Implement native messaging

build.gradle

@@ -19,7 +19,7 @@ buildscript {
 
 plugins {
     id 'com.gradle.build-scan' version '1.11'
-    id 'com.install4j.gradle' version '7.0.3'
+    id 'com.install4j.gradle' version '7.0.4'
     id 'com.github.johnrengelman.shadow' version '2.0.2'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.5.0-1'
@@ -50,7 +50,7 @@ apply from: 'xjc.gradle'
 group = "org.jabref"
 version = "4.2-dev"
 project.ext.threeDotVersion = "4.1.0.1"
-project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
+project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j7' : 'install4j7')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 mainClassName = "org.jabref.JabRefMain"
@@ -468,8 +468,16 @@ install4j {
     installDir = file(project.ext.install4jDir)
 }
 
+task generateFinalJabRefPS1File(type: Copy) {
+    from('buildres') {
+        include 'JabRef.ps1'
+    }
+    into 'build'
+    filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
+}
+
 // has to be defined AFTER 'dev' things to have the correct project.version
-task media(type: com.install4j.gradle.Install4jTask, dependsOn: "releaseJar") {
+task media(type: com.install4j.gradle.Install4jTask, dependsOn: ["releaseJar", "generateFinalJabRefPS1File"]) {
     projectFile = file('jabref.install4j')
     release = project.version
     winKeystorePassword = System.getenv('CERTIFICATE_PW')

buildres/JabRef.bat

@@ -0,0 +1,3 @@
+@echo off
+pushd %~dp0
+@powershell.exe -ExecutionPolicy Bypass -NoLogo -NonInteractive -NoProfile -WindowStyle Hidden -File ".\JabRef.ps1"

buildres/JabRef.ps1

@@ -0,0 +1,48 @@
+function Respond($response) {
+    $jsonResponse = $response | ConvertTo-Json
+
+    try {
+        $writer = New-Object System.IO.BinaryWriter([System.Console]::OpenStandardOutput())
+        $writer.Write([int]$jsonResponse.Length)
+        $writer.Write([System.Text.Encoding]::UTF8.GetBytes($jsonResponse))
+        $writer.Close()
+    } finally {
+        $writer.Dispose()
+    }
+}
+
+$jabRefJarFileName = "@jabRefJarFileName@"
+$jabRefJar = [System.IO.Path]::Combine($PSScriptRoot, $jabRefJarFileName)
+
+try {
+    $reader = New-Object System.IO.BinaryReader([System.Console]::OpenStandardInput())
+    $length = $reader.ReadInt32()
+    $messageRaw = [System.Text.Encoding]::UTF8.GetString($reader.ReadBytes($length))
+    $message = $messageRaw | ConvertFrom-Json
+
+    if ($message.Status -eq "validate") {
+        if (-not (Test-Path $jabRefJar)) {
+            return Respond @{message="jarNotFound";path=$jabRefJar}
+        } else {
+            return Respond @{message="jarFound"}
+        }
+    }
+
+    if (-not (Test-Path $jabRefJar)) {
+        $wshell = New-Object -ComObject Wscript.Shell
+        $popup = "Unable to locate '$jabRefJarFileName' in '$([System.IO.Path]::GetDirectoryName($jabRefJar))'."
+        $wshell.Popup($popup,0,"JabRef", 0x0 + 0x30)
+        return
+    }
+
+    #$wshell = New-Object -ComObject Wscript.Shell
+    #$wshell.Popup($message.Text,0,"JabRef", 0x0 + 0x30)
+
+    $messageText = $message.Text
+    $output = & java -jar $jabRefJar -importBibtex "$messageText" 2>&1
+    #$output = & echoargs -importBibtex $messageText 2>&1
+    #$wshell.Popup($output,0,"JabRef", 0x0 + 0x30)
+    return Respond @{message="ok";output="$output"}
+} finally {
+    $reader.Dispose()
+}

buildres/jabref.json

@@ -0,0 +1,9 @@
+{
+  "name": "org.jabref.jabref",
+  "description": "JabRef",
+  "path": "JabRef.bat",
+  "type": "stdio",
+  "allowed_extensions": [
+    "@jabfox"
+  ]
+}

jabref.install4j

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.3" transformSequenceNumber="7">
-  <directoryPresets config="build/releases/${compiler:buildFileName}" />
+<install4j version="7.0.4" transformSequenceNumber="7">
+  <directoryPresets config="./buildres/jabref.json" />
   <application name="JabRef" distributionSourceDir="" applicationId="0034-7691-1464-4754" mediaDir="build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="JabRef" publisher="JabRef Community" publisherWeb="https://www.jabref.org/" version="DEV" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="true" macSignature="????" macVolumeId="780dfea2d33a0244" javaMinVersion="1.8" javaMaxVersion="1.8" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="true" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
@@ -51,10 +51,13 @@
       <mountPoint id="22" root="" location="" mode="755" />
     </mountPoints>
     <entries>
-      <fileEntry mountPoint="22" file="build/releases/${compiler:buildFileName}" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
       <fileEntry mountPoint="22" file="./LICENSE.md" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
       <fileEntry mountPoint="22" file="./AUTHORS" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
+      <fileEntry mountPoint="22" file="build/releases/${compiler:buildFileName}" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
+      <fileEntry mountPoint="22" file="./build/JabRef.ps1" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
       <fileEntry mountPoint="22" file="./buildres/JabRef.VisualElementsManifest.xml" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
+      <fileEntry mountPoint="22" file="./buildres/JabRef.bat" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
+      <fileEntry mountPoint="22" file="./buildres/jabref.json" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" />
     </entries>
     <components />
   </files>
@@ -561,6 +564,30 @@ return console.askOkCancel(message, true);
                     </serializedBean>
                     <condition>!(Util.hasFullAdminRights() || Util.isAdminGroup())</condition>
                   </action>
+                  <action name="" id="352" customizedId="" beanClass="com.install4j.runtime.beans.actions.registry.SetRegistryValueAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
+                    <serializedBean>
+                      <java class="java.beans.XMLDecoder">
+                        <object class="com.install4j.runtime.beans.actions.registry.SetRegistryValueAction">
+                          <void property="keyName">
+                            <string>SOFTWARE\Mozilla\NativeMessagingHosts</string>
+                          </void>
+                          <void property="registryRoot">
+                            <object class="java.lang.Enum" method="valueOf">
+                              <class>com.install4j.api.windows.RegistryRoot</class>
+                              <string>HKEY_LOCAL_MACHINE</string>
+                            </object>
+                          </void>
+                          <void property="value">
+                            <string>/ve /d "${installer:sys.installationDir}\jabref.json" /f</string>
+                          </void>
+                          <void property="valueName">
+                            <string>org.jabref.jabref</string>
+                          </void>
+                        </object>
+                      </java>
+                    </serializedBean>
+                    <condition />
+                  </action>
                 </beans>
               </group>
             </actions>
@@ -896,6 +923,30 @@ return console.askYesNo(message, true);
                     </serializedBean>
                     <condition>!(Util.hasFullAdminRights() || Util.isAdminGroup())</condition>
                   </action>
+                  <action name="" id="353" customizedId="" beanClass="com.install4j.runtime.beans.actions.registry.DeleteRegistryItemAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
+                    <serializedBean>
+                      <java class="java.beans.XMLDecoder">
+                        <object class="com.install4j.runtime.beans.actions.registry.DeleteRegistryItemAction">
+                          <void property="keyName">
+                            <string>SOFTWARE\Mozilla\NativeMessagingHosts</string>
+                          </void>
+                          <void property="onlyIfEmpty">
+                            <boolean>false</boolean>
+                          </void>
+                          <void property="registryRoot">
+                            <object class="java.lang.Enum" method="valueOf">
+                              <class>com.install4j.api.windows.RegistryRoot</class>
+                              <string>HKEY_LOCAL_MACHINE</string>
+                            </object>
+                          </void>
+                          <void property="valueName">
+                            <string>org.jabref.jabref</string>
+                          </void>
+                        </object>
+                      </java>
+                    </serializedBean>
+                    <condition />
+                  </action>
                 </beans>
               </group>
             </actions>

src/main/java/org/jabref/Globals.java

@@ -31,7 +31,6 @@ public class Globals {
     public static final BuildInfo BUILD_INFO = new BuildInfo();
     // Remote listener
     public static final RemoteListenerServerLifecycle REMOTE_LISTENER = new RemoteListenerServerLifecycle();
-
     public static final ImportFormatReader IMPORT_FORMAT_READER = new ImportFormatReader();
     public static final TaskExecutor TASK_EXECUTOR = new DefaultTaskExecutor();
     // In the main program, this field is initialized in JabRef.java

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

@@ -102,7 +102,7 @@ private void openWindow() {
             for (Iterator<ParserResult> parserResultIterator = bibDatabases.iterator(); parserResultIterator.hasNext();) {
                 ParserResult pr = parserResultIterator.next();
                 // Define focused tab
-                if (pr.getFile().get().getAbsolutePath().equals(focusedFile)) {
+                if (pr.getFile().filter(path -> path.getAbsolutePath().equals(focusedFile)).isPresent()) {
                     first = true;
                 }
 

src/main/java/org/jabref/JabRefMain.java

@@ -20,7 +20,7 @@
 import org.jabref.logic.net.ProxyRegisterer;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.RemotePreferences;
-import org.jabref.logic.remote.client.RemoteListenerClient;
+import org.jabref.logic.remote.client.RemoteClient;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.JavaVersion;
 import org.jabref.logic.util.OS;
@@ -43,13 +43,8 @@ public class JabRefMain extends Application {
 
     public static void main(String[] args) {
         arguments = args;
-        launch(arguments);
-    }
 
-    @Override
-    public void start(Stage mainStage) throws Exception {
-        Platform.setImplicitExit(false);
-        SwingUtilities.invokeLater(() -> start(arguments));
+        launch(arguments);
     }
 
     /**
@@ -99,25 +94,9 @@ private static void ensureCorrectJavaVersion() {
     }
 
     private static void start(String[] args) {
-        FallbackExceptionHandler.installExceptionHandler();
-
+        // Init preferences
         JabRefPreferences preferences = JabRefPreferences.getInstance();
-
-        ensureCorrectJavaVersion();
-
-        ProxyPreferences proxyPreferences = preferences.getProxyPreferences();
-        ProxyRegisterer.register(proxyPreferences);
-        if (proxyPreferences.isUseProxy() && proxyPreferences.isUseAuthentication()) {
-            Authenticator.setDefault(new ProxyAuthenticator());
-        }
-
         Globals.prefs = preferences;
-        Globals.startBackgroundTasks();
-
-        // Note that the language was already set during the initialization of the preferences and it is safe to
-        // call the next function.
-        Globals.prefs.setLanguageDependentDefaultValues();
-
         // Perform Migrations
         // Perform checks and changes for users with a preference set from an older JabRef version.
         PreferencesMigrations.upgradePrefsToOrgJabRef();
@@ -130,6 +109,21 @@ private static void start(String[] args) {
         PreferencesMigrations.addCrossRefRelatedFieldsForAutoComplete();
         PreferencesMigrations.upgradeObsoleteLookAndFeels();
 
+        // Process arguments
+        ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START);
+
+        FallbackExceptionHandler.installExceptionHandler();
+
+        ensureCorrectJavaVersion();
+
+        ProxyPreferences proxyPreferences = preferences.getProxyPreferences();
+        ProxyRegisterer.register(proxyPreferences);
+        if (proxyPreferences.isUseProxy() && proxyPreferences.isUseAuthentication()) {
+            Authenticator.setDefault(new ProxyAuthenticator());
+        }
+
+        Globals.startBackgroundTasks();
+
         // Update handling of special fields based on preferences
         InternalBibtexFields
                 .updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
@@ -158,7 +152,7 @@ private static void start(String[] args) {
 
             if (!Globals.REMOTE_LISTENER.isOpen()) {
                 // we are not alone, there is already a server out there, try to contact already running JabRef:
-                if (RemoteListenerClient.sendToActiveJabRefInstance(args, remotePreferences.getPort())) {
+                if (new RemoteClient(remotePreferences.getPort()).sendCommandLineArguments(args)) {
                     // We have successfully sent our command line options through the socket to another JabRef instance.
                     // So we assume it's all taken care of, and quit.
                     LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
@@ -176,9 +170,6 @@ private static void start(String[] args) {
         // The preferences return the system newline character sequence as default
         OS.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
 
-        // Process arguments
-        ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START);
-
         // See if we should shut down now
         if (argumentProcessor.shouldShutDown()) {
             Globals.shutdownThreadPools();
@@ -191,4 +182,11 @@ private static void start(String[] args) {
                 .invokeLater(() -> new JabRefGUI(argumentProcessor.getParserResults(),
                         argumentProcessor.isBlank()));
     }
+
+    @Override
+    public void start(Stage mainStage) throws Exception {
+        Platform.setImplicitExit(false);
+        SwingUtilities.invokeLater(() -> start(arguments)
+        );
+    }
 }

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

@@ -32,7 +32,9 @@
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.OutputPrinter;
+import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.logging.JabRefLogger;
@@ -82,6 +84,19 @@ private static Optional<ParserResult> importToOpenBase(String argument) {
         return result;
     }
 
+    private static Optional<ParserResult> importBibtexToOpenBase(String argument) {
+        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
+        try {
+            List<BibEntry> entries = parser.parseEntries(argument);
+            ParserResult result = new ParserResult(entries);
+            result.setToOpenTab();
+            return Optional.of(result);
+        } catch (ParseException e) {
+            System.err.println(Localization.lang("Error occurred when parsing entry") + ": " + e.getLocalizedMessage());
+            return Optional.empty();
+        }
+    }
+
     private static Optional<ParserResult> importFile(String argument) {
         String[] data = argument.split(",");
 
@@ -346,6 +361,10 @@ private List<ParserResult> importAndOpenFiles() {
             importToOpenBase(cli.getImportToOpenBase()).ifPresent(loaded::add);
         }
 
+        if (!cli.isBlank() && cli.isBibtexImport()) {
+            importBibtexToOpenBase(cli.getBibtexImport()).ifPresent(loaded::add);
+        }
+
         return loaded;
     }
 

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

@@ -1,6 +1,5 @@
 package org.jabref.cli;
 
-import java.util.Arrays;
 import java.util.List;
 
 import org.jabref.Globals;
@@ -21,14 +20,13 @@ public class JabRefCLI {
     private final CommandLine cl;
     private List<String> leftOver;
 
-
     public JabRefCLI(String[] args) {
 
         Options options = getOptions();
 
         try {
             this.cl = new DefaultParser().parse(options, args);
-            this.leftOver = Arrays.asList(cl.getArgs());
+            this.leftOver = cl.getArgList();
         } catch (ParseException e) {
             LOGGER.warn("Problem parsing arguments", e);
 
@@ -96,6 +94,14 @@ public String getFileExport() {
         return cl.getOptionValue("output");
     }
 
+    public boolean isBibtexImport() {
+        return cl.hasOption("importBibtex");
+    }
+
+    public String getBibtexImport() {
+        return cl.getOptionValue("importBibtex");
+    }
+
     public boolean isFileImport() {
         return cl.hasOption("import");
     }
@@ -168,6 +174,14 @@ private Options getOptions() {
                 hasArg().
                 argName("FILE").build());
 
+        options.addOption(
+                Option.builder("ib")
+                      .longOpt("importBibtex")
+                      .desc(String.format("%s: %s[,importBibtex bibtexString]", Localization.lang("Import") + " " + Localization.BIBTEX, Localization.lang("filename")))
+                      .hasArg()
+                      .argName("FILE")
+                      .build());
+
         options.addOption(Option.builder("o").
                 longOpt("output").
                 desc(String.format("%s: %s[,export format]", Localization.lang("Output or export file"),