Merge branch 'JabRef:main' into main

.github/workflows/deployment.yml

@@ -37,10 +37,10 @@ jobs:
   build:
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
+      matrix: # if you change the os version rename all other occurrences
+        os: [ubuntu-22.04, windows-latest, macos-13]
         include:
-          - os: ubuntu-latest
+          - os: ubuntu-22.04
             displayName: linux
             archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
           - os: windows-latest
@@ -75,7 +75,7 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install pigz and cache (linux)
-        if: (matrix.os == 'ubuntu-latest')
+        if: (matrix.os == 'ubuntu-22.04')
         uses: awalsh128/cache-apt-pkgs-action@latest
         with:
           packages: pigz
@@ -212,7 +212,7 @@ jobs:
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Repack deb file for Debian
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-22.04') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           cd build/distribution
@@ -247,7 +247,7 @@ jobs:
         # macOS: Negated condition of "Upload to GitHub workflow artifacts store (macOS)"
         #        Reason: We either upload the non-notarized files - or notarize the files later (and upload these later)
         # needs to be on one line; multi line does not work
-        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-latest') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-22.04') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ [email protected]:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
@@ -268,7 +268,7 @@ jobs:
           compression-level: 0 # no compression
   announce:
     name: Comment on pull request
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: [build]
     if: ${{ github.event_name == 'pull_request' }}
     steps:

CHANGELOG.md

@@ -18,6 +18,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Fixed
 
 - We fixed an issue where a bib file with UFF-8 charset was wrongly loaded with a different charset [forum#5369](https://discourse.jabref.org/t/jabref-5-15-opens-bib-files-with-shift-jis-encoding-instead-of-utf-8/5369/)
+- We fixed an issue where new entries were inserted in the middle of the table instead of at the end. [#12371](https://github.com/JabRef/jabref/pull/12371)
+- We fixed an issue where removing the sort from the table did not restore the original order. [#12371](https://github.com/JabRef/jabref/pull/12371)
 
 ### Removed
 

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.29.3'
+    id 'org.openrewrite.rewrite' version '7.0.0'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -308,7 +308,7 @@ dependencies {
     // API
     implementation 'jakarta.ws.rs:jakarta.ws.rs-api:4.0.0'
     // Implementation of the API
-    implementation 'org.glassfish.jersey.core:jersey-server:3.1.9'
+    implementation 'org.glassfish.jersey.core:jersey-server:3.1.10'
     // injection framework
     implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.9'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
@@ -317,8 +317,8 @@ dependencies {
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
-    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.9'
-    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.9'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.10'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.10'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
@@ -401,7 +401,7 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.23.2"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:3.0.1"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -185,7 +185,28 @@ public MainTable(MainTableDataModel model,
         this.setItems(model.getEntriesFilteredAndSorted());
 
         // Enable sorting
-        model.getEntriesFilteredAndSorted().comparatorProperty().bind(this.comparatorProperty());
+        // Workaround for a JavaFX bug: https://bugs.openjdk.org/browse/JDK-8301761 (The sorting of the SortedList can become invalid)
+        // The default comparator of the SortedList does not consider the insertion index of entries that are equal according to the comparator.
+        // When two entries are equal based on the comparator, the entry that was inserted first should be considered smaller.
+        this.setSortPolicy(_ -> true);
+        model.getEntriesFilteredAndSorted().comparatorProperty().bind(
+                this.comparatorProperty().map(comparator -> {
+                    if (comparator == null) {
+                        return null;
+                    }
+
+                    return (entry1, entry2) -> {
+                        int result = comparator.compare(entry1, entry2);
+                        if (result != 0) {
+                            return result;
+                        }
+                        // If the entries are equal according to the comparator, compare them by their index in the database.
+                        // The comparison should ideally be based on the database index, but retrieving the index takes log(n). See {@link BibDatabase#indexOf}.
+                        // Using the entry ID is also valid since IDs are monotonically increasing.
+                        return entry1.getEntry().getId().compareTo(entry2.getEntry().getId());
+                    };
+                })
+        );
 
         // Store visual state
         new PersistenceVisualStateTable(this, mainTablePreferences.getColumnPreferences()).addListeners();

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

@@ -252,16 +252,24 @@ private boolean isFarAway(TextPosition previous, TextPosition current) {
             return Math.abs(Xgap) > XspaceThreshold && Math.abs(Ygap) > YspaceThreshold;
         }
 
-        private boolean isUnwantedText(TextPosition previousTextPosition, TextPosition textPosition) {
+        private boolean isUnwantedText(TextPosition previousTextPosition, TextPosition textPosition,
+                                       Map<Float, TextPosition> lastPositionMap, float fontSize) {
+            // This indicates that the text is at the start of the line, so it is needed.
             if (textPosition == null || previousTextPosition == null) {
                 return false;
             }
+            // We use the font size to identify titles. Blank characters don't have a font size, so we discard them.
+            // The space will be added back in the final result, but not in this method.
             if (StringUtil.isBlank(textPosition.getUnicode())) {
                 return true;
             }
-            // The title usually don't in the bottom 10% of a page.
-            return (textPosition.getPageHeight() - textPosition.getYDirAdj())
-                    < (textPosition.getPageHeight() * 0.1);
+            // Titles are generally not located in the bottom 10% of a page.
+            if ((textPosition.getPageHeight() - textPosition.getYDirAdj()) < (textPosition.getPageHeight() * 0.1)) {
+                return true;
+            }
+            // Characters in a title typically remain close together,
+            // so a distant character is unlikely to be part of the title.
+            return lastPositionMap.containsKey(fontSize) && isFarAway(lastPositionMap.get(fontSize), textPosition);
         }
 
         private Optional<String> findLargestFontText(List<TextPosition> textPositions) {
@@ -271,8 +279,7 @@ private Optional<String> findLargestFontText(List<TextPosition> textPositions) {
             for (TextPosition textPosition : textPositions) {
                 float fontSize = textPosition.getFontSizeInPt();
                 // Exclude unwanted text based on heuristics
-                if (isUnwantedText(previousTextPosition, textPosition) ||
-                    (lastPositionMap.containsKey(fontSize) && isFarAway(lastPositionMap.get(fontSize), textPosition))) {
+                if (isUnwantedText(previousTextPosition, textPosition, lastPositionMap, fontSize)) {
                     continue;
                 }
                 fontSizeTextMap.putIfAbsent(fontSize, new StringBuilder());

src/main/java/org/jabref/logic/search/query/SearchToSqlVisitor.java

@@ -207,6 +207,16 @@ public SqlQueryNode visitComparison(SearchParser.ComparisonContext ctx) {
             setFlags(searchFlags, REGULAR_EXPRESSION, true, true);
         }
 
+        // field = "" -> should find entries where the field is empty
+        // field != "" -> should find entries where the field is not empty
+        if (term.isEmpty()) {
+            if (searchFlags.contains(NEGATION)) {
+                searchFlags.remove(NEGATION);
+            } else {
+                searchFlags.add(NEGATION);
+            }
+        }
+
         return getFieldQueryNode(field.toLowerCase(Locale.ROOT), term, searchFlags);
     }
 

src/test/java/org/jabref/logic/search/query/SearchQuerySQLConversionTest.java

@@ -695,6 +695,38 @@ cte0 AS (
                             )
                         )
                         SELECT * FROM cte0 GROUP BY entryid"""
+                ),
+
+                Arguments.of(
+                        "file = \"\"",
+                        """
+                        WITH
+                        cte0 AS (
+                            SELECT main_table.entryid
+                            FROM bib_fields."tableName" AS main_table
+                            WHERE main_table.entryid NOT IN (
+                                SELECT inner_table.entryid
+                                FROM bib_fields."tableName" AS inner_table
+                                WHERE (
+                                    (inner_table.field_name = 'file') AND ((inner_table.field_value_literal ILIKE ('%%')) OR (inner_table.field_value_transformed ILIKE ('%%')))
+                                )
+                            )
+                        )
+                        SELECT * FROM cte0 GROUP BY entryid"""
+                ),
+
+                Arguments.of(
+                        "file != \"\"",
+                        """
+                        WITH
+                        cte0 AS (
+                            SELECT main_table.entryid
+                            FROM bib_fields."tableName" AS main_table
+                            WHERE (
+                                (main_table.field_name = 'file') AND ((main_table.field_value_literal ILIKE ('%%')) OR (main_table.field_value_transformed ILIKE ('%%')))
+                            )
+                        )
+                        SELECT * FROM cte0 GROUP BY entryid"""
                 )
         );
     }