MedlineImporterTest

src/main/java/net/sf/jabref/logic/util/strings/StringUtil.java

@@ -23,6 +23,7 @@
 import java.util.regex.Pattern;
 
 import net.sf.jabref.Globals;
+import net.sf.jabref.model.entry.Author;
 
 import com.google.common.base.CharMatcher;
 
@@ -625,6 +626,51 @@ public static String replaceSpecialCharacters(String s) {
         return result;
     }
 
+    /**
+     * Expand initials, e.g. EH Wissler -> E. H. Wissler or Wissler, EH -> Wissler, E. H.
+     *
+     * @param name
+     * @return The name after expanding initials.
+     */
+    public static String expandAuthorInitials(String name) {
+        String[] authors = name.split(" and ");
+        StringBuilder sb = new StringBuilder();
+        for (int i = 0; i < authors.length; i++) {
+            if (authors[i].contains(", ")) {
+                String[] names = authors[i].split(", ");
+                if (names.length > 0) {
+                    sb.append(names[0]);
+                    if (names.length > 1) {
+                        sb.append(", ");
+                    }
+                }
+                for (int j = 1; j < names.length; j++) {
+                    if (j == 1) {
+                        sb.append(Author.addDotIfAbbreviation(names[j]));
+                    } else {
+                        sb.append(names[j]);
+                    }
+                    if (j < (names.length - 1)) {
+                        sb.append(", ");
+                    }
+                }
+            } else {
+                String[] names = authors[i].split(" ");
+                if (names.length > 0) {
+                    sb.append(Author.addDotIfAbbreviation(names[0]));
+                }
+                for (int j = 1; j < names.length; j++) {
+                    sb.append(' ');
+                    sb.append(names[j]);
+                }
+            }
+            if (i < (authors.length - 1)) {
+                sb.append(" and ");
+            }
+        }
+        return sb.toString().trim();
+    }
+
     /**
      * Return a String with n spaces
      *

src/test/java/net/sf/jabref/importer/fileformat/MedlineImporterTest.java

@@ -0,0 +1,100 @@
+package net.sf.jabref.importer.fileformat;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import net.sf.jabref.Globals;
+import net.sf.jabref.JabRefPreferences;
+import net.sf.jabref.importer.OutputPrinterToNull;
+import net.sf.jabref.model.entry.BibEntry;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mockito;
+import org.mockito.runners.MockitoJUnitRunner;
+
+import static org.junit.Assert.assertEquals;
+
+/**
+ * Articles in the medline format can be downloaded from http://www.ncbi.nlm.nih.gov/pubmed/.
+ * 1. Search for a term and make sure you have selected the PubMed database
+ * 2. Select the results you want to export by checking their checkboxes
+ * 3. Press on the 'Send to' drop down menu on top of the search results
+ * 4. Select 'File' as Destination and 'XML' as Format
+ * 5. Press 'Create File' to download your search results in a medline xml file
+ *
+ * @author Daniel Mair/Bruehl
+ *
+ */
+@RunWith(MockitoJUnitRunner.class)
+public class MedlineImporterTest {
+
+    private MedlineImporter medlineImporter;
+    private static final String FILEFORMAT_PATH = "src/test/resources/net/sf/jabref/importer/fileformat";
+
+    /**
+     * Generates a List of all files in the package "/src/test/resources/net/sf/jabref/importer/fileformat"
+     * @return A list of Names
+     * @throws IOException
+     */
+    public List<String> getTestFiles() throws IOException {
+        List<String> files = new ArrayList<>();
+        try (DirectoryStream<Path> stream = Files.newDirectoryStream(Paths.get(FILEFORMAT_PATH))) {
+            stream.forEach(n -> files.add(n.getFileName().toString()));
+        }
+        return files;
+    }
+
+    @Before
+    public void setUp() throws Exception {
+        Globals.prefs = JabRefPreferences.getInstance();
+        this.medlineImporter = new MedlineImporter();
+    }
+
+    @Test
+    public void testExceptionOnInputStream() throws IOException {
+        try (InputStream is = Mockito.mock(InputStream.class)) {
+            Mockito.doThrow(new IOException()).when(is).read();
+            List<BibEntry> entry = medlineImporter.importEntries(is, new OutputPrinterToNull());
+            Assert.assertTrue(entry.isEmpty());
+        }
+    }
+
+    @Test
+    public void testGetItemsEmpty() {
+        MedlineHandler handler = new MedlineHandler();
+        assertEquals(Collections.emptyList(), handler.getItems());
+    }
+
+    @Test
+    public void testGetFormatName() {
+        assertEquals("Medline", medlineImporter.getFormatName());
+    }
+
+    @Test
+    public void testGetCLIId() {
+        assertEquals("medline", medlineImporter.getCLIId());
+    }
+
+    @Test
+    public void testIsRecognizedFormatReject() throws IOException {
+       List<String> list = getTestFiles().stream().filter(n -> !n.startsWith("MedlineImporter"))
+                .collect(Collectors.toList());
+
+        for (String str : list) {
+            try (InputStream is = MedlineImporter.class.getResourceAsStream(str)) {
+                Assert.assertFalse(medlineImporter.isRecognizedFormat(is));
+            }
+        }
+    }
+}

src/test/java/net/sf/jabref/importer/fileformat/MedlineImporterTestFiles.java

@@ -0,0 +1,79 @@
+package net.sf.jabref.importer.fileformat;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import net.sf.jabref.Globals;
+import net.sf.jabref.JabRefPreferences;
+import net.sf.jabref.importer.OutputPrinterToNull;
+import net.sf.jabref.logic.bibtex.BibEntryAssert;
+import net.sf.jabref.model.entry.BibEntry;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameter;
+import org.junit.runners.Parameterized.Parameters;
+
+import static org.junit.Assert.assertEquals;
+
+@RunWith(Parameterized.class)
+public class MedlineImporterTestFiles {
+
+    private final static String FILEFORMAT_PATH = "src/test/resources/net/sf/jabref/importer/fileformat";
+
+    private MedlineImporter medlineImporter;
+
+    @Parameter
+    public String fileName;
+
+
+    @Before
+    public void setUp() {
+        Globals.prefs = JabRefPreferences.getInstance();
+        medlineImporter = new MedlineImporter();
+    }
+
+    @Parameters(name = "{0}")
+    public static Collection<String> fileNames() throws IOException {
+        List<String> files = new ArrayList<>();
+        try (DirectoryStream<Path> stream = Files.newDirectoryStream(Paths.get(FILEFORMAT_PATH))) {
+            stream.forEach(n -> files.add(n.getFileName().toString()));
+        }
+        return files.stream().filter(n -> n.startsWith("MedlineImporterTest")).filter(n -> n.endsWith(".xml"))
+                .collect(Collectors.toList());
+    }
+
+    @Test
+    public void testIsRecognizedFormat() throws IOException {
+        try (InputStream stream = MedlineImporterTest.class.getResourceAsStream(fileName)) {
+            Assert.assertTrue(medlineImporter.isRecognizedFormat(stream));
+        }
+    }
+
+    @Test
+    @Ignore
+    public void testImportEntries() throws IOException {
+        try (InputStream inputStream = MedlineImporterTest.class.getResourceAsStream(fileName)) {
+            List<BibEntry> medlineEntries = medlineImporter.importEntries(inputStream, new OutputPrinterToNull());
+            String bibFileName = fileName.replace(".xml", ".bib");
+            if (medlineEntries.isEmpty()) {
+                assertEquals(Collections.emptyList(), medlineEntries);
+            } else {
+                BibEntryAssert.assertEquals(MedlineImporterTest.class, bibFileName, medlineEntries);
+            }
+        }
+    }
+}

src/test/resources/net/sf/jabref/importer/fileformat/MedlineImporterTestArticleID.bib

@@ -0,0 +1,14 @@
+% Encoding: UTF-8
+
+@article{,
+  abstract = {This abstract is a dummy.},
+  author = {Rhein, Joshua and Bahr, Nathan C. and Hemmert, Andrew C. and Cloud, Joann L. and Bellamkonda, Satya and Oswald, Cody and Lo, Eric and Nabeta, Henry and Kiggundu, Reuben and Akampurira, Andrew and Musubire, Abdu and Williams, Darlisha A. and Meya, David B. and Boulware, David R. and , A. S. T. R. O.-C. M. Team},
+  institution = {Division of Infectious Disease and International Health, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.},
+  journal = {Diagn Microbiol Infect Dis},
+  language = {eng},
+  medline-pst = {aheadofprint},
+  month = {Dec},
+  pmid = {26711635},
+  title = {Diagnostic performance of a multiplex PCR assay for meningitis in an HIV-infected population in Uganda.},
+  year = {2015}
+}