Merge branch 'main' into main

asifebrahim · web-flow · commit 8a942331a902 · 2025-07-09T21:59:38.000+05:30
diff --git a/.jbang/JabSrvLauncher.java b/.jbang/JabSrvLauncher.java
@@ -60,7 +60,7 @@
 //DEPS info.picocli:picocli:4.7.7
 //DEPS org.postgresql:postgresql:42.7.7
 //DEPS org.bouncycastle:bcprov-jdk18on:1.81
-//DEPS com.konghq:unirest-modules-gson:4.4.7
+//DEPS com.konghq:unirest-modules-gson:4.4.12
 //DEPS jakarta.ws.rs:jakarta.ws.rs-api:4.0.0
 //DEPS org.glassfish.jersey.core:jersey-server:3.1.10
 //DEPS org.glassfish.jersey.inject:jersey-hk2:3.1.10
@@ -72,7 +72,7 @@
 //DEPS org.glassfish.grizzly:grizzly-framework:4.0.2
 //DEPS jakarta.validation:jakarta.validation-api:3.1.1
 //DEPS org.hibernate.validator:hibernate-validator:9.0.1.Final
-//DEPS com.konghq:unirest-modules-gson:4.4.7
+//DEPS com.konghq:unirest-modules-gson:4.4.12
 //DEPS com.google.guava:guava:33.4.8-jre
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.4.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -74,6 +74,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where Document Viewer showed technical exceptions when opening entries with non-PDF files. [#13198](https://github.com/JabRef/jabref/issues/13198)
 - When creating a library, if you drag a PDF file containing only a single column, the dialog will now automatically close. [#13262](https://github.com/JabRef/jabref/issues/13262)
 - We fixed an issue where the tab showing the fulltext search results would appear blank after switching library. [#13241](https://github.com/JabRef/jabref/issues/13241)
+- Enhanced field selection logic in the Merge Entries dialog when fetching from DOI to prefer valid years and entry types. [#12549](https://github.com/JabRef/jabref/issues/12549)
 
 ### Removed
 
diff --git a/build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts b/build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts
diff --git a/build-logic/src/main/kotlin/org.jabref.gradle.base.targets.gradle.kts b/build-logic/src/main/kotlin/org.jabref.gradle.base.targets.gradle.kts
@@ -18,12 +18,12 @@ javaModulePackaging {
     target("ubuntu-22.04") {
         operatingSystem = OperatingSystemFamily.LINUX
         architecture = MachineArchitecture.X86_64
-        packageTypes = listOf("app-image", "deb")
+        packageTypes = listOf("app-image", "deb", "rpm")
     }
     target("ubuntu-22.04-arm") {
         operatingSystem = OperatingSystemFamily.LINUX
         architecture = MachineArchitecture.ARM64
-        packageTypes = listOf("app-image", "deb")
+        packageTypes = listOf("app-image", "deb", "rpm")
     }
     target("macos-13") {
         operatingSystem = OperatingSystemFamily.MACOS
diff --git a/jabgui/src/main/java/module-info.java b/jabgui/src/main/java/module-info.java
@@ -47,7 +47,7 @@
     provides org.kordamp.ikonli.IkonProvider
             with org.jabref.gui.icon.JabrefIconProvider;
 
-    requires org.reactfx;
+    requires reactfx;
     // endregion
 
     // region: Logging
@@ -92,7 +92,7 @@
     // region HTTP clients
     requires org.apache.httpcomponents.core5.httpcore5;
     requires org.jsoup;
-    requires com.konghq.unirest.java.core;
+    requires unirest.java.core;
     // requires unirest.modules.gson;
     // endregion
 
@@ -130,14 +130,14 @@
     // requires org.apache.xmpbox;
     // requires com.ibm.icu;
 
-    requires com.vladsch.flexmark;
-    requires com.vladsch.flexmark.html2md.converter;
-    requires com.vladsch.flexmark.util.ast;
-    requires com.vladsch.flexmark.util.data;
+    requires flexmark;
+    requires flexmark.html2md.converter;
+    requires flexmark.util.ast;
+    requires flexmark.util.data;
 
     // requires com.h2database.mvstore;
 
-    requires com.github.java.keyring;
+    requires java.keyring;
     // requires org.freedesktop.dbus;
 
     requires org.jooq.jool;
@@ -148,15 +148,15 @@
     // requires ai.djl.tokenizers;
     // requires jvm.openai;
     // requires langchain4j;
-    requires dev.langchain4j.core;
+    requires langchain4j.core;
     // requires langchain4j.google.ai.gemini;
     // requires langchain4j.hugging.face;
     // requires langchain4j.mistral.ai;
     // requires langchain4j.open.ai;
     // uses ai.djl.engine.EngineProvider;
     // uses ai.djl.repository.RepositoryFactory;
     // uses ai.djl.repository.zoo.ZooProvider;
-    // uses dev.langchain4j.spi.prompt.PromptTemplateFactory;
+    // uses langchain4j.spi.prompt.PromptTemplateFactory;
     // requires velocity.engine.core;
     // endregion
 
diff --git a/jabgui/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java b/jabgui/src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java
@@ -107,6 +107,7 @@ private void showMergeDialog(BibEntry originalEntry, BibEntry fetchedEntry, WebF
         dialog.setTitle(Localization.lang("Merge entry with %0 information", fetcher.getName()));
         dialog.setLeftHeaderText(Localization.lang("Original entry"));
         dialog.setRightHeaderText(Localization.lang("Entry from %0", fetcher.getName()));
+        dialog.autoSelectBetterFields();
         Optional<BibEntry> mergedEntry = dialogService.showCustomDialogAndWait(dialog).map(EntriesMergeResult::mergedEntry);
 
         if (mergedEntry.isPresent()) {
diff --git a/jabgui/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java b/jabgui/src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java
@@ -64,4 +64,8 @@ public void setRightHeaderText(String rightHeaderText) {
     public void configureDiff(ShowDiffConfig diffConfig) {
         threeWayMergeView.showDiff(diffConfig);
     }
+
+    public void autoSelectBetterFields() {
+        threeWayMergeView.autoSelectBetterFields();
+    }
 }
diff --git a/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/FieldRowView.java b/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/FieldRowView.java
@@ -208,6 +208,10 @@ public boolean hasEqualLeftAndRightValues() {
         return viewModel.hasEqualLeftAndRightValues();
     }
 
+    public void autoSelectBetterValue() {
+        viewModel.autoSelectBetterValue();
+    }
+
     @Override
     public String toString() {
         return "FieldRowView [shouldShowDiffs=" + shouldShowDiffs.get() + ", fieldNameCell=" + fieldNameCell + ", leftValueCell=" + leftValueCell + ", rightValueCell=" + rightValueCell + ", mergedValueCell=" + mergedValueCell + "]";
diff --git a/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/FieldRowViewModel.java b/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/FieldRowViewModel.java
@@ -16,10 +16,14 @@
 
 import org.jabref.gui.mergeentries.newmergedialog.fieldsmerger.FieldMerger;
 import org.jabref.gui.mergeentries.newmergedialog.fieldsmerger.FieldMergerFactory;
+import org.jabref.logic.bibtex.comparator.ComparisonResult;
+import org.jabref.logic.bibtex.comparator.YearFieldValuePlausibilityComparator;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.InternalField;
+import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.EntryTypeFactory;
+import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.strings.StringUtil;
 
 import com.tobiasdiez.easybind.EasyBind;
@@ -120,6 +124,25 @@ public FieldRowViewModel(Field field, BibEntry leftEntry, BibEntry rightEntry, B
         EasyBind.subscribe(hasEqualLeftAndRightBinding(), this::setIsFieldsMerged);
     }
 
+    public void autoSelectBetterValue() {
+        String leftValue = getLeftFieldValue();
+        String rightValue = getRightFieldValue();
+
+        if (StandardField.YEAR == field) {
+                YearFieldValuePlausibilityComparator comparator = new YearFieldValuePlausibilityComparator();
+                ComparisonResult comparison = comparator.compare(leftValue, rightValue);
+                if (ComparisonResult.RIGHT_BETTER == comparison) {
+                    selectRightValue();
+                } else if (ComparisonResult.LEFT_BETTER == comparison) {
+                    selectLeftValue();
+                }
+        } else if (InternalField.TYPE_HEADER == field) {
+            if (leftValue.equalsIgnoreCase(StandardEntryType.Misc.getName())) {
+                selectRightValue();
+            }
+        }
+    }
+
     public void selectNonEmptyValue() {
         if (StringUtil.isNullOrEmpty(leftFieldValue.get())) {
             selectRightValue();
diff --git a/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java b/jabgui/src/main/java/org/jabref/gui/mergeentries/newmergedialog/ThreeWayMergeView.java
@@ -200,4 +200,10 @@ public BibEntry getRightEntry() {
     public void saveConfiguration() {
         toolbar.saveToolbarConfiguration();
     }
+
+    public void autoSelectBetterFields() {
+        for (FieldRowView row : fieldRows) {
+            row.autoSelectBetterValue();
+        }
+    }
 }
diff --git a/jabgui/src/test/java/org/jabref/gui/mergeentries/FieldRowViewModelTest.java b/jabgui/src/test/java/org/jabref/gui/mergeentries/FieldRowViewModelTest.java
@@ -214,6 +214,24 @@ void unmergeFieldsShouldDoNothingIfFieldsAreNotMerged() {
         assertEquals(oldRightGroups, groupsField.getRightFieldValue());
     }
 
+    @Test
+    void newYearShouldBeSelectedForYearsWithLargeValueGap() {
+        BibEntry leftEntry = new BibEntry().withField(StandardField.YEAR, "1990");
+        BibEntry rightEntry = new BibEntry().withField(StandardField.YEAR, "2020");
+        FieldRowViewModel yearField = new FieldRowViewModel(StandardField.YEAR, leftEntry, rightEntry, mergedEntry, fieldMergerFactory);
+        yearField.autoSelectBetterValue();
+        assertEquals(FieldRowViewModel.Selection.RIGHT, yearField.getSelection());
+    }
+
+    @Test
+    void yearInRangeShouldBeSelected() {
+        BibEntry leftEntry = new BibEntry().withField(StandardField.YEAR, "1700");
+        BibEntry rightEntry = new BibEntry().withField(StandardField.YEAR, "2000");
+        FieldRowViewModel yearField = new FieldRowViewModel(StandardField.YEAR, leftEntry, rightEntry, mergedEntry, fieldMergerFactory);
+        yearField.autoSelectBetterValue();
+        assertEquals(FieldRowViewModel.Selection.RIGHT, yearField.getSelection());
+    }
+
     public FieldRowViewModel createViewModelForField(Field field) {
         return new FieldRowViewModel(field, leftEntry, rightEntry, mergedEntry, fieldMergerFactory);
     }
diff --git a/jablib/src/main/java/module-info.java b/jablib/src/main/java/module-info.java
@@ -153,20 +153,20 @@
     requires jakarta.ws.rs;
     requires org.apache.httpcomponents.core5.httpcore5;
     requires org.jsoup;
-    requires com.konghq.unirest.java.core;
-    requires com.konghq.unirest.modules.gson;
+    requires unirest.java.core;
+    requires unirest.modules.gson;
     // endregion
 
     // region: SQL databases
-    requires io.zonky.test.embedded.postgres;
+    requires embedded.postgres;
     requires org.tukaani.xz;
     requires org.postgresql.jdbc;
     // endregion
 
     // region: Apache Commons and other (similar) helper libraries
     requires com.google.common;
     requires io.github.javadiffutils;
-    requires info.debatty.java.string.similarity;
+    requires java.string.similarity;
     requires org.apache.commons.compress;
     requires org.apache.commons.csv;
     requires org.apache.commons.io;
@@ -177,27 +177,27 @@
 
     // region: latex2unicode
     requires com.github.tomtung.latex2unicode;
-    requires com.lihaoyi.fastparse;
+    requires fastparse;
     requires scala.library;
     // endregion
 
-    requires org.jbibtex;
-    requires de.undercouch.citeproc.java;
+    requires jbibtex;
+    requires citeproc.java;
 
-    requires de.rototor.snuggletex.core;
+    requires snuggletex.core;
 
     requires org.apache.pdfbox;
     requires org.apache.xmpbox;
     requires com.ibm.icu;
 
-    requires com.vladsch.flexmark;
-    requires com.vladsch.flexmark.html2md.converter;
-    requires com.vladsch.flexmark.util.ast;
-    requires com.vladsch.flexmark.util.data;
+    requires flexmark;
+    requires flexmark.html2md.converter;
+    requires flexmark.util.ast;
+    requires flexmark.util.data;
 
     requires com.h2database.mvstore;
 
-    requires com.github.java.keyring;
+    requires java.keyring;
     requires org.freedesktop.dbus;
 
     requires org.jooq.jool;
@@ -206,18 +206,18 @@
     requires ai.djl.api;
     requires ai.djl.pytorch_model_zoo;
     requires ai.djl.tokenizers;
-    requires io.github.stefanbratanov.jvm.openai;
-    requires dev.langchain4j;
-    requires dev.langchain4j.core;
-    requires dev.langchain4j.google.ai.gemini;
-    requires dev.langchain4j.hugging.face;
-    requires dev.langchain4j.mistral.ai;
-    requires dev.langchain4j.open.ai;
+    requires jvm.openai;
+    requires langchain4j;
+    requires langchain4j.core;
+    requires langchain4j.google.ai.gemini;
+    requires langchain4j.hugging.face;
+    requires langchain4j.mistral.ai;
+    requires langchain4j.open.ai;
     uses ai.djl.engine.EngineProvider;
     uses ai.djl.repository.RepositoryFactory;
     uses ai.djl.repository.zoo.ZooProvider;
     uses dev.langchain4j.spi.prompt.PromptTemplateFactory;
-    requires org.apache.velocity.engine.core;
+    requires velocity.engine.core;
     // endregion
 
     // region: Lucene
@@ -243,12 +243,13 @@
 
     // region: other libraries (alphabetically)
     requires cuid;
-    requires com.googlecode.dd.plist;
+    requires dd.plist;
     requires io.github.adr;
     // required by okhttp and some AI library
     requires kotlin.stdlib;
     requires mslinks;
     requires org.antlr.antlr4.runtime;
     requires org.libreoffice.uno;
+    requires org.jetbrains.annotations;
     // endregion
 }
diff --git a/jablib/src/main/java/org/jabref/logic/bibtex/comparator/ComparisonResult.java b/jablib/src/main/java/org/jabref/logic/bibtex/comparator/ComparisonResult.java
@@ -0,0 +1,7 @@
+package org.jabref.logic.bibtex.comparator;
+
+public enum ComparisonResult {
+    LEFT_BETTER,
+    RIGHT_BETTER,
+    UNDETERMINED
+}
diff --git a/jablib/src/main/java/org/jabref/logic/bibtex/comparator/FieldValuePlausibilityComparator.java b/jablib/src/main/java/org/jabref/logic/bibtex/comparator/FieldValuePlausibilityComparator.java
@@ -0,0 +1,12 @@
+package org.jabref.logic.bibtex.comparator;
+
+public abstract class FieldValuePlausibilityComparator {
+    /**
+     * Compares the plausibility of two field values.
+     *
+     * @param leftValue  value from the library (or candidate)
+     * @param rightValue value from the fetcher (or existing record)
+     * @return ComparisonResult indicating which field is more plausible: RIGHT_BETTER, LEFT_BETTER, or UNDETERMINED
+     */
+    public abstract ComparisonResult compare(String leftValue, String rightValue);
+}
diff --git a/jablib/src/main/java/org/jabref/logic/bibtex/comparator/YearFieldValuePlausibilityComparator.java b/jablib/src/main/java/org/jabref/logic/bibtex/comparator/YearFieldValuePlausibilityComparator.java
@@ -0,0 +1,62 @@
+package org.jabref.logic.bibtex.comparator;
+
+import java.time.Year;
+import java.util.Optional;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.jabref.logic.integrity.YearChecker;
+
+public class YearFieldValuePlausibilityComparator extends FieldValuePlausibilityComparator {
+
+    private static final Pattern YEAR_PATTERN = Pattern.compile("(\\d{4})");
+
+    /**
+     * Compares the plausibility of two field values.
+     *
+     * @param leftValue  value from the library (or candidate)
+     * @param rightValue value from the fetcher (or existing record)
+     * @return ComparisonResult indicating which year is more plausible: RIGHT_BETTER, LEFT_BETTER, or UNDETERMINED
+     */
+
+    @Override
+    public ComparisonResult compare(String leftValue, String rightValue) {
+        YearChecker checker = new YearChecker();
+
+        boolean leftValid = checker.checkValue(leftValue).isEmpty();
+
+        if (leftValid) {
+            Optional<Integer> leftYear = extractYear(leftValue);
+            Optional<Integer> rightYear = extractYear(rightValue);
+
+            boolean leftYearInRange = (leftYear.get() >= 1800) && (leftYear.get() <= Year.now().getValue() + 2);
+
+            if (leftYearInRange) {
+                int diff = Math.abs(leftYear.get() - rightYear.get());
+                if (diff > 10) {
+                    return rightYear.get() > leftYear.get()
+                            ? ComparisonResult.RIGHT_BETTER
+                            : ComparisonResult.LEFT_BETTER;
+                }
+                return ComparisonResult.UNDETERMINED; // years are close, undetermined
+            }
+            return ComparisonResult.RIGHT_BETTER;
+            }
+        return ComparisonResult.RIGHT_BETTER;
+    }
+
+    /**
+     * Extracts the first 4-digit number found in the string.
+     * Used to identify year-like values such as "About 2000" or "Published in 1999".
+     *
+     * @param value the input string possibly containing a year
+     * @return Optional containing the 4-digit year if found, otherwise Optional.empty()
+     */
+    private Optional<Integer> extractYear(String value) {
+        Matcher matcher = YEAR_PATTERN.matcher(value);
+        if (matcher.find()) {
+            return Optional.of(Integer.parseInt(matcher.group(1)));
+        }
+        return Optional.empty();
+    }
+}
diff --git a/jabsrv-cli/src/main/java/module-info.java b/jabsrv-cli/src/main/java/module-info.java
diff --git a/jabsrv/build.gradle.kts b/jabsrv/build.gradle.kts
diff --git a/jabsrv/src/main/java/module-info.java b/jabsrv/src/main/java/module-info.java

Original file line number	Diff line number	Diff line change
`@@ -64,4 +64,8 @@ public void setRightHeaderText(String rightHeaderText) {`
`64`	`64`	`public void configureDiff(ShowDiffConfig diffConfig) {`
`65`	`65`	`threeWayMergeView.showDiff(diffConfig);`
`66`	`66`	`}`
	`67`	`+`
	`68`	`+ public void autoSelectBetterFields() {`
	`69`	`+ threeWayMergeView.autoSelectBetterFields();`
	`70`	`+ }`
`67`	`71`	`}`
Original file line number	Diff line number	Diff line change
`@@ -200,4 +200,10 @@ public BibEntry getRightEntry() {`
`200`	`200`	`public void saveConfiguration() {`
`201`	`201`	`toolbar.saveToolbarConfiguration();`
`202`	`202`	`}`
	`203`	`+`
	`204`	`+ public void autoSelectBetterFields() {`
	`205`	`+ for (FieldRowView row : fieldRows) {`
	`206`	`+ row.autoSelectBetterValue();`
	`207`	`+ }`
	`208`	`+ }`
`203`	`209`	`}`