Open linked pdf files in bib files (#14275)

* add pdf opening ability

* fix jbang

* fix format

* fix checkstyle

* fix tests

* remove unused import

* Add debug

* .jbang scripts should not be included inside themselves

* Add ability to open pdfs in standalone nad gui mode

* update execution rights

* More `@NonNull`

* More `@NonNull`

* Fix data type

* Fix catch of NPE in context of Optionals

* Add `@NullMarked` and refactor Optional use

* More close constructors

* Add link to other tests

* Output field at parsing

* Initial test for BibDefinitionProvider

* address comments

* Fix file path on databasecontext

* Fix test

* Fix formatting

* Fix Path.of - and remove obsolete method

* Group ".remote" together in module-info

* Fix URI.from() architecture rule

* Fix test

---------

Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

Author: palukku

.jbang/JabLsLauncher.java

@@ -36,6 +36,7 @@
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspLinkHandler.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspParserHandler.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspRangeUtil.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/BibDefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProviderFactory.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/LatexDefinitionProvider.java

jablib/src/main/java/module-info.java

@@ -30,6 +30,7 @@
     exports org.jabref.logic.protectedterms;
     exports org.jabref.logic.remote;
     exports org.jabref.logic.remote.client;
+    exports org.jabref.logic.remote.server;
     exports org.jabref.logic.net.ssl;
     exports org.jabref.logic.citationstyle;
     exports org.jabref.architecture;
@@ -85,7 +86,6 @@
     exports org.jabref.logic.biblog;
     exports org.jabref.model.biblog;
     exports org.jabref.model.http;
-    exports org.jabref.logic.remote.server;
     exports org.jabref.logic.util.strings;
     exports org.jabref.model.openoffice;
     exports org.jabref.logic.openoffice;

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -88,6 +88,8 @@
 ///
 /// **Opposite class:**
 /// [`BibDatabaseWriter`](org.jabref.logic.exporter.BibDatabaseWriter)
+///
+/// FIXME: This class relies on `char`, but should use [java.lang.Character] to be fully Unicode compliant.
 public class BibtexParser implements Parser {
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexParser.class);
     private static final int LOOKAHEAD = 1024;
@@ -759,7 +761,7 @@ private void parseField(BibEntry entry) throws IOException {
         Field field = FieldFactory.parseField(parseTextToken());
 
         skipWhitespace();
-        consume('=');
+        consume(field, '=');
         String content = parseFieldContent(field);
         if (!content.isEmpty()) {
             if (entry.hasField(field)) {
@@ -1172,6 +1174,19 @@ private void consume(char expected) throws IOException {
         }
     }
 
+    private void consume(Field field, char expected) throws IOException {
+        int character = read();
+
+        if (character != expected) {
+            throw new IOException(
+                    "Error at line " + line
+                            + " after column " + column
+                            + " (" + field.getName() + "): Expected "
+                            + expected + " but received "
+                            + (char) character + " (" + character + ")");
+        }
+    }
+
     private boolean consumeUncritically(char expected) throws IOException {
         int character;
         // @formatter:off

jablib/src/main/java/org/jabref/logic/importer/util/FileFieldParser.java

@@ -4,10 +4,14 @@
 import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
 
 import org.jabref.logic.util.URLUtil;
 import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.util.Range;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -21,7 +25,7 @@ public class FileFieldParser {
 
     private boolean windowsPath;
 
-    public FileFieldParser(String value) {
+    private FileFieldParser(String value) {
         if (value == null) {
             this.value = null;
         } else {
@@ -46,11 +50,16 @@ public FileFieldParser(String value) {
     public static List<LinkedFile> parse(String value) {
         // We need state to have a more clean code. Thus, we instantiate the class and then return the result
         FileFieldParser fileFieldParser = new FileFieldParser(value);
-        return fileFieldParser.parse();
+        return fileFieldParser.parse().stream().map(LinkedFilePosition::linkedFile).collect(Collectors.toList());
     }
 
-    public List<LinkedFile> parse() {
-        List<LinkedFile> files = new ArrayList<>();
+    public static Map<LinkedFile, Range> parseToPosition(String value) {
+        FileFieldParser fileFieldParser = new FileFieldParser(value);
+        return fileFieldParser.parse().stream().collect(HashMap::new, (map, position) -> map.put(position.linkedFile(), position.range()), HashMap::putAll);
+    }
+
+    private List<LinkedFilePosition> parse() {
+        List<LinkedFilePosition> files = new ArrayList<>();
 
         if ((value == null) || value.trim().isEmpty()) {
             return files;
@@ -59,7 +68,7 @@ public List<LinkedFile> parse() {
         if (LinkedFile.isOnlineLink(value.trim())) {
             // needs to be modifiable
             try {
-                return List.of(new LinkedFile(URLUtil.create(value), ""));
+                return List.of(new LinkedFilePosition(new LinkedFile(URLUtil.create(value), ""), new Range(0, value.length() - 1)));
             } catch (MalformedURLException e) {
                 LOGGER.error("invalid url", e);
                 return files;
@@ -72,6 +81,7 @@ public List<LinkedFile> parse() {
         resetDataStructuresForNextElement();
         boolean inXmlChar = false;
         boolean escaped = false;
+        int startColumn = 0;
 
         for (int i = 0; i < value.length(); i++) {
             char c = value.charAt(i);
@@ -114,7 +124,8 @@ public List<LinkedFile> parse() {
                 }
             } else if (!escaped && (c == ';') && !inXmlChar) {
                 linkedFileData.add(charactersOfCurrentElement.toString());
-                files.add(convert(linkedFileData));
+                files.add(new LinkedFilePosition(convert(linkedFileData), new Range(startColumn, i)));
+                startColumn = i + 1;
 
                 // next iteration
                 resetDataStructuresForNextElement();
@@ -127,7 +138,7 @@ public List<LinkedFile> parse() {
             linkedFileData.add(charactersOfCurrentElement.toString());
         }
         if (!linkedFileData.isEmpty()) {
-            files.add(convert(linkedFileData));
+            files.add(new LinkedFilePosition(convert(linkedFileData), new Range(startColumn, value.length() - 1)));
         }
         return files;
     }
@@ -193,4 +204,7 @@ static LinkedFile convert(List<String> entry) {
         entry.clear();
         return field;
     }
+
+    private record LinkedFilePosition(LinkedFile linkedFile, Range range) {
+    }
 }

jablib/src/main/java/org/jabref/logic/util/io/FileUtil.java

@@ -403,9 +403,9 @@ public static Optional<Path> findSingleFileRecursively(String filename, Path roo
         return Optional.empty();
     }
 
-    public static Optional<Path> find(final BibDatabaseContext databaseContext,
+    public static Optional<Path> find(@NonNull BibDatabaseContext databaseContext,
                                       @NonNull String fileName,
-                                      FilePreferences filePreferences) {
+                                      @NonNull FilePreferences filePreferences) {
         return find(fileName, databaseContext.getFileDirectories(filePreferences));
     }
 
@@ -416,7 +416,7 @@ public static Optional<Path> find(final BibDatabaseContext databaseContext,
      * Will look in each of the given directories starting from the beginning and
      * returning the first found file to match if any.
      */
-    public static Optional<Path> find(String fileName, List<Path> directories) {
+    public static Optional<Path> find(@NonNull String fileName, @NonNull List<@NonNull Path> directories) {
         if (directories.isEmpty()) {
             // Fallback, if no directories to resolve are passed
             Path path = Path.of(fileName);

jablib/src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -69,8 +69,10 @@ public class BibDatabaseContext {
 
     @Nullable
     private DatabaseSynchronizer dbmsSynchronizer;
+
     @Nullable
     private CoarseChangeFilter dbmsListener;
+
     private DatabaseLocation location;
 
     public BibDatabaseContext() {
@@ -172,7 +174,7 @@ public boolean isStudy() {
      * @param preferences The fileDirectory preferences
      * @return List of existing absolute paths
      */
-    public List<Path> getFileDirectories(FilePreferences preferences) {
+    public @NonNull List<@NonNull Path> getFileDirectories(@NonNull FilePreferences preferences) {
         // Paths are a) ordered and b) should be contained only once in the result
         SequencedSet<Path> fileDirs = new LinkedHashSet<>(3);
 

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

@@ -28,10 +28,9 @@
 import org.jspecify.annotations.NullMarked;
 import org.jspecify.annotations.Nullable;
 
-/**
- * Represents the link to an external file (e.g. associated PDF file).
- * This class is {@link Serializable} which is needed for drag and drop in gui
- */
+/// Represents the link to an external file (e.g. associated PDF file).
+/// This class is {@link Serializable} which is needed for drag and drop in gui
+/// The conversion from String ([org.jabref.model.entry.field.StandardField.FILE]) is done at [org.jabref.logic.importer.util.FileFieldParser#parse(String)]
 @AllowedToUseLogic("Uses FileUtil from logic")
 @NullMarked
 public class LinkedFile implements Serializable {

jablib/src/test/java/org/jabref/logic/importer/ParserResultTest.java

@@ -18,6 +18,7 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.mock;
 
+// Other tests for reading can be found at [org.jabref.logic.importer.fileformat.BibtexImporterTest]
 class ParserResultTest {
     @Test
     void isEmptyForNewParseResult() {

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

@@ -219,6 +219,11 @@ private static Stream<Arguments> stringsToParseTest() throws MalformedURLExcepti
                 Arguments.of(
                         List.of(new LinkedFile("", "A:\\Zotero\\storage\\test.pdf", "")),
                         "A:\\Zotero\\storage\\test.pdf"
+                ),
+                // Mixed path
+                Arguments.of(
+                        List.of(new LinkedFile("", "C:/Users/Philip/Downloads/corti-et-al-2009-cocoa-and-cardiovascular-health.pdf", "PDF")),
+                        ":C\\:/Users/Philip/Downloads/corti-et-al-2009-cocoa-and-cardiovascular-health.pdf:PDF"
                 )
         );
     }

jablib/src/test/java/org/jabref/model/entry/identifier/RFCTest.java

@@ -1,6 +1,7 @@
 package org.jabref.model.entry.identifier;
 
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.Optional;
 
 import org.junit.jupiter.api.Test;
@@ -30,8 +31,8 @@ void invalidRfc() {
     }
 
     @Test
-    void getExternalUri() {
+    void getExternalUri() throws URISyntaxException {
         RFC rfc = new RFC("rfc7276");
-        assertEquals(Optional.of(URI.create("https://www.rfc-editor.org/rfc/rfc7276")), rfc.getExternalURI());
+        assertEquals(Optional.of(new URI("https://www.rfc-editor.org/rfc/rfc7276")), rfc.getExternalURI());
     }
 }