Merge remote-tracking branch 'upstream/master' into writebackupToTemp

* upstream/master: (58 commits)
  remove any newlines and spaces in isbn when fetching (#7023)
  add exception to error handler in integrity check
  Update journalList.mv
  Update to javafx15 (#7018)
  Squashed 'src/main/resources/csl-styles/' changes from 6fab78b..5297abd
  try to fix DEP issue with official jdk (#7008)
  Jstor Fetcher (#6992)
  Group: "Searching for keywords" searches for a single keyword ==> use singular (#6995)
  Merge parsing of bracketed patterns (#6989)
  6848 fixed the issue of clicking collapse all expanding tree (#6993)
  Enable auto sync per default for Open/Libre Office (#6985)
  Bump unirest-java from 3.11.00 to 3.11.01 (#7001)
  Bump byte-buddy-parent from 1.10.16 to 1.10.17 (#7004)
  Bump lucene-queryparser from 8.6.2 to 8.6.3 (#7002)
  Bump postgresql from 42.2.16 to 42.2.17 (#7005)
  Bump pascalgn/automerge-action from v0.11.0 to v0.12.0 (#7006)
  Bump flowless from 0.6.1 to 0.6.2 (#7003)
  Rewrite guidelines to Java 15 (#6973)
  Lint CHANGELOG.md
  Removing "BibTeX" when not specific to BibTeX (#6983)
  ...

.github/dependabot.yml

@@ -10,13 +10,16 @@ updates:
   ignore:
   - dependency-name: com.microsoft.azure:applicationinsights-core
     versions:
-    - ">= 2.5.a, <= 2.6.1" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+    - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
   - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
     versions:
-    - ">= 2.5.a, <= 2.6.1" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+    - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
   - dependency-name: de.jensd:fontawesomefx-materialdesignfont
     versions:
     - "> 1.7.22-4" # Strange versioning format
+  - dependency-name: org.fxmisc.richtext:richtextfx
+    versions:
+    - "< 0.10.6" # Blocked by https://github.com/FXMisc/RichTextFX/issues/967, wait for new release
 - package-ecosystem: "github-actions"
   directory: "/"
   schedule:

.github/workflows/automerge.yml

@@ -11,12 +11,12 @@ jobs:
         id: waitforstatuschecks
         uses: "WyriHaximus/[email protected]"
         with:
-          ignoreActions: automerge
+          ignoreActions: Automerge Dependabot
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.10.0
+        uses: pascalgn/automerge-action@v0.12.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

.github/workflows/deployment.yml

@@ -55,10 +55,16 @@ jobs:
       - name: Run GitVersion
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
-      - name: Set up JDK
+      - name: Set up JDK 15 for linux and mac
         uses: actions/setup-java@v1
         with:
           java-version: 15
+        if: matrix.os != 'windows-latest'
+      - name: Set up JDK 14 for windows
+        uses: actions/setup-java@v1
+        with:
+          java-version: 14
+        if: matrix.os == 'windows-latest'
       - name: Restore gradle cache
         uses: actions/cache@master
         with:

AUTHORS

@@ -29,6 +29,7 @@ Andreas Amann
 Andreas Buhr
 Andreas Rudert
 Andrew Collins
+Andrew Kuncevich
 Andrew Levit
 André Schlichting
 Andrés Sánchez
@@ -112,6 +113,7 @@ Eiswindyeti
 Ellen Reitmayr
 Erdem Derebasoglu
 Erdem Derebaşoğlu
+Eric Lau
 Erik Putrycz
 Ervin Kolenovic
 Escoul
@@ -167,6 +169,7 @@ Jan Kubovy
 Jan Schäfer
 Janosch Kutscherauer
 Jason Pickering
+Jasper Vandemalle
 Javier Muñoz Ferrara
 jcampbell11245
 Jeff Kerr
@@ -177,6 +180,7 @@ Jens Döcke
 joeyzgraggen
 Johannes Hupe
 Johannes Manner
+Johannes Theiner
 John David
 John Relph
 John Zedlewski
@@ -225,13 +229,13 @@ Lucas Beretti
 Luciana de Melo e Abud
 Lugduni Desrosiers
 Luis Romero
-m-mauersberger
 Mairieli Wessel
 Malik Atalla
 Malte Deiseroth
 Manuel Siebeneicher
 Manuel Wtfjoke
 Marcel Luethi
+Marco Aurélio Graciotto Silva
 Marco Konersmann
 Mariana Prudencio
 Marius Kleiner
@@ -374,6 +378,7 @@ Tianjian Lei
 Tim Kilian
 Tim van Rossum
 Tim Würtele
+Timucin Merdin
 Tobias Boceck
 Tobias Bouschen
 Tobias Denkinger

CHANGELOG.md

@@ -15,9 +15,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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 a new fetcher to enable users to search jstor.org [#6627](https://github.com/JabRef/jabref/issues/6627)
 
 ### Changed
 
+- We changed the default preferences for OpenOffice/LibreOffice integration to automatically sync the bibliography when
+inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://github.com/JabRef/jabref/issues/6957)
 - We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 - We removed two useless preferences in the groups preferences dialog. [#6836](https://github.com/JabRef/jabref/pull/6836)
@@ -29,18 +32,28 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We changed the title of the window "Manage field names and content" to have the same title as the corresponding menu item [#6895](https://github.com/JabRef/jabref/pull/6895)
 - We renamed the menus "View -> Previous citation style" and "View -> Next citation style" into "View -> Previous preview style" and "View -> Next preview style" and renamed the "Preview" style to "Customized preview style". [#6899](https://github.com/JabRef/jabref/pull/6899)
 - We changed the default preference option "Search and store files relative to library file location" to on, as this seems to be a more intuitive behaviour. [#6863](https://github.com/JabRef/jabref/issues/6863)
-- Improved detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
+- We changed the title of the window  "Manage field names and content":  to have the same title as the corresponding menu item  [#6895](https://github.com/JabRef/jabref/pull/6895)
+- We improved the detection of "short" DOIs [6880](https://github.com/JabRef/jabref/issues/6880)
+- We improved the duplicate detection when identifiers like DOI or arxiv are semantiaclly the same, but just syntactically differ (e.g. with or without http(s):// prefix). [#6707](https://github.com/JabRef/jabref/issues/6707)
+- We changed in the group interface "Generate groups from keywords in a BibTeX field" by "Generate groups from keywords in the following field". [#6983](https://github.com/JabRef/jabref/issues/6983)
+- We changed the name of a group type from "Searching for keywords" to "Searching for a keyword". [6995](https://github.com/JabRef/jabref/pull/6995)
 
 ### Fixed
 
-- We fixed an issue changing the icon link_variation_off that is not meaningful. [#6834][https://github.com/JabRef/jabref/issues/6834]
+- We fixed an issue changing the icon link_variation_off that is not meaningful. [#6834](https://github.com/JabRef/jabref/issues/6834)
 - We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
 - We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
 - We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)
+- We fixed the failure to Copy citation key and link. [#5835](https://github.com/JabRef/jabref/issues/5835)
 - We fixed an issue where the sort order of the entry table was reset after a restart of JabRef. [#6898](https://github.com/JabRef/jabref/pull/6898)
 - We fixed an issue where no longer a warning was displayed when inserting references into LibreOffice with an invalid "ReferenceParagraphFormat". [#6907](https://github.com/JabRef/jabref/pull/60907).
-- We fixed an issue where a selected field was not removed after the first click in the custom entry types dialog [#6934](https://github.com/JabRef/jabref/issues/6934)
-- We fixed an issue where a remove icon was shown for standard entry types in the custom entry types dialog [6906](https://github.com/JabRef/jabref/issues/6906)
+- We fixed an issue where a selected field was not removed after the first click in the custom entry types dialog. [#6934](https://github.com/JabRef/jabref/issues/6934)
+- We fixed an issue where a remove icon was shown for standard entry types in the custom entry types dialog. [#6906](https://github.com/JabRef/jabref/issues/6906)
+- We fixed an issue where it was impossible to connect to OpenOffice/LibreOffice on Mac OSX. [#6970](https://github.com/JabRef/jabref/pull/6970)
+- We fixed an issue with the python script used by browser plugins that failed to locate JabRef if not installed in its default location. [#6963](https://github.com/JabRef/jabref/pull/6963/files)
+- We fixed an issue where spaces and newlines in an isbn would generate an exception. [#6456](https://github.com/JabRef/jabref/issues/6456)
+- We fixed an issue where identity column header had incorrect foreground color in the  Dark theme. [#6796](https://github.com/JabRef/jabref/issues/6796)
+- We fixed an issue where clicking on Collapse All button in the Search for Unlinked Local Files expanded the directory structure erroneously [#6848](https://github.com/JabRef/jabref/issues/6848)
 
 ### Removed
 

build.gradle

@@ -12,11 +12,11 @@ import org.jabref.build.xjc.XjcTask
 plugins {
     id 'application'
     id "com.simonharrer.modernizer" version '2.1.0-1'
-    id 'me.champeau.gradle.jmh' version '0.5.1'
+    id 'me.champeau.gradle.jmh' version '0.5.2'
     id 'com.github.ben-manes.versions' version '0.33.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.22.0'
+    id 'org.beryx.jlink' version '2.22.1'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -97,7 +97,7 @@ configurations {
 }
 
 javafx {
-    version = "14"
+    version = "15"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -128,7 +128,7 @@ dependencies {
     libreoffice 'org.libreoffice:ridl:6.4.3'
     libreoffice 'org.libreoffice:unoil:6.4.3'
 
-    implementation 'io.github.java-diff-utils:java-diff-utils:4.7'
+    implementation 'io.github.java-diff-utils:java-diff-utils:4.8'
     implementation 'info.debatty:java-string-similarity:2.0.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
@@ -137,13 +137,13 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.8-1'
     implementation 'org.antlr:antlr4-runtime:4.8-1'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.2') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.6.3') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.6.2'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.0'
 
-    implementation 'org.postgresql:postgresql:42.2.16'
+    implementation 'org.postgresql:postgresql:42.2.17'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -163,14 +163,14 @@ dependencies {
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.1.0'
-    implementation 'org.fxmisc.flowless:flowless:0.6.1'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.5'
+    implementation 'org.fxmisc.flowless:flowless:0.6.2'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.0.2'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.10.00'
+    implementation 'com.konghq:unirest-java:3.11.01'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -204,10 +204,10 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.15'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.17'
     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:3.5.11'
+    testImplementation 'org.mockito:mockito-core:3.5.13'
     testImplementation 'org.xmlunit:xmlunit-core:2.7.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.7.0'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.14.1'
@@ -216,7 +216,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.36.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.36.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
     jython 'org.python:jython-standalone:2.7.2'
 }
@@ -664,6 +664,7 @@ jlink {
                     '--win-dir-chooser',
                     '--win-shortcut',
                     '--win-menu',
+                    '--win-menu-group', "JabRef",
                     '--temp', "$buildDir/installer",
                     '--resource-dir', "${projectDir}/buildres/windows",
                     '--file-associations', "${projectDir}/buildres/windows/bibtexAssociations.properties"

buildres/linux/jabrefHost.py

@@ -6,6 +6,7 @@
 
 import json
 import logging
+import os
 import platform
 import shlex
 import shutil
@@ -16,11 +17,16 @@
 
 # We assume that this python script is located in "jabref/lib" while the executable is "jabref/bin/JabRef"
 script_dir = Path(__file__).resolve().parent.parent
-JABREF_PATH = script_dir / "bin/JabRef"
-if not JABREF_PATH.exists():
-    JABREF_PATH = shutil.which("jabref")
-
-if not JABREF_PATH.exists():
+relpath_path = script_dir / "bin/JabRef"
+lowercase_path = shutil.which("jabref")
+uppercase_path = shutil.which("JabRef")
+if relpath_path.exists():
+    JABREF_PATH = relpath_path
+elif lowercase_path is not None and os.path.exists(lowercase_path):
+    JABREF_PATH = Path(lowercase_path)
+elif uppercase_path is not None and os.path.exists(uppercase_path):
+    JABREF_PATH = Path(uppercase_path)
+else:
     logging.error("Could not determine JABREF_PATH")
     sys.exit(-1)
 

config/README.md

@@ -1,9 +1,9 @@
 # IntelliJ IDEA Code Style Configuration
 
 IntelliJ IDEA comes with a powerful code formatter that helps you to keep the formatting consistent with the style JabRef uses.
-Style-checks are done for each pull request and installing this cody style configuration helps you to ensure that this test passes. To install it, you need to do the following steps:
+Style-checks are done for each pull request and installing this code style configuration helps you to ensure that this test passes. To install it, you need to do the following steps:
 
-1. Goto *Preferences* or press <kbd>Ctrl</kbd> + <kbd>Alt</kbd> + <kbd>S</kbd> (<kbd>Cmd</kbd> + <kbd>,</kbd> on Mac OS X)
+1. Go to *Preferences* or press <kbd>Ctrl</kbd> + <kbd>Alt</kbd> + <kbd>S</kbd> (<kbd>Cmd</kbd> + <kbd>,</kbd> on Mac OS X)
 2. Go to "Editor > Code Style"
 3. Click the gear (right of "Scheme: ...")
 4. Click "Import Scheme >"

docs/README.md

@@ -25,7 +25,7 @@ We are very happy that JabRef is part of [Software Engineering](https://en.wikip
 
 The package `org.jabref.cli` is responsible for handling the command line options.
 
-During development, one can configure IntelliJ to pass command line paramters:
+During development, one can configure IntelliJ to pass command line parameters:
 
 ![IntelliJ-run-configuration](.gitbook/assets/intellij-run-configuration-command-line%20%282%29.png)
 

docs/adr.md

@@ -15,7 +15,7 @@ Architectural decisions for JabRef:
 * [ADR-0010](https://github.com/JabRef/jabref/tree/master/docs/adr/0010-use-h2-as-internal-database.md) - Use H2 as Internal SQL Database
 * [ADR-0011](https://github.com/JabRef/jabref/tree/master/docs/adr/0011-test-external-links-in-documentation.md) - Test external links in documentation
 * [ADR-0012](https://github.com/JabRef/jabref/tree/master/docs/adr/0012-handle-different-bibEntry-formats-of-fetchers.md) - Handle different bibentry formats of fetchers by adding a layer
-* [ADR-0013](https://github.com/JabRef/jabref/tree/master/docs/adr/0013-add-native-support-biblatex-software.md) - Add Native Support for BibLatex-Sotware
+* [ADR-0013](https://github.com/JabRef/jabref/tree/master/docs/adr/0013-add-native-support-biblatex-software.md) - Add Native Support for BibLatex-Software
 fix checkstyle in adr
 * [ADR-0014](https://github.com/JabRef/jabref/tree/master/docs/adr/0014-separate-URL-creation-to-enable-proper-logging.md) - Separate URL creation to enable proper logging
 * [ADR-0015](https://github.com/JabRef/jabref/tree/master/docs/adr/0015-support-an-abstract-query-syntax-for-query-conversion.md) - Query syntax design

docs/adr/0004-use-mariadb-connector.md

@@ -21,7 +21,7 @@ Chosen option: "Use MariaDB Connector", because comes out best \(see below\).
 
 The [MariaDB Connector](https://mariadb.com/kb/en/library/about-mariadb-connector-j/) is a LGPL-licensed JDBC driver to connect to MySQL and MariaDB.
 
-* Good, because can be used as drop-in replacement for MySQL connectopr
+* Good, because can be used as drop-in replacement for MySQL connector
 
 ### Use MySQL Connector
 

docs/adr/0006-only-translated-strings-in-language-file.md

@@ -2,7 +2,7 @@
 
 ## Context and Problem Statement
 
-JabRef has translation files `JabRef_it.properties`, ... There are translated and unstranslated strings. Which ones should be in the translation file?
+JabRef has translation files `JabRef_it.properties`, ... There are translated and untranslated strings. Which ones should be in the translation file?
 
 ## Decision Drivers
 
@@ -31,8 +31,8 @@ Chosen option: "Only translated strings in language file", because comes out bes
 ### Translated and untranslated strings in language file, have value the untranslated string to indicate untranslated
 
 * Good, because no issues with FXML
-* Good, because Crowin supports it
-* Bad, because untranslated strings cannot be identified easily in latin languages
+* Good, because Crowdin supports it
+* Bad, because untranslated strings cannot be identified easily in Latin languages
 
 ### Translated and untranslated strings in language file, have empty to indicate untranslated
 

docs/adr/0008-use-public-final-instead-of-getters.md

@@ -19,4 +19,4 @@ Chosen option: "Offer public static field", because getters used to be a convent
 
 ### Negative Consequences
 
-* new comers could get confused, because getters/setters are still teached
+* newcomers could get confused, because getters/setters are still taught

docs/adr/0011-test-external-links-in-documentation.md

@@ -26,18 +26,18 @@ Chosen option: "\[option 1\]", because \[justification. e.g., only option, which
 
 ### Negative Consequences
 
-* Some external sites need to [be disabled](https://github.com/JabRef/jabref/pull/6542/files). For isntance, GitHub.com always returns "forbidden". A [filter for status is future work of the used tool](https://github.com/tcort/markdown-link-check/issues/94#issuecomment-634947466).
+* Some external sites need to [be disabled](https://github.com/JabRef/jabref/pull/6542/files). For instance, GitHub.com always returns "forbidden". A [filter for status is future work of the used tool](https://github.com/tcort/markdown-link-check/issues/94#issuecomment-634947466).
 
 ## Pros and Cons of the Options
 
 ### Check external links once a month
 
-* Good, because does not interfer with the normal development workflow
+* Good, because does not interfere with the normal development workflow
 * Bad, because an additional workflow is required
 
 ### Check external links in the "checkstyle" task
 
-* Good, because no seperate workflow is required
+* Good, because no separate workflow is required
 * Bad, because checks fail independent of the PR (because external web sites can go down and go up independent of a PR)
 
 ### Do not check external links