Merge remote-tracking branch 'upstream/master' into importerbackgroun…

…dtask

* upstream/master:
  Bump xmlunit-core from 2.8.1 to 2.8.2 (#7251)
  Bump classgraph from 4.8.97 to 4.8.98 (#7250)
  Bump bcprov-jdk15on from 1.67 to 1.68 (#7249)
  Bump xmlunit-matchers from 2.8.1 to 2.8.2 (#7252)
  Bump unirest-java from 3.11.06 to 3.11.09 (#7254)
  Bump org.beryx.jlink from 2.23.0 to 2.23.1 (#7253)
  Bump pascalgn/automerge-action from v0.12.0 to v0.13.0 (#7255)
  Added a check to integrate with the flatpak package (#7248)
  New translations JabRef_en.properties (Chinese Traditional) (#7247)
  Update code-howtos.md

.github/workflows/automerge.yml

@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.12.0
+        uses: pascalgn/automerge-action@v0.13.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

CHANGELOG.md

@@ -11,6 +11,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added the extension support and the external application support (For Texshow, Texmaker and LyX) to the flatpak [#7248](https://github.com/JabRef/jabref/pull/7248)
+
 ### Changed
 
 ### Fixed

build.gradle

@@ -14,7 +14,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.36.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.23.0'
+    id 'org.beryx.jlink' version '2.23.1'
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
     id 'com.adarshr.test-logger' version '2.1.1'
@@ -106,7 +106,7 @@ dependencies {
     implementation group: 'org.apache.tika', name: 'tika-core', version: '1.25'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.67'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.68'
 
     implementation 'commons-cli:commons-cli:1.4'
 
@@ -157,7 +157,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.0.3'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.11.06'
+    implementation 'com.konghq:unirest-java:3.11.09'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -186,7 +186,7 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.97'
+    testImplementation 'io.github.classgraph:classgraph:4.8.98'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.7.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
@@ -195,8 +195,8 @@ dependencies {
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:3.6.28'
-    testImplementation 'org.xmlunit:xmlunit-core:2.8.1'
-    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.1'
+    testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
+    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.15.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.15.0'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"

buildres/linux/jabrefHost.py

@@ -1,8 +1,4 @@
-#!/usr/bin/python3 -u
-
-# Note that running python with the `-u` flag is required on Windows,
-# in order to ensure that stdin and stdout are opened in binary, rather
-# than text, mode.
+#!/usr/bin/python3
 
 import json
 import logging
@@ -15,17 +11,24 @@
 import sys
 from pathlib import Path
 
-# We assume that this python script is located in "jabref/lib" while the executable is "jabref/bin/JabRef"
+# Try a set of possible launchers to execute JabRef
 script_dir = Path(__file__).resolve().parent.parent
 relpath_path = script_dir / "bin/JabRef"
 lowercase_path = shutil.which("jabref")
 uppercase_path = shutil.which("JabRef")
+
+# Relative path used in the portable install
 if relpath_path.exists():
     JABREF_PATH = relpath_path
+# Lowercase launcher used in deb/rpm/snap packages
 elif lowercase_path is not None and os.path.exists(lowercase_path):
     JABREF_PATH = Path(lowercase_path)
+# Uppercase launcher used in Arch AUR package
 elif uppercase_path is not None and os.path.exists(uppercase_path):
     JABREF_PATH = Path(uppercase_path)
+# FLatpak support
+elif subprocess.run(["flatpak", "info", "org.jabref.jabref"], capture_output=True).returncode == 0:
+    JABREF_PATH = "flatpak run org.jabref.jabref"
 else:
     logging.error("Could not determine JABREF_PATH")
     sys.exit(-1)
@@ -70,7 +73,7 @@ def send_message(message):
 
 def add_jabref_entry(data):
     """Send string via cli as literal to preserve special characters"""
-    cmd = [str(JABREF_PATH), "--importBibtex", r"{}".format(data)]
+    cmd = str(JABREF_PATH).split() + ["--importBibtex", r"{}".format(data)]
     logging.info("Try to execute command {}".format(cmd))
     try:
         response = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
@@ -90,7 +93,7 @@ def add_jabref_entry(data):
 logging.info(str(message))
 
 if "status" in message and message["status"] == "validate":
-    cmd = [str(JABREF_PATH), "--version"]
+    cmd = str(JABREF_PATH).split() + ["--version"]
     try:
         response = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
     except subprocess.CalledProcessError as exc: