Merge remote-tracking branch 'upstream/main' into controlsfx-tags

* upstream/main: fix merge conflict Squashed 'buildres/csl/csl-locales/' changes from 969d9567ac..55459cd79f Squashed 'buildres/csl/csl-styles/' changes from e740261..3d3573c Show pdf icon for mime type in maintable (#8935) Fix for Dark theme not readable (#8929) Find Unlinked files should ignore Thumbs.db, etc (#8800) Try to make reproducible builds (#8925) Link to new board (and refine text) Pass the data as a string (#8923) Add IntelliJ plugins to Gitpod configuration Add gradle support Fix extension name Remove obsolete closing bracket
JabRef · Jul 1, 2022 · ba3ffce · ba3ffce
2 parents 78010ec + eb1d7a9
commit ba3ffce
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diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile
@@ -5,4 +5,4 @@ FROM gitpod/workspace-full
 # All available versions can be listed using sdk ls java
 # More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
 RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
-             && sdk install java 18.0.1.1-open)"
+             && sdk install java 18.0.1.1-open"
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -2,7 +2,15 @@ image:
   file: .gitpod.Dockerfile
 tasks:
   - init: ./gradlew assemble
+jetbrains:
+  intellij:
+    plugins:
+      - CheckStyle-IDEA
+      - zielu.gittoolbox
 vscode:
   extensions:
     - redhat.java
-    - vscjava
+    - richardwillis.vscode-gradle
+    - vscjava.vscode-java-debug
+    - kiteco.kite
+    - DavidAnson.vscode-markdownlint
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,11 +13,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
 - We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
 
 ### Changed
 
+- The file column in the main table now shows the corresponding defined icon for the linked file [8930](https://github.com/JabRef/jabref/issues/8930).
+- We improved the color of the selected entries and the color of the summary in the Import Entries Dialog in the dark theme. [#7927](https://github.com/JabRef/jabref/issues/7927)
 - We upgraded to Lucene 9.2 for the fulltext search.
   Thus, the now created search index cannot be read from older versions of JabRef anylonger.
   ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
@@ -35,6 +38,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
 - We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
 - We fixed an issue where the content of a big shared database library is not shown [#8788](https://github.com/JabRef/jabref/issues/8788)
 - We fixed the unnecessary horizontal scroll bar in group panel [#8467](https://github.com/JabRef/jabref/issues/8467)

diff --git a/build.gradle b/build.gradle
@@ -81,7 +81,7 @@ repositories {
     mavenLocal()
     mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
-    maven { url 'https://repository.apache.org/snapshots' }
+    maven { url 'https://jitpack.io' }
 }
 
 configurations {
@@ -95,6 +95,10 @@ configurations {
     }
 }
 
+dependencyLocking {
+    lockAllConfigurations()
+}
+
 javafx {
     version = "18"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
@@ -166,7 +170,7 @@ dependencies {
     // JavaFX stuff
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
-    implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
+    implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
     implementation 'org.fxmisc.flowless:flowless:0.6.10'
@@ -211,15 +215,13 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
-    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:4.6.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
-    testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
-    testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
+    testImplementation "org.testfx:testfx-core:4.0.16-alpha"
+    testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:10.1'

diff --git a/buildres/csl/csl-locales/.github/workflows/merge.yaml b/buildres/csl/csl-locales/.github/workflows/merge.yaml
@@ -19,9 +19,9 @@ jobs:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       DISTRIBUTION_UPDATER_TOKEN: "${{ secrets.DISTRIBUTION_UPDATER_TOKEN }}"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'push'
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'workflow_dispatch'
       with:
         fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
       id: release
       run: echo ::set-output name=branch::v1.0.2
     - name: Checkout release branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ steps.release.outputs.branch }}
         path: './release'
@@ -63,7 +63,7 @@ jobs:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
       if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-locales/.github/workflows/sheldon.yaml b/buildres/csl/csl-locales/.github/workflows/sheldon.yaml
@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-locales/Gemfile.lock b/buildres/csl/csl-locales/Gemfile.lock
@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)

diff --git a/buildres/csl/csl-styles/.github/dependabot.yml b/buildres/csl/csl-styles/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/buildres/csl/csl-styles/.github/workflows/merge.yaml b/buildres/csl/csl-styles/.github/workflows/merge.yaml
@@ -19,9 +19,9 @@ jobs:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       DISTRIBUTION_UPDATER_TOKEN: "${{ secrets.DISTRIBUTION_UPDATER_TOKEN }}"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'push'
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'workflow_dispatch'
       with:
         fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
       id: release
       run: echo ::set-output name=branch::v1.0.2
     - name: Checkout release branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ steps.release.outputs.branch }}
         path: './release'
@@ -63,7 +63,7 @@ jobs:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
       if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-styles/.github/workflows/sheldon.yaml b/buildres/csl/csl-styles/.github/workflows/sheldon.yaml
@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

diff --git a/buildres/csl/csl-styles/Gemfile.lock b/buildres/csl/csl-styles/Gemfile.lock
@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)

diff --git a/buildres/csl/csl-styles/advanced-materials.csl b/buildres/csl/csl-styles/advanced-materials.csl
@@ -5,7 +5,7 @@
     <id>http://www.zotero.org/styles/advanced-materials</id>
     <link href="http://www.zotero.org/styles/advanced-materials" rel="self"/>
     <link href="http://www.zotero.org/styles/small" rel="template"/>
-    <link href="http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291521-4095/homepage/2089_authorresources.html" rel="documentation"/>
+    <link href="https://onlinelibrary.wiley.com/page/journal/15214095/homepage/author-guidelines" rel="documentation"/>
     <author>
       <name>Jimmy Lawrence</name>
       <email>jimmymisc@gmail.com</email>
@@ -16,13 +16,13 @@
     <issn>0935-9648</issn>
     <eissn>1521-4095</eissn>
     <summary>A style for Wiley's Advanced Materials</summary>
-    <updated>2012-09-27T22:06:38+00:00</updated>
+    <updated>2022-06-22T14:43:19+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <macro name="author">
     <names variable="author">
       <name initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" prefix=", " text-case="capitalize-first" suffix=" "/>
+      <label form="short" text-case="capitalize-first" prefix=", "/>
       <substitute>
         <names variable="editor"/>
         <names variable="translator"/>
@@ -32,7 +32,7 @@
   <macro name="editor">
     <names variable="editor">
       <label form="short" text-case="capitalize-first" suffix=".: " strip-periods="true"/>
-      <name initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+      <name delimiter-precedes-last="always" initialize-with=". "/>
     </names>
   </macro>
   <macro name="year-date">
@@ -124,7 +124,7 @@
             <text macro="year-date"/>
           </group>
         </else-if>
-        <else-if type="webpage">
+        <else-if type="webpage post post-weblog" match="any">
           <group delimiter=", ">
             <text variable="title" quotes="true"/>
             <text macro="access"/>

diff --git a/buildres/csl/csl-styles/american-society-for-horticultural-science.csl b/buildres/csl/csl-styles/american-society-for-horticultural-science.csl
@@ -13,7 +13,7 @@
     <category citation-format="author-date"/>
     <category field="biology"/>
     <category field="botany"/>
-    <updated>2021-07-27T13:34:10+00:00</updated>
+    <updated>2022-06-14T08:25:19+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <macro name="edition">
@@ -32,11 +32,13 @@
   <macro name="container">
     <choose>
       <if type="chapter paper-conference" match="any">
-        <text term="in" text-case="capitalize-first" font-style="italic" prefix=". " suffix=" "/>
-        <names variable="editor translator" delimiter=", " suffix=". ">
-          <name initialize-with="." delimiter=", " delimiter-precedes-last="never" and="symbol"/>
-          <label form="short" prefix=" (" suffix=")"/>
-        </names>
+        <group delimiter=": ">
+          <text term="in" text-case="capitalize-first" font-style="normal" prefix=". " suffix=" "/>
+          <names variable="editor translator" delimiter=", " suffix=". ">
+            <name initialize-with="." delimiter=", " delimiter-precedes-last="never" and="symbol"/>
+            <label form="short" prefix=" (" suffix=")"/>
+          </names>
+        </group>
         <group delimiter=", ">
           <text variable="container-title" text-case="title"/>
           <text variable="collection-title" text-case="title"/>
@@ -49,7 +51,7 @@
         </group>
       </else-if>
       <else>
-        <group prefix=". " delimiter=", ">
+        <group delimiter=", " prefix=". ">
           <text variable="container-title" form="short"/>
           <text variable="collection-title"/>
         </group>
@@ -86,14 +88,7 @@
     </names>
   </macro>
   <macro name="access">
-    <choose>
-      <if type="webpage">
-        <group>
-          <text value="URL" suffix=" "/>
-          <text variable="URL"/>
-        </group>
-      </if>
-    </choose>
+    <text variable="URL" prefix="&lt;" suffix="&gt;"/>
   </macro>
   <macro name="title">
     <choose>
@@ -106,10 +101,6 @@
           </group>
         </group>
       </if>
-      <else-if type="webpage">
-        <text variable="title"/>
-        <text value="WWW Document" prefix=" [" suffix="]"/>
-      </else-if>
       <else>
         <text variable="title"/>
       </else>
@@ -173,13 +164,13 @@
       </if>
       <else-if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
         <group delimiter=", " prefix=". ">
+          <text macro="edition"/>
+          <text macro="event"/>
+          <text macro="publisher"/>
           <group>
             <text variable="genre"/>
             <text variable="number" prefix=" No. "/>
           </group>
-          <text macro="edition"/>
-          <text macro="event"/>
-          <text macro="publisher"/>
         </group>
       </else-if>
       <else-if type="chapter paper-conference" match="any">
@@ -188,15 +179,21 @@
           <text macro="publisher"/>
         </group>
       </else-if>
+      <else-if type="webpage post post-weblog" match="any">
+        <group delimiter=". " prefix=". ">
+          <date form="text" date-parts="year-month-day" variable="issued"/>
+          <text macro="access"/>
+        </group>
+      </else-if>
     </choose>
   </macro>
   <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" collapse="year">
     <sort>
-      <key macro="issued"/>
       <key macro="author"/>
+      <key macro="issued"/>
     </sort>
-    <layout prefix="(" suffix=")" delimiter=", ">
-      <group delimiter=" ">
+    <layout delimiter="; " prefix="(" suffix=")">
+      <group delimiter=", ">
         <text macro="author-short"/>
         <text macro="issued"/>
       </group>
@@ -217,7 +214,6 @@
         </group>
         <text macro="locators"/>
       </group>
-      <text macro="access" prefix=". "/>
     </layout>
   </bibliography>
 </style>