Merge remote-tracking branch 'upstream/master' into test-module-issue

* upstream/master: (33 commits)
  Bump archunit-junit5-api from 0.14.1 to 0.15.0 (#7220)
  Bump unoloader from 7.0.3 to 7.0.4 (#7214)
  Bump guava from 30.0-jre to 30.1-jre (#7218)
  Bump xmpbox from 2.0.21 to 2.0.22 (#7217)
  Bump classgraph from 4.8.94 to 4.8.97 (#7211)
  Bump byte-buddy-parent from 1.10.18 to 1.10.19 (#7216)
  Bump archunit-junit5-engine from 0.14.1 to 0.15.0 (#7215)
  Bump org.beryx.jlink from 2.22.3 to 2.23.0 (#7212)
  Add missing author
  Remove field check for journal abbrev in entry editor (#7208)
  Improvements for Entry Preview (in the context of #7083 and in addition to #7093) (#7185)
  Fix pdf content importer exception if DOI is empty (#7207)
  New translations JabRef_en.properties (Turkish) (#7204)
  New Crowdin updates (#7198)
  New Crowdin updates (#7192)
  Added missing test
  Changed tests to parameterized tests
  Extraction of Globals.prefs.put and .get (#7121)
  Fix newly added entry not synced to db (#7178)
  Bump org.eclipse.jgit from 5.9.0.202009080501-r to 5.10.0.202012080955-r (#7187)
  ...

.github/workflows/stale.yml

@@ -2,17 +2,27 @@ name: Mark stale issues and pull requests
 
 on:
   schedule:
-  - cron: "0 0 * * *"
+  - cron: "20 19 * * *"
 
 jobs:
   stale:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@master
+    - uses: actions/stale@v3
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-message: 'This issue will be closed in 7 days due to inactivity :zzz: Please provide the requested information if the problem persists.'
+        days-before-stale: 180
+        days-before-close: 14
+        stale-issue-message: |
+          This issue has been inactive for half a year. Since JabRef is constantly evolving this issue may not be relevant any longer and it will be closed in two weeks if no further activity occurs.
+
+          As part of an effort to ensure that the JabRef team is focusing on important and valid issues, we would like to ask if you could update the issue if it still persists. This could be in the following form:
+
+          - If there has been a longer discussion, add a short summary of the most important points as a new comment (if not yet existing).
+          - Provide further steps or information on how to reproduce this issue.
+          - Upvote the initial post if you like to see it implemented soon. Votes are not the only metric that we use to determine the requests that are implemented, however, they do factor into our decision-making process.
+          - If all information is provided and still up-to-date, then just add a short comment that the issue is still relevant.
+
+          Thank you for your contribution!
         stale-issue-label: 'status: stale'
-        days-before-stale: 30
-        only-labels: 'status: waiting-for-customer-feedback'

AUTHORS

@@ -38,6 +38,7 @@ Anita Armbruster
 Antonio Ribeiro
 Arno Blouin
 Arthur Fröhlich
+AtrusRiven
 Atul Kaushik
 August Janse
 Ayachi Nene

CHANGELOG.md

@@ -17,8 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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 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)
@@ -28,8 +27,7 @@ to the page field for cases where the page numbers are missing. [#7019](https://
 
 ### 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 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)
@@ -48,7 +46,8 @@ inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://git
 - 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)
 - We changed the way JabRef displays the title of a tab and of the window. [4161](https://github.com/JabRef/jabref/issues/4161)
 - We changed connect timeouts for server requests to 30 seconds in general and 5 seconds for GROBID server (special) and improved user notifications on connection issues. [7026](https://github.com/JabRef/jabref/pull/7026)
-- We changed the way linked files are opened on Linux to use the native openFile method, compatible with confined packages. [7037](https://github.com/JabRef/jabref/pull/7037)
+- We changed the order of the library tab context menu items. [#7171](https://github.com/JabRef/jabref/issues/7171)
+- We changed the way linked files are opened on Linux to use the native openFile method, compatible with confined  packages. [7037](https://github.com/JabRef/jabref/pull/7037)
 - We refined the entry preview to show the full names of authors and editors, to list the editor only if no author is present, have the year ealier. [#7083](https://github.com/JabRef/jabref/issues/7083)
 
 ### Fixed
@@ -77,11 +76,15 @@ inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://git
 - We fixed an issue where the color of groups of type "free search expression" not persisting after restarting the application [#6999](https://github.com/JabRef/jabref/issues/6999)
 - We fixed an issue where modifications in the source tab where not saved without switching to another field before saving the library [#6622](https://github.com/JabRef/jabref/issues/6622)
 - We fixed an issue where the "Document Viewer" did not show the first page of the opened pdf document and did not show the correct total number of pages [#7108](https://github.com/JabRef/jabref/issues/7108)
+- We fixed an issue where the context menu was not updated after a file link was changed. [#5777](https://github.com/JabRef/jabref/issues/5777)
 - 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)
 
 ### Removed
 
 - 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)
 
 ## [5.1] – 2020-08-30
 

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 '2.22.3'
+    id 'org.beryx.jlink' version '2.23.0'
     // 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'
@@ -103,20 +103,20 @@ dependencies {
 
     implementation 'org.apache.pdfbox:pdfbox:2.0.21'
     implementation 'org.apache.pdfbox:fontbox:2.0.21'
-    implementation 'org.apache.pdfbox:xmpbox:2.0.21'
+    implementation 'org.apache.pdfbox:xmpbox:2.0.22'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.8'
     implementation 'com.h2database:h2-mvstore:1.4.200'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '1.24.1'
+    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 'commons-cli:commons-cli:1.4'
 
     implementation 'org.libreoffice:libreoffice:7.0.3'
-    implementation 'org.libreoffice:unoloader:7.0.3'
+    implementation 'org.libreoffice:unoloader:7.0.4'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.9'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -131,7 +131,7 @@ dependencies {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
-    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.9.0.202009080501-r'
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.10.0.202012080955-r'
 
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.0'
@@ -145,7 +145,7 @@ dependencies {
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:30.0-jre') {
+    implementation ('com.google.guava:guava:30.1-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -165,7 +165,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.0.3'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.11.05'
+    implementation 'com.konghq:unirest-java:3.11.06'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -194,19 +194,19 @@ 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:4.8.92'
+    testImplementation 'io.github.classgraph:classgraph:4.8.97'
     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'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.18'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.19'
     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'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.14.1'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.14.1'
+    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"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"

docs/getting-into-the-code/code-howtos.md

@@ -211,7 +211,7 @@ Optional<Path> file = FileHelper.expandFilename(database, fileText, preferences.
 
 ## How to work with Preferences
 
-`model` and `logic` must not know JabRefPreferences. See `ProxyPreferences` for encapsulated preferences and [https://github.com/JabRef/jabref/pull/658](https://github.com/JabRef/jabref/pull/658) for a detailed discussion.
+`model` and `logic` must not know `JabRefPreferences`. See `ProxyPreferences` for encapsulated preferences and [https://github.com/JabRef/jabref/pull/658](https://github.com/JabRef/jabref/pull/658) for a detailed discussion.
 
 See [https://github.com/JabRef/jabref/blob/master/src/main/java/org/jabref/logic/preferences/TimestampPreferences.java](https://github.com/JabRef/jabref/blob/master/src/main/java/org/jabref/logic/preferences/TimestampPreferences.java) \(via [https://github.com/JabRef/jabref/pull/3092](https://github.com/JabRef/jabref/pull/3092)\) for the current way how to deal with preferences.
 
@@ -291,9 +291,12 @@ Or even better, try to mock the preferences and insert them via dependency injec
 @Test
 public void getTypeReturnsBibLatexArticleInBibLatexMode() {
      // Mock preferences
-     JabrefPreferences mockedPrefs = mock(JabrefPreferences.class);
+     PreferencesService mockedPrefs = mock(PreferencesService.class);
+     GeneralPreferences mockedGeneralPrefs = mock(GeneralPReferences.class);
      // Switch to BibLatex mode
-     when(mockedPrefs.getBoolean("BiblatexMode")).thenReturn(true);
+     when(mockedPrefs.getGeneralPrefs()).thenReturn(mockedGeneralPrefs);
+     when(mockedGeneralPrefs.getDefaultBibDatabaseMode())
+        .thenReturn(BibDatabaseMode.BIBLATEX);
 
      // Now test
      EntryTypes biblatexentrytypes = new EntryTypes(mockedPrefs);

src/main/java/module-info.java

@@ -81,7 +81,7 @@
     requires org.apache.commons.lang3;
     requires org.antlr.antlr4.runtime;
     requires flowless;
-    requires org.apache.tika.core;
+    requires tika.core;
 
     requires flexmark;
     requires flexmark.ext.gfm.strikethrough;

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

@@ -456,8 +456,8 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
     private void importPreferences() {
         try {
             Globals.prefs.importPreferences(cli.getPreferencesImport());
-            Globals.entryTypesManager.addCustomOrModifiedTypes(Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
-                    Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
+            Globals.entryTypesManager.addCustomOrModifiedTypes(Globals.prefs.getBibEntryTypes(BibDatabaseMode.BIBTEX),
+                    Globals.prefs.getBibEntryTypes(BibDatabaseMode.BIBLATEX));
             List<TemplateExporter> customExporters = Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationRepository);
             LayoutFormatterPreferences layoutPreferences =
                     Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);