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

* upstream/master: (40 commits) Add test for regular expression pattern Snap GitHub ci (#5379) Bump src/main/resources/csl-locales from `e89e6b0` to `9785a6e` Bump src/main/resources/csl-styles from `36ac1f6` to `6169061` Bump mariadb-java-client from 2.4.4 to 2.5.0 Bump mockito-core from 3.0.0 to 3.1.0 Bump slf4j-api from 2.0.0-alpha0 to 2.0.0-alpha1 (#5403) Remove unnecessary code Fix JabFox integration Update CHANGELOG.md Add hacktoberfest shields.io badge Update CHANGELOG.md Fix various copy to clipboard issues (#5340) Fix 5359: Writing of Editor field is duplicated (#5392) Fix exception when merging entries Reenable prevcycle (#5385) Update deployment.yml revert 3fbe0a2 use submodules to fetch CSL styles properly add missing ',' ...
JabRef · Oct 9, 2019 · b13e470 · b13e470
2 parents 9f8ad5a + ccfa991
commit b13e470
Show file tree

Hide file tree

Showing 26 changed files with 349 additions and 495 deletions.
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -32,7 +32,16 @@ jobs:
     - name: Checkout source
       uses: actions/checkout@v1
       with:
-        fetch-depth: 1
+        depth: 1
+        submodules: true
+    - name: Extract branch name
+      shell: bash
+      run: |
+         ref=${GITHUB_REF#refs/heads/}
+         ref=${ref#refs/pull/}
+         ref=${ref%/merge}
+         echo "##[set-output name=branch;]${ref}"
+      id: extract_branch
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:
@@ -74,10 +83,14 @@ jobs:
     - name: Package application image
       run: ${{ matrix.archivePortable }}
       shell: bash
-    - name: Extract branch name
+    - name: Build and publish snap
+      if: matrix.os == 'ubuntu-latest' && steps.extract_branch.outputs.branch == 'master'
+      env:
+        SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
+      run: |
+          docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/"
+          # cd build/distribution/ && mdkir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg && snapcraft push --release=beta *.snap
       shell: bash
-      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
-      id: extract_branch
     - name: Upload to builds.jabref.org
       uses: garygrossgarten/github-action-scp@release
       with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
-- We added a short DOI field formatter which shortens DOI to more human readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
+- We added a short DOI field formatter which shortens DOI to more human-readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
 - We improved the display of group memberships by adding multiple colored bars if the entry belongs to more than one group. [#4574](https://github.com/JabRef/jabref/issues/4574)
 
 ### Fixed
@@ -22,17 +22,25 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where it was no longer possible to connect to LibreOffice. [#5261](https://github.com/JabRef/jabref/issues/5261)
 - The "All entries group" is no longer shown when no library is open.
 - We fixed an exception which occurred when closing JabRef. [#5348](https://github.com/JabRef/jabref/issues/5348)
+- We fixed a few problems that prevented JabFox to communicate with JabRef. [#4737](https://github.com/JabRef/jabref/issues/4737) [#4303](https://github.com/JabRef/jabref/issues/4303)
 - We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022) 
+- We fixed an error where an exception was thrown when merging entries. [#5169](https://github.com/JabRef/jabref/issues/5169)
 - After assigning an entry to a group, the item count is now properly colored to reflect the new membership of the entry. [#3112](https://github.com/JabRef/jabref/issues/3112)
 - The group panel is now properly updated when switching between libraries (or when closing/opening one). [#3142](https://github.com/JabRef/jabref/issues/3142)
 - We fixed an error where the number of matched entries shown in the group pane was not updated correctly. [#4441](https://github.com/JabRef/jabref/issues/4441)
 - We fixed an issue where empty keywords lead to a strange display of automatic keyword groups. [#5333](https://github.com/JabRef/jabref/issues/5333)
 - We fixed an error where the default color of a new group was white instead of dark gray. [#4868](https://github.com/JabRef/jabref/issues/4868)
 - We fixed an error mentioning "javafx.controls/com.sun.javafx.scene.control" that was thrown when interacting with the toolbar.
 - We fixed an error where a cleared search was restored after switching libraries. [#4846](https://github.com/JabRef/jabref/issues/4846) 
-- We fixed an exception which occured when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - The context menu for fields in the entry editor is back. [#5254](https://github.com/JabRef/jabref/issues/5254)
-- We fixed an exception which occurred when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed a problem where the "editor" information has been duplicated during saving a .bib-Database. [#5359](https://github.com/JabRef/jabref/issues/5359)
+- We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
+- We fixed various issues (including [#5263](https://github.com/JabRef/jabref/issues/5263)) related to copying entries to the clipboard
+
+
+
 
 ### Removed
 
@@ -101,11 +109,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - Moreover, empty deprecated fields are no longer shown
 - Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
-- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
+- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the URL, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
-- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or URL field and moves it to the `eprint` field.
   Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [#4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
@@ -124,18 +132,19 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
-- We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
-- We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
+- We add auto URL formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
+- We added a minimum height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
 - We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
 - We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
-- We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
+- We updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
 - We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
 - For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added description of how recommendations where chosen and better error handling to Related Articles tab
+- We added the ability to change the column widths directly in the main 
+. [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added a description of how recommendations were chosen and better error handling to Related Articles tab
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
@@ -144,7 +153,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
-- We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We made modifications to improve the contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
 - We added a warning for empty BibTeX keys in the entry editor. [#4440](https://github.com/JabRef/jabref/issues/4440)
 - We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
@@ -171,7 +180,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the group tree was not updated correctly after an entry was changed. https://github.com/JabRef/jabref/issues/3618
 - We fixed an issue where a right-click in the main table selected a wrong entry. https://github.com/JabRef/jabref/issues/3267
 - We fixed an issue where in rare cases entries where overlayed in the main table. https://github.com/JabRef/jabref/issues/3281
-- We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
+- We fixed an issue where selecting a group messed up the focus of the main table and the entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
 - We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
@@ -204,9 +213,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 - We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
-- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
+- We fixed an issue where option 'open terminal here' with custom command was passing the wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
-- We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
+- We fixed an issue where special characters where removed from non-label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 - We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](https://github.com/JabRef/jabref/issues/4932)
 - We fixed an issue where a database exception related to a missing timezone was too big. [#4827](https://github.com/JabRef/jabref/issues/4827)
@@ -222,13 +231,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
 - We removed the global search feature.
-- We removed the coloring of cells in the maintable according to whether the field is optional/required.
+- We removed the coloring of cells in the main table according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
   - Print entry preview: available through entry preview
   - All commands related to marking: marking is not yet reimplemented
   - Set/clear/append/rename fields: available through Edit menu
-  - Manage keywords: available through Edit menu
+  - Manage keywords: available through the Edit menu
   - Copy linked files to folder: available through File menu
   - Add/move/remove from group: removed completely (functionality still available through group interface)
 - We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# JabRef Bibliography Management
+# JabRef Bibliography Management [![Hacktoberfest](https://img.shields.io/github/hacktoberfest/2019/JabRef/jabref?suggestion_label=hacktoberfest)](https://www.jabref.org/hacktoberfest/2019.html)
 
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)

diff --git a/build.gradle b/build.gradle
@@ -138,7 +138,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.4.4'
+    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.0'
 
     compile 'org.postgresql:postgresql:42.2.8'
 
@@ -164,9 +164,10 @@ dependencies {
     compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-    compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
+    compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
     compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-20190915.182410-364'
     compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-20190915.182922-250'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-20190915.182837-57'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-20190915.182113-372'
     compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
@@ -204,7 +205,7 @@ dependencies {
     testCompile 'net.bytebuddy:byte-buddy-parent:1.10.1'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-20190915.182552-364'
-    testCompile 'org.mockito:mockito-core:3.0.0'
+    testCompile 'org.mockito:mockito-core:3.1.0'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile ('org.reflections:reflections:0.9.11') {
         exclude module: "jsr305"
@@ -505,14 +506,11 @@ modernizer {
 }
 
 // Release tasks
-task generateFinalJabRefPS1File(type: Copy) {
-    from('buildres') {
-        include 'JabRef.ps1'
-    }
-    into 'build'
-    filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
+task deleteInstallerTemp(type: Delete) {
+    delete "$buildDir/installer"
 }
 
+jpackage.dependsOn deleteInstallerTemp
 jlink {
     options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
     launcher {
@@ -583,7 +581,9 @@ jlink {
                     '--app-version', "${project.version}",
                     '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                     '--win-dir-chooser',
-                    '--win-shortcut'
+                    '--win-shortcut',
+                    '--temp', "$buildDir/installer",
+                    '--resource-dir', "${projectDir}/buildres"
             ]
         }
 
@@ -608,6 +608,14 @@ jlink {
         }
     }
 }
+tasks.jpackageImage.doLast {
+    copy {
+        from("/buildres/") {
+            include "jabref.json", "JabRefHost.bat", "JabRefHost.ps1"
+        }
+        into "$buildDir/distribution/JabRef"
+    }
+}
 
 jmh {
     warmupIterations = 5