Rewrite Bibtexml exporter

src/main/java/net/sf/jabref/logic/exporter/BibTeXMLExportFormat.java

@@ -0,0 +1,247 @@
+package net.sf.jabref.logic.exporter;
+
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.math.BigInteger;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.namespace.QName;
+
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Article;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Book;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Booklet;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Conference;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Entry;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.File;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Inbook;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Incollection;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Inproceedings;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Manual;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Mastersthesis;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Misc;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Phdthesis;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Proceedings;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Techreport;
+import net.sf.jabref.logic.importer.fileformat.bibtexml.Unpublished;
+import net.sf.jabref.model.database.BibDatabaseContext;
+import net.sf.jabref.model.entry.BibEntry;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+public class BibTeXMLExportFormat extends ExportFormat {
+
+    private static final String BIBTEXML_NAMESPACE_URI = "http://bibtexml.sf.net/";
+    private static final Locale ENGLISH = Locale.ENGLISH;
+    private static final Log LOGGER = LogFactory.getLog(BibTeXMLExportFormat.class);
+    private JAXBContext context;
+
+
+    public BibTeXMLExportFormat() {
+        super("BibTeXML", "bibtexml", null, null, ".xml");
+    }
+
+    @Override
+    public void performExport(final BibDatabaseContext databaseContext, final String resultFile, final Charset encoding,
+            List<BibEntry> entries) throws SaveException {
+        Objects.requireNonNull(databaseContext);
+        Objects.requireNonNull(entries);
+        if (entries.isEmpty()) { // Only export if entries exist
+            return;
+        }
+
+        File file = new File();
+        for (BibEntry bibEntry : entries) {
+            Entry entry = new Entry();
+
+            Optional<String> citeKey = bibEntry.getCiteKeyOptional();
+            if (citeKey.isPresent()) {
+                entry.setId(citeKey.get());
+            }
+
+            String type = bibEntry.getType().toLowerCase(ENGLISH);
+            switch (type) {
+                case "article":
+                    parse(new Article(), bibEntry, entry);
+                    break;
+                case "book":
+                    parse(new Book(), bibEntry, entry);
+                    break;
+                case "booklet":
+                    parse(new Booklet(), bibEntry, entry);
+                    break;
+                case "conference":
+                    parse(new Conference(), bibEntry, entry);
+                    break;
+                case "inbook":
+                    parseInbook(new Inbook(), bibEntry, entry);
+                    break;
+                case "incollection":
+                    parse(new Incollection(), bibEntry, entry);
+                    break;
+                case "inproceedings":
+                    parse(new Inproceedings(), bibEntry, entry);
+                    break;
+                case "mastersthesis":
+                    parse(new Mastersthesis(), bibEntry, entry);
+                    break;
+                case "manual":
+                    parse(new Manual(), bibEntry, entry);
+                    break;
+                case "misc":
+                    parse(new Misc(), bibEntry, entry);
+                    break;
+                case "phdthesis":
+                    parse(new Phdthesis(), bibEntry, entry);
+                    break;
+                case "proceedings":
+                    parse(new Proceedings(), bibEntry, entry);
+                    break;
+                case "techreport":
+                    parse(new Techreport(), bibEntry, entry);
+                    break;
+                case "unpublished":
+                    parse(new Unpublished(), bibEntry, entry);
+                    break;
+                default:
+                    LOGGER.warn("unexpected type appeared");
+                    break;
+            }
+            file.getEntry().add(entry);
+        }
+        createMarshallerAndWriteToFile(file, resultFile);
+    }
+
+    private void createMarshallerAndWriteToFile(File file, String resultFile) throws SaveException {
+        try {
+            if (context == null) {
+                context = JAXBContext.newInstance(File.class);
+            }
+            Marshaller marshaller = context.createMarshaller();
+            marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
+
+            marshaller.marshal(file, new java.io.File(resultFile));
+        } catch (JAXBException e) {
+            throw new SaveException(e);
+        }
+    }
+
+    /**
+     * Contains same logic as the parse method, but inbook needs a special treatment, because
+     * the contents of inbook are stored in a List of JAXBElements. So we first need to create
+     * a JAXBElement for every field and then add it to the content list.
+     */
+    private void parseInbook(Inbook inbook, BibEntry bibEntry, Entry entry) {
+        Map<String, String> fieldMap = bibEntry.getFieldMap();
+        for (Map.Entry<String, String> entryField : fieldMap.entrySet()) {
+            String value = entryField.getValue();
+            String key = entryField.getKey();
+            if ("year".equals(key)) {
+                XMLGregorianCalendar calendar;
+                try {
+                    calendar = DatatypeFactory.newInstance().newXMLGregorianCalendar(value);
+
+                    JAXBElement<XMLGregorianCalendar> year = new JAXBElement<>(
+                            new QName(BIBTEXML_NAMESPACE_URI, "year"), XMLGregorianCalendar.class, calendar);
+                    inbook.getContent().add(year);
+                } catch (DatatypeConfigurationException e) {
+                    LOGGER.error("A configuration error occured");
+                }
+            } else if ("number".equals(key)) {
+                JAXBElement<BigInteger> number = new JAXBElement<>(new QName(BIBTEXML_NAMESPACE_URI, "number"),
+                        BigInteger.class, new BigInteger(value));
+                inbook.getContent().add(number);
+            } else {
+                JAXBElement<String> element = new JAXBElement<>(new QName(BIBTEXML_NAMESPACE_URI, key), String.class,
+                        value);
+                inbook.getContent().add(element);
+            }
+        }
+
+        //set the entryType to the entry
+        entry.setInbook(inbook);
+    }
+
+    /**
+     * Generic method that gets an instance of an entry type (article, book, booklet ...). It also
+     * gets one bibEntry. Then the method checks all fields of the entry and then for all fields the method
+     * uses the set method of the entry type with the fieldname. So for example if a bib entry has the field
+     * author and the value for it is "Max Mustermann" and the given type is an article, then this method
+     * will invoke <Code>article.setAuthor("Max Mustermann")</Code>. <br>
+     * <br>
+     * The second part of this method is that the entry type will be set to the entry. So e.g., if the type is
+     * article then <Code>entry.setArticle(article)</Code> will be invoked.
+     *
+     * @param entryType The type parameterized type of the entry.
+     * @param bibEntry  The bib entry, which fields will be set to the entryType.
+     * @param entry     The bibtexml entry. The entryType will be set to this entry.
+     */
+    private <T> void parse(T entryType, BibEntry bibEntry, Entry entry) {
+        List<Method> declaredSetMethods = getListOfSetMethods(entryType);
+        Map<String, String> fieldMap = bibEntry.getFieldMap();
+        for (Map.Entry<String, String> entryField : fieldMap.entrySet()) {
+            String value = entryField.getValue();
+            String key = entryField.getKey();
+            for (Method method : declaredSetMethods) {
+                String methodNameWithoutSet = method.getName().replace("set", "").toLowerCase(ENGLISH);
+                try {
+
+                    if ("year".equals(key) && key.equals(methodNameWithoutSet)) {
+                        try {
+
+                            XMLGregorianCalendar calendar = DatatypeFactory.newInstance()
+                                    .newXMLGregorianCalendar(value);
+                            method.invoke(entryType, calendar);
+                        } catch (DatatypeConfigurationException e) {
+                            LOGGER.error("A configuration error occured");
+                        }
+                        break;
+                    } else if ("number".equals(key) && key.equals(methodNameWithoutSet)) {
+                        method.invoke(entryType, new BigInteger(value));
+                        break;
+                    } else if (key.equals(methodNameWithoutSet)) {
+                        method.invoke(entryType, value);
+                        break;
+                    }
+                } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+                    LOGGER.error("Could not invoke method", e);
+                }
+            }
+
+            //set the entryType to the entry
+            List<Method> entryMethods = getListOfSetMethods(entryType);
+            for (Method method : entryMethods) {
+                String methodWithoutSet = method.getName().replace("set", "");
+                String simpleClassName = entryType.getClass().getSimpleName().replaceAll("\\[", "").replaceAll("\\]",
+                        "");
+                if (methodWithoutSet.equals(simpleClassName)) {
+                    try {
+                        method.invoke(entry, entryType);
+                    } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+                        LOGGER.warn("Could not set the type to the entry");
+                    }
+                }
+            }
+        }
+    }
+
+    private <T> List<Method> getListOfSetMethods(T entryType) {
+        return Arrays.asList(entryType.getClass().getDeclaredMethods()).stream()
+                .filter(method -> method.getName().startsWith("set")).collect(Collectors.toList());
+    }
+
+}

src/main/java/net/sf/jabref/logic/exporter/ExportFormats.java

@@ -31,7 +31,7 @@ public static void initAllExports(Map<String, ExportFormat> customFormats,
         ExportFormats.putFormat(new ExportFormat("DIN 1505", "din1505", "din1505winword", "din1505", ".rtf",
                 layoutPreferences, savePreferences));
         ExportFormats.putFormat(
-                new ExportFormat("BibTeXML", "bibtexml", "bibtexml", null, ".xml", layoutPreferences, savePreferences));
+new BibTeXMLExportFormat());
         ExportFormats.putFormat(
                 new ExportFormat("BibO RDF", "bibordf", "bibordf", null, ".rdf", layoutPreferences, savePreferences));
         ExportFormats.putFormat(new ExportFormat(Localization.lang("HTML table"), "tablerefs", "tablerefs", "tablerefs",

src/test/java/net/sf/jabref/logic/exporter/BibTeXMLExporterTestFiles.java

@@ -0,0 +1,89 @@
+package net.sf.jabref.logic.exporter;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import net.sf.jabref.logic.importer.fileformat.BibtexImporter;
+import net.sf.jabref.model.database.BibDatabaseContext;
+import net.sf.jabref.model.entry.BibEntry;
+import net.sf.jabref.preferences.JabRefPreferences;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameter;
+import org.junit.runners.Parameterized.Parameters;
+import org.xmlunit.builder.Input;
+import org.xmlunit.builder.Input.Builder;
+import org.xmlunit.diff.DefaultNodeMatcher;
+import org.xmlunit.diff.ElementSelectors;
+import org.xmlunit.matchers.CompareMatcher;
+
+
+@RunWith(Parameterized.class)
+public class BibTeXMLExporterTestFiles {
+
+    public BibDatabaseContext databaseContext;
+    public Charset charset;
+    public File tempFile;
+    public BibTeXMLExportFormat bibtexmlExportFormat;
+    public BibtexImporter testImporter;
+
+    @Parameter
+    public String filename;
+    public Path resourceDir;
+
+    @Rule
+    public TemporaryFolder testFolder = new TemporaryFolder();
+
+
+    @Parameters(name = "{0}")
+    public static Collection<String> fileNames() throws IOException, URISyntaxException {
+        try (Stream<Path> stream = Files.list(Paths.get(BibTeXMLExporterTestFiles.class.getResource("").toURI()))) {
+            return stream.map(n -> n.getFileName().toString()).filter(n -> n.endsWith(".bib"))
+                    .filter(n -> n.startsWith("BibTeXML")).collect(Collectors.toList());
+        }
+    }
+
+    @Before
+    public void setUp() throws Exception {
+        resourceDir = Paths.get(BibTeXMLExporterTestFiles.class.getResource("").toURI());
+        databaseContext = new BibDatabaseContext();
+        charset = StandardCharsets.UTF_8;
+        bibtexmlExportFormat = new BibTeXMLExportFormat();
+        tempFile = testFolder.newFile();
+        testImporter = new BibtexImporter(JabRefPreferences.getInstance().getImportFormatPreferences());
+    }
+
+    @Test
+    public final void testPerformExport() throws IOException, SaveException {
+        String xmlFileName = filename.replace(".bib", ".xml");
+        Path importFile = resourceDir.resolve(filename);
+        String tempFilename = tempFile.getCanonicalPath();
+
+        List<BibEntry> entries = testImporter.importDatabase(importFile, StandardCharsets.UTF_8).getDatabase()
+                .getEntries();
+
+        bibtexmlExportFormat.performExport(databaseContext, tempFile.getPath(), charset, entries);
+
+        Builder control = Input.from(Files.newInputStream(resourceDir.resolve(xmlFileName)));
+        Builder test = Input.from(Files.newInputStream(Paths.get(tempFilename)));
+
+        Assert.assertThat(test, CompareMatcher.isSimilarTo(control)
+                .withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText)).throwComparisonFailure());
+    }
+}

src/test/resources/net/sf/jabref/logic/exporter/BibTeXMLExporterTestArticle.bib

@@ -0,0 +1,11 @@
+% Encoding: UTF-8
+
+@Article{Mustermann2016,
+  author =   {Max Mustermann},
+  title =    {Java tricks},
+  journal =  {Java Journal},
+  year =     {2016},
+  pages =    {2},
+  month =    {February},
+  keywords = {java}
+}

src/test/resources/net/sf/jabref/logic/exporter/BibTeXMLExporterTestArticle.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<file xmlns="http://bibtexml.sf.net/">
+    <entry id="Mustermann2016">
+        <article>
+            <author>Max Mustermann</author>
+            <title>Java tricks</title>
+            <journal>Java Journal</journal>
+            <year>2016</year>
+            <pages>2</pages>
+            <month>February</month>
+            <keywords>java</keywords>
+        </article>
+    </entry>
+</file>

src/test/resources/net/sf/jabref/logic/exporter/BibTeXMLExporterTestArticleWithoutID.bib

@@ -0,0 +1,11 @@
+% Encoding: UTF-8
+
+@Article{,
+  author =   {Max Mustermann},
+  title =    {Java tricks},
+  journal =  {Java Journal},
+  year =     {2016},
+  pages =    {2},
+  month =    {February},
+  keywords = {java}
+}