Merge remote-tracking branch 'upstream/main' into fixUrlLink

* upstream/main:
  Add some JavaDoc to Fetchers
  Support two argument form of \abx@aux@cite macro in DefaultAuxParser (#8549)

CHANGELOG.md

@@ -26,6 +26,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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
 

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 {@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/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/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}}