Merge branch 'main' into fix-for-issue-10548

CHANGELOG.md

@@ -12,7 +12,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - We added a "view as BibTeX" option before importing an entry from the citation relation tab. [#11826](https://github.com/JabRef/jabref/issues/11826)
-- We added probable search hits instead of exact matches. Sorting by hit score can be done by the new score table column. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We added support finding LaTeX-encoded special characters based on plain Unicode and vice versa. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - When a search hits a file, the file icon of that entry is changed accordingly. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We added an AI-based chat for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
@@ -42,8 +41,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
-- The search syntax is changed to [Apache Lucene syntax](https://lucene.apache.org/core/9_11_1/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#Overview) (also to be similar to the [online search syntax](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax)). [#11542](https://github.com/JabRef/jabref/pull/11542/)
-- When searching using a regular expression, one needs to enclose the search string in `/`. [#11542](https://github.com/JabRef/jabref/pull/11542/)
 - A search in "any" fields ignores the [groups](https://docs.jabref.org/finding-sorting-and-cleaning-entries/groups). [#7996](https://github.com/JabRef/jabref/issues/7996)
 - When a communication error with an [online service](https://docs.jabref.org/collect/import-using-online-bibliographic-database) occurs, JabRef displays the HTTP error. [#11223](https://github.com/JabRef/jabref/issues/11223)
 - The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
@@ -98,12 +95,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where recently opened files were not displayed in the main menu properly. [#9042](https://github.com/JabRef/jabref/issues/9042)
 - We fixed an issue where the DOI lookup would show an error when a DOI was found for an entry. [#11850](https://github.com/JabRef/jabref/issues/11850)
 - We fixed an issue where <kbd>Tab</kbd> cannot be used to jump to next field in some single-line fields. [#11785](https://github.com/JabRef/jabref/issues/11785)
+- We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 - We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)
 
 ### Removed
 
-- We removed support for case-sensitive and exact search. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed the description of search strings. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed support for importing using the SilverPlatterImporter (`Record INSPEC`). [#11576](https://github.com/JabRef/jabref/pull/11576)
 - We removed support for automatically generating file links using the CLI (`--automaticallySetFileLinks`).

build.gradle

@@ -29,9 +29,9 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.23.4'
+    id 'org.openrewrite.rewrite' version '6.25.1'
 
-    id "org.itsallcode.openfasttrace" version "3.0.0"
+    id "org.itsallcode.openfasttrace" version "3.0.1"
 }
 
 // Enable following for debugging
@@ -238,7 +238,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.58.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.60.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -304,7 +304,7 @@ dependencies {
     // Implementation of the API
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.9'
     // injection framework
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.8'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.9'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
@@ -370,11 +370,14 @@ dependencies {
     // Even if "compileOnly" is used, IntelliJ always adds to module-info.java. To avoid issues during committing, we use "implementation" instead of "compileOnly"
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
+    implementation 'io.zonky.test:embedded-postgres:2.0.7'
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
+
     testImplementation 'io.github.classgraph:classgraph:4.8.177'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
 
-    testImplementation 'org.mockito:mockito-core:5.14.1'
+    testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
@@ -795,9 +798,13 @@ jlink {
         requires 'org.apache.commons.lang3'
         requires 'org.apache.commons.logging'
         requires 'org.apache.commons.text'
+        requires 'org.apache.commons.codec'
+        requires 'org.apache.commons.io'
+        requires 'org.apache.commons.compress'
         requires 'org.freedesktop.dbus'
         requires 'org.jsoup'
         requires 'org.slf4j'
+        requires 'org.tukaani.xz';
         uses 'ai.djl.engine.EngineProvider'
         uses 'ai.djl.repository.RepositoryFactory'
         uses 'ai.djl.repository.zoo.ZooProvider'
@@ -809,6 +816,7 @@ jlink {
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
+        uses 'org.postgresql.shaded.com.ongres.stringprep.Profile'
 
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'

external-libraries.md

@@ -357,10 +357,10 @@ License: MIT
 ```
 
 ```yaml
-Id:io.github.adr:e-adr
-Project:EmbeddedArchitecturalDecisionRecords
-URL:https://github.com/adr/e-adr/
-License:EPL-2.0
+Id:      io.github.adr:e-adr
+Project: EmbeddedArchitecturalDecisionRecords
+URL:     https://github.com/adr/e-adr/
+License: EPL-2.0
 ```
 
 ```yaml
@@ -370,6 +370,13 @@ URL:     https://github.com/java-diff-utils/java-diff-utils
 License: Apache-2.0
 ```
 
+```yaml
+Id:      io.zonky.test:embedded-postgres
+Project: embedded-postgres
+URL:     https://github.com/zonkyio/embedded-postgres
+License: Apache-2.0
+```
+
 ```yaml
 Id:      jakarta.annotation:jakarata.annotation-api
 Project: Jakarta Annotations
@@ -806,6 +813,7 @@ de.undercouch:citeproc-java:3.1.0
 eu.lestard:doc-annotations:0.2
 info.debatty:java-string-similarity:2.0.0
 io.github.java-diff-utils:java-diff-utils:4.12
+io.zonky.test:embedded-postgres:2.0.7
 jakarta.activation:jakarta.activation-api:2.1.3
 jakarta.annotation:jakarta.annotation-api:2.1.1
 jakarta.inject:jakarta.inject-api:2.0.1
@@ -821,6 +829,7 @@ net.jodah:typetools:0.6.1
 net.synedra:validatorfx:0.5.0
 one.jpro.jproutils:tree-showing:0.2.2
 org.antlr:antlr4-runtime:4.13.2
+org.apache.commons:commons-compress:1.27.1
 org.apache.commons:commons-csv:1.11.0
 org.apache.commons:commons-lang3:3.17.0
 org.apache.commons:commons-text:1.12.0
@@ -897,6 +906,7 @@ org.slf4j:slf4j-api:2.0.16
 org.tinylog:slf4j-tinylog:2.7.0
 org.tinylog:tinylog-api:2.7.0
 org.tinylog:tinylog-impl:2.7.0
+org.tukaani:xz:1.9
 org.yaml:snakeyaml:2.3
 pt.davidafsilva.apple:jkeychain:1.1.0
 tech.units:indriya:2.2

src/main/antlr4/org/jabref/search/Search.g4

@@ -4,49 +4,82 @@
  * These search expressions are used for searching the bibtex library. They are heavily used for search groups.
  */
 grammar Search;
+options { caseInsensitive = true; }
 
-WS: [ \t] -> skip; // whitespace is ignored/skipped
+WS: [ \t\n\r]+ -> skip; // whitespace is ignored/skipped
 
-LPAREN:'(';
-RPAREN:')';
+LPAREN: '(';
+RPAREN: ')';
 
-EQUAL:'='; // semantically the same as CONTAINS
-EEQUAL:'=='; // semantically the same as MATCHES
-NEQUAL:'!=';
+EQUAL: '='; // case insensitive contains, semantically the same as CONTAINS
+CEQUAL: '=!'; // case sensitive contains
 
-AND:[aA][nN][dD]; // 'and' case insensitive
-OR:[oO][rR]; // 'or' case insensitive
-CONTAINS:[cC][oO][nN][tT][aA][iI][nN][sS]; // 'contains' case insensitive
-MATCHES:[mM][aA][tT][cC][hH][eE][sS]; // 'matches' case insensitive
-NOT:[nN][oO][tT]; // 'not' case insensitive
+EEQUAL: '=='; // exact match case insensitive, semantically the same as MATCHES
+CEEQUAL: '==!'; // exact match case sensitive
 
-STRING:QUOTE (~'"')* QUOTE;
-QUOTE:'"';
+REQUAL: '=~'; // regex check case insensitive
+CREEQUAL: '=~!'; // regex check case sensitive
 
-FIELDTYPE:LETTER+;
-// fragments are not accessible from the code, they are only for describing the grammar better
-fragment LETTER : ~[ \t"()=!];
+NEQUAL: '!='; //  negated case insensitive contains
+NCEQUAL: '!=!'; // negated case sensitive contains
 
+NEEQUAL: '!=='; // negated case insensitive exact match
+NCEEQUAL: '!==!'; // negated case sensitive exact match
 
-start:
-    expression EOF;
+NREQUAL: '!=~'; // negated regex check case insensitive
+NCREEQUAL: '!=~!'; // negated regex check case sensitive
 
-// labels are used to refer to parts of the rules in the generated code later on
-// label=actualThingy
-expression:
-    LPAREN expression RPAREN                         #parenExpression  // example: (author=miller)
-    | NOT expression                                 #unaryExpression  // example: not author = miller
-    | left=expression operator=AND right=expression  #binaryExpression // example: author = miller and title = test
-    | left=expression operator=OR right=expression   #binaryExpression // example: author = miller or title = test
-    | comparison                                     #atomExpression
+AND: 'AND';
+OR: 'OR';
+CONTAINS: 'CONTAINS';
+MATCHES: 'MATCHES';
+NOT: 'NOT';
+
+FIELD: [A-Z]+;
+STRING_LITERAL: '"' ('\\"' | ~["])* '"';    // " should be escaped with a backslash
+TERM: ('\\' [=!~()] | ~[ \t\n\r=!~()])+;    // =!~() should be escaped with a backslash
+
+start
+    : EOF
+    | andExpression EOF
+    ;
+
+andExpression
+    : expression+                                         #implicitAndExpression   // example: author = miller year = 2010 --> equivalent to: author = miller AND year = 2010
+    ;
+
+expression
+    : LPAREN andExpression RPAREN                         #parenExpression        // example: (author = miller)
+    | NOT expression                                      #negatedExpression      // example: NOT author = miller
+    | left = expression bin_op = AND right = expression   #binaryExpression       // example: author = miller AND year = 2010
+    | left = expression bin_op = OR right = expression    #binaryExpression       // example: author = miller OR year = 2010
+    | comparison                                          #comparisonExpression   // example: miller OR author = miller
+    ;
+
+comparison
+    : FIELD operator searchValue    // example: author = miller
+    | searchValue                   // example: miller
     ;
 
-comparison:
-    left=name operator=(CONTAINS | MATCHES | EQUAL | EEQUAL | NEQUAL) right=name // example: author != miller
-    | right=name                                                                 // example: miller (search all fields)
+operator
+    : EQUAL
+    | CEQUAL
+    | EEQUAL
+    | CEEQUAL
+    | REQUAL
+    | CREEQUAL
+    | NEQUAL
+    | NCEQUAL
+    | NEEQUAL
+    | NCEEQUAL
+    | NREQUAL
+    | NCREEQUAL
+    | CONTAINS
+    | MATCHES
     ;
 
-name:
-    STRING // example: "miller"
-    | FIELDTYPE // example: author
+searchValue
+    : STRING_LITERAL
+    | FIELD
+    | TERM
     ;

src/main/java/module-info.java

@@ -97,6 +97,8 @@
     // endregion
 
     // region: SQL databases
+    requires embedded.postgres;
+    requires org.tukaani.xz;
     requires ojdbc10;
     requires org.postgresql.jdbc;
     requires org.mariadb.jdbc;
@@ -108,6 +110,7 @@
     requires io.github.javadiffutils;
     requires java.string.similarity;
     requires org.apache.commons.cli;
+    requires org.apache.commons.compress;
     requires org.apache.commons.csv;
     requires org.apache.commons.io;
     requires org.apache.commons.lang3;
@@ -160,8 +163,8 @@
     // endregion
 
     // region: Lucene
-    /**
-     * In case the version is updated, please also increment {@link org.jabref.model.search.SearchFieldConstants#VERSION} to trigger reindexing.
+    /*
+     * In case the version is updated, please also increment {@link org.jabref.model.search.LinkedFilesConstants.VERSION} to trigger reindexing.
      */
     uses org.apache.lucene.codecs.lucene100.Lucene100Codec;
     requires org.apache.lucene.analysis.common;

src/main/java/org/jabref/Launcher.java

@@ -9,6 +9,7 @@
 import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.search.PostgreServer;
 import org.jabref.logic.util.HeadlessExecutorService;
 import org.jabref.migrations.PreferencesMigrations;
 
@@ -38,6 +39,9 @@ public static void main(String[] args) {
 
         PreferencesMigrations.runMigrations(preferences);
 
+        PostgreServer postgreServer = new PostgreServer();
+        Injector.setModelOrService(PostgreServer.class, postgreServer);
+
         JabRefGUI.setup(uiCommands, preferences, fileUpdateMonitor);
         JabRefGUI.launch(JabRefGUI.class, args);
     }

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -53,7 +53,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
-import org.jabref.model.search.SearchQuery;
+import org.jabref.model.search.query.SearchQuery;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
@@ -458,8 +458,8 @@ private boolean exportMatches(List<ParserResult> loaded) {
 
         List<BibEntry> matches;
         try {
-            // extract current thread task executor from luceneManager
-            matches = new DatabaseSearcher(query, databaseContext, new CurrentThreadTaskExecutor(), cliPreferences.getFilePreferences()).getMatches();
+            // extract current thread task executor from indexManager
+            matches = new DatabaseSearcher(query, databaseContext, new CurrentThreadTaskExecutor(), cliPreferences).getMatches();
         } catch (IOException e) {
             LOGGER.error("Error occurred when searching", e);
             return false;

src/main/java/org/jabref/gui/JabRefGUI.java

@@ -32,6 +32,7 @@
 import org.jabref.logic.net.ProxyRegisterer;
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.server.RemoteListenerServerManager;
+import org.jabref.logic.search.PostgreServer;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.FallbackExceptionHandler;
 import org.jabref.logic.util.HeadlessExecutorService;
@@ -395,6 +396,9 @@ public static void shutdownThreadPools() {
         LOGGER.trace("Shutting down directoryMonitor");
         DirectoryMonitor directoryMonitor = Injector.instantiateModelOrService(DirectoryMonitor.class);
         directoryMonitor.shutdown();
+        LOGGER.trace("Shutting down postgreServer");
+        PostgreServer postgreServer = Injector.instantiateModelOrService(PostgreServer.class);
+        postgreServer.shutdown();
         LOGGER.trace("Shutting down HeadlessExecutorService");
         HeadlessExecutorService.INSTANCE.shutdownEverything();
         LOGGER.trace("Finished shutdownThreadPools");