Merge branch 'updateGradle7' into test-module-issue

* updateGradle7: (39 commits)
  try upgrading gradle
  Only disable  move to file dir when path equals (#7269)
  Improved detection of long DOI's within text (#7260)
  Add missing author and fix name
  Fix style of highlighted checkboxes while searching in preferences (#7258)
  Updates to institution citation keys (#7210)
  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
  GitBook: [master] 5 pages and 25 assets modified
  New Crowdin updates (#7246)
  add language mapping for chinese
  remove chinese content
  ...

Author: Siedlerchr

.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"

.github/workflows/deployment.yml

@@ -1,6 +1,7 @@
 name: Deployment
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - master

.github/workflows/tests.yml

@@ -261,6 +261,6 @@ jobs:
           echo
           echo "In case you want to use a different one, please comment here and adjust your name in your git configuration for future commits"
           echo
-          echo "Just adding yourself into the AUHTORS file does not help as it is overwritten by our script ./scripts/generate-authors."
+          echo "Just adding yourself into the AUTHORS file does not help as it is overwritten by our script ./scripts/generate-authors."
           echo "Read more on the AUTHORS file at found at https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits"
           exit 1

AUTHORS

@@ -133,6 +133,7 @@ Felix Luthman
 Felix Wilke
 Fernando Santagata
 ffffatgoose
+Fiyinfolu Eludire
 Florian Beetz
 Florian Straßer
 Foivos Christoulakis
@@ -163,6 +164,7 @@ Hollyqqqqq
 Houssem Nasri
 hrandrianasolo
 Hussain Arif
+IfIWantedTo
 Igor Chernyavsky
 Igor Steinmacher
 Illes Solt

CHANGELOG.md

@@ -1,4 +1,3 @@
-
 # Changelog
 
 All notable changes to this project will be documented in this file.
@@ -12,13 +11,27 @@ 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
+
+- We fixed an issue with the style of highlighted check boxes while searching in preferences. [#7226](https://github.com/JabRef/jabref/issues/7226)
+- We fixed an issue where the option "Move file to file directory" was disabled in the entry editor for all files [#7194](https://github.com/JabRef/jabref/issues/7194)
+
+### Removed
+
+## [5.2] – 2020-12-24
+
+### Added
+
 - We added a validation to check if the current database location is shared, preventing an exception when Pulling Changes From Shared Database. [#6959](https://github.com/JabRef/jabref/issues/6959)
 - We added a query parser and mapping layer to enable conversion of queries formulated in simplified lucene syntax by the user into api queries. [#6799](https://github.com/JabRef/jabref/pull/6799)
 - We added some basic functionality to customise the look of JabRef by importing a css theme file. [#5790](https://github.com/JabRef/jabref/issues/5790)
 - We added connection check function in network preference setting [#6560](https://github.com/JabRef/jabref/issues/6560)
 - We added support for exporting to YAML. [#6974](https://github.com/JabRef/jabref/issues/6974)
 - We added a DOI format and organization check to detect [American Physical Society](https://journals.aps.org/) journals to copy the article ID to the page field for cases where the page numbers are missing. [#7019](https://github.com/JabRef/jabref/issues/7019)
-- We added a new fetcher to enable users to search jstor.org [#6627](https://github.com/JabRef/jabref/issues/6627)
 - We added an error message in the New Entry dialog that is shown in case the fetcher did not find anything . [#7000](https://github.com/JabRef/jabref/issues/7000)
 - We added a new formatter to output shorthand month format. [#6579](https://github.com/JabRef/jabref/issues/6579)
 - We added support for the new Microsoft Edge browser in all platforms. [#7056](https://github.com/JabRef/jabref/pull/7056)
@@ -80,9 +93,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the password for a shared SQL database was not remembered [#6869](https://github.com/JabRef/jabref/issues/6869)
 - We fixed an issue where newly added entires were not synced to a shared SQL database [#7176](https://github.com/JabRef/jabref/issues/7176)
 - We fixed an issue where the PDF-Content importer threw an exception when no DOI number is present at the first page of the PDF document [#7203](https://github.com/JabRef/jabref/issues/7203)
+- We fixed an issue where authors that only have last names were incorrectly identified as institutes when generating citation keys [#7199](https://github.com/JabRef/jabref/issues/7199)
+- We fixed an issue where institutes were incorrectly identified as universities when generating citation keys [#6942](https://github.com/JabRef/jabref/issues/6942)
 
 ### Removed
 
+- We removed the Google Scholar fetcher and the ACM fetcher do not work due to traffic limitations [#6369](https://github.com/JabRef/jabref/issues/6369)
 - We removed the menu entry "Manage external file types" because it's already in 'Preferences' dialog [#6991](https://github.com/JabRef/jabref/issues/6991)
 - We removed the integrity check "Abbreviation detected" for the field journal/journaltitle in the entry editor [#3925](https://github.com/JabRef/jabref/issues/3925)
 
@@ -483,7 +499,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.1...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.2...HEAD
+[5.2]: https://github.com/JabRef/jabref/compare/v5.1...v5.2
 [5.1]: https://github.com/JabRef/jabref/compare/v5.0...v5.1
 [5.0]: https://github.com/JabRef/jabref/compare/v5.0-beta...v5.0
 [5.0-beta]: https://github.com/JabRef/jabref/compare/v5.0-alpha...v5.0-beta

build.gradle

@@ -13,8 +13,8 @@ plugins {
     id 'me.champeau.gradle.jmh' version '0.5.2'
     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.openjfx.javafxplugin' version '0.0.9'
+    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'
@@ -38,23 +38,21 @@ version = project.findProperty('projVersion') ?: '100.0.0'
 java {
     sourceCompatibility = JavaVersion.VERSION_14
     targetCompatibility = JavaVersion.VERSION_14
+    
 }
 
 application {
     mainClassName = "org.jabref.gui.JabRefLauncher"
     mainModule ='org.jabref'
 }
+modularity.disableEffectiveArgumentsAdjustment()
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
 // These should be removed, as well as the files in the lib folder, as soon as they have valid module names
 modularity.patchModule("test", "fastparse_2.12-1.0.0.jar")
 modularity.patchModule("test2", "fastparse-utils_2.12-1.0.0.jar")
 modularity.patchModule("test3", "sourcecode_2.12-0.1.4.jar")
 
-// These are the Java version requirements we will check on each start of JabRef
-ext.minRequiredJavaVersion = "1.8.0_171"
-ext.allowJava9 = true
-
 sourceSets {
     main {
         java {
@@ -92,10 +90,6 @@ configurations {
     }
 }
 
-javafx {
-    version = "15"
-    modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
-}
 
 dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
@@ -111,7 +105,7 @@ 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'
 
@@ -153,6 +147,12 @@ dependencies {
     implementation group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.5'
 
     // JavaFX stuff
+    
+    // https://mvnrepository.com/artifact/org.openjfx/javafx-controls
+	implementation group: 'org.openjfx', name: 'javafx-controls', version: '15.0.1'
+	implementation group: 'org.openjfx', name: 'javafx-fxml', version: '15.0.1'
+	implementation group: 'org.openjfx', name: 'javafx-web', version: '15.0.1'
+    
     implementation 'de.jensd:fontawesomefx-commons:11.0'
     implementation 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-11'
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
@@ -165,7 +165,7 @@ 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'
@@ -194,7 +194,7 @@ 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'
@@ -203,8 +203,8 @@ 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"
@@ -275,15 +275,12 @@ processResources {
                 "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'),
                 "springerNatureAPIKey": System.getenv('SpringerNatureAPIKey'),
                 "astrophysicsDataSystemAPIKey": System.getenv('AstrophysicsDataSystemAPIKey'),
-                "ieeeAPIKey": System.getenv('IEEEAPIKey'),
-                "minRequiredJavaVersion": minRequiredJavaVersion,
-                "allowJava9": allowJava9
-
+                "ieeeAPIKey": System.getenv('IEEEAPIKey')
         )
         filteringCharset = 'UTF-8'
     }
 
-    filesMatching("resource/**/meta.xml") {
+    filesMatching(["resources/resource/ods/meta.xml", "resources/resource/openoffice/meta.xml"]) {
         expand version: project.version
     }
 }

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:

crowdin.yml

@@ -5,3 +5,5 @@ files:
       two_letters_code:
         pt-BR: pt_BR
         id: in
+        zh-CN: zh_CN
+        zh-TW: zh_TW