Merge remote-tracking branch 'upstream/main' into bibtestFiles

* upstream/main: Bump org.apache.lucene:lucene-core from 9.9.1 to 9.9.2 (#10860) Bump org.junit.jupiter:junit-jupiter from 5.10.1 to 5.10.2 (#10863) Bump org.apache.lucene:lucene-highlighter from 9.9.1 to 9.9.2 (#10861) Bump org.tinylog:tinylog-api from 2.6.2 to 2.7.0 (#10862) Bump org.apache.lucene:lucene-queryparser from 9.9.1 to 9.9.2 (#10859) Bump gradle/wrapper-validation-action from 1 to 2 (#10858) Bump codecov/codecov-action from 3 to 4 (#10857) Bump peter-evans/create-pull-request from 5 to 6 (#10856) Update Gradle Wrapper from 8.5 to 8.6. (#10854) Enable auto merge of gradle wrapper update Jump to entry from cli (#10578) Fix closing of JabRef in case of issues with index writer (#10840) Update deployment-arm64.yml Fix secrents presence chcek
JabRef · Feb 6, 2024 · 6b4a7c0 · 6b4a7c0
2 parents b7e1bb4 + 7001cb3
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -17,7 +17,8 @@ jobs:
         (
           startsWith(github.event.pull_request.title, '[Bot] ') || 
           startsWith(github.event.pull_request.title, 'Bump ') || 
-          startsWith(github.event.pull_request.title, 'New Crowdin updates')
+          startsWith(github.event.pull_request.title, 'New Crowdin updates') ||
+          startsWith(github.event.pull_request.title, 'Update Gradle Wrapper from')
         )
       )
     steps:

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -42,15 +42,23 @@ jobs:
             displayName: macOS (Arm64)
             suffix: '_arm64'
     runs-on: ${{ matrix.os }}
+    outputs:
+      major: ${{ steps.gitversion.outputs.Major }}
+      minor: ${{ steps.gitversion.outputs.Minor }}
+      branchname: ${{ steps.gitversion.outputs.branchName }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Check secrets presence
         id: checksecrets
         shell: bash
         run: |
-         [ -n "$BUILDJABREFPRIVATEKEY" ] || exit 1
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
+          else
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
+          fi
         env:
-         BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v4
         with:

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -36,7 +36,7 @@ jobs:
           git add -f src/main/resources/csl-styles
           git add -f src/main/resources/csl-locales
           git diff-index --quiet HEAD || git commit -m 'Update CSL styles'
-      - uses: peter-evans/create-pull-request@v5
+      - uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
           branch: refresh-csl

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -41,7 +41,7 @@ jobs:
         run: |
           git add -f buildres/abbrv.jabref.org
           git diff-index --quiet HEAD || git commit -m 'Update journal abbreviation lists'
-      - uses: peter-evans/create-pull-request@v5
+      - uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
           branch: update-journal-lists

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -293,7 +293,7 @@ jobs:
           CI: "true"
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           DBMS: "postgresql"
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -306,7 +306,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           show-progress: 'false'
-      - uses: gradle/wrapper-validation-action@v1
+      - uses: gradle/wrapper-validation-action@v2
   # This ensures that no git merge conflict markers (<<<, ...) are contained
   merge_conflict_job:
     name: Find merge conflicts

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a fetcher for [ISIDORE](https://isidore.science/), simply paste in the link into the text field or the last 6 digits in the link that identify that paper. [#10423](https://github.com/JabRef/jabref/issues/10423)
 - When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
 - We added a new group icon column to the main table showing the icons of the entry's groups. [#10801](https://github.com/JabRef/jabref/pull/10801)
+- We added ability to jump to an entry in the command line using `-j CITATIONKEY`. [koppor#540](https://github.com/koppor/jabref/issues/540)
 - We added a new boolean to the style files for Openoffice/Libreoffice integration to switch between ZERO_WIDTH_SPACE (default) and no space. [#10843](https://github.com/JabRef/jabref/pull/10843)
 
 ### Changed

diff --git a/build.gradle b/build.gradle
@@ -119,11 +119,11 @@ dependencies {
         exclude group: 'org.junit.jupiter'
     }
 
-    implementation 'org.apache.lucene:lucene-core:9.9.1'
-    implementation 'org.apache.lucene:lucene-queryparser:9.9.1'
+    implementation 'org.apache.lucene:lucene-core:9.9.2'
+    implementation 'org.apache.lucene:lucene-queryparser:9.9.2'
     implementation 'org.apache.lucene:lucene-queries:9.9.1'
     implementation 'org.apache.lucene:lucene-analysis-common:9.9.1'
-    implementation 'org.apache.lucene:lucene-highlighter:9.9.1'
+    implementation 'org.apache.lucene:lucene-highlighter:9.9.2'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.10.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
@@ -188,7 +188,7 @@ dependencies {
     implementation 'com.konghq:unirest-java:3.14.5'
 
     implementation 'org.slf4j:slf4j-api:2.0.11'
-    implementation "org.tinylog:tinylog-api:2.6.2"
+    implementation "org.tinylog:tinylog-api:2.7.0"
     implementation "org.tinylog:slf4j-tinylog:2.6.2"
     implementation "org.tinylog:tinylog-impl:2.6.2"
 
@@ -241,7 +241,7 @@ dependencies {
     implementation 'org.jspecify:jspecify:0.3.0'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.165'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.10.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.1'
 
     testImplementation 'org.mockito:mockito-core:5.10.0'

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=9d926787066a081739e8200858338b4a69e837c3a821a33aca9db09dd4a41026
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+distributionSha256Sum=9631d53cf3e74bfa726893aee1f8994fee4e060c401335946dba2156f440f24c
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

diff --git a/gradlew.bat b/gradlew.bat
@@ -43,11 +43,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -57,11 +57,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -16,6 +16,7 @@
 import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.JabRefException;
+import org.jabref.logic.UiCommand;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.exporter.AtomicFileWriter;
@@ -64,28 +65,31 @@
 import org.slf4j.LoggerFactory;
 
 public class ArgumentProcessor {
-
     private static final Logger LOGGER = LoggerFactory.getLogger(ArgumentProcessor.class);
-    private final JabRefCLI cli;
 
-    // Written once by processArguments()
-    private List<ParserResult> parserResults = List.of();
+    public enum Mode { INITIAL_START, REMOTE_START }
+
+    private final JabRefCLI cli;
 
     private final Mode startupMode;
+
     private final PreferencesService preferencesService;
     private final FileUpdateMonitor fileUpdateMonitor;
     private final BibEntryTypesManager entryTypesManager;
-    private boolean noGUINeeded;
+
+    private boolean guiNeeded;
+    private final List<UiCommand> uiCommands = new ArrayList<>();
 
     /**
      * First call the constructor, then call {@link #processArguments()}.
-     * Afterward, you can access the {@link #getParserResults()} and other getters.
+     * Afterward, you can access the {@link #getUiCommands()}.
      */
     public ArgumentProcessor(String[] args,
                              Mode startupMode,
                              PreferencesService preferencesService,
                              FileUpdateMonitor fileUpdateMonitor,
-                             BibEntryTypesManager entryTypesManager) throws org.apache.commons.cli.ParseException {
+                             BibEntryTypesManager entryTypesManager)
+            throws org.apache.commons.cli.ParseException {
         this.cli = new JabRefCLI(args);
         this.startupMode = startupMode;
         this.preferencesService = preferencesService;
@@ -121,6 +125,7 @@ private Optional<ParserResult> importBibtexToOpenBase(String argument, ImportFor
     }
 
     private Optional<ParserResult> importFile(String argument) {
+        LOGGER.debug("Importing file {}", argument);
         String[] data = argument.split(",");
 
         String address = data[0];
@@ -185,22 +190,21 @@ private Optional<ParserResult> importFile(Path file, String importFormat) {
         }
     }
 
-    public List<ParserResult> getParserResults() {
-        return parserResults;
-    }
-
     public void processArguments() {
+        uiCommands.clear();
+
         if ((startupMode == Mode.INITIAL_START) && cli.isShowVersion()) {
             cli.displayVersion();
         }
 
         if ((startupMode == Mode.INITIAL_START) && cli.isHelp()) {
             JabRefCLI.printUsage(preferencesService);
-            noGUINeeded = true;
-            this.parserResults = Collections.emptyList();
+            guiNeeded = false;
             return;
         }
 
+        guiNeeded = true;
+
         // Check if we should reset all preferences to default values:
         if (cli.isPreferencesReset()) {
             resetPreferences(cli.getPreferencesReset());
@@ -211,7 +215,6 @@ public void processArguments() {
             importPreferences();
         }
 
-        // List to put imported/loaded database(s) in.
         List<ParserResult> loaded = importAndOpenFiles();
 
         if (!cli.isBlank() && cli.isFetcherEngine()) {
@@ -221,7 +224,6 @@ public void processArguments() {
         if (cli.isExportMatches()) {
             if (!loaded.isEmpty()) {
                 if (!exportMatches(loaded)) {
-                    this.parserResults = Collections.emptyList();
                     return;
                 }
             } else {
@@ -277,7 +279,17 @@ public void processArguments() {
             doAuxImport(loaded);
         }
 
-        this.parserResults = loaded;
+        if (cli.isBlank()) {
+            uiCommands.add(new UiCommand.BlankWorkspace());
+        }
+
+        if (!cli.isBlank() && cli.isJumpToKey()) {
+            uiCommands.add(new UiCommand.JumpToEntryKey(cli.getJumpToKey()));
+        }
+
+        if (!cli.isBlank() && !loaded.isEmpty()) {
+            uiCommands.add(new UiCommand.OpenDatabases(loaded));
+        }
     }
 
     private void writeMetadataToPdf(List<ParserResult> loaded,
@@ -460,7 +472,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
                 default -> {
                     System.err.println(Localization.lang("Output file missing").concat(". \n \t ")
                                                    .concat(Localization.lang("Usage")).concat(": ") + JabRefCLI.getExportMatchesSyntax());
-                    noGUINeeded = true;
+                    guiNeeded = false;
                     return false;
                 }
             }
@@ -510,6 +522,9 @@ private void doAuxImport(List<ParserResult> loaded) {
         }
     }
 
+    /**
+     * @return List of opened files (could be .bib, but also other formats). May also contain error results.
+     */
     private List<ParserResult> importAndOpenFiles() {
         List<ParserResult> loaded = new ArrayList<>();
         List<String> toImport = new ArrayList<>();
@@ -527,6 +542,7 @@ private List<ParserResult> importAndOpenFiles() {
                                 Path.of(aLeftOver),
                                 preferencesService.getImportFormatPreferences(),
                                 fileUpdateMonitor);
+                        // In contrast to org.jabref.gui.LibraryTab.onDatabaseLoadingSucceed, we do not execute OpenDatabaseAction.performPostOpenActions(result, dialogService);
                     } catch (IOException ex) {
                         pr = ParserResult.fromError(ex);
                         LOGGER.error("Error opening file '{}'", aLeftOver, ex);
@@ -773,15 +789,11 @@ private Optional<ParserResult> fetch(String fetchCommand) {
         }
     }
 
-    public boolean isBlank() {
-        return cli.isBlank();
-    }
-
     public boolean shouldShutDown() {
-        return cli.isDisableGui() || cli.isShowVersion() || noGUINeeded;
+        return cli.isDisableGui() || cli.isShowVersion() || !guiNeeded;
     }
 
-    public enum Mode {
-        INITIAL_START, REMOTE_START
+    public List<UiCommand> getUiCommands() {
+        return uiCommands;
     }
 }
diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -169,6 +169,14 @@ public String getWriteMetadatatoPdf() {
                         cl.hasOption("embeddBibfileInPdf") ? cl.getOptionValue("embeddBibfileInPdf") : null;
     }
 
+    public String getJumpToKey() {
+        return cl.getOptionValue("jumpToKey");
+    }
+
+    public boolean isJumpToKey() {
+        return cl.hasOption("jumpToKey");
+    }
+
     private static Options getOptions() {
         Options options = new Options();
 
@@ -275,7 +283,7 @@ private static Options getOptions() {
         options.addOption(Option
                 .builder()
                 .longOpt("embeddBibfileInPdf")
-                .desc("%s: '%s'".formatted(Localization.lang("Embed BibTeXEntry in PDF."), "-w pathToMyOwnPaper.pdf"))
+                .desc("%s: '%s'".formatted(Localization.lang("Embed BibTeX as attached file in PDF."), "-w pathToMyOwnPaper.pdf"))
                 .hasArg()
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());
@@ -288,6 +296,14 @@ private static Options getOptions() {
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());
 
+        options.addOption(Option
+                .builder("j")
+                .longOpt("jumpToKey")
+                .desc("%s: '%s'".formatted(Localization.lang("Jump to the entry of the given citation key."), "-j key"))
+                .hasArg()
+                .argName("CITATIONKEY")
+                .build());
+
         return options;
     }