Merge branch 'JabRef:main' into main

leaf-soba · Sep 10, 2024 · b952b2e · b952b2e
2 parents 7d09ec5 + d02a504
commit b952b2e
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -332,6 +332,22 @@ jobs:
         env:
           CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
 
+  requirements_coverage:
+    name: "Validate requiremenet coverage"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21.0.2
+          distribution: 'temurin'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+      - run: ./gradlew traceRequirements
+
   # This is https://github.com/marketplace/actions/gradle-wrapper-validation
   # It ensures that the jar file is from gradle and not by a strange third party.
   gradlevalidation:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We enabled creating a new file link manually. [#11017](https://github.com/JabRef/jabref/issues/11017)
 - We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
 - We reintroduced the floating search in the main table. [#4237](https://github.com/JabRef/jabref/issues/4237)
+- We added a switch not to store the linked file URL, because it caused troubles at other apps. [#11735](https://github.com/JabRef/jabref/pull/11735)
 - When starting a new SLR, the selected catalogs now persist within and across JabRef sessions. [koppor#614](https://github.com/koppor/jabref/issues/614)
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 
@@ -42,6 +43,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We enhanced the indexing speed. [#11502](https://github.com/JabRef/jabref/pull/11502)
 - ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
+- The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)
 - We improved the display of long messages in the integrity check dialog. [#11619](https://github.com/JabRef/jabref/pull/11619)
 
 ### Fixed
@@ -64,6 +66,9 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the full-text search results were incomplete. [#8626](https://github.com/JabRef/jabref/issues/8626)
 - We fixed an issue where search result highlighting was incorrectly highlighting the boolean operators. [#11595](https://github.com/JabRef/jabref/issues/11595)
 - We fixed an issue where search result highlighting was broken at complex searches. [#8067](https://github.com/JabRef/jabref/issues/8067)
+- We fixed an exception when searching for unlinked files. [#11731](https://github.com/JabRef/jabref/issues/11731)
+- We fixed an issue where two contradicting notifications were shown when cutting an entry in the main table. [#11724](https://github.com/JabRef/jabref/pull/11724)
+- We fixed an issue where unescaped braces in the arXiv fetcher were not treated. [#11704](https://github.com/JabRef/jabref/issues/11704)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -30,6 +30,8 @@ plugins {
     id 'idea'
 
     id 'org.openrewrite.rewrite' version '6.20.0'
+
+    id "org.itsallcode.openfasttrace" version "3.0.0"
 }
 
 // Enable following for debugging
@@ -255,10 +257,12 @@ dependencies {
 
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
+    // region HTTP clients
     implementation 'org.jsoup:jsoup:1.18.1'
     implementation 'com.konghq:unirest-java-core:4.4.4'
     implementation 'com.konghq:unirest-modules-gson:4.4.4'
     implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
+    // endregion
 
     implementation 'org.slf4j:slf4j-api:2.0.16'
     implementation 'org.tinylog:tinylog-api:2.7.0'
@@ -321,7 +325,7 @@ dependencies {
     implementation 'com.github.vatbub:mslinks:1.0.6.2'
 
     // YAML formatting
-    implementation 'org.yaml:snakeyaml:2.2'
+    implementation 'org.yaml:snakeyaml:2.3'
 
     // AI
     implementation 'dev.langchain4j:langchain4j:0.33.0'
@@ -330,11 +334,11 @@ dependencies {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
     }
     implementation('dev.langchain4j:langchain4j-mistral-ai:0.33.0')
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.33.0')
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.34.0')
     implementation 'ai.djl:api:0.29.0'
     implementation 'ai.djl.pytorch:pytorch-model-zoo:0.29.0'
     implementation 'ai.djl.huggingface:tokenizers:0.29.0'
-    implementation 'io.github.stefanbratanov:jvm-openai:0.10.0'
+    implementation 'io.github.stefanbratanov:jvm-openai:0.11.0'
     // openai depends on okhttp, which needs kotlin - see https://github.com/square/okhttp/issues/5299 for details
     implementation ('com.squareup.okhttp3:okhttp:4.12.0') {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
@@ -365,7 +369,7 @@ 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:2.17.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.18.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -896,3 +900,7 @@ jmh {
     iterations = 10
     fork = 2
 }
+
+requirementTracing {
+    inputDirectories = files('docs', 'src/main/java', 'src/test/java')
+}
diff --git a/buildres/abbrv.jabref.org b/buildres/abbrv.jabref.org
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -112,3 +112,5 @@ If you want to indicate that a pull request is not yet complete **before** creat
 
 For improving developer's documentation, go on at the [docs/ subdirectory of JabRef's code](https://github.com/JabRef/jabref/tree/main/docs) and edit the file.
 GitHub offers a good guide at [Editing files in another user's repository](https://help.github.com/en/github/managing-files-in-a-repository/editing-files-in-another-users-repository).
+
+One can also add [callouts](https://just-the-docs.github.io/just-the-docs-tests/components/callouts/).
diff --git a/docs/requirements/ai.md b/docs/requirements/ai.md
@@ -0,0 +1,16 @@
+---
+parent: Requirements
+---
+# AI
+
+## User Interface
+
+### Chatting with AI
+`req~ai.chat.new-message-based-on-previous~1`
+
+To enable simple editing and resending of previous messages, <kbd>Cursor Up</kbd> should show last message.
+This should only happen if the current text field is empty.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->
diff --git a/docs/requirements/index.md b/docs/requirements/index.md
@@ -0,0 +1,49 @@
+---
+nav_order: 7
+has_children: true
+---
+# Requirements
+
+This part of the documentation collects requirements using [OpenFastTrace](https://github.com/itsallcode/openfasttrace).
+
+## Specifying requirements
+
+One writes directly below a Markdown heading a requirement identifier.
+
+Example:
+
+```markdown
+### Example
+`req~ai.example~1`
+```
+
+It is important that there is no empty line directly after the heading.
+
+{: note}
+One needs to add `<!-- markdownlint-disable-file MD022 -->` to the end of the file, because the id of the requirement needs to follow the heading directly.
+
+## Linking implementations
+
+Then, one writes down at the requirement.
+Directly at the end, one writes that it requires an implementation:
+
+```markdown
+Needs: impl
+```
+
+One can also state that there should be detailed design document (`dsn`).
+However, typically in JabRef, we go from the requirement directly to the implementation.
+
+Then, at the implementation, a comment is added this implementation is covered:
+
+```java
+// [impl->req~ai.example~1]
+```
+
+When executing the gradle task `traceRequirements`, `build/tracing.txt` is generated.
+In case of a tracing error, one can inspect this file to see which requirements were not covered.
+
+## More Information
+
+- [User manual of OpenFastTrace](https://github.com/itsallcode/openfasttrace/blob/main/doc/user_guide.md)
+- We cannot copy and paste real examples here, because of [openfasttrace#280](https://github.com/itsallcode/openfasttrace/issues/280).
diff --git a/rewrite.yml b/rewrite.yml
@@ -206,3 +206,6 @@ recipeList:
   - org.openrewrite.java.testing.junit5.RemoveTryCatchFailBlocks
   - org.openrewrite.java.testing.junit5.LifecycleNonPrivate
   - org.openrewrite.java.testing.junit5.StaticImports
+
+  # Logging
+  - org.openrewrite.java.logging.slf4j.Slf4jBestPractices
diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -89,11 +89,11 @@
     // dependency injection using HK2
     requires org.glassfish.hk2.api;
 
-    // region: http clients
-    requires unirest.java.core;
-    requires unirest.modules.gson;
+    // region HTTP clients
     requires org.apache.httpcomponents.core5.httpcore5;
     requires org.jsoup;
+    requires unirest.java.core;
+    requires unirest.modules.gson;
     // endregion
 
     // region: SQL databases
@@ -155,7 +155,7 @@
 
     // region: Lucene
     /**
-     * In case the version is updated, please also adapt {@link org.jabref.model.search.SearchFieldConstants#VERSION} to the newly used version.
+     * In case the version is updated, please also increment {@link org.jabref.model.search.SearchFieldConstants#VERSION} to trigger reindexing.
      */
     uses org.apache.lucene.codecs.lucene99.Lucene99Codec;
     requires org.apache.lucene.analysis.common;

diff --git a/src/main/java/org/jabref/Launcher.java b/src/main/java/org/jabref/Launcher.java
@@ -36,7 +36,6 @@
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreferencesService;
-import org.jabref.preferences.ai.AiApiKeyProvider;
 
 import com.airhacks.afterburner.injection.Injector;
 import org.apache.commons.cli.ParseException;
@@ -64,7 +63,6 @@ public static void main(String[] args) {
             // Initialize preferences
             final JabRefPreferences preferences = JabRefPreferences.getInstance();
             Injector.setModelOrService(PreferencesService.class, preferences);
-            Injector.setModelOrService(AiApiKeyProvider.class, preferences);
 
             // Early exit in case another instance is already running
             if (!handleMultipleAppInstances(args, preferences.getRemotePreferences())) {

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -14,7 +14,6 @@
 import java.util.prefs.BackingStoreException;
 
 import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
-import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.util.CurrentThreadTaskExecutor;
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.UiCommand;
@@ -99,16 +98,13 @@ public ArgumentProcessor(String[] args,
     }
 
     /**
-     * Will open a file (like importFile), but will also request JabRef to focus on this database
+     * Will open a file (like {@link #importFile(String)}, but will also request JabRef to focus on this database.
      *
-     * @param argument See importFile.
      * @return ParserResult with setToOpenTab(true)
      */
-    private Optional<ParserResult> importToOpenBase(String argument) {
-        Optional<ParserResult> result = importFile(argument);
-
+    private Optional<ParserResult> importToOpenBase(String importArguments) {
+        Optional<ParserResult> result = importFile(importArguments);
         result.ifPresent(ParserResult::setToOpenTab);
-
         return result;
     }
 
@@ -125,9 +121,13 @@ private Optional<ParserResult> importBibtexToOpenBase(String argument, ImportFor
         }
     }
 
-    private Optional<ParserResult> importFile(String argument) {
-        LOGGER.debug("Importing file {}", argument);
-        String[] data = argument.split(",");
+    /**
+     *
+     * @param importArguments Format: <code>fileName[,format]</code>
+     */
+    private Optional<ParserResult> importFile(String importArguments) {
+        LOGGER.debug("Importing file {}", importArguments);
+        String[] data = importArguments.split(",");
 
         String address = data[0];
         Path file;
@@ -295,7 +295,7 @@ public void processArguments() {
     }
 
     private void writeMetadataToPdf(List<ParserResult> loaded,
-                                    String filesAndCitekeys,
+                                    String filesAndCiteKeys,
                                     XmpPreferences xmpPreferences,
                                     FilePreferences filePreferences,
                                     BibDatabaseMode databaseMode,
@@ -314,7 +314,7 @@ private void writeMetadataToPdf(List<ParserResult> loaded,
         XmpPdfExporter xmpPdfExporter = new XmpPdfExporter(xmpPreferences);
         EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter = new EmbeddedBibFilePdfExporter(databaseMode, entryTypesManager, fieldPreferences);
 
-        if ("all".equals(filesAndCitekeys)) {
+        if ("all".equals(filesAndCiteKeys)) {
             for (BibEntry entry : databaseContext.getEntries()) {
                 writeMetadataToPDFsOfEntry(
                         databaseContext,
@@ -332,7 +332,7 @@ private void writeMetadataToPdf(List<ParserResult> loaded,
 
         List<String> citeKeys = new ArrayList<>();
         List<String> pdfs = new ArrayList<>();
-        for (String fileOrCiteKey : filesAndCitekeys.split(",")) {
+        for (String fileOrCiteKey : filesAndCiteKeys.split(",")) {
             if (fileOrCiteKey.toLowerCase(Locale.ROOT).endsWith(".pdf")) {
                 pdfs.add(fileOrCiteKey);
             } else {
@@ -368,7 +368,7 @@ private void writeMetadataToPDFsOfEntry(BibDatabaseContext databaseContext,
                                             EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter,
                                             JournalAbbreviationRepository abbreviationRepository,
                                             boolean writeXMP,
-                                            boolean embeddBibfile) {
+                                            boolean embedBibfile) {
         try {
             if (writeXMP) {
                 if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, filePreferences, entry, List.of(entry), abbreviationRepository)) {
@@ -377,7 +377,7 @@ private void writeMetadataToPDFsOfEntry(BibDatabaseContext databaseContext,
                     System.err.printf("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.%n", citeKey);
                 }
             }
-            if (embeddBibfile) {
+            if (embedBibfile) {
                 if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, filePreferences, entry, List.of(entry), abbreviationRepository)) {
                     System.out.printf("Successfully embedded metadata on at least one linked file of %s%n", citeKey);
                 } else {
@@ -461,6 +461,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
 
         List<BibEntry> matches;
         try {
+            // extract current thread task executor from luceneManager
             matches = new DatabaseSearcher(query, databaseContext, new CurrentThreadTaskExecutor(), preferencesService.getFilePreferences()).getMatches();
         } catch (IOException e) {
             LOGGER.error("Error occurred when searching", e);
@@ -729,12 +730,17 @@ private void resetPreferences(String value) {
     private void automaticallySetFileLinks(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
-            LOGGER.info(Localization.lang("Automatically setting file links"));
+            LOGGER.info("Automatically setting file links for {}",
+                    parserResult.getDatabaseContext().getDatabasePath()
+                                .map(Path::getFileName)
+                                .map(Path::toString).orElse("UNKNOWN"));
+
             AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
                     parserResult.getDatabaseContext(),
                     preferencesService.getFilePreferences(),
                     preferencesService.getAutoLinkPreferences());
-            util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
+
+            util.linkAssociatedFiles(database.getEntries(), (linkedFile, bibEntry) -> bibEntry.addFile(linkedFile));
         }
     }
 

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -110,7 +110,7 @@ public static String getContentsPrimary() {
                 try {
                     return (String) contents.getTransferData(DataFlavor.stringFlavor);
                 } catch (UnsupportedFlavorException | IOException e) {
-                    LOGGER.warn(e.getMessage());
+                    LOGGER.warn("", e);
                 }
             }
         }

diff --git a/src/main/java/org/jabref/gui/FallbackExceptionHandler.java b/src/main/java/org/jabref/gui/FallbackExceptionHandler.java
@@ -19,7 +19,7 @@ public static void installExceptionHandler() {
 
     @Override
     public void uncaughtException(Thread thread, Throwable exception) {
-        LOGGER.error("Uncaught exception occurred in " + thread, exception);
+        LOGGER.error("Uncaught exception occurred in {}", thread, exception);
         UiTaskExecutor.runInJavaFXThread(() -> {
                     DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
                     dialogService.showErrorDialogAndWait("Uncaught exception occurred in " + thread, exception);

diff --git a/src/main/java/org/jabref/gui/JabRefGUI.java b/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -40,7 +40,6 @@
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.GuiPreferences;
 import org.jabref.preferences.JabRefPreferences;
-import org.jabref.preferences.ai.AiApiKeyProvider;
 
 import com.airhacks.afterburner.injection.Injector;
 import com.tobiasdiez.easybind.EasyBind;
@@ -161,7 +160,6 @@ public void initialize() {
                 preferencesService.getAiPreferences(),
                 preferencesService.getFilePreferences(),
                 preferencesService.getCitationKeyPatternPreferences(),
-                Injector.instantiateModelOrService(AiApiKeyProvider.class),
                 dialogService,
                 taskExecutor);
         Injector.setModelOrService(AiService.class, aiService);
Original file line number	Diff line number	Diff line change
Expand Up		@@ -112,3 +112,5 @@ If you want to indicate that a pull request is not yet complete before creat

		For improving developer's documentation, go on at the [docs/ subdirectory of JabRef's code](https://github.com/JabRef/jabref/tree/main/docs) and edit the file.
		GitHub offers a good guide at [Editing files in another user's repository](https://help.github.com/en/github/managing-files-in-a-repository/editing-files-in-another-users-repository).

		One can also add [callouts](https://just-the-docs.github.io/just-the-docs-tests/components/callouts/).