diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index e44b50251e1..70cad8a62dd 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -37,9 +37,10 @@ jobs:
- name: Run check style reporter
uses: nikitasavinov/checkstyle-action@master
with:
- reporter: github-pr-check
+ reporter: github-pr-review
+ github_token: ${{ secrets.GITHUB_TOKEN }}
checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
- checkstyle_version: '10.1'
+ checkstyle_version: '10.3'
- name: Run checkstyle gradle
run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
- name: Run markdown-lint
diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile
new file mode 100644
index 00000000000..86a0be3410e
--- /dev/null
+++ b/.gitpod.Dockerfile
@@ -0,0 +1,8 @@
+# See https://www.gitpod.io/docs/java-in-gitpod/ for a full documentation of Java in GitPod
+
+FROM gitpod/workspace-full
+
+# All available versions can be listed using sdk ls java
+# More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
+RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
+ && sdk install java 18.0.1.1-open)"
diff --git a/.gitpod.yml b/.gitpod.yml
new file mode 100644
index 00000000000..ca3b96bdf76
--- /dev/null
+++ b/.gitpod.yml
@@ -0,0 +1,8 @@
+image:
+ file: .gitpod.Dockerfile
+tasks:
+ - init: ./gradlew assemble
+vscode:
+ extensions:
+ - redhat.java
+ - vscjava
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ad04d7fde61..4bad6edb909 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
- We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
- JabRef now writes log files. Linux: `$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
@@ -29,9 +30,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- The Medline/Pubmed search now also supports the [default fields and operators for searching](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax). [forum#3554](https://discourse.jabref.org/t/native-pubmed-search/3354)
- We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
- When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
+- We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
+- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
### Fixed
+- 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)
- We fixed an issue where the notification bar message, icon and actions appeared to be invisible. [#8761](https://github.com/JabRef/jabref/issues/8761)
@@ -39,7 +43,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where an exception for DOI search occurred when the DOI contained urlencoded characters. [#8787](https://github.com/JabRef/jabref/issues/8787)
- We fixed an issue which allow us to select and open identifiers from a popup list in the maintable [#8758](https://github.com/JabRef/jabref/issues/8758), [8802](https://github.com/JabRef/jabref/issues/8802)
- We fixed an issue where the escape button had no functionality within the "Filter groups" textfield. [koppor#562](https://github.com/koppor/jabref/issues/562)
-- We fixed an issue where right clicking a group and choose "remove selected entries from this group" leads to error when Bibtex source tab is selected. [#8012](https://github.com/JabRef/jabref/issues/8012)
+- We fixed an issue where the exception that there are invalid characters in filename. [#8786](https://github.com/JabRef/jabref/issues/8786)
- When the proxy configuration removed the proxy user/password, this change is applied immediately.
- We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
diff --git a/README.md b/README.md
index fecab06fd8d..23cc6f637f6 100644
--- a/README.md
+++ b/README.md
@@ -71,7 +71,7 @@ An explanation of donation possibilities and usage of donations is available at
[](https://www.openhub.net/p/jabref)
[](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
[](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
-[](https://codecov.io/github/JabRef/jabref?branch=master)
+[](https://codecov.io/github/JabRef/jabref?branch=main)
Want to be part of a free and open-source project that tens of thousands of scientists use every day?
Check out the ways you can contribute, below:
diff --git a/build.gradle b/build.gradle
index 3c83d91f55d..b2867237e17 100644
--- a/build.gradle
+++ b/build.gradle
@@ -120,9 +120,9 @@ dependencies {
implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
- implementation 'com.h2database:h2-mvstore:2.1.212'
+ implementation 'com.h2database:h2-mvstore:2.1.214'
- implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.0'
+ implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
implementation 'com.ibm.icu:icu4j-charset:71.1'
// required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
@@ -130,26 +130,26 @@ dependencies {
implementation 'commons-cli:commons-cli:1.5.0'
- implementation 'org.libreoffice:libreoffice:7.3.3'
- implementation 'org.libreoffice:unoloader:7.3.3'
+ implementation 'org.libreoffice:libreoffice:7.3.4'
+ implementation 'org.libreoffice:unoloader:7.3.4'
implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
implementation 'info.debatty:java-string-similarity:2.0.0'
antlr3 'org.antlr:antlr:3.5.3'
- implementation 'org.antlr:antlr-runtime:3.5.2'
+ implementation 'org.antlr:antlr-runtime:3.5.3'
antlr4 'org.antlr:antlr4:4.9.3'
implementation 'org.antlr:antlr4-runtime:4.9.3'
- implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.1.0.202203080745-r'
+ implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.2.0.202206071550-r'
implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.13.3'
implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.3'
implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
- implementation 'org.postgresql:postgresql:42.3.5'
+ implementation 'org.postgresql:postgresql:42.4.0'
implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
// causing module issues
@@ -169,7 +169,7 @@ dependencies {
implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
implementation 'de.saxsys:mvvmfx:1.8.0'
implementation 'com.tobiasdiez:easybind:2.2'
- implementation 'org.fxmisc.flowless:flowless:0.6.9'
+ implementation 'org.fxmisc.flowless:flowless:0.6.10'
implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.45.2') {
@@ -211,7 +211,9 @@ dependencies {
testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
- testImplementation 'org.mockito:mockito-core:4.5.1'
+ 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'
@@ -266,7 +268,8 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
"generateMedlineSource",
"generateBibtexmlSource",
"generateEndnoteSource",
- "generateModsSource"]) {
+ "generateModsSource",
+ "generateCitaviSource"]) {
group = 'JabRef'
description 'Generates all necessary (Java) source files.'
}
@@ -320,6 +323,15 @@ task generateEndnoteSource(type: XjcTask) {
javaPackage = "org.jabref.logic.importer.fileformat.endnote"
}
+task generateCitaviSource(type: XjcTask) {
+ group = 'JabRef'
+ description = "Generates java files for the citavi importer."
+
+ schemaFile = "src/main/resources/xjc/citavi/citavi.xsd"
+ outputDirectory = "src-gen/main/java/"
+ javaPackage = "org.jabref.logic.importer.fileformat.citavi"
+}
+
task generateModsSource(type: XjcTask) {
group = 'JabRef'
description = "Generates java files for the mods importer."
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 43eb84d3cb2..61d0772e817 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -6,7 +6,7 @@ repositories {
}
dependencies {
- implementation 'com.h2database:h2-mvstore:2.1.212'
+ implementation 'com.h2database:h2-mvstore:2.1.214'
implementation 'org.apache.commons:commons-csv:1.9.0'
implementation 'org.slf4j:slf4j-api:2.0.0-alpha7'
}
diff --git a/buildres/csl/csl-styles/Gemfile.lock b/buildres/csl/csl-styles/Gemfile.lock
index 3dfefe1a56a..e7c7f102fa9 100644
--- a/buildres/csl/csl-styles/Gemfile.lock
+++ b/buildres/csl/csl-styles/Gemfile.lock
@@ -65,10 +65,10 @@ GEM
mini_portile2 (2.8.0)
multipart-post (2.1.1)
namae (1.1.1)
- nokogiri (1.13.4)
+ nokogiri (1.13.6)
mini_portile2 (~> 2.8.0)
racc (~> 1.4)
- nokogiri (1.13.4-x64-mingw32)
+ nokogiri (1.13.6-x64-mingw32)
racc (~> 1.4)
octokit (4.21.0)
faraday (>= 0.9)
diff --git a/buildres/csl/csl-styles/dependent/avian-research.csl b/buildres/csl/csl-styles/dependent/avian-research.csl
index 3ca017cd9d3..0c4ca1bcf24 100644
--- a/buildres/csl/csl-styles/dependent/avian-research.csl
+++ b/buildres/csl/csl-styles/dependent/avian-research.csl
@@ -1,16 +1,15 @@
diff --git a/buildres/csl/csl-styles/economie-et-statistique.csl b/buildres/csl/csl-styles/economie-et-statistique.csl
index 3e77cb301d7..3bbcb4313ee 100644
--- a/buildres/csl/csl-styles/economie-et-statistique.csl
+++ b/buildres/csl/csl-styles/economie-et-statistique.csl
@@ -1,5 +1,5 @@
-
diff --git a/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl b/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl
index a8d56d3c5f7..f017c7c9f94 100644
--- a/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl
+++ b/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl
@@ -6,7 +6,7 @@
FAO
http://www.zotero.org/styles/food-and-agriculture-organization-of-the-united-nations
-
+
Bin Liu
lieubean@gmail.com
@@ -15,12 +15,23 @@
Julian Plummer
julian.plummer@gmail.com
+ https://www.linkedin.com/in/julian-plummer/
+
+
+ Amy Knauff
+
+ https://www.linkedin.com/in/amy-knauff-92655442/
+
+
+ Stephanie Wright
+
+ https://www.linkedin.com/in/piriet/
- This style is created to meet the citation and bibliographical requirements of FAOSTYLE, and has been tested with Zotero and Mendeley. Last update: March 2017.
- 2021-06-07T23:29:39+02:00
+ This style is created to meet the citation and bibliographical requirements of FAOSTYLE, and has been tested with Zotero and Mendeley. Last update: February 2022.
+ 2022-02-02T16:03:38+00:00
This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License
@@ -28,8 +39,8 @@
undated
- also available at
- Paper presented at
+ Presentation at
+ Adopted
@@ -42,7 +53,7 @@
-
+
@@ -80,7 +91,7 @@
-
+
@@ -90,60 +101,90 @@
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
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+
+
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+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
-
-
-
-
-
-
-
-
-
+
+
-
-
-
-
+
-
-
-
-
-
-
-
-
@@ -151,220 +192,195 @@
-
+
-
-
-
+
+
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
-
-
-
-
-
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-
-
+
+
+
+
-
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+
+
+
-
-
-
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-
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-
-
+
+
+
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+
+
+
+
-
+
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-
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-
-
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-
+
+
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+
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+
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+
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+
-
+
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
-
-
+
+
+
-
-
-
-
-
-
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-
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+
+
+
+
+
+
-
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+
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+
+
+
-
+
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+
+
+
-
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+
+
-
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+
+
+
+
+
+
-
+
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+
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+
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+
+
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+
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+
+
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+
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+
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+
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+
+
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+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+
+
+
diff --git a/buildres/csl/csl-styles/frontiers-in-ecology-and-the-environment.csl b/buildres/csl/csl-styles/frontiers-in-ecology-and-the-environment.csl
index b8a24308b08..ed858f24304 100644
--- a/buildres/csl/csl-styles/frontiers-in-ecology-and-the-environment.csl
+++ b/buildres/csl/csl-styles/frontiers-in-ecology-and-the-environment.csl
@@ -1,11 +1,11 @@
-
diff --git a/buildres/csl/csl-styles/glossa.csl b/buildres/csl/csl-styles/glossa.csl
index 60a489bbcc1..a5db572f78d 100644
--- a/buildres/csl/csl-styles/glossa.csl
+++ b/buildres/csl/csl-styles/glossa.csl
@@ -1,5 +1,5 @@
-
diff --git a/buildres/csl/csl-styles/meta.csl b/buildres/csl/csl-styles/meta.csl
new file mode 100644
index 00000000000..843a260b514
--- /dev/null
+++ b/buildres/csl/csl-styles/meta.csl
@@ -0,0 +1,938 @@
+
+
diff --git a/buildres/csl/csl-styles/population.csl b/buildres/csl/csl-styles/population.csl
index 4a650687147..3e75caa2912 100644
--- a/buildres/csl/csl-styles/population.csl
+++ b/buildres/csl/csl-styles/population.csl
@@ -1,5 +1,5 @@
-
diff --git a/buildres/csl/csl-styles/pour-reussir-note.csl b/buildres/csl/csl-styles/pour-reussir-note.csl
index 884c78ffe94..4cc02a54b98 100644
--- a/buildres/csl/csl-styles/pour-reussir-note.csl
+++ b/buildres/csl/csl-styles/pour-reussir-note.csl
@@ -1,19 +1,25 @@
-
diff --git a/buildres/csl/csl-styles/universitat-bern-institut-fur-musikwissenschaft-note.csl b/buildres/csl/csl-styles/universitat-bern-institut-fur-musikwissenschaft-note.csl
index e474459ba0c..537dea9a205 100644
--- a/buildres/csl/csl-styles/universitat-bern-institut-fur-musikwissenschaft-note.csl
+++ b/buildres/csl/csl-styles/universitat-bern-institut-fur-musikwissenschaft-note.csl
@@ -1,5 +1,5 @@
-