From e09a9c98528892775c65146d2a2b1d9044c09fb5 Mon Sep 17 00:00:00 2001
From: gradle-update-robot <gradle-update-robot@regolo.cc>
Date: Mon, 12 Apr 2021 05:07:12 +0000
Subject: [PATCH 01/40] Update Gradle Wrapper from 6.8.3 to 7.0.

Signed-off-by: gradle-update-robot <gradle-update-robot@regolo.cc>
---
 gradle/wrapper/gradle-wrapper.properties | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 442d9132ea3..d6aa5ac2215 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip
+distributionSha256Sum=eb8b89184261025b0430f5b2233701ff1377f96da1ef5e278af6ae8bac5cc305
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

From 25594e01cf6f0526fd4a7edb6b3010d520c088ac Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 12 Apr 2021 08:26:06 +0200
Subject: [PATCH 02/40] fix gradle compile errors

---
 build.gradle                                           |  6 +++---
 buildSrc/build.gradle                                  |  6 +++---
 .../main/groovy/org/jabref/build/xjc/XjcTask.groovy    | 10 ++++++++--
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/build.gradle b/build.gradle
index c53810e99e6..99b43877fcf 100644
--- a/build.gradle
+++ b/build.gradle
@@ -202,12 +202,12 @@ dependencies {
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.1'
 
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.22'
-    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'
+    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:3.8.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.17.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.17.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.17.0'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 9f99d5fbc0a..f06c7e7dee5 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -5,9 +5,9 @@ repositories {
 }
 
 dependencies {
-    compile 'com.h2database:h2-mvstore:1.4.200'
-    compile 'org.apache.commons:commons-csv:1.8'
-    compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
+    implementation 'com.h2database:h2-mvstore:1.4.200'
+    implementation 'org.apache.commons:commons-csv:1.8'
+    implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
 }
 
 sourceSets{
diff --git a/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy b/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy
index 2b6fd9b7bbd..8b68e35ab98 100644
--- a/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy
+++ b/buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy
@@ -2,6 +2,8 @@ package org.jabref.build.xjc
 
 import org.gradle.api.DefaultTask
 import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.InputFile
+import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.Optional
 import org.gradle.api.tasks.TaskAction
 
@@ -30,7 +32,7 @@ class XjcTask extends DefaultTask {
         }
     }
 
-    @Input
+    @InputFile
     File getSchemaFile() {
         if (schemaFile == null) {
             return null
@@ -42,6 +44,7 @@ class XjcTask extends DefaultTask {
         this.schemaFile = schemaFile
     }
 
+    @OutputDirectory
     File getOutputDirectory() {
         if (outputDirectory == null) {
             return null
@@ -54,6 +57,7 @@ class XjcTask extends DefaultTask {
         updateOutput()
     }
 
+    @Input
     String getJavaPackage() {
         return javaPackage
     }
@@ -63,6 +67,7 @@ class XjcTask extends DefaultTask {
         updateOutput()
     }
 
+    @Input
     String getEncoding() {
         if(encoding == null ) {
             // use UTF-8 as default encoding
@@ -76,6 +81,7 @@ class XjcTask extends DefaultTask {
         this.encoding = encoding
     }
 
+    @Input
     String getArguments() {
         return arguments
     }
@@ -84,7 +90,7 @@ class XjcTask extends DefaultTask {
         this.arguments = args
     }
 
-    @Input
+    @InputFile
     File getBindingFile() {
         if (bindingFile == null) {
             return null

From b5e4a812d88fa14183327be637950bbaed93ecfe Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 12 Apr 2021 08:48:38 +0200
Subject: [PATCH 03/40] update cache workflows

---
 .github/workflows/deployment.yml     |  8 +++++---
 .github/workflows/tests-fetchers.yml | 19 +++++++------------
 .github/workflows/tests.yml          | 17 ++++++-----------
 3 files changed, 18 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index 1607cb3fe8c..a117969563a 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -67,10 +67,12 @@ jobs:
           java-version: 14
         if: matrix.os == 'windows-latest'
       - name: Restore gradle cache
-        uses: actions/cache@master
+        uses: actions/cache@v2
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
             ${{ runner.os }}-gradle-
       - name: Setup OSX key chain on OSX
diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
index 3d485287efc..a31a33ce2ec 100644
--- a/.github/workflows/tests-fetchers.yml
+++ b/.github/workflows/tests-fetchers.yml
@@ -37,20 +37,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
-        name: Restore gradle cache
+      - name: Restore gradle cache
+        uses: actions/cache@v2
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle-
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 05e80ee68f1..6c6288112da 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -27,20 +27,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
+      - uses: actions/cache@v2
         name: Restore gradle cache
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle-
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:

From ff0f5582253278005973dbf49f725c5883156eb2 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 12 Apr 2021 19:39:28 +0200
Subject: [PATCH 04/40] update cachem, rename key to gradle 7

---
 .github/workflows/deployment.yml |  4 +-
 .github/workflows/tests.yml      | 80 ++++++++++++--------------------
 2 files changed, 32 insertions(+), 52 deletions(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index a117969563a..9c2ea587980 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -72,9 +72,9 @@ jobs:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-
+            ${{ runner.os }}-gradle7-
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
         uses: apple-actions/import-codesign-certs@v1
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6c6288112da..e61d16528fc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -27,15 +27,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v2
-        name: Restore gradle cache
+      - name: Restore gradle cache
+        uses: actions/cache@v2
         with:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.os }}-gradle-
+            ${{ runner.os }}-gradle7-
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
@@ -58,20 +58,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
+      - uses: actions/cache@v2
         name: Restore gradle cache
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle7-
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest
         env:
@@ -102,20 +97,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
-        name: Restore gradle cache
+      - name: Restore gradle cache
+        uses: actions/cache@v2
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle7-
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
         env:
@@ -148,20 +138,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
+      - uses: actions/cache@v2
         name: Restore gradle cache
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle7-
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
         env:
@@ -198,20 +183,15 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
-        name: Restore gradle cache
+      - name: Restore gradle cache
+        uses: actions/cache@v2
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.OS }}-gradle-${{ env.cache-name }}-
-            ${{ runner.OS }}-gradle-
-            ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+            ${{ runner.os }}-gradle7-
       - name: Update test coverage metrics
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);

From 5849c32326968a5b719c3d51665d4d55e1bef6a9 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 12 Apr 2021 23:14:49 +0200
Subject: [PATCH 05/40] Try to fix compile issue

---
 build.gradle | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/build.gradle b/build.gradle
index 98cee4e93d1..303ebec5217 100644
--- a/build.gradle
+++ b/build.gradle
@@ -85,6 +85,9 @@ repositories {
 configurations {
     antlr3
     antlr4
+    testCompile {
+      extendsFrom javaCompile
+    }
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
     compile {

From a1ff517983876453a3214b9f1fffb38c95efaaac Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 12 Apr 2021 23:22:06 +0200
Subject: [PATCH 06/40] Update build.gradle

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 303ebec5217..6b38c3ca1e2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -86,7 +86,7 @@ configurations {
     antlr3
     antlr4
     testCompile {
-      extendsFrom javaCompile
+      extendsFrom testImplementation
     }
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation

From 9dc446b8ec6159b0553163336b6d58aec434444c Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 12 Apr 2021 23:34:42 +0200
Subject: [PATCH 07/40] disable daemon and watch-fs

---
 .github/workflows/deployment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index c8c3acf89e6..e44f7c87bdd 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -21,6 +21,7 @@ env:
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
   OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
+  GRADLE_OPTS: -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
 
 jobs:
   build:

From 64769ecf8c2ad0e5c6ffcc1c710e7095c8b4c4c2 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 16 Apr 2021 20:12:04 +0200
Subject: [PATCH 08/40] try to use tasks register

---
 build.gradle | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build.gradle b/build.gradle
index 6b38c3ca1e2..77510723be1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,5 +1,6 @@
 import groovy.json.JsonSlurper
 import org.gradle.internal.os.OperatingSystem
+import org.gradle.work.DisableCachingByDefault
 import org.jabref.build.JournalAbbreviationConverter
 import org.jabref.build.xjc.XjcPlugin
 import org.jabref.build.xjc.XjcTask
@@ -300,8 +301,7 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
     group = 'JabRef'
     description 'Generates all necessary (Java) source files.'
 }
-
-task generateBstGrammarSource(type: JavaExec) {
+tasks.register("generateBstGrammarSource", JavaExec) {
     main = "org.antlr.Tool"
     classpath = configurations.antlr3
     group = "JabRef"
@@ -311,7 +311,7 @@ task generateBstGrammarSource(type: JavaExec) {
     args = ["-o", "$projectDir/src/main/generated/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
 }
 
-task generateSearchGrammarSource(type: JavaExec) {
+tasks.register("generateSearchGrammarSource", JavaExec) {
     main = "org.antlr.v4.Tool"
     classpath = configurations.antlr4
     group = 'JabRef'

From f1b6a50712835a640bca4c7693446fcfc43b8210 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sat, 17 Apr 2021 17:07:27 +0200
Subject: [PATCH 09/40] Try to ensure source generation

---
 .github/workflows/deployment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index da56e0ce438..ff1dd40b6e2 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -96,7 +96,7 @@ jobs:
       - name: Build runtime image
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" generateSource jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
         if: matrix.os == 'macos-latest'

From 21585b4f29f9034228e6a397d60727e5e3a2b673 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 25 Apr 2021 18:20:35 +0200
Subject: [PATCH 10/40] Add extension for compile to make jlink work

---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index 38f217d5cd3..4486f64a4ae 100644
--- a/build.gradle
+++ b/build.gradle
@@ -92,6 +92,7 @@ configurations {
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
     compile {
+        extendsFrom implementation
         exclude group: "javax.activation"
     }
 }

From 7ea349654d33678f49454720a403e10086852e57 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 25 Apr 2021 18:29:29 +0200
Subject: [PATCH 11/40] try with new cache

---
 .github/workflows/deployment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index ff1dd40b6e2..f921d87c449 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -75,9 +75,9 @@ jobs:
           path: |
             ~/.gradle/caches
             ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          key: ${{ runner.os }}-gradle7x-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
           restore-keys: |
-            ${{ runner.os }}-gradle7-
+            ${{ runner.os }}-gradle7x-
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
         uses: apple-actions/import-codesign-certs@v1

From 012dfb97ce17e068a8b2cdaa881259bddc9b8d98 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 26 Apr 2021 19:56:31 +0200
Subject: [PATCH 12/40] update modularity plugin

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 518f1449fe5..40581165f1f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,7 +13,7 @@ plugins {
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.3'
     id 'com.github.ben-manes.versions' version '0.38.0'
-    id 'org.javamodularity.moduleplugin' version '1.7.0'
+    id 'org.javamodularity.moduleplugin' version '1.8.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
     id 'org.beryx.jlink' version '2.23.7'
     // nicer test outputs during running and completion

From 5b6e522d4c77c62e9a8237a78601327ca3e10023 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 27 Apr 2021 07:13:23 +0200
Subject: [PATCH 13/40] Try with org.javamodularity.moduleplugin:1.8.1

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 40581165f1f..721545cfbb1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,7 +13,7 @@ plugins {
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.3'
     id 'com.github.ben-manes.versions' version '0.38.0'
-    id 'org.javamodularity.moduleplugin' version '1.8.0'
+    id 'org.javamodularity.moduleplugin' version '1.8.1'
     id 'org.openjfx.javafxplugin' version '0.0.9'
     id 'org.beryx.jlink' version '2.23.7'
     // nicer test outputs during running and completion

From e756362298fb13c611eff3a9d1b1e13fdd89e684 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Tue, 27 Apr 2021 07:13:53 +0200
Subject: [PATCH 14/40] Remove quickfix

---
 build.gradle | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/build.gradle b/build.gradle
index 721545cfbb1..ccdf0173bb9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -86,9 +86,6 @@ repositories {
 configurations {
     antlr3
     antlr4
-    testCompile {
-      extendsFrom testImplementation
-    }
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
     compile {

From 01b53fb98f2eb41a6c65843bcd334436a915b85e Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 18:11:31 +0200
Subject: [PATCH 15/40] specify outputs dir and use modulary 1.8.2

---
 build.gradle | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index ccdf0173bb9..8a1ba3a0cae 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,7 +13,7 @@ plugins {
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.3'
     id 'com.github.ben-manes.versions' version '0.38.0'
-    id 'org.javamodularity.moduleplugin' version '1.8.1'
+    id 'org.javamodularity.moduleplugin' version '1.8.2'
     id 'org.openjfx.javafxplugin' version '0.0.9'
     id 'org.beryx.jlink' version '2.23.7'
     // nicer test outputs during running and completion
@@ -306,6 +306,7 @@ tasks.register("generateBstGrammarSource", JavaExec) {
     description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
 
     inputs.dir('src/main/antlr3/org/jabref/bst/')
+    outputs.dir("src/main/generated/org/jabref/logic/bst/")
     args = ["-o", "$projectDir/src/main/generated/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
 }
 
@@ -316,6 +317,7 @@ tasks.register("generateSearchGrammarSource", JavaExec) {
     description = "Generates java files for Search.g antlr4."
 
     inputs.dir("src/main/antlr4/org/jabref/search/")
+    outputs.dir("src/main/generated/org/jabref/search/")
     args  = ["-o","$projectDir/src/main/generated/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
 }
 

From 858e5fba30464b5393df30000dab161eb68be61c Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 18:18:18 +0200
Subject: [PATCH 16/40] dowmgrade plugin

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 8a1ba3a0cae..948ac4f20e2 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,7 +13,7 @@ plugins {
     id "com.simonharrer.modernizer" version '2.1.0-1'
     id 'me.champeau.gradle.jmh' version '0.5.3'
     id 'com.github.ben-manes.versions' version '0.38.0'
-    id 'org.javamodularity.moduleplugin' version '1.8.2'
+    id 'org.javamodularity.moduleplugin' version '1.8.1'
     id 'org.openjfx.javafxplugin' version '0.0.9'
     id 'org.beryx.jlink' version '2.23.7'
     // nicer test outputs during running and completion

From 068cfdd7b6c84f841bef27b27d3d53de7dcacc79 Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 18:30:56 +0200
Subject: [PATCH 17/40] Update deployment.yml

revert adding generate source
---
 .github/workflows/deployment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index f921d87c449..9b10456ba3d 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -96,7 +96,7 @@ jobs:
       - name: Build runtime image
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" generateSource jpackage
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
         if: matrix.os == 'macos-latest'

From 4adaa3f9a91f45819e630b5fd9403dd2121153e0 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 18:45:47 +0200
Subject: [PATCH 18/40] add duplicate strategy exclude

---
 build.gradle | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 948ac4f20e2..43f3d4c877c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -268,6 +268,7 @@ processResources {
         if (gradle.taskGraph.hasTask(":jpackage")) {
             logger.info('Adding buildres/csl to resources')
             from("buildres/csl")
+            duplicatesStrategy = DuplicatesStrategy.EXCLUDE
         }
     }
 
@@ -641,8 +642,6 @@ jlink {
     }
 
     jpackage {
-        // In order for this to work, you need to dowload jpackage from https://jdk.java.net/jpackage/
-        // and put the path to the jdk-14 folder in the environment variable BADASS_JLINK_JPACKAGE_HOME
         outputDir = "distribution"
 
         if (OperatingSystem.current().isWindows()) {

From 69b3682d7f54c2eab1a850bd8320dcff2ca0d1ee Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 19:26:39 +0200
Subject: [PATCH 19/40] set inferModularity to false

---
 build.gradle | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/build.gradle b/build.gradle
index 43f3d4c877c..39ed398d2c1 100644
--- a/build.gradle
+++ b/build.gradle
@@ -39,6 +39,8 @@ version = project.findProperty('projVersion') ?: '100.0.0'
 java {
     sourceCompatibility = JavaVersion.VERSION_14
     targetCompatibility = JavaVersion.VERSION_14
+    modularity.inferModulePath.set(false) //workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
+
 }
 
 application {
@@ -56,6 +58,7 @@ modularity.patchModule("test3", "sourcecode_2.12-0.1.4.jar")
 // See also https://github.com/java9-modularity/gradle-modules-plugin/issues/165
 modularity.disableEffectiveArgumentsAdjustment()
 
+
 sourceSets {
     main {
         java {

From 1f37009194395bb367625867d9bcccd4855fe410 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 21:33:38 +0200
Subject: [PATCH 20/40] Fix empty lines

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 39ed398d2c1..7ccc4a285ab 100644
--- a/build.gradle
+++ b/build.gradle
@@ -303,6 +303,7 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
     group = 'JabRef'
     description 'Generates all necessary (Java) source files.'
 }
+
 tasks.register("generateBstGrammarSource", JavaExec) {
     main = "org.antlr.Tool"
     classpath = configurations.antlr3
@@ -441,7 +442,6 @@ javadoc {
     }
 }
 
-
 test {
     useJUnitPlatform {
         excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest'

From d3515056f809ab32001f48993bc33508e1c06a21 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 21:34:32 +0200
Subject: [PATCH 21/40] Fix empty lines

---
 build.gradle | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 7ccc4a285ab..66d1125af6d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -58,7 +58,6 @@ modularity.patchModule("test3", "sourcecode_2.12-0.1.4.jar")
 // See also https://github.com/java9-modularity/gradle-modules-plugin/issues/165
 modularity.disableEffectiveArgumentsAdjustment()
 
-
 sourceSets {
     main {
         java {

From 398875acfbd92f2c47cc9bf1279b75affb47fc85 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 21:36:16 +0200
Subject: [PATCH 22/40] Fix empty line

---
 build.gradle | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 66d1125af6d..2e3674781c5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -40,7 +40,6 @@ java {
     sourceCompatibility = JavaVersion.VERSION_14
     targetCompatibility = JavaVersion.VERSION_14
     modularity.inferModulePath.set(false) //workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
-
 }
 
 application {

From 7b63bbcaff3d586f17eae805ce083ab6d564a0c3 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:08:24 +0200
Subject: [PATCH 23/40] Disable full strack traces ALWAYS

---
 build.gradle | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 2e3674781c5..4972eb8f3f3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -21,7 +21,8 @@ plugins {
     id 'com.adarshr.test-logger' version '3.0.0'
 }
 
-gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.ALWAYS
+// Enable following for debugging
+// gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.
 
 apply plugin: 'java'
 apply plugin: 'application'

From 2ae05b94fe48e266fa71e218230c3a9360e088aa Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 22:20:58 +0200
Subject: [PATCH 24/40] add duplicate strategy

---
 .../org/jabref/build/JournalAbbreviationConverter.groovy       | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/buildSrc/src/main/groovy/org/jabref/build/JournalAbbreviationConverter.groovy b/buildSrc/src/main/groovy/org/jabref/build/JournalAbbreviationConverter.groovy
index 85fabd28569..bfeec72191b 100644
--- a/buildSrc/src/main/groovy/org/jabref/build/JournalAbbreviationConverter.groovy
+++ b/buildSrc/src/main/groovy/org/jabref/build/JournalAbbreviationConverter.groovy
@@ -22,10 +22,13 @@ abstract class JournalAbbreviationConverter extends DefaultTask {
         def targetFile = outputDir.file("journalList.mv").get().asFile
         targetFile.delete()
         MVStore.open(targetFile.toString()).withCloseable { store ->
+
             MVMap<String, String> fullToAbbreviation = store.openMap("FullToAbbreviation")
             MVMap<String, String> abbreviationToFull = store.openMap("AbbreviationToFull")
 
             inputDir.getAsFileTree().filter({ File f -> f.name.endsWith(".csv") }).getFiles().each { file ->
+                duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+
                 def abbreviations = JournalAbbreviationLoader.readJournalListFromFile(file.toPath())
                 fullToAbbreviation.putAll(
                         abbreviations

From 168b110e9b7da0561ead96841a51692ee4b6f162 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:24:13 +0200
Subject: [PATCH 25/40] Small code improvments

- Remove obsolete import org.gradle.work.DisableCachingByDefault
- Empty lines to make plugin id comments more readable
- Nicer Groovy code (= ;)

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
---
 build.gradle | 70 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 39 insertions(+), 31 deletions(-)

diff --git a/build.gradle b/build.gradle
index 4972eb8f3f3..4a81026de88 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,6 +1,5 @@
 import groovy.json.JsonSlurper
 import org.gradle.internal.os.OperatingSystem
-import org.gradle.work.DisableCachingByDefault
 import org.jabref.build.JournalAbbreviationConverter
 import org.jabref.build.xjc.XjcPlugin
 import org.jabref.build.xjc.XjcTask
@@ -10,12 +9,21 @@ import org.jabref.build.xjc.XjcTask
 
 plugins {
     id 'application'
+
     id "com.simonharrer.modernizer" version '2.1.0-1'
+
     id 'me.champeau.gradle.jmh' version '0.5.3'
+
     id 'com.github.ben-manes.versions' version '0.38.0'
+
+    // 1.8.2 does not work in our case (tends to be buggy)
+    // See https://github.com/java9-modularity/gradle-modules-plugin/issues/188 for details
     id 'org.javamodularity.moduleplugin' version '1.8.1'
+
     id 'org.openjfx.javafxplugin' version '0.0.9'
+
     id 'org.beryx.jlink' version '2.23.7'
+
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
     id 'com.adarshr.test-logger' version '3.0.0'
@@ -44,8 +52,8 @@ java {
 }
 
 application {
-    mainClassName = "org.jabref.gui.JabRefLauncher"
-    mainModule = 'org.jabref'
+    mainClass.set('org.jabref.gui.JabRefLauncher')
+    mainModule.set('org.jabref')
 }
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
@@ -226,7 +234,7 @@ dependencyUpdates {
 }
 
 // We have some dependencies which cannot be updated due to various reasons.
-dependencyUpdates.resolutionStrategy = {
+dependencyUpdates.resolutionStrategy {
     componentSelection { rules ->
         rules.all { ComponentSelection selection ->
             boolean rejected = ['alpha', 'snapshot', 'beta', 'rc', 'cr', 'm', 'preview', 'b', 'ea'].any { qualifier ->
@@ -573,30 +581,30 @@ jlink {
     // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
     // Execute ./gradlew suggestMergedModuleInfo and include the suggested directives here.
     mergedModule {
-        requires 'java.compiler';
-        requires 'java.datatransfer';
-        requires 'java.desktop';
-        requires 'java.logging';
-        requires 'java.management';
-        requires 'java.naming';
-        requires 'java.net.http';
-        requires 'java.scripting';
-        requires 'java.security.jgss';
-        requires 'java.security.sasl';
-        requires 'java.sql';
-        requires 'java.sql.rowset';
-        requires 'java.transaction.xa';
-        requires 'java.rmi';
-        requires 'java.xml';
-        requires 'jdk.jfr';
-        requires 'jdk.jsobject';
-        requires 'jdk.unsupported';
-        requires 'jdk.unsupported.desktop';
-        requires 'jdk.security.jgss';
-        requires 'jdk.xml.dom';
-        requires 'com.google.gson';
-        requires 'com.sun.xml.fastinfoset';
-        requires 'com.sun.xml.txw2';
+        requires 'java.compiler'
+        requires 'java.datatransfer'
+        requires 'java.desktop'
+        requires 'java.logging'
+        requires 'java.management'
+        requires 'java.naming'
+        requires 'java.net.http'
+        requires 'java.scripting'
+        requires 'java.security.jgss'
+        requires 'java.security.sasl'
+        requires 'java.sql'
+        requires 'java.sql.rowset'
+        requires 'java.transaction.xa'
+        requires 'java.rmi'
+        requires 'java.xml'
+        requires 'jdk.jfr'
+        requires 'jdk.jsobject'
+        requires 'jdk.unsupported'
+        requires 'jdk.unsupported.desktop'
+        requires 'jdk.security.jgss'
+        requires 'jdk.xml.dom'
+        requires 'com.google.gson'
+        requires 'com.sun.xml.fastinfoset'
+        requires 'com.sun.xml.txw2'
         requires 'org.slf4j'
         uses 'org.apache.logging.log4j.util.PropertySource'
         uses 'org.apache.logging.log4j.core.util.WatchEventService'
@@ -610,10 +618,10 @@ jlink {
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
-        uses 'org.eclipse.jgit.transport.SshSessionFactory';
-        uses 'org.eclipse.jgit.lib.GpgSigner';
+        uses 'org.eclipse.jgit.transport.SshSessionFactory'
+        uses 'org.eclipse.jgit.lib.GpgSigner'
         uses 'javax.xml.bind.JAXBContextFactory'
-        provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat';
+        provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat'
         provides 'javax.annotation.processing.Processor' with 'org.apache.logging.log4j.plugins.processor.PluginProcessor'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.apache.logging.log4j.message.ThreadDumpMessage.ThreadInfoFactory' with 'org.apache.logging.log4j.core.message.ExtendedThreadInfoFactory'

From 36307745e5aa7988c9b67a7ba4b7a9e4f794c4d1 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:30:15 +0200
Subject: [PATCH 26/40] Remove jcenter()

---
 build.gradle | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 4a81026de88..197fc4b8418 100644
--- a/build.gradle
+++ b/build.gradle
@@ -88,7 +88,6 @@ sourceSets {
 
 repositories {
     mavenLocal()
-    jcenter()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://repository.apache.org/snapshots' }
 }

From d192a7e07f4050ad5eb0ae13ca4f0ac4c3a59ff9 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:35:09 +0200
Subject: [PATCH 27/40] Fix mavenCentral

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index 7efba3db171..e40c0bd40f0 100644
--- a/build.gradle
+++ b/build.gradle
@@ -88,6 +88,7 @@ sourceSets {
 
 repositories {
     mavenLocal()
+    mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://repository.apache.org/snapshots' }
 }

From f14becd03fc8fa2455996d4cd584257ca3cdac14 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:35:19 +0200
Subject: [PATCH 28/40] Fix groovy

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index e40c0bd40f0..079b41dc552 100644
--- a/build.gradle
+++ b/build.gradle
@@ -563,7 +563,7 @@ task deleteInstallerTemp(type: Delete) {
 
 jpackage.dependsOn deleteInstallerTemp
 jlink {
-    options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
+    addOptions('--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages')
     launcher {
         name = 'JabRef'
     }

From b86837fd65383d7637a41e53c47e2e7c96aefd78 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 22:35:29 +0200
Subject: [PATCH 29/40] add maven central

---
 build.gradle          | 1 +
 buildSrc/build.gradle | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 7efba3db171..96db2702ba5 100644
--- a/build.gradle
+++ b/build.gradle
@@ -87,6 +87,7 @@ sourceSets {
 }
 
 repositories {
+    mavenCentral()
     mavenLocal()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
     maven { url 'https://repository.apache.org/snapshots' }
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index f06c7e7dee5..c0517933943 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -1,7 +1,7 @@
 apply plugin: 'java'
 
 repositories {
-    jcenter()
+   mavenCentral()
 }
 
 dependencies {

From 5126721d8f5209828dc2197ab21e247bc788131b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Sun, 2 May 2021 22:39:04 +0200
Subject: [PATCH 30/40] add maven central

---
 buildSrc/build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index c0517933943..d261ffc32dd 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -1,7 +1,7 @@
 apply plugin: 'java'
 
 repositories {
-   mavenCentral()
+  mavenCentral()
 }
 
 dependencies {

From 532596cb7bd667053356aefee88adf63f37c41c3 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 22:44:11 +0200
Subject: [PATCH 31/40] Switch to mavenCentral

---
 buildSrc/build.gradle | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index f06c7e7dee5..a86edc93a83 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -1,7 +1,8 @@
 apply plugin: 'java'
 
 repositories {
-    jcenter()
+    mavenLocal()
+    mavenCentral()
 }
 
 dependencies {

From 8b35c217084b5e8b7f15bed4a0735357be6fae50 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 2 May 2021 23:13:11 +0200
Subject: [PATCH 32/40] Improve readability

Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
---
 build.gradle | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/build.gradle b/build.gradle
index 079b41dc552..a2ce486eee9 100644
--- a/build.gradle
+++ b/build.gradle
@@ -27,17 +27,17 @@ plugins {
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
     id 'com.adarshr.test-logger' version '3.0.0'
+
+    id 'jacoco'
+
+    id 'checkstyle'
+
+    id 'project-report'
 }
 
 // Enable following for debugging
 // gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.
 
-apply plugin: 'java'
-apply plugin: 'application'
-apply plugin: 'project-report'
-apply plugin: 'jacoco'
-apply plugin: 'me.champeau.gradle.jmh'
-apply plugin: 'checkstyle'
 apply plugin: XjcPlugin
 
 apply from: 'eclipse.gradle'
@@ -48,7 +48,10 @@ version = project.findProperty('projVersion') ?: '100.0.0'
 java {
     sourceCompatibility = JavaVersion.VERSION_14
     targetCompatibility = JavaVersion.VERSION_14
-    modularity.inferModulePath.set(false) //workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
+
+    // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
+    // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
+    modularity.inferModulePath.set(false)
 }
 
 application {
@@ -376,7 +379,10 @@ task generateJournalAbbreviationList(type: JournalAbbreviationConverter) {
     group = 'JabRef'
     description = "Converts the comma-separated journal abbreviation file to a H2 MVStore."
 
+    // This directory is filled by "refresh-journal-lists.yml"
+    // It takes the contents of https://github.com/JabRef/abbrv.jabref.org.git
     inputDir = file("build/journals")
+
     outputDir = file("src/main/resources/journals")
 }
 
@@ -770,5 +776,3 @@ task downloadDependencies {
         }
     }
 }
-
-

From aec1a2066b92e872a2e680504806b3704ed47dbf Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 06:50:44 +0200
Subject: [PATCH 33/40] Resolve quirks with generateJournalAbbreviationList by
 copying java classes to buildSrc

---
 .github/workflows/refresh-journal-lists.yml   |   4 +-
 buildSrc/build.gradle                         |   2 +-
 .../jabref/logic/journals/Abbreviation.java   |  88 ++++++++++++
 .../logic/journals/AbbreviationFormat.java    |  22 +++
 .../logic/journals/AbbreviationParser.java    |  76 ++++++++++
 .../logic/journals/AbbreviationWriter.java    |  39 +++++
 .../journals/JournalAbbreviationLoader.java   |  54 +++++++
 .../JournalAbbreviationPreferences.java       |  27 ++++
 .../JournalAbbreviationRepository.java        | 133 ++++++++++++++++++
 .../jabref/logic/journals/package-info.java   |   7 +
 10 files changed, 450 insertions(+), 2 deletions(-)
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationFormat.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationParser.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationWriter.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationPreferences.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationRepository.java
 create mode 100644 buildSrc/src/copied/java/org/jabref/logic/journals/package-info.java

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
index cef2c760cec..a144641e950 100644
--- a/.github/workflows/refresh-journal-lists.yml
+++ b/.github/workflows/refresh-journal-lists.yml
@@ -43,10 +43,12 @@ jobs:
           mkdir -p $GITHUB_WORKSPACE/build/journals
           cp * $GITHUB_WORKSPACE/build/journals/
 
+          # ensure that the .java classes are the most recent ones
+          cp $GITHUB_WORKSPACE/src/main/java/org/jabref/logic/journals/* $GITHUB_WORKSPACE/buildSrc/src/copied/java/org/jabref/logic/journals
+
           # create .mv file
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
-
       - uses: peter-evans/create-pull-request@v3
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index a86edc93a83..fb4bcb94721 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -14,7 +14,7 @@ dependencies {
 sourceSets{
     main {
         java {
-            srcDir "${project.rootDir}/../src/main/java/org/jabref/logic/journals"
+            srcDir "src/copied"
         }
     }
 }
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java b/buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java
new file mode 100644
index 00000000000..b6c8d4ddf89
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/Abbreviation.java
@@ -0,0 +1,88 @@
+package org.jabref.logic.journals;
+
+import java.util.Objects;
+
+public class Abbreviation implements Comparable<Abbreviation> {
+
+    private final String name;
+    private final String abbreviation;
+    private final String shortestUniqueAbbreviation;
+
+    public Abbreviation(String name, String abbreviation) {
+        this(name, abbreviation, "");
+    }
+
+    public Abbreviation(String name, String abbreviation, String shortestUniqueAbbreviation) {
+        this.name = name;
+        this.abbreviation = abbreviation;
+        this.shortestUniqueAbbreviation = shortestUniqueAbbreviation.trim();
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getAbbreviation() {
+        return abbreviation;
+    }
+
+    public String getShortestUniqueAbbreviation() {
+        String result = shortestUniqueAbbreviation;
+        if (result.isEmpty()) {
+            return getAbbreviation();
+        }
+        return result;
+    }
+
+    public String getMedlineAbbreviation() {
+        return getAbbreviation().replace(".", " ").replace("  ", " ").trim();
+    }
+
+    @Override
+    public int compareTo(Abbreviation toCompare) {
+        return getName().compareTo(toCompare.getName());
+    }
+
+    public String getNext(String current) {
+        String currentTrimmed = current.trim();
+
+        if (getMedlineAbbreviation().equals(currentTrimmed)) {
+            return getShortestUniqueAbbreviation().equals(getAbbreviation()) ? getName() : getShortestUniqueAbbreviation();
+        } else if (getShortestUniqueAbbreviation().equals(currentTrimmed) && !getShortestUniqueAbbreviation().equals(getAbbreviation())) {
+            return getName();
+        } else if (getName().equals(currentTrimmed)) {
+            return getAbbreviation();
+        } else {
+            return getMedlineAbbreviation();
+        }
+    }
+
+    @Override
+    public String toString() {
+        return String.format("Abbreviation{name=%s, abbreviation=%s, medlineAbbreviation=%s, shortestUniqueAbbreviation=%s}",
+                this.name,
+                this.abbreviation,
+                this.getMedlineAbbreviation(),
+                this.shortestUniqueAbbreviation);
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (this == obj) {
+            return true;
+        }
+
+        if (obj == null || getClass() != obj.getClass()) {
+            return false;
+        }
+
+        Abbreviation that = (Abbreviation) obj;
+
+        return Objects.equals(getName(), that.getName());
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(getName());
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationFormat.java b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationFormat.java
new file mode 100644
index 00000000000..e4713773a3d
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationFormat.java
@@ -0,0 +1,22 @@
+package org.jabref.logic.journals;
+
+import org.apache.commons.csv.CSVFormat;
+
+public final class AbbreviationFormat {
+
+    public static final char DELIMITER = ';';
+    public static final char ESCAPE = '\\';
+    public static final char QUOTE = '"';
+
+    private AbbreviationFormat() {
+    }
+
+    public static CSVFormat getCSVFormat() {
+        return CSVFormat.DEFAULT
+                .withIgnoreEmptyLines(true)
+                .withDelimiter(DELIMITER)
+                .withEscape(ESCAPE)
+                .withQuote(QUOTE)
+                .withTrim();
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationParser.java b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationParser.java
new file mode 100644
index 00000000000..6506469d7da
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationParser.java
@@ -0,0 +1,76 @@
+package org.jabref.logic.journals;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.csv.CSVParser;
+import org.apache.commons.csv.CSVRecord;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Reads abbreviation files (CSV format) into a list of Abbreviations.
+ */
+public class AbbreviationParser {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbbreviationParser.class);
+
+    private final Set<Abbreviation> abbreviations = new HashSet<>(5000);
+
+    public void readJournalListFromResource(String resourceFileName) {
+        try (InputStream stream = JournalAbbreviationRepository.class.getResourceAsStream(resourceFileName);
+             BufferedReader reader = new BufferedReader(new InputStreamReader(stream, StandardCharsets.UTF_8))) {
+            readJournalList(reader);
+        } catch (IOException e) {
+            LOGGER.error(String.format("Could not read journal list from file %s", resourceFileName), e);
+        }
+    }
+
+    public void readJournalListFromFile(Path file) throws IOException {
+        readJournalListFromFile(file, StandardCharsets.UTF_8);
+    }
+
+    public void readJournalListFromFile(Path file, Charset encoding) throws IOException {
+        try (BufferedReader reader = Files.newBufferedReader(file, encoding)) {
+            readJournalList(reader);
+        }
+    }
+
+    /**
+     * Read the given file, which should contain a list of journal names and their abbreviations. Each line should be
+     * formatted as: "Full Journal Name;Abbr. Journal Name;[Shortest Unique Abbreviation]"
+     *
+     * @param reader a given file into a Reader object
+     */
+    private void readJournalList(Reader reader) throws IOException {
+        try (CSVParser csvParser = new CSVParser(reader, AbbreviationFormat.getCSVFormat())) {
+            for (CSVRecord csvRecord : csvParser) {
+                String name = csvRecord.size() > 0 ? csvRecord.get(0) : "";
+                String abbreviation = csvRecord.size() > 1 ? csvRecord.get(1) : "";
+                String shortestUniqueAbbreviation = csvRecord.size() > 2 ? csvRecord.get(2) : "";
+
+                // Check name and abbreviation
+                if (name.isEmpty() || abbreviation.isEmpty()) {
+                    return;
+                }
+
+                abbreviations.add(new Abbreviation(name, abbreviation, shortestUniqueAbbreviation));
+            }
+        }
+    }
+
+    public List<Abbreviation> getAbbreviations() {
+        return new LinkedList<>(abbreviations);
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationWriter.java b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationWriter.java
new file mode 100644
index 00000000000..d922ddd488d
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/AbbreviationWriter.java
@@ -0,0 +1,39 @@
+package org.jabref.logic.journals;
+
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+
+import org.apache.commons.csv.CSVPrinter;
+
+/**
+ * This class provides handy static methods to save abbreviations to the file system.
+ */
+public final class AbbreviationWriter {
+
+    private AbbreviationWriter() {
+    }
+
+    /**
+     * This method will write the list of abbreviations to a file on the file system specified by the given path. If the
+     * file already exists its content will be overridden, otherwise a new file will be created.
+     *
+     * @param path          to a file (doesn't have to exist just yet)
+     * @param abbreviations as a list specifying which entries should be written
+     */
+    public static void writeOrCreate(Path path, List<Abbreviation> abbreviations, Charset encoding) throws IOException {
+        try (OutputStreamWriter writer = new OutputStreamWriter(Files.newOutputStream(path), encoding);
+             CSVPrinter csvPrinter = new CSVPrinter(writer, AbbreviationFormat.getCSVFormat())) {
+            for (Abbreviation entry : abbreviations) {
+                if (entry.getShortestUniqueAbbreviation().isEmpty()) {
+                    csvPrinter.printRecord(entry.getName(), entry.getAbbreviation());
+                } else {
+                    csvPrinter.printRecord(entry.getName(), entry.getAbbreviation(), entry.getShortestUniqueAbbreviation());
+                }
+            }
+        }
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java
new file mode 100644
index 00000000000..72f0664b046
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationLoader.java
@@ -0,0 +1,54 @@
+package org.jabref.logic.journals;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Collections;
+import java.util.List;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class JournalAbbreviationLoader {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(JournalAbbreviationLoader.class);
+
+    public static List<Abbreviation> readJournalListFromFile(Path file) throws IOException {
+        LOGGER.debug(String.format("Reading journal list from file %s", file));
+        AbbreviationParser parser = new AbbreviationParser();
+        parser.readJournalListFromFile(file);
+        return parser.getAbbreviations();
+    }
+
+    public static JournalAbbreviationRepository loadRepository(JournalAbbreviationPreferences journalAbbreviationPreferences) {
+        JournalAbbreviationRepository repository;
+        // Initialize with built-in list
+        try {
+            Path tempJournalList = Files.createTempDirectory("journal").resolve("journalList.mv");
+            Files.copy(JournalAbbreviationRepository.class.getResourceAsStream("/journals/journalList.mv"), tempJournalList);
+            repository = new JournalAbbreviationRepository(tempJournalList);
+        } catch (IOException e) {
+            LOGGER.error("Error while copying journal list", e);
+            return null;
+        }
+
+        // Read external lists
+        List<String> lists = journalAbbreviationPreferences.getExternalJournalLists();
+        if (!(lists.isEmpty())) {
+            Collections.reverse(lists);
+            for (String filename : lists) {
+                try {
+                    repository.addCustomAbbreviations(readJournalListFromFile(Path.of(filename)));
+                } catch (IOException e) {
+                    LOGGER.error(String.format("Cannot read external journal list file %s", filename), e);
+                }
+            }
+        }
+        return repository;
+    }
+
+    public static JournalAbbreviationRepository loadBuiltInRepository() {
+        return loadRepository(new JournalAbbreviationPreferences(Collections.emptyList(), StandardCharsets.UTF_8));
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationPreferences.java b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationPreferences.java
new file mode 100644
index 00000000000..300592b0172
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationPreferences.java
@@ -0,0 +1,27 @@
+package org.jabref.logic.journals;
+
+import java.nio.charset.Charset;
+import java.util.List;
+
+public class JournalAbbreviationPreferences {
+
+    private final Charset defaultEncoding;
+    private List<String> externalJournalLists;
+
+    public JournalAbbreviationPreferences(List<String> externalJournalLists, Charset defaultEncoding) {
+        this.externalJournalLists = externalJournalLists;
+        this.defaultEncoding = defaultEncoding;
+    }
+
+    public List<String> getExternalJournalLists() {
+        return externalJournalLists;
+    }
+
+    public void setExternalJournalLists(List<String> externalJournalLists) {
+        this.externalJournalLists = externalJournalLists;
+    }
+
+    public Charset getDefaultEncoding() {
+        return defaultEncoding;
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationRepository.java b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationRepository.java
new file mode 100644
index 00000000000..523e1323be1
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationRepository.java
@@ -0,0 +1,133 @@
+package org.jabref.logic.journals;
+
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.h2.mvstore.MVMap;
+import org.h2.mvstore.MVStore;
+
+/**
+ * A repository for all journal abbreviations, including add and find methods.
+ */
+public class JournalAbbreviationRepository {
+
+    private final MVMap<String, String> fullToAbbreviation;
+    private final MVMap<String, String> abbreviationToFull;
+    private final List<Abbreviation> customAbbreviations;
+
+    public JournalAbbreviationRepository(Path journalList) {
+        MVStore store = new MVStore.Builder().readOnly().fileName(journalList.toAbsolutePath().toString()).open();
+        this.fullToAbbreviation = store.openMap("FullToAbbreviation");
+        this.abbreviationToFull = store.openMap("AbbreviationToFull");
+        this.customAbbreviations = new ArrayList<>();
+    }
+
+    private static boolean isMatched(String name, Abbreviation abbreviation) {
+        return name.equalsIgnoreCase(abbreviation.getName())
+                || name.equalsIgnoreCase(abbreviation.getAbbreviation())
+                || name.equalsIgnoreCase(abbreviation.getMedlineAbbreviation())
+                || name.equalsIgnoreCase(abbreviation.getShortestUniqueAbbreviation());
+    }
+
+    private static boolean isMatchedAbbreviated(String name, Abbreviation abbreviation) {
+        boolean isAbbreviated = name.equalsIgnoreCase(abbreviation.getAbbreviation())
+                || name.equalsIgnoreCase(abbreviation.getMedlineAbbreviation())
+                || name.equalsIgnoreCase(abbreviation.getShortestUniqueAbbreviation());
+        boolean isExpanded = name.equalsIgnoreCase(abbreviation.getName());
+        return isAbbreviated && !isExpanded;
+    }
+
+    /**
+     * Returns true if the given journal name is contained in the list either in its full form (e.g Physical Review
+     * Letters) or its abbreviated form (e.g. Phys. Rev. Lett.).
+     */
+    public boolean isKnownName(String journalName) {
+        String journal = journalName.trim();
+
+        boolean isKnown = customAbbreviations.stream().anyMatch(abbreviation -> isMatched(journal, abbreviation));
+        if (isKnown) {
+            return true;
+        }
+
+        return fullToAbbreviation.containsKey(journal) || abbreviationToFull.containsKey(journal);
+    }
+
+    /**
+     * Returns true if the given journal name is in its abbreviated form (e.g. Phys. Rev. Lett.). The test is strict,
+     * i.e. journals whose abbreviation is the same as the full name are not considered
+     */
+    public boolean isAbbreviatedName(String journalName) {
+        String journal = journalName.trim();
+
+        return customAbbreviations.stream().anyMatch(abbreviation -> isMatchedAbbreviated(journal, abbreviation))
+                || abbreviationToFull.containsKey(journal);
+    }
+
+    /**
+     * Attempts to get the abbreviation of the journal given.
+     *
+     * @param input The journal name (either abbreviated or full name).
+     */
+    public Optional<Abbreviation> get(String input) {
+        String journal = input.trim();
+
+        Optional<Abbreviation> customAbbreviation = customAbbreviations.stream()
+                                                                       .filter(abbreviation -> isMatched(journal, abbreviation))
+                                                                       .findAny();
+        if (customAbbreviation.isPresent()) {
+            return customAbbreviation;
+        }
+
+        return Optional.ofNullable(fullToAbbreviation.get(journal))
+                       .map(abbreviation -> new Abbreviation(journal, abbreviation))
+                       .or(() -> Optional.ofNullable(abbreviationToFull.get(journal)).map(fullName -> new Abbreviation(fullName, journal)));
+    }
+
+    public void addCustomAbbreviation(Abbreviation abbreviation) {
+        Objects.requireNonNull(abbreviation);
+
+        // We do not want to keep duplicates, thus remove the old abbreviation
+        // (abbreviation equality is tested on name only, so we cannot use a Set instead)
+        customAbbreviations.remove(abbreviation);
+        customAbbreviations.add(abbreviation);
+    }
+
+    public List<Abbreviation> getCustomAbbreviations() {
+        return customAbbreviations;
+    }
+
+    public void addCustomAbbreviations(Collection<Abbreviation> abbreviationsToAdd) {
+        abbreviationsToAdd.forEach(this::addCustomAbbreviation);
+    }
+
+    public Optional<String> getNextAbbreviation(String text) {
+        return get(text).map(abbreviation -> abbreviation.getNext(text));
+    }
+
+    public Optional<String> getDefaultAbbreviation(String text) {
+        return get(text).map(Abbreviation::getAbbreviation);
+    }
+
+    public Optional<String> getMedlineAbbreviation(String text) {
+        return get(text).map(Abbreviation::getMedlineAbbreviation);
+    }
+
+    public Optional<String> getShortestUniqueAbbreviation(String text) {
+        return get(text).map(Abbreviation::getShortestUniqueAbbreviation);
+    }
+
+    public Set<String> getFullNames() {
+        return fullToAbbreviation.keySet();
+    }
+
+    public List<Abbreviation> getAllLoaded() {
+        return fullToAbbreviation.entrySet().stream().map(entry ->
+                new Abbreviation(entry.getKey(), entry.getValue())).collect(Collectors.toList());
+    }
+}
diff --git a/buildSrc/src/copied/java/org/jabref/logic/journals/package-info.java b/buildSrc/src/copied/java/org/jabref/logic/journals/package-info.java
new file mode 100644
index 00000000000..7a967bbd91d
--- /dev/null
+++ b/buildSrc/src/copied/java/org/jabref/logic/journals/package-info.java
@@ -0,0 +1,7 @@
+/**
+ * The files in this directory are copied from JabRef's main source.
+ * We need top have a copy, because
+ * a) symblinks do not work on git for windows out of the box (<a href="https://stackoverflow.com/a/59761201/873282">https://stackoverflow.com/a/59761201/873282</a>)
+ * b) using a source directory of another project causes issues in i) gradle 7, ii) IntelliJ 2020 and later
+ */
+package org.jabref.logic.journals;

From ad66a8ceee67f25eda3e1d0a374f9994ee80df8b Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 07:42:44 +0200
Subject: [PATCH 34/40] Refine documentation for buildSrc

---
 build.gradle                                       |  1 -
 .../guidelines-for-setting-up-a-local-workspace.md | 14 ++++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/build.gradle b/build.gradle
index a2ce486eee9..6e96f9e7e70 100644
--- a/build.gradle
+++ b/build.gradle
@@ -74,7 +74,6 @@ sourceSets {
         java {
             srcDirs = ["src/main/java", "src/main/generated"]
         }
-
         resources {
             srcDirs = ["src/main/java", "src/main/resources"]
         }
diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
index f17c8b70681..c68a7cb24fd 100644
--- a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
+++ b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
@@ -114,7 +114,7 @@ Navigate to **File \| Settings \| Build, Execution, Deployment \| Build Tools \|
 
 To prepare IntelliJ's build system two additional steps are required:
 
-* Navigate to **File \| Settings \| Build, Execution, Deployment \| Compiler \| Java Compiler**, and under "Override compiler parameters per-module" add \(\[+\]\) the following compiler arguments for the `JabRef.main` module:
+* Navigate to **File \| Settings \| Build, Execution, Deployment \| Compiler \| Java Compiler**, and under "Override compiler parameters per-module" add \(\[+\]\) the following compiler arguments for the `JabRef.main` module. Otherwise, you will get: `java: package com.sun.javafx.scene.control is not visible (package com.sun.javafx.scene.control is declared in module javafx.controls, which does not export it to module org.jabref)`
 
   ```text
    --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref
@@ -171,7 +171,7 @@ To use IntelliJ IDEA's internal build system when you build JabRef through **Bui
 
 Essentially, you now have the best of both worlds: You can run Gradle tasks using the Gradle Tool Window and unless you haven't made changes to input files that generate sources, you can compile and run with IntelliJ's faster internal build system.
 
-In case all steps are followed, and there are still issues with `SearchBaseVisitor` \(e.g., `Error:(16, 25) java: package org.jabref.search does not exist`\), you have to delete `generated\org\jabref\gui\logging\plugins\Log4jPlugins.java`. This is independent of having enabled or disabled Annotation Processing \(see above at "Enable Annotation Processing"\).
+In case all steps are followed, and there are still issues with `SearchBaseVisitor` \(e.g., `Error:(16, 25) java: package org.jabref.search does not exist`\), you have to delete `src\main\generated\org\jabref\gui\logging\plugins\Log4jPlugins.java`. This is independent of having enabled or disabled Annotation Processing \(see above at "Enable Annotation Processing"\).
 
 #### Using JabRef's code style
 
@@ -271,11 +271,17 @@ Another indication is following output
 java.lang.UnsupportedClassVersionError: org/javamodularity/moduleplugin/ModuleSystemPlugin has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
 ```
 
-### Problems with generated source files
+### Issues with generated source files
 
 In rare cases you might encounter problems due to out-dated automatically generated source files. Running `./gradlew clean` deletes these old copies. Do not forget to run at least `./gradlew eclipse` or `./gradlew build` afterwards to regenerate the source files.
+``
+### Issues with `buildSrc`
 
-### Problems with openjfx libraries in local maven repository
+1. Open the context menu of `buildSrc`.
+1. Select "Load/Unload modules".
+1. Unload `jabRef.buildSrc`.
+
+### Issues with openjfx libraries in local maven repository
 
 There might be problems with building if you have openjfx libraries in local maven repository, resulting in errors like this:
 

From 1b3a1fe0d6a1ad2c1b153a228f84356810205a92 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 08:17:19 +0200
Subject: [PATCH 35/40] Generated sources flow into "src-gen/" directory having
 the same layout as "src/"

src-gen/main/java instead of src/main/generated
---
 .gitignore   |  1 +
 build.gradle | 32 ++++++++++++++++++++++----------
 2 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index ba242f57346..fd187d3f735 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
 # no generated files in version control
 src/main/gen/
 src/main/generated/
+src-gen/
 
 # private data
 /buildres/jabref-cert-2016.p12
diff --git a/build.gradle b/build.gradle
index 6e96f9e7e70..ae15b9be950 100644
--- a/build.gradle
+++ b/build.gradle
@@ -33,6 +33,8 @@ plugins {
     id 'checkstyle'
 
     id 'project-report'
+
+    id 'idea'
 }
 
 // Enable following for debugging
@@ -72,7 +74,8 @@ modularity.disableEffectiveArgumentsAdjustment()
 sourceSets {
     main {
         java {
-            srcDirs = ["src/main/java", "src/main/generated"]
+            // src-gen reasoning: https://stackoverflow.com/a/64612308/873282
+            srcDirs = ["src/main/java", "src-gen/main/java"]
         }
         resources {
             srcDirs = ["src/main/java", "src/main/resources"]
@@ -273,6 +276,7 @@ task checkOutdatedDependencies(dependsOn: dependencyUpdates) {
 
 clean {
     delete "src/main/generated"
+    delete "src-gen"
 }
 
 processResources {
@@ -321,8 +325,8 @@ tasks.register("generateBstGrammarSource", JavaExec) {
     description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
 
     inputs.dir('src/main/antlr3/org/jabref/bst/')
-    outputs.dir("src/main/generated/org/jabref/logic/bst/")
-    args = ["-o", "$projectDir/src/main/generated/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
+    outputs.dir("src-gen/main/java/org/jabref/logic/bst/")
+    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
 }
 
 tasks.register("generateSearchGrammarSource", JavaExec) {
@@ -332,8 +336,8 @@ tasks.register("generateSearchGrammarSource", JavaExec) {
     description = "Generates java files for Search.g antlr4."
 
     inputs.dir("src/main/antlr4/org/jabref/search/")
-    outputs.dir("src/main/generated/org/jabref/search/")
-    args  = ["-o","$projectDir/src/main/generated/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
+    outputs.dir("src-gen/main/java/org/jabref/search/")
+    args  = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
 }
 
 task generateMedlineSource(type: XjcTask) {
@@ -341,7 +345,7 @@ task generateMedlineSource(type: XjcTask) {
     description = "Generates java files for the medline importer."
 
     schemaFile = "src/main/resources/xjc/medline/medline.xsd"
-    outputDirectory = "src/main/generated"
+    outputDirectory = "src-gen/main/java"
     javaPackage = "org.jabref.logic.importer.fileformat.medline"
 }
 
@@ -350,7 +354,7 @@ task generateBibtexmlSource(type: XjcTask) {
     description = "Generates java files for the bibtexml importer."
 
     schemaFile = "src/main/resources/xjc/bibtexml/bibtexml.xsd"
-    outputDirectory = "src/main/generated/"
+    outputDirectory = "src-gen/main/java/"
     javaPackage = "org.jabref.logic.importer.fileformat.bibtexml"
 }
 
@@ -359,7 +363,7 @@ task generateEndnoteSource(type: XjcTask) {
     description = "Generates java files for the endnote importer."
 
     schemaFile = "src/main/resources/xjc/endnote/endnote.xsd"
-    outputDirectory = "src/main/generated/"
+    outputDirectory = "src-gen/main/java/"
     javaPackage = "org.jabref.logic.importer.fileformat.endnote"
 }
 
@@ -369,7 +373,7 @@ task generateModsSource(type: XjcTask) {
 
     schemaFile = "src/main/resources/xjc/mods/mods-3-7.xsd"
     bindingFile = "src/main/resources/xjc/mods/mods-binding.xjb"
-    outputDirectory = "src/main/generated/"
+    outputDirectory = "src-gen/main/java"
     javaPackage = "org.jabref.logic.importer.fileformat.mods"
     arguments = '-npa'
 }
@@ -393,7 +397,7 @@ compileJava {
     options.compilerArgs << "-Xlint:none"
     dependsOn "generateSource"
 
-    options.annotationProcessorGeneratedSourcesDirectory = file("${projectDir}/src/main/generated")
+    options.annotationProcessorGeneratedSourcesDirectory = file("src-gen/main/java")
 
     moduleOptions {
         // TODO: Remove access to internal api
@@ -775,3 +779,11 @@ task downloadDependencies {
         }
     }
 }
+
+idea {
+    module {
+        // documentation: https://docs.gradle.org/current/dsl/org.gradle.plugins.ide.idea.model.IdeaModule.html
+        generatedSourceDirs += file("src-gen/main/java")
+        downloadJavadoc = true
+    }
+}

From 35ce3a672cced49ff6cd0b82ff828d0b89869f09 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 3 May 2021 16:30:11 +0200
Subject: [PATCH 36/40] add checkstyle suppression

---
 config/checkstyle/suppressions.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/checkstyle/suppressions.xml b/config/checkstyle/suppressions.xml
index 2169d4246f3..471a9f57d82 100644
--- a/config/checkstyle/suppressions.xml
+++ b/config/checkstyle/suppressions.xml
@@ -6,6 +6,7 @@
 
 <suppressions>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]generated[\\/]" />
+    <suppress checks="[a-zA-Z0-9]*" files="[\\/]src-gen[\\/]" />
     <!-- We ignore this file because it's a modification of the original java code https://github.com/openjdk/jfx/blob/jfx15/modules/javafx.controls/src/main/java/javafx/scene/control/skin/TitledPaneSkin.java -->
     <suppress checks="[a-zA-Z0-9]*" files="CustomTitledPaneSkin.java" />
 </suppressions>

From 295a62fe8d09cd77172504bb9cefab9ba5ec0419 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 3 May 2021 16:36:44 +0200
Subject: [PATCH 37/40] fix markdownlint

---
 .../guidelines-for-setting-up-a-local-workspace.md           | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
index c68a7cb24fd..d7a8bedaec6 100644
--- a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
+++ b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
@@ -104,10 +104,10 @@ To configure IntelliJ IDEA for developing JabRef, you should first ensure that y
 
 After that, you can open `jabref/build.gradle` as a project. It is crucial that Java 15 is used consistently for the JabRef project which includes ensuring the right settings for your project structure, Gradle build, and run configurations.
 
-Ensure you have a Java 15 SDK configured by navigating to **File \| Project Structure \| Platform Settings \| SDKs**. If you don't have one, add a new Java JDK and point it to the location of a JDK 15.  
+Ensure you have a Java 15 SDK configured by navigating to **File \| Project Structure \| Platform Settings \| SDKs**. If you don't have one, add a new Java JDK and point it to the location of a JDK 15.
 ![Project Settings](../.gitbook/assets/intellij-choose-jdk-adoptopenjdk-on-windows-project-settings.png)
 
-Navigate to **File \| Project Structure \| Project** and ensure that the projects' SDK is Java 15  
+Navigate to **File \| Project Structure \| Project** and ensure that the projects' SDK is Java 15
 ![Use JDK 15 as project SDK](../.gitbook/assets/intellij-choose-jdk15-project-default.png)
 
 Navigate to **File \| Settings \| Build, Execution, Deployment \| Build Tools \| Gradle** and select the "Project SDK" as the Gradle JVM at the bottom.
@@ -275,6 +275,7 @@ java.lang.UnsupportedClassVersionError: org/javamodularity/moduleplugin/ModuleSy
 
 In rare cases you might encounter problems due to out-dated automatically generated source files. Running `./gradlew clean` deletes these old copies. Do not forget to run at least `./gradlew eclipse` or `./gradlew build` afterwards to regenerate the source files.
 ``
+
 ### Issues with `buildSrc`
 
 1. Open the context menu of `buildSrc`.

From e42432efe2c6ec6fb3edc1633788005eb41ab8b6 Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 22:53:22 +0200
Subject: [PATCH 38/40] JabRef runs out ouf IntelliJ again

---
 build.gradle                                   |  2 +-
 ...delines-for-setting-up-a-local-workspace.md | 18 +++++++++++++++---
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/build.gradle b/build.gradle
index ae15b9be950..1ad41944e37 100644
--- a/build.gradle
+++ b/build.gradle
@@ -783,7 +783,7 @@ task downloadDependencies {
 idea {
     module {
         // documentation: https://docs.gradle.org/current/dsl/org.gradle.plugins.ide.idea.model.IdeaModule.html
-        generatedSourceDirs += file("src-gen/main/java")
+        generatedSourceDirs += file('src-gen/main/java')
         downloadJavadoc = true
     }
 }
diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
index d7a8bedaec6..d4ba946990b 100644
--- a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
+++ b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
@@ -146,8 +146,6 @@ After that a new entry called "jabref \[run\]" will appear in the run configurat
 
 #### Using IntelliJ's internal build system
 
-**Note that these steps do not work on IntelliJ 2020.x.**. You have to keep using gradle for executing tasks. See [IDEA-249391](https://youtrack.jetbrains.com/issue/IDEA-249391) for details.
-
 You should use IntelliJ IDEA's internal build system for compiling and running JabRef during development, because it is usually more responsive. Thereby, **it's important** that you understand that JabRef relies on generated sources which are only build through Gradle. Therefore, to build or update these dependencies you need to run the `assemble` Gradle task at least once.
 
 To use IntelliJ IDEA's internal build system when you build JabRef through **Build \| Build Project** or use the provided "JabRef Main" run configuration, ensure that
@@ -157,7 +155,19 @@ To use IntelliJ IDEA's internal build system when you build JabRef through **Bui
 
   ![Ignore the Gradle project &quot;buildSrc&quot;](../.gitbook/assets/intellij-gradle-config-ignore-buildSrc%20%282%29%20%282%29%20%282%29%20%283%29.png)
 
-* Delete `org.jabref.gui.logging.plugins.Log4jPlugins` \(location: `generated\org\jabref\gui\logging\plugins\Log4jPlugins.java`\). Otherwise, you will see following error:
+* Add `src-gen` as root:
+
+    1. Right click on the project "jabref".
+    1. Select "Open Module Settings"
+    1. Expand "JabRef"
+    1. Select "main"
+    1. Select tab "Sources"
+    1. Click "+ Add Content Root"
+    1. Select the `src-gen` directory
+    1. Click "OK". When expanding "main", "java" should have been selected as source
+    1. Click "OK" to save the changes
+
+* Delete `org.jabref.gui.logging.plugins.Log4jPlugins` \(location: `src-gen/main/java/org/jabref/gui/logging/plugins/Log4jPlugins.java`\). Otherwise, you will see following error:
 
   ```text
   Error:java: Unable to create Plugin Service Class org.jabref.gui.logging.plugins.Log4jPlugins
@@ -173,6 +183,8 @@ Essentially, you now have the best of both worlds: You can run Gradle tasks usin
 
 In case all steps are followed, and there are still issues with `SearchBaseVisitor` \(e.g., `Error:(16, 25) java: package org.jabref.search does not exist`\), you have to delete `src\main\generated\org\jabref\gui\logging\plugins\Log4jPlugins.java`. This is independent of having enabled or disabled Annotation Processing \(see above at "Enable Annotation Processing"\).
 
+~~Note that the above steps might not work on IntelliJ 2020.x.**. You have to keep using gradle for executing tasks. See [IDEA-249391](https://youtrack.jetbrains.com/issue/IDEA-249391) for details.~~
+
 #### Using JabRef's code style
 
 Contributions to JabRef's source code need to have a code formatting that is consistent with existing source code. For that purpose, JabRef provides code-style and check-style definitions.

From dd32aa08226012da3c5ce5ca42c02be37b5fbdec Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 23:02:32 +0200
Subject: [PATCH 39/40] Add some try-again hint

---
 .../guidelines-for-setting-up-a-local-workspace.md              | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
index d4ba946990b..f63c5009c55 100644
--- a/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
+++ b/docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace.md
@@ -167,6 +167,8 @@ To use IntelliJ IDEA's internal build system when you build JabRef through **Bui
     1. Click "OK". When expanding "main", "java" should have been selected as source
     1. Click "OK" to save the changes
 
+* In case the above step does not work, run with gradle, import gradle project again, and try again.
+
 * Delete `org.jabref.gui.logging.plugins.Log4jPlugins` \(location: `src-gen/main/java/org/jabref/gui/logging/plugins/Log4jPlugins.java`\). Otherwise, you will see following error:
 
   ```text

From 3f19cab375a7c9e36b6f1d24f0f7ba8d0b06ba8f Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Mon, 3 May 2021 23:08:21 +0200
Subject: [PATCH 40/40] Remove idea config block -> we do it manually

---
 build.gradle | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/build.gradle b/build.gradle
index 1ad41944e37..e2c51041907 100644
--- a/build.gradle
+++ b/build.gradle
@@ -779,11 +779,3 @@ task downloadDependencies {
         }
     }
 }
-
-idea {
-    module {
-        // documentation: https://docs.gradle.org/current/dsl/org.gradle.plugins.ide.idea.model.IdeaModule.html
-        generatedSourceDirs += file('src-gen/main/java')
-        downloadJavadoc = true
-    }
-}