Merge branch 'main' into Ignore-initial-unprotected-uppercase

JabRef · Oct 13, 2023 · 3697ced · 3697ced
2 parents 4cf4119 + 44864fc
commit 3697ced
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -24,4 +24,4 @@ jobs:
         run: gh pr merge --auto "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
-          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}
diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel deployment run
-        uses: styfle/cancel-workflow-action@0.11.0
+        uses: styfle/cancel-workflow-action@0.12.0
         with:
           ignore_sha: true
           workflow_id: 9813 # workflow "Deployment"

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -14,36 +14,23 @@ jobs:
       - uses: actions/checkout@v4
         with:
           persist-credentials: true
-          fetch-depth: 0
           submodules: 'true'
           show-progress: 'false'
       - name: Initialize git
         run: |
           git config --local core.editor /usr/bin/cat
           git config user.name 'github-actions[bot]'
           git config user.email 'github-actions[bot]@users.noreply.github.com'
-      - name: Update buildres/csl/csl-styles
+      - name: Update src/main/resources/csl-styles
         run: |
-          cd buildres/csl/csl-styles
+          cd src/main/resources/csl-styles
           git checkout master
           git pull
-          cd ..
-          cd ..
-          cd ..
-          cp buildres/csl/csl-styles/acm-siggraph.csl src/main/resources/csl-styles/
-          cp buildres/csl/csl-styles/apa.csl src/main/resources/csl-styles/
-          cp buildres/csl/csl-styles/ieee.csl src/main/resources/csl-styles/
-          cp buildres/csl/csl-styles/turabian-author-date.csl src/main/resources/csl-styles/
-      - name: Update buildres/csl/csl-locales
+      - name: Update src/main/resources/csl-locales
         run: |
-          cd buildres/csl/csl-locales
+          cd src/main/resources/csl-locales
           git checkout master
           git pull
-          cd ..
-          cd ..
-          cd ..
-          cp buildres/csl/csl-locales/locales.json src/main/resources/csl-locales/
-          cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
       - uses: peter-evans/create-pull-request@v5
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}

diff --git a/.gitmodules b/.gitmodules
@@ -2,8 +2,8 @@
   path = buildres/abbrv.jabref.org
   url = https://github.com/JabRef/abbrv.jabref.org.git
 [submodule "buildres/csl-styles"]
-  path = buildres/csl/csl-styles
+  path = src/main/resources/csl-styles
   url = https://github.com/citation-style-language/styles.git
 [submodule "buildres/csl-locales"]
-  path = buildres/csl/csl-locales
+  path = src/main/resources/csl-locales
   url = https://github.com/citation-style-language/locales.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,10 +27,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When searching for an identifier in the "Web search", the title of the search window is now "Identifier-based Web Search". [#10391](https://github.com/JabRef/jabref/pull/10391)
 - The ampersand checker now skips verbatim fields (`file`, `url`, ...). [#10419](https://github.com/JabRef/jabref/pull/10419)
 - If no existing document is selected for exporting "XMP annotated pdf" JabRef will now create a new PDF file with a sample text and the metadata. [#10102](https://github.com/JabRef/jabref/issues/10102)
-- We modified the DOI cleanup to infer the DOI from an ArXiV ID if it's present. [10426](https://github.com/JabRef/jabref/issues/10426)
+- We modified the DOI cleanup to infer the DOI from an ArXiV ID if it's present. [#10426](https://github.com/JabRef/jabref/issues/10426)
+- The ISI importer uses the field `comment` for notes (instead of `review). [#10478](https://github.com/JabRef/jabref/pull/10478)
+- If no existing document is selected for exporting "Embedded BibTeX pdf" JabRef will now create a new PDF file with a sample text and the metadata. [#10101](https://github.com/JabRef/jabref/issues/10101)
 
 ### Fixed
 
+- We fixed an issue where "Move URL in note field to url field" in the cleanup dialog caused an exception if no note field was present [forum#3999](https://discourse.jabref.org/t/cleanup-entries-cant-get-it-to-work/3999)
 - It is possible again to use "current table sort order" for the order of entries when saving. [#9869](https://github.com/JabRef/jabref/issues/9869)
 - Passwords can be stored in GNOME key ring. [#10274](https://github.com/JabRef/jabref/issues/10274)
 - We fixed an issue where groups based on an aux file could not be created due to an exception [#10350](https://github.com/JabRef/jabref/issues/10350)
@@ -42,6 +45,10 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - JabRef does not hang anymore when exporting via CLI. [#10380](https://github.com/JabRef/jabref/issues/10380)
 - We fixed an issue where it was not possible to save a library on a network share under macOS due to an exception when acquiring a file lock [#10452](https://github.com/JabRef/jabref/issues/10452)
 - We fixed an issue where exporting "XMP annotated pdf" without selecting an existing document would produce an exception. [#10102](https://github.com/JabRef/jabref/issues/10102)
+- We fixed an issue where the "Enabled" column in the "Protected terms files" tab in the preferences could not be resized [#10285](https://github.com/JabRef/jabref/issues/10285)
+- We fixed an issue where after creation of a new library, the new library was not focused. [koppor#592](https://github.com/koppor/jabref/issues/592)
+- We fixed an issue where double clicking on an url in the file field would trigger an exception instead of opening the browser [#10480](https://github.com/JabRef/jabref/pull/10480)
+- We fixed an issue where exporting "Embedded BibTeX pdf" without selecting an existing document would produce an exception. [#10101](https://github.com/JabRef/jabref/issues/10101)
 
 ### Removed
 
@@ -83,7 +90,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a privacy policy. [#10064](https://github.com/JabRef/jabref/issues/10064)
 - We added a tooltip to show the number of entries in a group [#10208](https://github.com/JabRef/jabref/issues/10208)
 - We fixed an issue where it was no longer possible to add or remove selected entries to groups via context menu [#10404](https://github.com/JabRef/jabref/issues/10404), [#10317](https://github.com/JabRef/jabref/issues/10317) [#10374](https://github.com/JabRef/jabref/issues/10374)
-- We fixed an issue where "Move URL in note field to url field" in the cleanup dialog caused an exception if no note field was present [forum#3999](https://discourse.jabref.org/t/cleanup-entries-cant-get-it-to-work/3999)
 
 ### Changed
 

diff --git a/build.gradle b/build.gradle
@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.3.16'
+    id 'org.openrewrite.rewrite' version '6.3.18'
 }
 
 // Enable following for debugging
@@ -237,7 +237,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.0'
 
-    testImplementation 'org.mockito:mockito-core:5.5.0'
+    testImplementation 'org.mockito:mockito-core:5.6.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.1.0'
@@ -246,12 +246,12 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.3'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.4'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     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:2.3.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.3.1"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -264,14 +264,6 @@ clean {
 }
 
 processResources {
-    gradle.taskGraph.whenReady {
-        if (gradle.taskGraph.hasTask(":jpackage")) {
-            logger.info('Adding buildres/csl to resources')
-            from("buildres/csl")
-            duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-        }
-    }
-
     filteringCharset = 'UTF-8'
 
     filesMatching("build.properties") {

diff --git a/...etting-into-the-code/guidelines-for-setting-up-a-local-workspace/pre-03-code.md b/...etting-into-the-code/guidelines-for-setting-up-a-local-workspace/pre-03-code.md
@@ -25,17 +25,18 @@ In the following, we will use `c:\git-repositories` as base folder:
 cd \
 mkdir git-repositories
 cd git-repositories
-git clone --depth=10 https://github.com/JabRef/jabref.git JabRef
-cd jabref
+git clone --recurse-submodules https://github.com/JabRef/jabref.git JabRef
+cd JabRef
 git remote rename origin upstream
 git remote add origin https://github.com/YOUR_USERNAME/jabref.git
+git fetch --all
 git branch --set-upstream-to=origin/main main
 ```
 
 {: .important }
-> Note that putting the repo JabRef directly on `C:\` or any other drive letter on Windows causes compile errors (**negative example**: `C:\jabref`).
+> `--recurse-submodules` is necessary to have the required files available to JabRef. (Background: It concerns the files from [citation-style-language/styles](https://github.com/citation-style-language/styles) and more).
 >
-> Further, if you are building on Windows, make sure that the absolute path to the location of the clone does not contain folders starting with '`u`' (**negative example**: `C:\university\jabref`) as this may currently also cause [compile errors](https://github.com/JabRef/jabref/issues/9783).
+> Note that putting the repo JabRef directly on `C:\` or any other drive letter on Windows causes compile errors (**negative example**: `C:\jabref`).
 >
 > Please really ensure that you pass `JabRef` as parameter. Otherwise, you will get `java.lang.IllegalStateException: Module entity with name: jabref should be available`. See [IDEA-317606](https://youtrack.jetbrains.com/issue/IDEA-317606/Changing-only-the-case-of-the-Gradle-root-project-name-causes-exception-while-importing-project-java.lang.IllegalStateException) for details.
 
@@ -47,9 +48,6 @@ git branch --set-upstream-to=origin/main main
 > To prevent this, first the `upstream` repository is cloned.
 > This repository seems to live in the caches of GitHub.
 >
-> The `--depth--10` is used to limit the download to \~20 MB instead of downloading the complete history (\~800 MB).
-> If you want to dig in our commit history, feel free to download everything.
->
 > Now, you have two remote repositories, where `origin` is yours and `upstream` is the one of the JabRef organization.
 >
 > You can see it with `git remote -v`:

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=591855b517fc635b9e04de1d05d5e76ada3f89f5fc76f87978d1b245b4f69225
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
+distributionSha256Sum=3e1af3ae886920c3ac87f7a91f816c0c7c436f276a6eefdb3da152100fef72ae
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

diff --git a/gradlew b/gradlew
@@ -145,15 +145,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -202,11 +202,11 @@ fi
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -716,6 +716,7 @@ public void addTab(LibraryTab libraryTab, boolean raisePanel) {
         tabbedPane.getTabs().add(libraryTab);
         if (raisePanel) {
             tabbedPane.getSelectionModel().select(libraryTab);
+            tabbedPane.requestFocus();
         }
 
         libraryTab.setOnCloseRequest(event -> {

diff --git a/src/main/java/org/jabref/gui/auximport/AuxParserResultViewModel.java b/src/main/java/org/jabref/gui/auximport/AuxParserResultViewModel.java
@@ -1,5 +1,7 @@
 package org.jabref.gui.auximport;
 
+import java.util.stream.Collectors;
+
 import org.jabref.logic.auxparser.AuxParserResult;
 import org.jabref.logic.l10n.Localization;
 
@@ -13,22 +15,22 @@ public AuxParserResultViewModel(AuxParserResult auxParserResult) {
 
     /**
      * Prints parsing statistics
+     *
+     * @param includeMissingEntries shows the missing entries as text (the GUI renderes them at another place)
      */
     public String getInformation(boolean includeMissingEntries) {
-        StringBuilder result = new StringBuilder();
+        String missingEntries = "";
+        if (includeMissingEntries && (this.auxParserResult.getUnresolvedKeysCount() > 0)) {
+            missingEntries = this.auxParserResult.getUnresolvedKeys().stream().collect(Collectors.joining(", ", " (", ")"));
+        }
 
+        StringBuilder result = new StringBuilder();
         result.append(Localization.lang("keys in library")).append(' ').append(this.auxParserResult.getMasterDatabase().getEntryCount()).append('\n')
               .append(Localization.lang("found in AUX file")).append(' ').append(this.auxParserResult.getFoundKeysInAux()).append('\n')
               .append(Localization.lang("resolved")).append(' ').append(this.auxParserResult.getResolvedKeysCount()).append('\n')
-              .append(Localization.lang("not found")).append(' ').append(this.auxParserResult.getUnresolvedKeysCount()).append('\n')
+              .append(Localization.lang("not found")).append(' ').append(this.auxParserResult.getUnresolvedKeysCount()).append(missingEntries).append('\n')
               .append(Localization.lang("crossreferenced entries included")).append(' ').append(this.auxParserResult.getCrossRefEntriesCount()).append('\n')
               .append(Localization.lang("strings included")).append(' ').append(this.auxParserResult.getInsertedStrings()).append('\n');
-
-        if (includeMissingEntries && (this.auxParserResult.getUnresolvedKeysCount() > 0)) {
-            for (String entry : this.auxParserResult.getUnresolvedKeys()) {
-                result.append(entry).append('\n');
-            }
-        }
         if (this.auxParserResult.getNestedAuxCount() > 0) {
             result.append(Localization.lang("nested AUX files")).append(' ').append(this.auxParserResult.getNestedAuxCount());
         }

diff --git a/src/main/java/org/jabref/gui/auximport/FromAuxDialog.fxml b/src/main/java/org/jabref/gui/auximport/FromAuxDialog.fxml
@@ -7,28 +7,40 @@
 <?import javafx.scene.control.ListView?>
 <?import javafx.scene.control.TextArea?>
 <?import javafx.scene.control.TextField?>
+<?import javafx.scene.control.Tooltip?>
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 <?import javafx.scene.text.Font?>
+<?import org.jabref.gui.icon.JabRefIconView?>
+
 <DialogPane xmlns:fx="http://javafx.com/fxml/1" prefHeight="650.0" prefWidth="500.0"
             xmlns="http://javafx.com/javafx/8.0.121" fx:controller="org.jabref.gui.auximport.FromAuxDialog">
     <content>
         <VBox spacing="30">
             <VBox spacing="5.0">
                 <Label text="%LaTeX AUX file:"/>
-                <HBox spacing="10">
+                <HBox spacing="10" alignment="BASELINE_LEFT">
                     <TextField fx:id="auxFileField" HBox.hgrow="ALWAYS"/>
-                    <Button onAction="#browseButtonClicked" text="%Browse"/>
+                    <Button onAction="#browseButtonClicked"
+                            styleClass="icon-button,narrow"
+                            minWidth="20.0" minHeight="20.0" prefHeight="20.0" prefWidth="20.0">
+                        <graphic>
+                            <JabRefIconView glyph="OPEN"/>
+                        </graphic>
+                        <tooltip>
+                            <Tooltip text="%Browse"/>
+                        </tooltip>
+                    </Button>
                 </HBox>
-                <Button defaultButton="true" onAction="#parseActionPerformed" text="%Parse"/>
+                <Button defaultButton="true" onAction="#parseActionPerformed" text="%Parse" maxWidth="Infinity"/>
             </VBox>
             <VBox spacing="5">
                 <Label text="%Result">
                     <font>
                         <Font name="System Bold"/>
                     </font>
                 </Label>
-                <TextArea fx:id="statusInfos" editable="false" prefHeight="300.0"/>
+                <TextArea fx:id="statusInfos" editable="false" prefHeight="300.0" wrapText="true"/>
                 <Label text="%Unknown BibTeX entries:"/>
                 <ListView fx:id="notFoundList" prefHeight="200"/>
             </VBox>

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -150,6 +150,7 @@ private static void openIsbn(String isbn, PreferencesService preferencesService)
 
     /**
      * Open an external file, attempting to use the correct viewer for it.
+     * If the "file" is an online link, instead open it with the browser
      *
      * @param databaseContext The database this file belongs to.
      * @param link            The filename.
@@ -160,7 +161,7 @@ public static boolean openExternalFileAnyFormat(final BibDatabaseContext databas
                                                     String link,
                                                     final Optional<ExternalFileType> type) throws IOException {
         if (REMOTE_LINK_PATTERN.matcher(link.toLowerCase(Locale.ROOT)).matches()) {
-            openExternalFilePlatformIndependent(type, link, filePreferences);
+            openBrowser(link, filePreferences);
             return true;
         }
         Optional<Path> file = FileUtil.find(databaseContext, link, filePreferences);

diff --git a/src/main/java/org/jabref/gui/importer/GenerateEntryFromIdAction.java b/src/main/java/org/jabref/gui/importer/GenerateEntryFromIdAction.java
@@ -58,7 +58,10 @@ public void execute() {
         BackgroundTask<Optional<BibEntry>> backgroundTask = searchAndImportEntryInBackground();
         backgroundTask.titleProperty().set(Localization.lang("Import by ID"));
         backgroundTask.showToUser(true);
-        backgroundTask.onRunning(() -> dialogService.notify("%s".formatted(backgroundTask.messageProperty().get())));
+        backgroundTask.onRunning(() -> {
+            entryFromIdPopOver.hide();
+            dialogService.notify("%s".formatted(backgroundTask.messageProperty().get()));
+        });
         backgroundTask.onFailure(exception -> {
             String fetcherExceptionMessage = exception.getMessage();
 
@@ -95,8 +98,6 @@ public void execute() {
             } else {
                 dialogService.notify("No entry found or import canceled");
             }
-
-            entryFromIdPopOver.hide();
         });
         backgroundTask.executeWith(taskExecutor);
     }

diff --git a/src/main/java/org/jabref/gui/mergeentries/DiffHighlightingEllipsingTextFlow.java b/src/main/java/org/jabref/gui/mergeentries/DiffHighlightingEllipsingTextFlow.java
@@ -153,7 +153,7 @@ private String ellipseString(String s) {
     }
 
     public final void setEllipsisString(String value) {
-        ellipsisString.set((value == null) ? "" : value);
+        ellipsisString.set(value == null ? "" : value);
     }
 
     public String getEllipsisString() {