Merge remote-tracking branch 'upstream/master'

* upstream/master:
  Update CHANGELOG.md
  Fix inconsistent capitalisation of downloaded files
  Improve arXiv fetcher (#6113)

CHANGELOG.md

@@ -13,11 +13,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- We improved the arXiv fetcher. Now it should find entries even more reliably and does no longer include the version (e.g `v1`) in the `eprint` field. [forum#1941](https://discourse.jabref.org/t/remove-version-in-arxiv-import/1941)
 - We moved the group search bar and the button "New group" from bottom to top position to make it more prominent. [#6112](https://github.com/JabRef/jabref/pull/6112)
 
+
 ### Fixed
 
 - We fixed an issue where opening a library from the recent libraries menu was not possible. [#5939](https://github.com/JabRef/jabref/issues/5939)
+- We fixed an issue with inconsistent capitalization of file extensions when downloading files [#6115](https://github.com/JabRef/jabref/issues/6115)
 
 ### Removed
 

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -421,10 +421,10 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
         BackgroundTask<Path> downloadTask = BackgroundTask
                 .wrap(() -> {
                     Optional<ExternalFileType> suggestedType = inferFileType(urlDownload);
-                    String suggestedTypeName = suggestedType.orElse(StandardExternalFileType.PDF).getName();
+                    ExternalFileType externalFileType = suggestedType.orElse(StandardExternalFileType.PDF);
+                    String suggestedTypeName = externalFileType.getName();
                     linkedFile.setFileType(suggestedTypeName);
-
-                    String suggestedName = linkedFileHandler.getSuggestedFileName(suggestedTypeName);
+                    String suggestedName = linkedFileHandler.getSuggestedFileName(externalFileType.getExtension());
                     return targetDirectory.resolve(suggestedName);
                 })
                 .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))

src/main/java/org/jabref/logic/importer/fetcher/ArXiv.java

@@ -10,8 +10,6 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import javax.xml.parsers.DocumentBuilder;
@@ -59,8 +57,6 @@ public class ArXiv implements FulltextFetcher, SearchBasedFetcher, IdBasedFetche
     private static final Logger LOGGER = LoggerFactory.getLogger(ArXiv.class);
 
     private static final String API_URL = "https://export.arxiv.org/api/query";
-    private static final String ARXIV_URL_PREFIX_FOR_ID = "(https?://arxiv.org/abs/)";
-    private static final Pattern URL_PATTERN = Pattern.compile(ARXIV_URL_PREFIX_FOR_ID);
 
     private final ImportFormatPreferences importFormatPreferences;
 
@@ -106,7 +102,7 @@ private Optional<ArXivEntry> searchForEntry(String searchQuery) throws FetcherEx
 
     private Optional<ArXivEntry> searchForEntryById(String id) throws FetcherException {
         Optional<ArXivIdentifier> identifier = ArXivIdentifier.parse(id);
-        if (!identifier.isPresent()) {
+        if (identifier.isEmpty()) {
             return Optional.empty();
         }
 
@@ -263,10 +259,8 @@ public List<BibEntry> performSearch(String query) throws FetcherException {
 
     @Override
     public Optional<BibEntry> performSearchById(String identifier) throws FetcherException {
-        String cleanedIdentifier = identifier.replaceAll(" ", "");
-        cleanedIdentifier = ArXivEntry.createIdString(cleanedIdentifier);
-
-        return searchForEntryById(cleanedIdentifier).map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.getKeywordSeparator()));
+        return searchForEntryById(identifier)
+                .map((arXivEntry) -> arXivEntry.toBibEntry(importFormatPreferences.getKeywordSeparator()));
     }
 
     @Override
@@ -372,18 +366,7 @@ public Optional<URL> getPdfUrl() {
          * Returns the arXiv identifier
          */
         public Optional<String> getIdString() {
-            return urlAbstractPage.map(ArXivEntry::createIdString);
-        }
-
-        public static String createIdString(String id) {
-                Matcher matcher = URL_PATTERN.matcher(id);
-                if (matcher.find()) {
-                    // Remove leading http(s)://arxiv.org/abs/ from abstract url to get arXiv ID
-                    return id.substring(matcher.group(1).length());
-                } else {
-                    return id;
-                }
-
+            return urlAbstractPage.flatMap(ArXivIdentifier::parse).map(ArXivIdentifier::getNormalizedWithoutVersion);
         }
 
         public Optional<ArXivIdentifier> getId() {

src/main/java/org/jabref/model/entry/identifier/ArXivIdentifier.java

@@ -9,49 +9,59 @@
 
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.strings.StringUtil;
 
 /**
  * Identifier for the arXiv. See https://arxiv.org/help/arxiv_identifier
  */
 public class ArXivIdentifier implements Identifier {
 
+    private static final String ARXIV_PREFIX = "http(s)?://arxiv.org/(abs|pdf)/|arxiv|arXiv";
     private final String identifier;
     private final String classification;
+    private final String version;
 
     ArXivIdentifier(String identifier) {
-        this(identifier, "");
+        this(identifier, "", "");
     }
 
     ArXivIdentifier(String identifier, String classification) {
+        this(identifier, "", classification);
+    }
+
+    ArXivIdentifier(String identifier, String version, String classification) {
         this.identifier = identifier.trim();
+        this.version = version.trim();
         this.classification = classification.trim();
     }
 
     public static Optional<ArXivIdentifier> parse(String value) {
-        Pattern identifierPattern = Pattern.compile("(arxiv|arXiv)?\\s?:?\\s?(?<id>\\d{4}.\\d{4,5}(v\\d+)?)\\s?(\\[(?<classification>\\S+)\\])?");
-        Matcher identifierMatcher = identifierPattern.matcher(value);
+        String identifier = value.replaceAll(" ", "");
+        Pattern identifierPattern = Pattern.compile("(" + ARXIV_PREFIX + ")?\\s?:?\\s?(?<id>\\d{4}.\\d{4,5})(v(?<version>\\d+))?\\s?(\\[(?<classification>\\S+)\\])?");
+        Matcher identifierMatcher = identifierPattern.matcher(identifier);
         if (identifierMatcher.matches()) {
             String id = identifierMatcher.group("id");
             String classification = identifierMatcher.group("classification");
             if (classification == null) {
                 classification = "";
             }
-            return Optional.of(new ArXivIdentifier(id, classification));
+            String version = identifierMatcher.group("version");
+            if (version == null) {
+                version = "";
+            }
+            return Optional.of(new ArXivIdentifier(id, version, classification));
         }
 
-        Pattern oldIdentifierPattern = Pattern.compile("(arxiv|arXiv)?\\s?:?\\s?(?<id>(?<classification>[a-z\\-]+(\\.[A-Z]{2})?)/\\d{7})");
-        Matcher oldIdentifierMatcher = oldIdentifierPattern.matcher(value);
+        Pattern oldIdentifierPattern = Pattern.compile("(" + ARXIV_PREFIX + ")?\\s?:?\\s?(?<id>(?<classification>[a-z\\-]+(\\.[A-Z]{2})?)/\\d{7})(v(?<version>\\d+))?");
+        Matcher oldIdentifierMatcher = oldIdentifierPattern.matcher(identifier);
         if (oldIdentifierMatcher.matches()) {
             String id = oldIdentifierMatcher.group("id");
             String classification = oldIdentifierMatcher.group("classification");
-            return Optional.of(new ArXivIdentifier(id, classification));
-        }
-
-        Pattern urlPattern = Pattern.compile("(http://arxiv.org/abs/)(?<id>\\S+)");
-        Matcher urlMatcher = urlPattern.matcher(value);
-        if (urlMatcher.matches()) {
-            String id = urlMatcher.group("id");
-            return Optional.of(new ArXivIdentifier(id));
+            String version = oldIdentifierMatcher.group("version");
+            if (version == null) {
+                version = "";
+            }
+            return Optional.of(new ArXivIdentifier(id, version, classification));
         }
 
         return Optional.empty();
@@ -99,6 +109,14 @@ public Field getDefaultField() {
 
     @Override
     public String getNormalized() {
+        if (StringUtil.isNotBlank(version)) {
+            return identifier + "v" + version;
+        } else {
+            return identifier;
+        }
+    }
+
+    public String getNormalizedWithoutVersion() {
         return identifier;
     }
 

src/test/java/org/jabref/logic/importer/fetcher/ArXivTest.java

@@ -22,14 +22,14 @@
 import static org.mockito.Mockito.when;
 
 @FetcherTest
-public class ArXivTest {
+class ArXivTest {
 
     private ArXiv finder;
     private BibEntry entry;
     private BibEntry sliceTheoremPaper;
 
     @BeforeEach
-    public void setUp() {
+    void setUp() {
         ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class);
         when(importFormatPreferences.getKeywordSeparator()).thenReturn(',');
         finder = new ArXiv(importFormatPreferences);
@@ -41,107 +41,107 @@ public void setUp() {
         sliceTheoremPaper.setField(StandardField.TITLE, "Slice theorem for Fréchet group actions and covariant symplectic field theory");
         sliceTheoremPaper.setField(StandardField.DATE, "2014-05-09");
         sliceTheoremPaper.setField(StandardField.ABSTRACT, "A general slice theorem for the action of a Fr\\'echet Lie group on a Fr\\'echet manifolds is established. The Nash-Moser theorem provides the fundamental tool to generalize the result of Palais to this infinite-dimensional setting. The presented slice theorem is illustrated by its application to gauge theories: the action of the gauge transformation group admits smooth slices at every point and thus the gauge orbit space is stratified by Fr\\'echet manifolds. Furthermore, a covariant and symplectic formulation of classical field theory is proposed and extensively discussed. At the root of this novel framework is the incorporation of field degrees of freedom F and spacetime M into the product manifold F * M. The induced bigrading of differential forms is used in order to carry over the usual symplectic theory to this new setting. The examples of the Klein-Gordon field and general Yang-Mills theory illustrate that the presented approach conveniently handles the occurring symmetries.");
-        sliceTheoremPaper.setField(StandardField.EPRINT, "1405.2249v1");
+        sliceTheoremPaper.setField(StandardField.EPRINT, "1405.2249");
         sliceTheoremPaper.setField(StandardField.FILE, ":http\\://arxiv.org/pdf/1405.2249v1:PDF");
         sliceTheoremPaper.setField(StandardField.EPRINTTYPE, "arXiv");
         sliceTheoremPaper.setField(StandardField.EPRINTCLASS, "math-ph");
         sliceTheoremPaper.setField(StandardField.KEYWORDS, "math-ph, math.DG, math.MP, math.SG, 58B99, 58Z05, 58B25, 22E65, 58D19, 53D20, 53D42");
     }
 
     @Test
-    public void findFullTextForEmptyEntryResultsEmptyOptional() throws IOException {
+    void findFullTextForEmptyEntryResultsEmptyOptional() throws IOException {
         assertEquals(Optional.empty(), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextRejectsNullParameter() {
+    void findFullTextRejectsNullParameter() {
         assertThrows(NullPointerException.class, () -> finder.findFullText(null));
     }
 
     @Test
-    public void findFullTextByDOI() throws IOException {
+    void findFullTextByDOI() throws IOException {
         entry.setField(StandardField.DOI, "10.1529/biophysj.104.047340");
         entry.setField(StandardField.TITLE, "Pause Point Spectra in DNA Constant-Force Unzipping");
 
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/cond-mat/0406246v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByEprint() throws IOException {
+    void findFullTextByEprint() throws IOException {
         entry.setField(StandardField.EPRINT, "1603.06570");
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/1603.06570v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByEprintWithPrefix() throws IOException {
+    void findFullTextByEprintWithPrefix() throws IOException {
         entry.setField(StandardField.EPRINT, "arXiv:1603.06570");
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/1603.06570v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByEprintWithUnknownDOI() throws IOException {
+    void findFullTextByEprintWithUnknownDOI() throws IOException {
         entry.setField(StandardField.DOI, "10.1529/unknown");
         entry.setField(StandardField.EPRINT, "1603.06570");
 
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/1603.06570v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByTitle() throws IOException {
+    void findFullTextByTitle() throws IOException {
         entry.setField(StandardField.TITLE, "Pause Point Spectra in DNA Constant-Force Unzipping");
 
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/cond-mat/0406246v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByTitleAndPartOfAuthor() throws IOException {
+    void findFullTextByTitleAndPartOfAuthor() throws IOException {
         entry.setField(StandardField.TITLE, "Pause Point Spectra in DNA Constant-Force Unzipping");
         entry.setField(StandardField.AUTHOR, "Weeks and Lucks");
 
         assertEquals(Optional.of(new URL("http://arxiv.org/pdf/cond-mat/0406246v1")), finder.findFullText(entry));
     }
 
     @Test
-    public void notFindFullTextByUnknownDOI() throws IOException {
+    void notFindFullTextByUnknownDOI() throws IOException {
         entry.setField(StandardField.DOI, "10.1529/unknown");
         assertEquals(Optional.empty(), finder.findFullText(entry));
     }
 
     @Test
-    public void notFindFullTextByUnknownId() throws IOException {
+    void notFindFullTextByUnknownId() throws IOException {
         entry.setField(StandardField.EPRINT, "1234.12345");
         assertEquals(Optional.empty(), finder.findFullText(entry));
     }
 
     @Test
-    public void findFullTextByDOINotAvailableInCatalog() throws IOException {
+    void findFullTextByDOINotAvailableInCatalog() throws IOException {
         entry.setField(StandardField.DOI, "10.1016/0370-2693(77)90015-6");
         entry.setField(StandardField.TITLE, "Superspace formulation of supergravity");
 
         assertEquals(Optional.empty(), finder.findFullText(entry));
     }
 
     @Test
-    public void searchEntryByPartOfTitle() throws Exception {
+    void searchEntryByPartOfTitle() throws Exception {
         assertEquals(Collections.singletonList(sliceTheoremPaper),
                 finder.performSearch("ti:\"slice theorem for Frechet\""));
     }
 
     @Test
-    public void searchEntryByPartOfTitleWithAcuteAccent() throws Exception {
+    void searchEntryByPartOfTitleWithAcuteAccent() throws Exception {
         assertEquals(Collections.singletonList(sliceTheoremPaper),
                 finder.performSearch("ti:\"slice theorem for Fréchet\""));
     }
 
     @Test
-    public void searchEntryByOldId() throws Exception {
+    void searchEntryByOldId() throws Exception {
         BibEntry expected = new BibEntry();
         expected.setType(StandardEntryType.Article);
         expected.setField(StandardField.AUTHOR, "H1 Collaboration");
         expected.setField(StandardField.TITLE, "Multi-Electron Production at High Transverse Momenta in ep Collisions at HERA");
         expected.setField(StandardField.DATE, "2003-07-07");
         expected.setField(StandardField.ABSTRACT, "Multi-electron production is studied at high electron transverse momentum in positron- and electron-proton collisions using the H1 detector at HERA. The data correspond to an integrated luminosity of 115 pb-1. Di-electron and tri-electron event yields are measured. Cross sections are derived in a restricted phase space region dominated by photon-photon collisions. In general good agreement is found with the Standard Model predictions. However, for electron pair invariant masses above 100 GeV, three di-electron events and three tri-electron events are observed, compared to Standard Model expectations of 0.30 \\pm 0.04 and 0.23 \\pm 0.04, respectively.");
-        expected.setField(StandardField.EPRINT, "hep-ex/0307015v1");
+        expected.setField(StandardField.EPRINT, "hep-ex/0307015");
         expected.setField(StandardField.FILE, ":http\\://arxiv.org/pdf/hep-ex/0307015v1:PDF");
         expected.setField(StandardField.EPRINTTYPE, "arXiv");
         expected.setField(StandardField.EPRINTCLASS, "hep-ex");
@@ -153,61 +153,61 @@ public void searchEntryByOldId() throws Exception {
     }
 
     @Test
-    public void searchEntryByIdWith4DigitsAndVersion() throws Exception {
+    void searchEntryByIdWith4DigitsAndVersion() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("1405.2249v1"));
     }
 
     @Test
-    public void searchEntryByIdWith4Digits() throws Exception {
+    void searchEntryByIdWith4Digits() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("1405.2249"));
     }
 
     @Test
-    public void searchEntryByIdWith4DigitsAndPrefix() throws Exception {
+    void searchEntryByIdWith4DigitsAndPrefix() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("arXiv:1405.2249"));
     }
 
     @Test
-    public void searchEntryByIdWith4DigitsAndPrefixAndNotTrimmed() throws Exception {
+    void searchEntryByIdWith4DigitsAndPrefixAndNotTrimmed() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("arXiv : 1405. 2249"));
     }
 
     @Test
-    public void searchEntryByIdWith5Digits() throws Exception {
+    void searchEntryByIdWith5Digits() throws Exception {
         assertEquals(Optional.of(
                 "An Optimal Convergence Theorem for Mean Curvature Flow of Arbitrary Codimension in Hyperbolic Spaces"),
                 finder.performSearchById("1503.06747").flatMap(entry -> entry.getField(StandardField.TITLE)));
     }
 
     @Test
-    public void searchWithMalformedIdThrowsException() throws Exception {
+    void searchWithMalformedIdThrowsException() throws Exception {
         assertThrows(FetcherException.class, () -> finder.performSearchById("123412345"));
     }
 
     @Test
-    public void searchIdentifierForSlicePaper() throws Exception {
+    void searchIdentifierForSlicePaper() throws Exception {
         sliceTheoremPaper.clearField(StandardField.EPRINT);
 
-        assertEquals(ArXivIdentifier.parse("1405.2249v1"), finder.findIdentifier(sliceTheoremPaper));
+        assertEquals(ArXivIdentifier.parse("1405.2249"), finder.findIdentifier(sliceTheoremPaper));
     }
 
     @Test
-    public void searchEmptyId() throws Exception {
+    void searchEmptyId() throws Exception {
         assertEquals(Optional.empty(), finder.performSearchById(""));
     }
 
     @Test
-    public void searchWithHttpUrl() throws Exception {
+    void searchWithHttpUrl() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("http://arxiv.org/abs/1405.2249"));
     }
 
     @Test
-    public void searchWithHttpsUrl() throws Exception {
+    void searchWithHttpsUrl() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("https://arxiv.org/abs/1405.2249"));
     }
 
     @Test
-    public void searchWithHttpsUrlNotTrimmed() throws Exception {
+    void searchWithHttpsUrlNotTrimmed() throws Exception {
         assertEquals(Optional.of(sliceTheoremPaper), finder.performSearchById("https : // arxiv . org / abs / 1405 . 2249 "));
     }
 }