +4,6 @@ import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; -import java.io.Serializable; import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Collections; @@ -15,62 +14,24 @@ import java.util.Objects; import java.util.Optional; +import javax.xml.XMLConstants; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLStreamException; import javax.xml.stream.XMLStreamReader; +import javax.xml.stream.events.XMLEvent; import org.jabref.logic.importer.Importer; import org.jabref.logic.importer.ParseException; import org.jabref.logic.importer.Parser; import org.jabref.logic.importer.ParserResult; -import org.jabref.logic.importer.fileformat.medline.Abstract; -import org.jabref.logic.importer.fileformat.medline.AbstractText; -import org.jabref.logic.importer.fileformat.medline.AffiliationInfo; import org.jabref.logic.importer.fileformat.medline.ArticleId; -import org.jabref.logic.importer.fileformat.medline.ArticleIdList; -import org.jabref.logic.importer.fileformat.medline.ArticleTitle; -import org.jabref.logic.importer.fileformat.medline.Author; -import org.jabref.logic.importer.fileformat.medline.AuthorList; -import org.jabref.logic.importer.fileformat.medline.Book; -import org.jabref.logic.importer.fileformat.medline.BookDocument; -import org.jabref.logic.importer.fileformat.medline.BookTitle; -import org.jabref.logic.importer.fileformat.medline.Chemical; -import org.jabref.logic.importer.fileformat.medline.ContributionDate; -import org.jabref.logic.importer.fileformat.medline.DateCompleted; -import org.jabref.logic.importer.fileformat.medline.DateCreated; -import org.jabref.logic.importer.fileformat.medline.DateRevised; -import org.jabref.logic.importer.fileformat.medline.ELocationID; -import org.jabref.logic.importer.fileformat.medline.GeneSymbolList; -import org.jabref.logic.importer.fileformat.medline.GeneralNote; -import org.jabref.logic.importer.fileformat.medline.ISSN; import org.jabref.logic.importer.fileformat.medline.Investigator; -import org.jabref.logic.importer.fileformat.medline.InvestigatorList; -import org.jabref.logic.importer.fileformat.medline.Journal; -import org.jabref.logic.importer.fileformat.medline.JournalIssue; -import org.jabref.logic.importer.fileformat.medline.Keyword; -import org.jabref.logic.importer.fileformat.medline.KeywordList; -import org.jabref.logic.importer.fileformat.medline.MedlineCitation; -import org.jabref.logic.importer.fileformat.medline.MedlineJournalInfo; import org.jabref.logic.importer.fileformat.medline.MeshHeading; -import org.jabref.logic.importer.fileformat.medline.MeshHeadingList; -import org.jabref.logic.importer.fileformat.medline.OtherID; -import org.jabref.logic.importer.fileformat.medline.Pagination; +import org.jabref.logic.importer.fileformat.medline.OtherId; import org.jabref.logic.importer.fileformat.medline.PersonalNameSubject; -import org.jabref.logic.importer.fileformat.medline.PersonalNameSubjectList; -import org.jabref.logic.importer.fileformat.medline.PubDate; -import org.jabref.logic.importer.fileformat.medline.PublicationType; -import org.jabref.logic.importer.fileformat.medline.Publisher; -import org.jabref.logic.importer.fileformat.medline.PubmedArticle; -import org.jabref.logic.importer.fileformat.medline.PubmedArticleSet; -import org.jabref.logic.importer.fileformat.medline.PubmedBookArticle; -import org.jabref.logic.importer.fileformat.medline.PubmedBookArticleSet; -import org.jabref.logic.importer.fileformat.medline.PubmedBookData; -import org.jabref.logic.importer.fileformat.medline.QualifierName; -import org.jabref.logic.importer.fileformat.medline.Section; -import org.jabref.logic.importer.fileformat.medline.Sections; -import org.jabref.logic.importer.fileformat.medline.Text; import org.jabref.logic.util.StandardFileType; import org.jabref.model.entry.BibEntry; +import org.jabref.model.entry.Date; import org.jabref.model.entry.Month; import org.jabref.model.entry.field.Field; import org.jabref.model.entry.field.FieldFactory; @@ -80,10 +41,6 @@ import org.jabref.model.strings.StringUtil; import com.google.common.base.Joiner; -import jakarta.xml.bind.JAXBContext; -import jakarta.xml.bind.JAXBElement; -import jakarta.xml.bind.JAXBException; -import jakarta.xml.bind.Unmarshaller; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -98,7 +55,6 @@ public class MedlineImporter extends Importer implements Parser { private static final String KEYWORD_SEPARATOR = "; "; private static final Locale ENGLISH = Locale.ENGLISH; - private Unmarshaller unmarshaller; private static String join(List list, String string) { return Joiner.on(string).join(list); @@ -140,130 +96,294 @@ public boolean isRecognizedFormat(BufferedReader reader) throws IOException { } @Override - public ParserResult importDatabase(BufferedReader reader) throws IOException { - Objects.requireNonNull(reader); + public ParserResult importDatabase(BufferedReader input) throws IOException { + Objects.requireNonNull(input); List bibItems = new ArrayList<>(); try { - Object unmarshalledObject = unmarshallRoot(reader); - - // check whether we have an article set, an article, a book article or a book article set - if (unmarshalledObject instanceof PubmedArticleSet) { - PubmedArticleSet articleSet = (PubmedArticleSet) unmarshalledObject; - for (Object article : articleSet.getPubmedArticleOrPubmedBookArticle()) { - if (article instanceof PubmedArticle) { - PubmedArticle currentArticle = (PubmedArticle) article; - parseArticle(currentArticle, bibItems); - } - if (article instanceof PubmedBookArticle) { - PubmedBookArticle currentArticle = (PubmedBookArticle) article; - parseBookArticle(currentArticle, bibItems); + XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance(); + + // prevent xxe (https://rules.sonarsource.com/java/RSPEC-2755) + xmlInputFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_SCHEMA, ""); + // required for reading Unicode characters such as ö + xmlInputFactory.setProperty(XMLInputFactory.IS_COALESCING, true); + + XMLStreamReader reader = xmlInputFactory.createXMLStreamReader(input); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "PubmedArticle" -> { + parseArticle(reader, bibItems, elementName); + } + case "PubmedBookArticle" -> { + parseBookArticle(reader, bibItems, elementName); + } } } - } else if (unmarshalledObject instanceof PubmedArticle) { - PubmedArticle article = (PubmedArticle) unmarshalledObject; - parseArticle(article, bibItems); - } else if (unmarshalledObject instanceof PubmedBookArticle) { - PubmedBookArticle currentArticle = (PubmedBookArticle) unmarshalledObject; - parseBookArticle(currentArticle, bibItems); - } else { - PubmedBookArticleSet bookArticleSet = (PubmedBookArticleSet) unmarshalledObject; - for (PubmedBookArticle bookArticle : bookArticleSet.getPubmedBookArticle()) { - parseBookArticle(bookArticle, bibItems); - } } - } catch (JAXBException | XMLStreamException e) { + } catch (XMLStreamException e) { LOGGER.debug("could not parse document", e); return ParserResult.fromError(e); } + return new ParserResult(bibItems); } - private Object unmarshallRoot(BufferedReader reader) throws JAXBException, XMLStreamException { - initUmarshaller(); + private void parseBookArticle(XMLStreamReader reader, List bibItems, String startElement) + throws XMLStreamException { + Map fields = new HashMap<>(); - XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory(); - XMLStreamReader xmlStreamReader = xmlInputFactory.createXMLStreamReader(reader); + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "BookDocument" -> { + parseBookDocument(reader, fields, elementName); + } + case "PublicationStatus" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.PUBSTATE, reader.getText()); + } + } + } + } - // go to the root element - while (!xmlStreamReader.isStartElement()) { - xmlStreamReader.next(); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } } - return unmarshaller.unmarshal(xmlStreamReader); - } + BibEntry entry = new BibEntry(StandardEntryType.Article); + entry.setField(fields); - private void initUmarshaller() throws JAXBException { - if (unmarshaller == null) { - // Lazy init because this is expensive - JAXBContext context = JAXBContext.newInstance("org.jabref.logic.importer.fileformat.medline"); - unmarshaller = context.createUnmarshaller(); - } + bibItems.add(entry); } - private void parseBookArticle(PubmedBookArticle currentArticle, List bibItems) { - Map fields = new HashMap<>(); - if (currentArticle.getBookDocument() != null) { - BookDocument bookDocument = currentArticle.getBookDocument(); - fields.put(StandardField.PMID, bookDocument.getPMID().getContent()); - if (bookDocument.getDateRevised() != null) { - DateRevised dateRevised = bookDocument.getDateRevised(); - addDateRevised(fields, dateRevised); - } - if (bookDocument.getAbstract() != null) { - Abstract abs = bookDocument.getAbstract(); - addAbstract(fields, abs); - } - if (bookDocument.getPagination() != null) { - Pagination pagination = bookDocument.getPagination(); - addPagination(fields, pagination); - } - if (bookDocument.getSections() != null) { - ArrayList result = new ArrayList<>(); - Sections sections = bookDocument.getSections(); - for (Section section : sections.getSection()) { - for (Serializable content : section.getSectionTitle().getContent()) { - if (content instanceof String) { - result.add((String) content); + private void parseBookDocument(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + // multiple occurrences of the following fields can be present + List sectionTitleList = new ArrayList<>(); + List keywordList = new ArrayList<>(); + List publicationTypeList = new ArrayList<>(); + List articleTitleList = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "PMID" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + fields.put(StandardField.PMID, reader.getText()); } } + case "DateRevised", "ContributionDate" -> { + parseDate(reader, fields, elementName); + } + case "Abstract" -> { + addAbstract(reader, fields, elementName); + } + case "Pagination" -> { + addPagination(reader, fields, elementName); + } + case "Section" -> { + parseSections(reader, sectionTitleList); + } + case "Keyword" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + keywordList.add(reader.getText()); + } + } + case "PublicationType" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + publicationTypeList.add(reader.getText()); + } + } + case "ArticleTitle" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + articleTitleList.add(reader.getText()); + } + } + case "Book" -> { + parseBookInformation(reader, fields, elementName); + } } - fields.put(new UnknownField("sections"), join(result, "; ")); } - if (bookDocument.getKeywordList() != null) { - addKeyWords(fields, bookDocument.getKeywordList()); - } - if (bookDocument.getContributionDate() != null) { - addContributionDate(fields, bookDocument.getContributionDate()); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } - if (bookDocument.getPublicationType() != null) { - List result = new ArrayList<>(); - for (PublicationType type : bookDocument.getPublicationType()) { - if (type.getContent() != null) { - result.add(type.getContent()); + } + + // populate multiple occurrence fields + if (!sectionTitleList.isEmpty()) { + fields.put(new UnknownField("sections"), join(sectionTitleList, "; ")); + } + addKeywords(fields, keywordList); + if (!publicationTypeList.isEmpty()) { + fields.put(new UnknownField("pubtype"), join(publicationTypeList, ", ")); + } + if (!articleTitleList.isEmpty()) { + fields.put(new UnknownField("article"), join(articleTitleList, ", ")); + } + } + + private void parseBookInformation(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + List isbnList = new ArrayList<>(); + List titleList = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "PublisherName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.PUBLISHER, reader.getText()); + } + } + case "PublisherLocation" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("publocation"), reader.getText()); + } + } + case "BookTitle" -> { + handleTextElement(reader, titleList, elementName); + } + case "PubDate" -> { + addPubDate(reader, fields, elementName); + } + case "AuthorList" -> { + handleAuthorList(reader, fields, elementName); + } + case "Volume" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.VOLUME, reader.getText()); + } + } + case "Edition" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.EDITION, reader.getText()); + } + } + case "Medium" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("medium"), reader.getText()); + } + } + case "ReportNumber" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("reportnumber"), reader.getText()); + } + } + case "ELocationID" -> { + String eidType = reader.getAttributeValue(null, "EIdType"); + reader.next(); + if (isCharacterXMLEvent(reader)) { + handleElocationId(fields, reader, eidType); + } + } + case "Isbn" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + isbnList.add(reader.getText()); + } } } - fields.put(new UnknownField("pubtype"), join(result, ", ")); } - if (bookDocument.getArticleTitle() != null) { - ArticleTitle articleTitle = bookDocument.getArticleTitle(); - ArrayList titles = new ArrayList<>(); - for (Serializable content : articleTitle.getContent()) { - if (content instanceof String) { - titles.add((String) content); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } + } + + if (!isbnList.isEmpty()) { + fields.put(StandardField.ISBN, join(isbnList, ", ")); + } + + if (!titleList.isEmpty()) { + putIfValueNotNull(fields, StandardField.TITLE, join(titleList, " ")); + } + } + + private void handleElocationId(Map fields, XMLStreamReader reader, String eidType) { + if (eidType.equals("doi")) { + fields.put(StandardField.DOI, reader.getText()); + } + if (eidType.equals("pii")) { + fields.put(new UnknownField("pii"), reader.getText()); + } + } + + private void parseSections(XMLStreamReader reader, List sectionTitleList) throws XMLStreamException { + int sectionLevel = 0; + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "SectionTitle" -> { + reader.next(); + if (isCharacterXMLEvent(reader) && sectionLevel == 0) { + // we only collect SectionTitles from root level Sections + sectionTitleList.add(reader.getText()); + } + } + case "Section" -> { + sectionLevel++; } } - fields.put(new UnknownField("article"), join(titles, ", ")); } - if (bookDocument.getBook() != null) { - addBookInformation(fields, bookDocument.getBook()); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals("Section")) { + if (sectionLevel == 0) { + break; + } else { + sectionLevel--; + } } } + } + + private void parseArticle(XMLStreamReader reader, List bibItems, String startElement) + throws XMLStreamException { + Map fields = new HashMap<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "MedlineCitation" -> { + parseMedlineCitation(reader, fields, elementName); + } + case "PubmedData" -> { + parsePubmedData(reader, fields, elementName); + } + } + } - if (currentArticle.getPubmedBookData() != null) { - PubmedBookData bookData = currentArticle.getPubmedBookData(); - putIfValueNotNull(fields, StandardField.PUBSTATE, bookData.getPublicationStatus()); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } } BibEntry entry = new BibEntry(StandardEntryType.Article); @@ -272,373 +392,752 @@ private void parseBookArticle(PubmedBookArticle currentArticle, List b bibItems.add(entry); } - private void addBookInformation(Map fields, Book book) { - if (book.getPublisher() != null) { - Publisher publisher = book.getPublisher(); - putIfValueNotNull(fields, new UnknownField("publocation"), publisher.getPublisherLocation()); - putStringFromSerializableList(fields, StandardField.PUBLISHER, publisher.getPublisherName().getContent()); - } - if (book.getBookTitle() != null) { - BookTitle title = book.getBookTitle(); - putStringFromSerializableList(fields, StandardField.TITLE, title.getContent()); - } - if (book.getPubDate() != null) { - addPubDate(fields, book.getPubDate()); - } - if (book.getAuthorList() != null) { - List authorLists = book.getAuthorList(); - // authorLists size should be one - if (authorLists.size() == 1) { - for (AuthorList authorList : authorLists) { - handleAuthors(fields, authorList); + private void parsePubmedData(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + String publicationStatus = ""; + List articleIdList = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "PublicationStatus" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + publicationStatus = reader.getText(); + } + } + case "ArticleId" -> { + String idType = reader.getAttributeValue(null, "IdType"); + reader.next(); + if (isCharacterXMLEvent(reader)) { + articleIdList.add(new ArticleId(idType, reader.getText())); + } + } } - } else { - LOGGER.info(String.format("Size of authorlist was %s", authorLists.size())); } - } - putIfValueNotNull(fields, StandardField.VOLUME, book.getVolume()); - putIfValueNotNull(fields, StandardField.EDITION, book.getEdition()); - putIfValueNotNull(fields, new UnknownField("medium"), book.getMedium()); - putIfValueNotNull(fields, new UnknownField("reportnumber"), book.getReportNumber()); - - if (book.getELocationID() != null) { - for (ELocationID id : book.getELocationID()) { - addElocationID(fields, id); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - if (book.getIsbn() != null) { - fields.put(StandardField.ISBN, join(book.getIsbn(), ", ")); + + if (fields.get(new UnknownField("revised")) != null) { + putIfValueNotNull(fields, StandardField.PUBSTATE, publicationStatus); + if (!articleIdList.isEmpty()) { + addArticleIdList(fields, articleIdList); + } } } - private void putStringFromSerializableList(Map fields, Field field, List contentList) { - StringBuilder result = new StringBuilder(); - for (Serializable content : contentList) { - if (content instanceof String) { - result.append((String) content); + private void parseMedlineCitation(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + // multiple occurrences of the following fields can be present + List citationSubsets = new ArrayList<>(); + List meshHeadingList = new ArrayList<>(); + List personalNameSubjectList = new ArrayList<>(); + List otherIdList = new ArrayList<>(); + List keywordList = new ArrayList<>(); + List spaceFlightMissionList = new ArrayList<>(); + List investigatorList = new ArrayList<>(); + List generalNoteList = new ArrayList<>(); + + String status = reader.getAttributeValue(null, "Status"); + String owner = reader.getAttributeValue(null, "Owner"); + int latestVersion = 0; + fields.put(new UnknownField("status"), status); + fields.put(StandardField.OWNER, owner); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "DateCreated", "DateCompleted", "DateRevised" -> { + parseDate(reader, fields, elementName); + } + case "Article" -> { + parseArticleInformation(reader, fields); + } + case "PMID" -> { + String versionStr = reader.getAttributeValue(null, "Version"); + reader.next(); + if (versionStr != null) { + int version = Integer.parseInt(versionStr); + if (isCharacterXMLEvent(reader) && version > latestVersion) { + latestVersion = version; + fields.put(StandardField.PMID, reader.getText()); + } + } + } + case "MedlineJournalInfo" -> { + parseMedlineJournalInfo(reader, fields, elementName); + } + case "ChemicalList" -> { + parseChemicalList(reader, fields, elementName); + } + case "CitationSubset" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + citationSubsets.add(reader.getText()); + } + } + case "GeneSymbolList" -> { + parseGeneSymbolList(reader, fields, elementName); + } + case "MeshHeading" -> { + parseMeshHeading(reader, meshHeadingList, elementName); + } + case "NumberOfReferences" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("references"), reader.getText()); + } + } + case "PersonalNameSubject" -> { + parsePersonalNameSubject(reader, personalNameSubjectList, elementName); + } + case "OtherID" -> { + String otherIdSource = reader.getAttributeValue(null, "Source"); + reader.next(); + if (isCharacterXMLEvent(reader)) { + String content = reader.getText(); + otherIdList.add(new OtherId(otherIdSource, content)); + } + } + case "Keyword" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + keywordList.add(reader.getText()); + } + } + case "SpaceFlightMission" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + spaceFlightMissionList.add(reader.getText()); + } + } + case "Investigator" -> { + parseInvestigator(reader, investigatorList, elementName); + } + case "GeneralNote" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + generalNoteList.add(reader.getText()); + } + } + } + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - if (result.length() > 0) { - fields.put(field, result.toString()); + + // populate multiple occurrence fields + if (!citationSubsets.isEmpty()) { + fields.put(new UnknownField("citation-subset"), join(citationSubsets, ", ")); + } + addMeshHeading(fields, meshHeadingList); + addPersonalNames(fields, personalNameSubjectList); + addOtherId(fields, otherIdList); + addKeywords(fields, keywordList); + if (!spaceFlightMissionList.isEmpty()) { + fields.put(new UnknownField("space-flight-mission"), join(spaceFlightMissionList, ", ")); } + addInvestigators(fields, investigatorList); + addNotes(fields, generalNoteList); } - private void addContributionDate(Map fields, ContributionDate contributionDate) { - if ((contributionDate.getDay() != null) && (contributionDate.getMonth() != null) - && (contributionDate.getYear() != null)) { - String result = convertToDateFormat(contributionDate.getYear(), contributionDate.getMonth(), - contributionDate.getDay()); - fields.put(new UnknownField("contribution"), result); + private void parseInvestigator(XMLStreamReader reader, List investigatorList, String startElement) + throws XMLStreamException { + String lastName = ""; + String foreName = ""; + List affiliationList = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "LastName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + lastName = reader.getText(); + } + } + case "ForeName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + foreName = reader.getText(); + } + } + case "Affiliation" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + affiliationList.add(reader.getText()); + } + } + } + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } } - } - private String convertToDateFormat(String year, String month, String day) { - return String.format("%s-%s-%s", year, month, day); + investigatorList.add(new Investigator(lastName, foreName, affiliationList)); } - private void parseArticle(PubmedArticle article, List bibItems) { - Map fields = new HashMap<>(); + private void parsePersonalNameSubject(XMLStreamReader reader, List personalNameSubjectList, String startElement) + throws XMLStreamException { + String lastName = ""; + String foreName = ""; + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "LastName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + lastName = reader.getText(); + } + } + case "ForeName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + foreName = reader.getText(); + } + } + } + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } + } - if (article.getPubmedData() != null) { - if (article.getMedlineCitation().getDateRevised() != null) { - DateRevised dateRevised = article.getMedlineCitation().getDateRevised(); - addDateRevised(fields, dateRevised); - putIfValueNotNull(fields, StandardField.PUBSTATE, article.getPubmedData().getPublicationStatus()); - if (article.getPubmedData().getArticleIdList() != null) { - ArticleIdList articleIdList = article.getPubmedData().getArticleIdList(); - addArticleIdList(fields, articleIdList); + personalNameSubjectList.add(new PersonalNameSubject(lastName, foreName)); + } + + private void parseMeshHeading(XMLStreamReader reader, List meshHeadingList, String startElement) + throws XMLStreamException { + String descriptorName = ""; + List qualifierNames = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "DescriptorName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + descriptorName = reader.getText(); + } + } + case "QualifierName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + qualifierNames.add(reader.getText()); + } + } } } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; + } } - if (article.getMedlineCitation() != null) { - MedlineCitation medlineCitation = article.getMedlineCitation(); - fields.put(new UnknownField("status"), medlineCitation.getStatus()); - DateCreated dateCreated = medlineCitation.getDateCreated(); - if (medlineCitation.getDateCreated() != null) { - fields.put(new UnknownField("created"), - convertToDateFormat(dateCreated.getYear(), dateCreated.getMonth(), dateCreated.getDay())); + meshHeadingList.add(new MeshHeading(descriptorName, qualifierNames)); + } + + private void parseGeneSymbolList(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + List geneSymbols = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + if (elementName.equals("GeneSymbol")) { + reader.next(); + if (isCharacterXMLEvent(reader)) { + geneSymbols.add(reader.getText()); + } + } } - fields.put(new UnknownField("pubmodel"), medlineCitation.getArticle().getPubModel()); - if (medlineCitation.getDateCompleted() != null) { - DateCompleted dateCompleted = medlineCitation.getDateCompleted(); - fields.put(new UnknownField("completed"), - convertToDateFormat(dateCompleted.getYear(), dateCompleted.getMonth(), dateCompleted.getDay())); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } + } - fields.put(StandardField.PMID, medlineCitation.getPMID().getContent()); - fields.put(StandardField.OWNER, medlineCitation.getOwner()); + if (!geneSymbols.isEmpty()) { + fields.put(new UnknownField("gene-symbols"), join(geneSymbols, ", ")); + } + } - addArticleInformation(fields, medlineCitation.getArticle().getContent()); + private void parseChemicalList(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + List chemicalNames = new ArrayList<>(); - MedlineJournalInfo medlineJournalInfo = medlineCitation.getMedlineJournalInfo(); - putIfValueNotNull(fields, new UnknownField("country"), medlineJournalInfo.getCountry()); - putIfValueNotNull(fields, new UnknownField("journal-abbreviation"), medlineJournalInfo.getMedlineTA()); - putIfValueNotNull(fields, new UnknownField("nlm-id"), medlineJournalInfo.getNlmUniqueID()); - putIfValueNotNull(fields, new UnknownField("issn-linking"), medlineJournalInfo.getISSNLinking()); - if (medlineCitation.getChemicalList() != null) { - if (medlineCitation.getChemicalList().getChemical() != null) { - addChemicals(fields, medlineCitation.getChemicalList().getChemical()); + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + if (elementName.equals("NameOfSubstance")) { + reader.next(); + if (isCharacterXMLEvent(reader)) { + chemicalNames.add(reader.getText()); + } } } - if (medlineCitation.getCitationSubset() != null) { - fields.put(new UnknownField("citation-subset"), join(medlineCitation.getCitationSubset(), ", ")); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } - if (medlineCitation.getGeneSymbolList() != null) { - addGeneSymbols(fields, medlineCitation.getGeneSymbolList()); + } + + fields.put(new UnknownField("chemicals"), join(chemicalNames, ", ")); + } + + private void parseMedlineJournalInfo(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "Country" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("country"), reader.getText()); + } + } + case "MedlineTA" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("journal-abbreviation"), reader.getText()); + } + } + case "NlmUniqueID" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("nlm-id"), reader.getText()); + } + } + case "ISSNLinking" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("issn-linking"), reader.getText()); + } + } + } } - if (medlineCitation.getMeshHeadingList() != null) { - addMeashHeading(fields, medlineCitation.getMeshHeadingList()); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } - putIfValueNotNull(fields, new UnknownField("references"), medlineCitation.getNumberOfReferences()); - if (medlineCitation.getPersonalNameSubjectList() != null) { - addPersonalNames(fields, medlineCitation.getPersonalNameSubjectList()); + } + } + + private void parseArticleInformation(XMLStreamReader reader, Map fields) throws XMLStreamException { + List titleList = new ArrayList<>(); + String pubmodel = reader.getAttributeValue(null, "PubModel"); + fields.put(new UnknownField("pubmodel"), pubmodel); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "Journal" -> { + parseJournal(reader, fields); + } + case "ArticleTitle" -> { + handleTextElement(reader, titleList, elementName); + } + case "Pagination" -> { + addPagination(reader, fields, elementName); + } + case "ELocationID" -> { + String eidType = reader.getAttributeValue(null, "EIdType"); + String validYN = reader.getAttributeValue(null, "ValidYN"); + reader.next(); + if (isCharacterXMLEvent(reader) && "Y".equals(validYN)) { + handleElocationId(fields, reader, eidType); + } + } + case "Abstract" -> { + addAbstract(reader, fields, elementName); + } + case "AuthorList" -> { + handleAuthorList(reader, fields, elementName); + } + } } - if (medlineCitation.getOtherID() != null) { - addOtherId(fields, medlineCitation.getOtherID()); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals("Article")) { + break; } - if (medlineCitation.getKeywordList() != null) { - addKeyWords(fields, medlineCitation.getKeywordList()); + } + + if (!titleList.isEmpty()) { + fields.put(StandardField.TITLE, StringUtil.stripBrackets(join(titleList, " "))); + } + } + + private void parseJournal(XMLStreamReader reader, Map fields) throws XMLStreamException { + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "Title" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.JOURNAL, reader.getText()); + } + } + case "ISSN" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.ISSN, reader.getText()); + } + } + case "Volume" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.VOLUME, reader.getText()); + } + } + case "Issue" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.ISSUE, reader.getText()); + } + } + case "PubDate" -> { + addPubDate(reader, fields, elementName); + } + } } - if (medlineCitation.getSpaceFlightMission() != null) { - fields.put(new UnknownField("space-flight-mission"), join(medlineCitation.getSpaceFlightMission(), ", ")); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals("Journal")) { + break; } - if (medlineCitation.getInvestigatorList() != null) { - addInvestigators(fields, medlineCitation.getInvestigatorList()); + } + } + + private void parseDate(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + Optional year = Optional.empty(); + Optional month = Optional.empty(); + Optional day = Optional.empty(); + + // mapping from date XML element to field name + Map dateFieldMap = Map.of( + "DateCreated", "created", + "DateCompleted", "completed", + "DateRevised", "revised", + "ContributionDate", "contribution", + "PubDate", "" + ); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "Year" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + year = Optional.of(reader.getText()); + } + } + case "Month" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + month = Optional.of(reader.getText()); + } + } + case "Day" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + day = Optional.of(reader.getText()); + } + } + } } - if (medlineCitation.getGeneralNote() != null) { - addNotes(fields, medlineCitation.getGeneralNote()); + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - BibEntry entry = new BibEntry(StandardEntryType.Article); - entry.setField(fields); - - bibItems.add(entry); + Optional date = Date.parse(year, month, day); + date.ifPresent(dateValue -> + fields.put(new UnknownField(dateFieldMap.get(startElement)), dateValue.getNormalized())); } - private void addArticleIdList(Map fields, ArticleIdList articleIdList) { - for (ArticleId id : articleIdList.getArticleId()) { - if (id.getIdType() != null) { - if ("pubmed".equals(id.getIdType())) { - fields.put(StandardField.PMID, id.getContent()); + private void addArticleIdList(Map fields, List articleIdList) { + for (ArticleId id : articleIdList) { + if (!id.idType().isBlank()) { + if ("pubmed".equals(id.idType())) { + fields.computeIfAbsent(StandardField.PMID, k -> id.content()); } else { - fields.put(FieldFactory.parseField(StandardEntryType.Article, id.getIdType()), id.getContent()); + fields.computeIfAbsent(FieldFactory.parseField(StandardEntryType.Article, id.idType()), k -> id.content()); } } } } - private void addNotes(Map fields, List generalNote) { + private void addNotes(Map fields, List generalNoteList) { List notes = new ArrayList<>(); - for (GeneralNote note : generalNote) { - if (note != null) { - notes.add(note.getContent()); + + for (String note : generalNoteList) { + if (!note.isBlank()) { + notes.add(note); } } - fields.put(StandardField.NOTE, join(notes, ", ")); + + if (!notes.isEmpty()) { + fields.put(StandardField.NOTE, join(notes, ", ")); + } } - private void addInvestigators(Map fields, InvestigatorList investigatorList) { + private void addInvestigators(Map fields, List investigatorList) { List investigatorNames = new ArrayList<>(); List affiliationInfos = new ArrayList<>(); - String name; + // add the investigators like the authors - if (investigatorList.getInvestigator() != null) { - List investigators = investigatorList.getInvestigator(); - for (Investigator investigator : investigators) { - name = investigator.getLastName(); - if (investigator.getForeName() != null) { - name += ", " + investigator.getForeName(); + if (!investigatorList.isEmpty()) { + for (Investigator investigator : investigatorList) { + StringBuilder result = new StringBuilder(investigator.lastName()); + if (!investigator.foreName().isBlank()) { + result.append(", ").append(investigator.foreName()); } - investigatorNames.add(name); + investigatorNames.add(result.toString()); // now add the affiliation info - if (investigator.getAffiliationInfo() != null) { - for (AffiliationInfo info : investigator.getAffiliationInfo()) { - for (Serializable affiliation : info.getAffiliation().getContent()) { - if (affiliation instanceof String) { - affiliationInfos.add((String) affiliation); - } - } - } - fields.put(new UnknownField("affiliation"), join(affiliationInfos, ", ")); + if (!investigator.affiliationList().isEmpty()) { + affiliationInfos.addAll(investigator.affiliationList()); } } + + if (!affiliationInfos.isEmpty()) { + fields.put(new UnknownField("affiliation"), join(affiliationInfos, ", ")); + } + fields.put(new UnknownField("investigator"), join(investigatorNames, " and ")); } } - private void addKeyWords(Map fields, List allKeywordLists) { - List keywordStrings = new ArrayList<>(); - // add keywords to the list - for (KeywordList keywordList : allKeywordLists) { - for (Keyword keyword : keywordList.getKeyword()) { - for (Serializable content : keyword.getContent()) { - if (content instanceof String) { - keywordStrings.add((String) content); - } - } - } - } - // Check whether MeshHeadingList exist or not + private void addKeywords(Map fields, List keywordList) { + // Check whether MeshHeadingList exists or not if (fields.get(StandardField.KEYWORDS) == null) { - fields.put(StandardField.KEYWORDS, join(keywordStrings, KEYWORD_SEPARATOR)); + fields.put(StandardField.KEYWORDS, join(keywordList, KEYWORD_SEPARATOR)); } else { - if (keywordStrings.size() > 0) { + if (!keywordList.isEmpty()) { // if it exists, combine the MeshHeading with the keywords - String result = join(keywordStrings, "; "); + String result = join(keywordList, "; "); result = fields.get(StandardField.KEYWORDS) + KEYWORD_SEPARATOR + result; fields.put(StandardField.KEYWORDS, result); } } } - private void addOtherId(Map fields, List otherID) { - for (OtherID id : otherID) { - if ((id.getSource() != null) && (id.getContent() != null)) { - fields.put(FieldFactory.parseField(StandardEntryType.Article, id.getSource()), id.getContent()); + private void addOtherId(Map fields, List otherIdList) { + for (OtherId id : otherIdList) { + if (!id.source().isBlank() && !id.content().isBlank()) { + fields.put(FieldFactory.parseField(StandardEntryType.Article, id.source()), id.content()); } } } - private void addPersonalNames(Map fields, PersonalNameSubjectList personalNameSubjectList) { + private void addPersonalNames(Map fields, List personalNameSubjectList) { if (fields.get(StandardField.AUTHOR) == null) { // if no authors appear, then add the personal names as authors List personalNames = new ArrayList<>(); - if (personalNameSubjectList.getPersonalNameSubject() != null) { - List personalNameSubject = personalNameSubjectList.getPersonalNameSubject(); - for (PersonalNameSubject personalName : personalNameSubject) { - String name = personalName.getLastName(); - if (personalName.getForeName() != null) { - name += ", " + personalName.getForeName(); - } - personalNames.add(name); + + if (!personalNameSubjectList.isEmpty()) { + for (PersonalNameSubject personalNameSubject : personalNameSubjectList) { + StringBuilder result = new StringBuilder(personalNameSubject.lastName()); + if (!personalNameSubject.foreName().isBlank()) { + result.append(", ").append(personalNameSubject.foreName()); + } + personalNames.add(result.toString()); } + fields.put(StandardField.AUTHOR, join(personalNames, " and ")); } } } - private void addMeashHeading(Map fields, MeshHeadingList meshHeadingList) { - ArrayList keywords = new ArrayList<>(); - for (MeshHeading keyword : meshHeadingList.getMeshHeading()) { - StringBuilder result = new StringBuilder(keyword.getDescriptorName().getContent()); - if (keyword.getQualifierName() != null) { - for (QualifierName qualifier : keyword.getQualifierName()) { - result.append(", ").append(qualifier.getContent()); + private void addMeshHeading(Map fields, List meshHeadingList) { + List keywords = new ArrayList<>(); + + if (!meshHeadingList.isEmpty()) { + for (MeshHeading meshHeading : meshHeadingList) { + StringBuilder result = new StringBuilder(meshHeading.descriptorName()); + if (meshHeading.qualifierNames() != null) { + for (String qualifierName : meshHeading.qualifierNames()) { + result.append(", ").append(qualifierName); + } } + keywords.add(result.toString()); } - keywords.add(result.toString()); + + fields.put(StandardField.KEYWORDS, join(keywords, KEYWORD_SEPARATOR)); } - fields.put(StandardField.KEYWORDS, join(keywords, KEYWORD_SEPARATOR)); } - private void addGeneSymbols(Map fields, GeneSymbolList geneSymbolList) { - List geneSymbols = geneSymbolList.getGeneSymbol(); - fields.put(new UnknownField("gene-symbols"), join(geneSymbols, ", ")); - } + private void addPubDate(XMLStreamReader reader, Map fields, String startElement) throws XMLStreamException { + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "MedlineDate" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + fields.put(StandardField.YEAR, extractYear(reader.getText())); + } + } + case "Year" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + fields.put(StandardField.YEAR, reader.getText()); + } + } + case "Month" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + Optional month = Month.parse(reader.getText()); + month.ifPresent(monthValue -> fields.put(StandardField.MONTH, monthValue.getJabRefFormat())); + } + } + case "Season" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + fields.put(new UnknownField("season"), reader.getText()); + } + } + } + } - private void addChemicals(Map fields, List chemicals) { - List chemicalNames = new ArrayList<>(); - for (Chemical chemical : chemicals) { - if (chemical != null) { - chemicalNames.add(chemical.getNameOfSubstance().getContent()); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - fields.put(new UnknownField("chemicals"), join(chemicalNames, ", ")); } - private void addArticleInformation(Map fields, List content) { - for (Object object : content) { - if (object instanceof Journal) { - Journal journal = (Journal) object; - putIfValueNotNull(fields, StandardField.JOURNAL, journal.getTitle()); - - ISSN issn = journal.getISSN(); - if (issn != null) { - putIfValueNotNull(fields, StandardField.ISSN, issn.getContent()); + private void addAbstract(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { + List abstractTextList = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "CopyrightInformation" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, new UnknownField("copyright"), reader.getText()); + } + } + case "AbstractText" -> { + handleTextElement(reader, abstractTextList, elementName); + } } + } - JournalIssue journalIssue = journal.getJournalIssue(); - putIfValueNotNull(fields, StandardField.VOLUME, journalIssue.getVolume()); - putIfValueNotNull(fields, StandardField.ISSUE, journalIssue.getIssue()); - - addPubDate(fields, journalIssue.getPubDate()); - } else if (object instanceof ArticleTitle) { - ArticleTitle articleTitle = (ArticleTitle) object; - fields.put(StandardField.TITLE, StringUtil.stripBrackets(articleTitle.getContent().toString())); - } else if (object instanceof Pagination) { - Pagination pagination = (Pagination) object; - addPagination(fields, pagination); - } else if (object instanceof ELocationID) { - ELocationID eLocationID = (ELocationID) object; - addElocationID(fields, eLocationID); - } else if (object instanceof Abstract) { - Abstract abs = (Abstract) object; - addAbstract(fields, abs); - } else if (object instanceof AuthorList) { - AuthorList authors = (AuthorList) object; - handleAuthors(fields, authors); + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - } - private void addElocationID(Map fields, ELocationID eLocationID) { - if (eLocationID.getEIdType().equals("doi")) { - fields.put(StandardField.DOI, eLocationID.getContent()); - } - if (eLocationID.getEIdType().equals("pii")) { - fields.put(new UnknownField("pii"), eLocationID.getContent()); + if (!abstractTextList.isEmpty()) { + fields.put(StandardField.ABSTRACT, join(abstractTextList, " ")); } } - private void addPubDate(Map fields, PubDate pubDate) { - if (pubDate.getYear() == null) { - // if year of the pubdate is null, the medlineDate shouldn't be null - fields.put(StandardField.YEAR, extractYear(pubDate.getMedlineDate())); - } else { - fields.put(StandardField.YEAR, pubDate.getYear()); - if (pubDate.getMonth() != null) { - Optional month = Month.parse(pubDate.getMonth()); - if (month.isPresent()) { - fields.put(StandardField.MONTH, month.get().getJabRefFormat()); + /** + * Handles text entities that can have inner tags such as {@literal <}i{@literal >}, {@literal <}b{@literal >} etc. + * We ignore the tags and return only the characters present in the enclosing parent element. + * + */ + private void handleTextElement(XMLStreamReader reader, List textList, String startElement) + throws XMLStreamException { + StringBuilder result = new StringBuilder(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "sup", "sub" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + result.append("(").append(reader.getText()).append(")"); + } + } } - } else if (pubDate.getSeason() != null) { - fields.put(new UnknownField("season"), pubDate.getSeason()); + } else if (isCharacterXMLEvent(reader)) { + result.append(reader.getText().trim()).append(" "); } - } - } - private void addAbstract(Map fields, Abstract abs) { - putIfValueNotNull(fields, new UnknownField("copyright"), abs.getCopyrightInformation()); - List abstractText = new ArrayList<>(); - for (AbstractText text : abs.getAbstractText()) { - for (Serializable textContent : text.getContent()) { - if (textContent instanceof String) { - abstractText.add((String) textContent); - } + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } - fields.put(StandardField.ABSTRACT, join(abstractText, " ")); + + textList.add(result.toString().trim()); } - private void addPagination(Map fields, Pagination pagination) { + private void addPagination(XMLStreamReader reader, Map fields, String startElement) + throws XMLStreamException { String startPage = ""; String endPage = ""; - for (JAXBElement element : pagination.getContent()) { - if ("MedlinePgn".equals(element.getName().getLocalPart())) { - putIfValueNotNull(fields, StandardField.PAGES, fixPageRange(element.getValue())); - } else if ("StartPage".equals(element.getName().getLocalPart())) { - // it could happen, that the article has only a start page - startPage = element.getValue() + endPage; - putIfValueNotNull(fields, StandardField.PAGES, startPage); - } else if ("EndPage".equals(element.getName().getLocalPart())) { - endPage = element.getValue(); - // but it should not happen, that a endpage appears without startpage - fields.put(StandardField.PAGES, fixPageRange(startPage + "-" + endPage)); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "MedlinePgn" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + putIfValueNotNull(fields, StandardField.PAGES, fixPageRange(reader.getText())); + } + } + case "StartPage" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + // it could happen, that the article has only a start page + startPage = reader.getText() + endPage; + putIfValueNotNull(fields, StandardField.PAGES, startPage); + } + } + case "EndPage" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + endPage = reader.getText(); + // but it should not happen, that a endpage appears without startpage + fields.put(StandardField.PAGES, fixPageRange(startPage + "-" + endPage)); + } + } + } + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } } @@ -648,31 +1147,68 @@ private String extractYear(String medlineDate) { return medlineDate.substring(0, 4); } - private void handleAuthors(Map fields, AuthorList authors) { + private void handleAuthorList(XMLStreamReader reader, Map fields, String startElement) throws XMLStreamException { List authorNames = new ArrayList<>(); - for (Author author : authors.getAuthor()) { - if (author.getCollectiveName() != null) { - Text collectiveNames = author.getCollectiveName(); - for (Serializable content : collectiveNames.getContent()) { - if (content instanceof String) { - authorNames.add((String) content); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "Author" -> { + parseAuthor(reader, authorNames); } } - } else { - String authorName = author.getLastName(); - if (author.getForeName() != null) { - authorName += ", " + author.getForeName(); - } - authorNames.add(authorName); + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals(startElement)) { + break; } } + fields.put(StandardField.AUTHOR, join(authorNames, " and ")); } - private void addDateRevised(Map fields, DateRevised dateRevised) { - if ((dateRevised.getDay() != null) && (dateRevised.getMonth() != null) && (dateRevised.getYear() != null)) { - fields.put(new UnknownField("revised"), - convertToDateFormat(dateRevised.getYear(), dateRevised.getMonth(), dateRevised.getDay())); + private void parseAuthor(XMLStreamReader reader, List authorNames) throws XMLStreamException { + StringBuilder authorName = new StringBuilder(); + List collectiveNames = new ArrayList<>(); + + while (reader.hasNext()) { + reader.next(); + if (isStartXMLEvent(reader)) { + String elementName = reader.getName().getLocalPart(); + switch (elementName) { + case "CollectiveName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + collectiveNames.add(reader.getText()); + } + } + case "LastName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + authorName = new StringBuilder(reader.getText()); + } + } + case "ForeName" -> { + reader.next(); + if (isCharacterXMLEvent(reader)) { + authorName.append(", ").append(reader.getText()); + } + } + } + } + + if (isEndXMLEvent(reader) && reader.getName().getLocalPart().equals("Author")) { + break; + } + } + + if (collectiveNames.size() > 0) { + authorNames.addAll(collectiveNames); + } + if (!authorName.toString().isBlank()) { + authorNames.add(authorName.toString()); } } @@ -683,7 +1219,8 @@ private void putIfValueNotNull(Map fields, Field field, String va } /** - * Convert medline page ranges from short form to full form. Medline reports page ranges in a shorthand format. The last page is reported using only the digits which differ from the first page. i.e. 12345-51 refers to the actual range 12345-12351 + * Convert medline page ranges from short form to full form. Medline reports page ranges in a shorthand format. + * The last page is reported using only the digits which differ from the first page. i.e. 12345-51 refers to the actual range 12345-12351 */ private String fixPageRange(String pageRange) { int minusPos = pageRange.indexOf('-'); @@ -700,6 +1237,18 @@ private String fixPageRange(String pageRange) { return startPage + "--" + endPage; } + private boolean isCharacterXMLEvent(XMLStreamReader reader) { + return reader.getEventType() == XMLEvent.CHARACTERS; + } + + private boolean isStartXMLEvent(XMLStreamReader reader) { + return reader.getEventType() == XMLEvent.START_ELEMENT; + } + + private boolean isEndXMLEvent(XMLStreamReader reader) { + return reader.getEventType() == XMLEvent.END_ELEMENT; + } + @Override public List parseEntries(InputStream inputStream) throws ParseException { try { diff --git a/src/main/java/org/jabref/logic/importer/fileformat/medline/ArticleId.java b/src/main/java/org/jabref/logic/importer/fileformat/medline/ArticleId.java new file mode 100644 index 00000000000..3a8be1b9b63 --- /dev/null +++ b/src/main/java/org/jabref/logic/importer/fileformat/medline/ArticleId.java @@ -0,0 +1,7 @@ +package org.jabref.logic.importer.fileformat.medline; + +public record ArticleId( + String idType, + String content +) { +} diff --git a/src/main/java/org/jabref/logic/importer/fileformat/medline/Investigator.java b/src/main/java/org/jabref/logic/importer/fileformat/medline/Investigator.java new file mode 100644 index 00000000000..64ea31e6206 --- /dev/null +++ b/src/main/java/org/jabref/logic/importer/fileformat/medline/Investigator.java @@ -0,0 +1,10 @@ +package org.jabref.logic.importer.fileformat.medline; + +import java.util.List; + +public record Investigator( + String lastName, + String foreName, + List affiliationList +) { +} diff --git a/src/main/java/org/jabref/logic/importer/fileformat/medline/MeshHeading.java b/src/main/java/org/jabref/logic/importer/fileformat/medline/MeshHeading.java new file mode 100644 index 00000000000..a78f65f9727 --- /dev/null +++ b/src/main/java/org/jabref/logic/importer/fileformat/medline/MeshHeading.java @@ -0,0 +1,9 @@ +package org.jabref.logic.importer.fileformat.medline; + +import java.util.List; + +public record MeshHeading( + String descriptorName, + List qualifierNames +) { +} diff --git a/src/main/java/org/jabref/logic/importer/fileformat/medline/OtherId.java b/src/main/java/org/jabref/logic/importer/fileformat/medline/OtherId.java new file mode 100644 index 00000000000..4429436c332 --- /dev/null +++ b/src/main/java/org/jabref/logic/importer/fileformat/medline/OtherId.java @@ -0,0 +1,7 @@ +package org.jabref.logic.importer.fileformat.medline; + +public record OtherId( + String source, + String content +) { +} diff --git a/src/main/java/org/jabref/logic/importer/fileformat/medline/PersonalNameSubject.java b/src/main/java/org/jabref/logic/importer/fileformat/medline/PersonalNameSubject.java new file mode 100644 index 00000000000..bda9c6aefff --- /dev/null +++ b/src/main/java/org/jabref/logic/importer/fileformat/medline/PersonalNameSubject.java @@ -0,0 +1,7 @@ +package org.jabref.logic.importer.fileformat.medline; + +public record PersonalNameSubject( + String lastName, + String foreName +) { +} diff --git a/src/main/java/org/jabref/logic/util/OS.java b/src/main/java/org/jabref/logic/util/OS.java index fabbadbd2c9..52a29bcdedc 100644 --- a/src/main/java/org/jabref/logic/util/OS.java +++ b/src/main/java/org/jabref/logic/util/OS.java @@ -8,7 +8,7 @@ public class OS { public static final String NEWLINE = System.lineSeparator(); - public static final String APP_DIR_APP_NAME = "JabRef"; + public static final String APP_DIR_APP_NAME = "jabref"; public static final String APP_DIR_APP_AUTHOR = "org.jabref"; // File separator obtained from system diff --git a/src/main/java/org/jabref/logic/util/io/BackupFileUtil.java b/src/main/java/org/jabref/logic/util/io/BackupFileUtil.java index f669f2ee567..c378386c1ed 100644 --- a/src/main/java/org/jabref/logic/util/io/BackupFileUtil.java +++ b/src/main/java/org/jabref/logic/util/io/BackupFileUtil.java @@ -10,7 +10,6 @@ import java.util.Optional; import org.jabref.logic.util.BackupFileType; -import org.jabref.logic.util.BuildInfo; import org.jabref.logic.util.OS; import net.harawata.appdirs.AppDirsFactory; @@ -25,11 +24,11 @@ private BackupFileUtil() { } public static Path getAppDataBackupDir() { - Path directory = Path.of(AppDirsFactory.getInstance().getUserDataDir( - OS.APP_DIR_APP_NAME, - new BuildInfo().version.toString(), - OS.APP_DIR_APP_AUTHOR)) - .resolve("backups"); + Path directory = Path.of(AppDirsFactory.getInstance() + .getUserDataDir( + OS.APP_DIR_APP_NAME, + "backups", + OS.APP_DIR_APP_AUTHOR)); return directory; } @@ -72,7 +71,7 @@ public static Path getPathForNewBackupFileAndCreateDirectory(Path targetFile, Ba * * @param targetFile the full path of the file to backup */ - public static Optional getPathOfLatestExisingBackupFile(Path targetFile, BackupFileType fileType) { + public static Optional getPathOfLatestExistingBackupFile(Path targetFile, BackupFileType fileType) { // The code is similar to "getPathForNewBackupFileAndCreateDirectory" String extension = "." + fileType.getExtensions().get(0); diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java index f3202faa549..4781e359d7d 100644 --- a/src/main/java/org/jabref/preferences/JabRefPreferences.java +++ b/src/main/java/org/jabref/preferences/JabRefPreferences.java @@ -530,7 +530,10 @@ private JabRefPreferences() { // SSL defaults.put(TRUSTSTORE_PATH, Path.of(AppDirsFactory.getInstance() - .getUserDataDir(OS.APP_DIR_APP_NAME, "ssl", OS.APP_DIR_APP_AUTHOR)) + .getUserDataDir( + OS.APP_DIR_APP_NAME, + "ssl", + OS.APP_DIR_APP_AUTHOR)) .resolve("truststore.jks").toString()); defaults.put(POS_X, 0); diff --git a/src/main/resources/xjc/medline/medline.xsd b/src/main/resources/xjc/medline/medline.xsd deleted file mode 100644 index 9c2f73a5bdd..00000000000 --- a/src/main/resources/xjc/medline/medline.xsd +++ /dev/null @@ -1,314 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.bib b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.bib new file mode 100644 index 00000000000..f64ae9d0921 --- /dev/null +++ b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.bib @@ -0,0 +1,26 @@ +@Article{, + author = {Moreno-Grau, Sonia and Hernández, Isabel and Heilmann-Heimbach, Stefanie and Ruiz, Susana and Rosende-Roca, Maitée and Mauleón, Ana and Vargas, Liliana and Rodríguez-Gómez, Octavio and Alegret, Montserrat and Espinosa, Ana and Ortega, Gemma and Aguilera, Nuria and Abdelnour, Carla and Neuroimaging Initiative, Alzheimer's Disease and Gil, Silvia and Maier, Wolfgang and Sotolongo-Grau, Oscar and Tárraga, Lluís and Ramirez, Alfredo and López-Arrrieta, Jesús and Antúnez, Carmen and Serrano-Ríos, Manuel and Boada, Mercè and Ruiz, Agustín}, + journal = {Oncotarget}, + title = {Genome-wide significant risk factors on chromosome 19 and the APOE locus.}, + year = {2018}, + issn = {1949-2553}, + month = may, + pages = {24590--24600}, + volume = {9}, + abstract = {The apolipoprotein E ( APOE ) gene on chromosome 19q13.32, was the first, and remains the strongest, genetic risk factor for Alzheimer's disease (AD). Additional signals associated with AD have been located in chromosome 19, including ABCA7 (19p13.3) and CD33 ( 19q13.41). The ABCA7 gene has been replicated in most populations. However, the contribution to AD of other signals close to APOE gene remains controversial. Possible explanations for inconsistency between reports include long range linkage disequilibrium (LRLD). We analysed the contribution of ABCA7 and CD33 loci to AD risk and explore LRLD patterns across APOE region. To evaluate AD risk conferred by ABCA7 rs4147929:G>A and CD33 rs3865444:C>A, we used a large Spanish population (1796 AD cases, 2642 controls). The ABCA7 rs4147929:G>A SNP effect was nominally replicated in the Spanish cohort and reached genome-wide significance after meta-analysis (odds ratio (OR)=1.15, 95% confidence interval (95% CI)=1.12-1.19; P = 1.60 x 10 (-19)). CD33 rs3865444:C>A was not associated with AD in the dataset. The meta-analysis was also negative (OR=0.98, 95% CI=0.93-1.04; P =0.48). After exploring LRLD patterns between APOE and CD33 in several datasets, we found significant LD (D' >0.20; P <0.030) between APOE -Ɛ2 and CD33 rs3865444C>A in two of five datasets, suggesting the presence of a non-universal long range interaction between these loci affecting to some populations. In conclusion, we provide here evidence of genetic association of the ABCA7 locus in the Spanish population and also propose a plausible explanation for the controversy on the contribution of CD33 to AD susceptibility.}, + country = {United States}, + doi = {10.18632/oncotarget.25083}, + issn-linking = {1949-2553}, + issue = {37}, + journal-abbreviation = {Oncotarget}, + keywords = {ABCA7; APOE; CD33; Gerotarget; late onset Alzheimer’s disease; linkage disequilibrium}, + nlm-id = {101532965}, + owner = {NLM}, + pii = {25083}, + pmc = {PMC5973862}, + pmid = {29872490}, + pubmodel = {Electronic-eCollection}, + pubstate = {epublish}, + revised = {2019-11-20}, + status = {PubMed-not-MEDLINE}, +} diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.xml b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.xml new file mode 100644 index 00000000000..fa4c03e3f4d --- /dev/null +++ b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestArticleItalics.xml @@ -0,0 +1,652 @@ + + + + 29872490 + + 2019 + 11 + 20 + +
+ + 1949-2553 + + 9 + 37 + + 2018 + May + 15 + + + Oncotarget + Oncotarget + + Genome-wide significant risk factors on chromosome 19 and the + APOE locus. + + + 24590 + 24600 + 24590-24600 + + 10.18632/oncotarget.25083 + + The apolipoprotein E ( + APOE) gene on chromosome 19q13.32, was the first, and remains the strongest, genetic risk factor for Alzheimer's disease (AD). Additional signals associated with AD have been located in chromosome 19, including + ABCA7 (19p13.3) and + CD33 (19q13.41). The + ABCA7 gene has been replicated in most populations. However, the contribution to AD of other signals close to + APOE gene remains controversial. Possible explanations for inconsistency between reports include long range linkage disequilibrium (LRLD). We analysed the contribution of + ABCA7 and + CD33 loci to AD risk and explore LRLD patterns across + APOE region. To evaluate AD risk conferred by + ABCA7 rs4147929:G>A and + CD33 rs3865444:C>A, we used a large Spanish population (1796 AD cases, 2642 controls). The + ABCA7 rs4147929:G>A SNP effect was nominally replicated in the Spanish cohort and reached genome-wide significance after meta-analysis (odds ratio (OR)=1.15, 95% confidence interval (95% CI)=1.12-1.19; + P = 1.60 x 10 + -19). + CD33 rs3865444:C>A was not associated with AD in the dataset. The meta-analysis was also negative (OR=0.98, 95% CI=0.93-1.04; + P=0.48). After exploring LRLD patterns between + APOE and + CD33 in several datasets, we found significant LD (D' >0.20; + P <0.030) between + APOE-Ɛ2 and + CD33 rs3865444C>A in two of five datasets, suggesting the presence of a non-universal long range interaction between these loci affecting to some populations. In conclusion, we provide here evidence of genetic association of the + ABCA7 locus in the Spanish population and also propose a plausible explanation for the controversy on the contribution of + CD33 to AD susceptibility. + + + + + Moreno-Grau + Sonia + S + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Hernández + Isabel + I + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Heilmann-Heimbach + Stefanie + S + + Institute of Human Genetics, University of Bonn, Bonn, Germany. + + + Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany. + + + + Ruiz + Susana + S + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Rosende-Roca + Maitée + M + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Mauleón + Ana + A + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Vargas + Liliana + L + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Rodríguez-Gómez + Octavio + O + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Alegret + Montserrat + M + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Espinosa + Ana + A + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Ortega + Gemma + G + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Aguilera + Nuria + N + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Abdelnour + Carla + C + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Neuroimaging Initiative + Alzheimer's Disease + AD + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + Institute of Human Genetics, University of Bonn, Bonn, Germany. + + + Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany. + + + Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany. + + + German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany. + + + Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany. + + + Memory Unit, University Hospital La Paz-Cantoblanco, Madrid, Spain. + + + Dementia Unit, University Hospital Virgen de la Arrixaca, Murcia, Spain. + + + Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM, Spain, Hospital Clínico San Carlos, Madrid, Spain. + + + + Gil + Silvia + S + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Maier + Wolfgang + W + + Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany. + + + German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany. + + + + Sotolongo-Grau + Oscar + O + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Tárraga + Lluís + L + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Ramirez + Alfredo + A + + Institute of Human Genetics, University of Bonn, Bonn, Germany. + + + Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany. + + + Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany. + + + + López-Arrrieta + Jesús + J + + Memory Unit, University Hospital La Paz-Cantoblanco, Madrid, Spain. + + + + Antúnez + Carmen + C + + Dementia Unit, University Hospital Virgen de la Arrixaca, Murcia, Spain. + + + + Serrano-Ríos + Manuel + M + + Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM, Spain, Hospital Clínico San Carlos, Madrid, Spain. + + + + Boada + Mercè + M + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + Ruiz + Agustín + A + + Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Univesitat Internacional de Catalunya, Barcelona, Spain. + + + + eng + + + U01 AG024904 + AG + NIA NIH HHS + United States + + + + Journal Article + + + 2018 + 05 + 15 + +
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PLoS Genet. 2011;7:e1001308. + + PMC3040659 + 21379329 + + + + Zhang Q, Calus MP, Guldbrandtsen B, Lund MS, Sahana G. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genet. 2015;16:88. + + PMC4509611 + 26195126 + + + + + + diff --git a/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestNbib.bib b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestNbib.bib index 6d897517d74..29dddebede9 100644 --- a/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestNbib.bib +++ b/src/test/resources/org/jabref/logic/importer/fileformat/MedlineImporterTestNbib.bib @@ -27,7 +27,7 @@ @article{ pubmodel = {Print-Electronic}, pubstate = {ppublish}, references = {23}, - revised = {2015-9-15}, + revised = {2015-09-15}, season = {Spring}, space-flight-mission = {fly}, status = {MEDLINE},