Merge branch 'main' into fix-rpm-uninstall

JabRef · Dec 1, 2024 · 9dc5c32 · 9dc5c32
2 parents ec5d4fc + 37593bf
commit 9dc5c32
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diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -69,12 +69,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -81,12 +81,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].2
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.moderne/moderne.yml b/.moderne/moderne.yml
@@ -0,0 +1,3 @@
+specs: specs.moderne.ai/v1/cli
+java:
+  selectedJdk: '23'
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added a Markdown export layout. [#12220](https://github.com/JabRef/jabref/pull/12220)
 - 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 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)
@@ -43,8 +44,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
 - We added support to automatically open a `.bib` file in the current/parent folder if no other library is opened. [koppor#377](https://github.com/koppor/jabref/issues/377)
 - We added a search bar for filtering keyboard shortcuts. [#11686](https://github.com/JabRef/jabref/issues/11686)
+- We added new modifiers `camel_case`, `camel_case_n`, `short_title`, and `very_short_title` for the [citation key generator](https://docs.jabref.org/setup/citationkeypatterns). [#11367](https://github.com/JabRef/jabref/issues/11367)
 - By double clicking on a local citation in the Citation Relations Tab you can now jump the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
 - We use the menu icon for background tasks as a progress indicator to visualise an import's progress when dragging and dropping several PDF files into the main table. [#12072](https://github.com/JabRef/jabref/pull/12072)
+- The PDF content importer now supports importing title from upto the second page of the PDF. [#12139](https://github.com/JabRef/jabref/issues/12139)
 
 ### Changed
 
@@ -77,6 +80,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the defualt [unwanted charachters](https://docs.jabref.org/setup/citationkeypatterns#removing-unwanted-characters) in the citation key generator and allow a dash (`-`) and colon (`:`) being part of a citation key. [#12144](https://github.com/JabRef/jabref/pull/12144)
 - The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
 - We disabled the actions "Open Terminal here" and "Reveal in file explorer" for unsaved libraries. [#11920](https://github.com/JabRef/jabref/issues/11920)
+- JabRef now opens the corresponding directory in the library properties when "Browse" is clicked. [#12223](https://github.com/JabRef/jabref/pull/12223)
 
 ### Fixed
 
@@ -113,11 +117,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the "Do not ask again" checkbox was not working, when asking for permission to use Grobid [koppor#556](https://github.com/koppor/jabref/issues/566).
 - We fixed an issue where we display warning message for moving attached open files. [#10121](https://github.com/JabRef/jabref/issues/10121)
 - 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 when handling URLs containing a pipe (`|`) character. [#11876](https://github.com/JabRef/jabref/issues/11876)
 - 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 when opening attached files in [extra file columns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#adding-additional-columns-to-entry-table-for-file-types). [#12005](https://github.com/JabRef/jabref/issues/12005)
 - 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)
 - We fixed an issue when the preview was out of sync. [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
+- We fixed an issue when click on entry at "Check Integrity" wasn't properly focusing the entry and field. [#11997](https://github.com/JabRef/jabref/issues/11997)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.27.0'
+    id 'org.openrewrite.rewrite' version '6.27.2'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -54,13 +54,14 @@ java {
 
     toolchain {
         // If this is updated, also update
-        // - .gitpod.Dockerfile
+        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         // - .devcontainer/devcontainer.json#L34 and
+        // - .gitpod.Dockerfile
+        // - .moderne/moderne.yml
         // - .github/workflows/deployment*.yml
         // - .github/workflows/tests*.yml
         // - .github/workflows/update-gradle-wrapper.yml
         // - docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md
-        // - build.gradle -> jacoco -> toolVersion (because JaCoCo does not support newest JDK out of the box. Check versions at https://www.jacoco.org/jacoco/trunk/doc/changes.html)
         languageVersion = JavaLanguageVersion.of(23)
         // See https://docs.gradle.org/current/javadoc/org/gradle/jvm/toolchain/JvmVendorSpec.html for a full list
         // vendor = JvmVendorSpec.AMAZON
@@ -278,7 +279,7 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.1'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.2'
 
     implementation('de.undercouch:citeproc-java:3.1.0') {
         exclude group: 'org.antlr'
@@ -341,7 +342,7 @@ dependencies {
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-mistral-ai:0.36.0') {
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.36.2') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -370,17 +371,17 @@ dependencies {
     implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:2.0.21'
     // endregion
 
-    implementation 'commons-io:commons-io:2.17.0'
+    implementation 'commons-io:commons-io:2.18.0'
 
     // 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 'io.zonky.test:embedded-postgres:2.1.0'
     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:5.11.3'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.11.3'
 
     testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
@@ -400,7 +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:2.19.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.22.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -13,6 +13,7 @@
 import java.util.SortedSet;
 import java.util.stream.Collectors;
 
+import javafx.application.Platform;
 import javafx.fxml.FXML;
 import javafx.geometry.Side;
 import javafx.scene.control.Button;
@@ -61,6 +62,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.EntryConverter;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.util.DirectoryMonitorManager;
 import org.jabref.model.util.FileUpdateMonitor;
@@ -463,11 +465,26 @@ private void fetchAndMerge(EntryBasedFetcher fetcher) {
 
     public void setFocusToField(Field field) {
         UiTaskExecutor.runInJavaFXThread(() -> {
+        Field actualField = field;
+        boolean fieldFound = false;
             for (Tab tab : tabbed.getTabs()) {
+                tabbed.getSelectionModel().select(tab);
                 if ((tab instanceof FieldsEditorTab fieldsEditorTab)
-                        && fieldsEditorTab.getShownFields().contains(field)) {
+                        && fieldsEditorTab.getShownFields().contains(actualField)) {
                     tabbed.getSelectionModel().select(tab);
-                    fieldsEditorTab.requestFocus(field);
+                    Platform.runLater(() -> {
+                        fieldsEditorTab.requestFocus(actualField);
+                    });
+                    // This line explicitly brings focus back to the main window containing the Entry Editor.
+                    getScene().getWindow().requestFocus();
+                    fieldFound = true;
+                    break;
+                }
+            }
+            if (!fieldFound) {
+                Field aliasField = EntryConverter.FIELD_ALIASES.get(field);
+                if (aliasField != null) {
+                    setFocusToField(aliasField);
                 }
             }
         });

diff --git a/...rg/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java b/...rg/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java
@@ -1,14 +1,14 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.util.List;
 
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.fetcher.CustomizableKeyFetcher;
 import org.jabref.logic.net.URLDownload;
+import org.jabref.logic.util.URLUtil;
 import org.jabref.model.entry.BibEntry;
 
 import com.google.gson.Gson;
@@ -38,7 +38,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
 
         URL citationsUrl;
         try {
-            citationsUrl = URI.create(getAPIUrl("citations", entry)).toURL();
+            citationsUrl = URLUtil.create(getAPIUrl("citations", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }
@@ -62,7 +62,7 @@ public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
 
         URL referencesUrl;
         try {
-            referencesUrl = URI.create(getAPIUrl("references", entry)).toURL();
+            referencesUrl = URLUtil.create(getAPIUrl("references", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -38,6 +37,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.BackgroundTask;
 import org.jabref.logic.util.TaskExecutor;
+import org.jabref.logic.util.URLUtil;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -186,7 +186,7 @@ private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
 
     public boolean downloadFile(String urlText) {
         try {
-            URL url = URI.create(urlText).toURL();
+            URL url = URLUtil.create(urlText);
             addFromURLAndDownload(url);
             return true;
         } catch (MalformedURLException exception) {

diff --git a/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java b/src/main/java/org/jabref/gui/fieldeditors/URLUtil.java
@@ -1,89 +1,22 @@
 package org.jabref.gui.fieldeditors;
 
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
-import java.net.URLDecoder;
-import java.nio.charset.StandardCharsets;
-import java.util.Objects;
 import java.util.Optional;
 
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.frame.ExternalApplicationsPreferences;
 
+/**
+ * URL utilities for URLs in the JabRef GUI.
+ * <p>
+ * For logic-oriented URL utilities see {@link org.jabref.logic.util.URLUtil}.
+ */
 public class URLUtil {
-    private static final String URL_EXP = "^(https?|ftp)://.+";
-
-    // Detect Google search URL
-    private static final String GOOGLE_SEARCH_EXP = "^https?://(?:www\\.)?google\\.[\\.a-z]+?/url.*";
 
     private URLUtil() {
     }
 
-    /**
-     * Cleans URLs returned by Google search.
-     *
-     * <example>
-     *  If you copy links from search results from Google, all links will be enriched with search meta data, e.g.
-     *  https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&&url=http%3A%2F%2Fwww.inrg.csie.ntu.edu.tw%2Falgorithm2014%2Fhomework%2FWagner-74.pdf&ei=DifeVYHkDYWqU5W0j6gD&usg=AFQjCNFl638rl5KVta1jIMWLyb4CPSZidg&sig2=0hSSMw9XZXL3HJWwEcJtOg
-     * </example>
-     *
-     * @param url the Google search URL string
-     * @return the cleaned Google URL or @code{url} if no search URL was detected
-     */
-    public static String cleanGoogleSearchURL(String url) {
-        Objects.requireNonNull(url);
-
-        if (!url.matches(GOOGLE_SEARCH_EXP)) {
-            return url;
-        }
-        // Extract destination URL
-        try {
-            URL searchURL = URI.create(url).toURL();
-            // URL parameters
-            String query = searchURL.getQuery();
-            // no parameters
-            if (query == null) {
-                return url;
-            }
-            // extract url parameter
-            String[] pairs = query.split("&");
-
-            for (String pair : pairs) {
-                // "clean" url is decoded value of "url" parameter
-                if (pair.startsWith("url=")) {
-                    String value = pair.substring(pair.indexOf('=') + 1);
-
-                    String decode = URLDecoder.decode(value, StandardCharsets.UTF_8);
-                    // url?
-                    if (decode.matches(URL_EXP)) {
-                        return decode;
-                    }
-                }
-            }
-            return url;
-        } catch (MalformedURLException e) {
-            return url;
-        }
-    }
-
-    /**
-     * Checks whether the given String is a URL.
-     * <p>
-     * Currently only checks for a protocol String.
-     *
-     * @param url the String to check for a URL
-     * @return true if <c>url</c> contains a valid URL
-     */
-    public static boolean isURL(String url) {
-        try {
-            URI.create(url).toURL();
-            return true;
-        } catch (MalformedURLException | IllegalArgumentException e) {
-            return false;
-        }
-    }
-
     /**
      * Look for the last '.' in the link, and return the following characters.
      * <p>
@@ -96,7 +29,7 @@ public static Optional<String> getSuffix(final String link, ExternalApplications
         String strippedLink = link;
         try {
             // Try to strip the query string, if any, to get the correct suffix:
-            URL url = URI.create(link).toURL();
+            URL url = org.jabref.logic.util.URLUtil.create(link);
             if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
                 strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
             }

diff --git a/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/UrlEditorViewModel.java
@@ -13,6 +13,7 @@
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.URLUtil;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.strings.StringUtil;