Merge remote-tracking branch 'upstream/main' into dependabot/gradle/c…

…om.puppycrawl.tools-checkstyle-10.0

* upstream/main:
  Fix online link detection in entry editor (#8514)
  Add some JavaDoc to Fetchers
  Support two argument form of \abx@aux@cite macro in DefaultAuxParser (#8549)
  Bump guava from 31.0.1-jre to 31.1-jre (#8543)
  Bump org.beryx.jlink from 2.24.4 to 2.25.0 (#8548)
  Bump postgresql from 42.3.2 to 42.3.3 (#8546)
  Bump richtextfx from 0.10.7 to 0.10.9 (#8547)
  Bump archunit-junit5-engine from 0.22.0 to 0.23.1 (#8545)
  Bump actions/checkout from 2 to 3 (#8542)

.github/workflows/check-links.yaml

@@ -13,7 +13,7 @@ jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: 'yes'

.github/workflows/deployment.yml

@@ -51,7 +51,7 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
@@ -152,7 +152,7 @@ jobs:
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion

.github/workflows/gource.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Determine dates

.github/workflows/refresh-csl-subtrees.yml

@@ -13,7 +13,7 @@ jobs:
     if: github.repository == 'JabRef/jabref'
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           fetch-depth: 0

.github/workflows/refresh-journal-lists.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           persist-credentials: false

.github/workflows/snap.yml

@@ -30,7 +30,7 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
       - name: Run snapcraft build

.github/workflows/tests-fetchers.yml

@@ -37,7 +37,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -50,7 +50,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -82,7 +82,7 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -116,7 +116,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -154,7 +154,7 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -174,5 +174,5 @@ jobs:
     name: "Validate Gradle Wrapper"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gradle/wrapper-validation-action@v1

.github/workflows/update-gradle-wrapper.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Update Gradle Wrapper
         uses: gradle-update/update-gradle-wrapper-action@v1

CHANGELOG.md

@@ -21,10 +21,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where online links in the file field were not detected correctly and could produce an exception [#8150](https://github.com/JabRef/jabref/issues/8510)
 - We fixed an issue where an exception could occur when saving the preferences [#7614](https://github.com/JabRef/jabref/issues/7614)
 - We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
 - We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
 - We fixed an issue where pasting a URL was replacing + signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
+- We fixed an issue where creating subsidiary files from aux files created with some versions of biblatex would produce incorrect results. [#8513](https://github.com/JabRef/jabref/issues/8513)
 
 ### Removed
 

build.gradle

@@ -18,7 +18,7 @@ plugins {
 
     id 'org.openjfx.javafxplugin' version '0.0.12'
 
-    id 'org.beryx.jlink' version '2.24.4'
+    id 'org.beryx.jlink' version '2.25.0'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -147,14 +147,14 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
 
-    implementation 'org.postgresql:postgresql:42.3.2'
+    implementation 'org.postgresql:postgresql:42.3.3'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:31.0.1-jre') {
+    implementation ('com.google.guava:guava:31.1-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -168,7 +168,7 @@ dependencies {
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
     implementation 'org.fxmisc.flowless:flowless:0.6.8'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.1'
@@ -211,7 +211,7 @@ dependencies {
     testImplementation 'org.mockito:mockito-core:4.3.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"

src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java

@@ -32,7 +32,7 @@
 public class DefaultAuxParser implements AuxParser {
     private static final Logger LOGGER = LoggerFactory.getLogger(DefaultAuxParser.class);
 
-    private static final Pattern CITE_PATTERN = Pattern.compile("\\\\(citation|abx@aux@cite)\\{(.+)\\}");
+    private static final Pattern CITE_PATTERN = Pattern.compile("\\\\(citation|abx@aux@cite)(\\{\\d+\\})?\\{(?<citationkey>.+)\\}");
     private static final Pattern INPUT_PATTERN = Pattern.compile("\\\\@input\\{(.+)\\}");
 
     private final BibDatabase masterDatabase;
@@ -108,7 +108,7 @@ private void matchCitation(AuxParserResult result, String line) {
         Matcher citeMatch = CITE_PATTERN.matcher(line);
 
         while (citeMatch.find()) {
-            String keyString = citeMatch.group(2);
+            String keyString = citeMatch.group("citationkey");
             String[] keys = keyString.split(",");
 
             for (String key : keys) {

src/main/java/org/jabref/logic/importer/EntryBasedFetcher.java

@@ -6,7 +6,7 @@
 
 /**
  * Searches web resources for bibliographic information based on a {@link BibEntry}.
- * Useful to complete an existing entry with fetched information.
+ * Useful to <emph>complete</emph> an existing entry with fetched information.
  * May return multiple search hits.
  */
 public interface EntryBasedFetcher extends WebFetcher {

src/main/java/org/jabref/logic/importer/IdBasedFetcher.java

@@ -6,6 +6,7 @@
 
 /**
  * Searches web resources for bibliographic information based on an identifier.
+ * Examples are ISBN numbers and DOIs.
  */
 public interface IdBasedFetcher extends WebFetcher {
 

src/main/java/org/jabref/logic/importer/SearchBasedFetcher.java

@@ -15,6 +15,9 @@
 /**
  * Searches web resources for bibliographic information based on a free-text query.
  * May return multiple search hits.
+ * <p>
+ *    This interface is used for web resources which directly return BibTeX data ({@link BibEntry})
+ * </p>
  */
 public interface SearchBasedFetcher extends WebFetcher {
 

src/main/java/org/jabref/logic/importer/SearchBasedParserFetcher.java

@@ -13,12 +13,25 @@
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**
- * Provides a convenient interface for search-based fetcher, which follow the usual three-step procedure:
+ * Provides a convenient interface for search-based fetcher, which follows the usual three-step procedure:
  * <ol>
  *     <li>Open a URL based on the search query</li>
  *     <li>Parse the response to get a list of {@link BibEntry}</li>
  *     <li>Post-process fetched entries</li>
  * </ol>
+ * <p>
+ *     This interface is used for web resources which do NOT provide BibTeX data {@link BibEntry}.
+ *     JabRef's infrastructure to convert arbitrary input data to BibTeX is {@link Parser}.
+ * </p>
+ * <p>
+ *     This interface inherits {@link SearchBasedFetcher}, because the methods <code>performSearch</code> have to be provided by both.
+ *     As non-BibTeX web fetcher one could do "magic" stuff without this helper interface and directly use {@link WebFetcher}, but this is more work.
+ * </p>
+ * <p>
+ *     Note that this interface "should" be an abstract class.
+ *     However, Java does not support multi inheritance with classes (but with interfaces).
+ *     We need multi inheritance, because a fetcher might implement multiple query types (such as id fetching {@link IdBasedFetcher}), complete entry {@link EntryBasedFetcher}, and search-based fetcher (this class).
+ * </p>
  */
 public interface SearchBasedParserFetcher extends SearchBasedFetcher {
 

src/main/java/org/jabref/logic/importer/fileformat/ACMPortalParser.java

@@ -71,8 +71,8 @@ public List<String> parseDoiSearchPage(InputStream stream) throws ParseException
             Elements doiHrefs = doc.select("div.issue-item__content-right > h5 > span > a");
 
             for (Element elem : doiHrefs) {
-                String fullSegement = elem.attr("href");
-                String doi = fullSegement.substring(fullSegement.indexOf("10"));
+                String fullSegment = elem.attr("href");
+                String doi = fullSegment.substring(fullSegment.indexOf("10"));
                 doiList.add(doi);
             }
         } catch (IOException ex) {

src/main/java/org/jabref/model/entry/LinkedFile.java

@@ -11,6 +11,7 @@
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.regex.Pattern;
 
 import javafx.beans.Observable;
 import javafx.beans.property.SimpleStringProperty;
@@ -26,6 +27,9 @@
  */
 public class LinkedFile implements Serializable {
 
+    private static final String REGEX_URL = "^((?:https?\\:\\/\\/|www\\.)(?:[-a-z0-9]+\\.)*[-a-z0-9]+.*)";
+    private static final Pattern URL_PATTERN = Pattern.compile(REGEX_URL);
+
     private static final LinkedFile NULL_OBJECT = new LinkedFile("", Path.of(""), "");
 
     // We have to mark these properties as transient because they can't be serialized directly
@@ -145,7 +149,7 @@ private void readObject(ObjectInputStream in) throws IOException {
      */
     public static boolean isOnlineLink(String toCheck) {
         String normalizedFilePath = toCheck.trim().toLowerCase();
-        return normalizedFilePath.startsWith("http://") || normalizedFilePath.startsWith("https://") || normalizedFilePath.contains("www.");
+        return URL_PATTERN.matcher(normalizedFilePath).matches();
     }
 
     @Override

src/test/java/org/jabref/logic/auxparser/AuxParserTest.java

@@ -64,6 +64,33 @@ void testNormal() throws URISyntaxException, IOException {
         }
     }
 
+    @Test
+    void testTwoArgMacro() throws URISyntaxException, IOException {
+        // Result should be identical to that of testNormal
+
+        InputStream originalStream = AuxParserTest.class.getResourceAsStream("origin.bib");
+        Path auxFile = Path.of(AuxParserTest.class.getResource("papertwoargmacro.aux").toURI());
+        try (InputStreamReader originalReader = new InputStreamReader(originalStream, StandardCharsets.UTF_8)) {
+            ParserResult result = new BibtexParser(importFormatPreferences, new DummyFileUpdateMonitor()).parse(originalReader);
+
+            AuxParser auxParser = new DefaultAuxParser(result.getDatabase());
+            AuxParserResult auxResult = auxParser.parse(auxFile);
+
+            assertTrue(auxResult.getGeneratedBibDatabase().hasEntries());
+            assertEquals(0, auxResult.getUnresolvedKeysCount());
+            BibDatabase newDB = auxResult.getGeneratedBibDatabase();
+            List<BibEntry> newEntries = newDB.getEntries();
+            assertEquals(2, newEntries.size());
+            assertTrue(newEntries.get(0).hasChanged());
+            assertTrue(newEntries.get(1).hasChanged());
+            assertEquals(2, auxResult.getResolvedKeysCount());
+            assertEquals(2, auxResult.getFoundKeysInAux());
+            assertEquals(auxResult.getFoundKeysInAux() + auxResult.getCrossRefEntriesCount(),
+                    auxResult.getResolvedKeysCount() + auxResult.getUnresolvedKeysCount());
+            assertEquals(0, auxResult.getCrossRefEntriesCount());
+        }
+    }
+
     @Test
     void testNotAllFound() throws URISyntaxException, IOException {
         InputStream originalStream = AuxParserTest.class.getResourceAsStream("origin.bib");

src/test/java/org/jabref/logic/importer/util/FileFieldParserTest.java

@@ -138,17 +138,34 @@ private static Stream<Arguments> stringsToParseTestData() throws Exception {
                         "desc:file.pdf:PDF:asdf"
                 ),
 
+                // www inside filename
+                Arguments.of(
+                        Collections.singletonList(new LinkedFile("", Path.of("/home/www.google.de.pdf"), "")),
+                        ":/home/www.google.de.pdf"
+                ),
+
                 // url
                 Arguments.of(
                          Collections.singletonList(new LinkedFile(new URL("https://books.google.de/"), "")),
                          "https://books.google.de/"
                 ),
 
+                // url with www
+                Arguments.of(
+                             Collections.singletonList(new LinkedFile(new URL("https://www.google.de/"), "")),
+                             "https://www.google.de/"
+                ),
+
                 // url as file
                 Arguments.of(
                              Collections.singletonList(new LinkedFile("", new URL("http://ceur-ws.org/Vol-438"), "URL")),
                              ":http\\://ceur-ws.org/Vol-438:URL"
-                )
+                ),
+                // url as file with desc
+                Arguments.of(
+                             Collections.singletonList(new LinkedFile("desc", new URL("http://ceur-ws.org/Vol-438"), "URL")),
+                             "desc:http\\://ceur-ws.org/Vol-438:URL"
+               )
         );
     }
 

src/test/resources/org/jabref/logic/auxparser/papertwoargmacro.aux

@@ -0,0 +1,8 @@
+\relax
+\abx@aux@cite{0}{Darwin1888}
+\abx@aux@cite{0}{Einstein1920}
+\bibstyle{plain}
+\bibdata{origin}
+\bibcite{Darwin1888}{1}
+\bibcite{Einstein1920}{2}
+\@writefile{toc}{\contentsline {section}{\numberline {1}}{1}}