Merge remote-tracking branch 'upstream/maintable-beta' into editStrin…

…gsjavafx

* upstream/maintable-beta: (188 commits)
  Fix checkstyle
  Exchange Ignore by Disabled (#3912)
  Remove all @author comments and empty method/class comments
  Clean unused imports
  Fix missing icons and wrong package for custom icons
  Consistent FX color scheme for JabRef (#3839)
  javafx replacement for file dialog (#3005)
  Reenable closing of entry preview by pressing Esc (#3883)
  Load all field editors using ViewLoader
  Use JabRef icons in FXML
  Move icon stuff to new package gui.icon
  Load EntryEditor using new ViewLoader
  Improve tooltip tests
  Fix import thread problem
  Don't use null as parameter in DialogService
  Make it easier to create FXML dialogs (#3880)
  update slf4j from 1.8.0-beta1 -> 1.8.0-beta2
  New translations JabRef_en.properties (Tagalog)
  New translations JabRef_en.properties (Italian)
  New translations Menu_en.properties (Italian)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/JabRefFrame.java

.github/PULL_REQUEST_TEMPLATE.md

@@ -7,6 +7,7 @@
 
 - [ ] Change in CHANGELOG.md described
 - [ ] Tests created for changes
-- [ ] Screenshots added (for bigger UI changes)
 - [ ] Manually tested changed features in running JabRef
+- [ ] Screenshots added in PR description (for bigger UI changes)
+- [ ] Ensured that [the git commit message is a good one](https://github.com/joelparkerhenderson/git_commit_message)
 - [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)

.travis.yml

@@ -17,11 +17,11 @@ env:
   global:
     - GRADLE_OPTS=-Dorg.gradle.daemon=false
   matrix:
+    - TEST_SUITE=checkstyle
     - TEST_SUITE=check OPTIONS=modernizer
     - TEST_SUITE=fetcherTest
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
-    - TEST_SUITE=checkstyle
     - TEST_SUITE=codecov
     - DEPENDENCY_UPDATES=check
 
@@ -60,6 +60,7 @@ after_failure:
 branches:
   only:
     - master
+    - maintable-beta
 
 # cache gradle dependencies
 # https://docs.travis-ci.com/user/languages/java#Caching

CHANGELOG.md

@@ -12,6 +12,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Added "*.*" (any file type) to the Import File Filter Dialog. [#3757] (https://github.com/JabRef/jabref/issues/3757)
 - Abbreviate journal names functionality is now running parallel, increasing performance significantly. [#2831] (https://github.com/JabRef/jabref/issues/2831)
 - Changed order of items in context menu [#298] (https://github.com/koppor/jabref/issues/298)
 - Changed ID-based entry generator to store the last used fetcher. [#2796] (https://github.com/JabRef/jabref/issues/2796)
@@ -30,26 +31,33 @@ For more details refer to the [field mapping help page](http://help.jabref.org/e
 - We added Facebook and Twitter icons in the toolbar to link to our [Facebook](https://www.facebook.com/JabRef/) and [Twitter](https://twitter.com/jabref_org) pages.
 - Renamed the _Review_ Tab into _Comments_ Tab
 - We no longer print empty lines when exporting an entry in RIS format [#3634](https://github.com/JabRef/jabref/issues/3634)
+- We added the option to download linked URLs in the context menu in the entry editor.
 - We improved file saving so that hard links are now preserved when a save is performed [#2633](https://github.com/JabRef/jabref/issues/2633)
 - We changed the default dialog option when removing a [file link](http://help.jabref.org/en/FileLinks#adding-external-links-to-an-entry) from an entry.
 The new default removes the linked file from the entry instead of deleting the file from disk. [#3679](https://github.com/JabRef/jabref/issues/3679)
-- The group editing window can now also be called by double-clicking the group to be edited. [koppor#277](https://github.com/koppor/jabref/issues/277)
 - The magnifier icon at the search shows the [search mode](https://help.jabref.org/en/Search#search-modes) again. [#3535](https://github.com/JabRef/jabref/issues/3535)
 - We added a new cleanup operation that replaces ligatures with their expanded form. [#3613](https://github.com/JabRef/jabref/issues/3613)
+- We added the function to parse German month names. [#3536](https://github.com/JabRef/jabref/pull/3536)
 - Pressing <kbd>ESC</kbd> while searching will clear the search field and select the first entry, if available, in the table. [koppor#293](https://github.com/koppor/jabref/issues/293)
+- We changed the metadata reading and writing. DublinCore is now the only metadata format, JabRef supports. (https://github.com/JabRef/jabref/pull/3710)
+- We added another CLI functionality for reading and writing metadata to pdfs. (see https://github.com/JabRef/jabref/pull/3756 and see http://help.jabref.org/en/CommandLine)
+- We no longer print errors in field values during autosave into the log [#3811](https://github.com/JabRef/jabref/issues/3811)
+
 
 ### Fixed
 - We fixed several performance problems with the management of journal abbreviations [#3323](https://github.com/JabRef/jabref/issues/3323)
 - We fixed an issue where changing the type of an entry did not update the label in the tool bar of the entry editor and the contents of the currently visible entry editor tab
 - We fixed an issue where pressing space caused the cursor to jump to the start of the text field. [#3471](https://github.com/JabRef/jabref/issues/3471)
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 - Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
+- We fixed an issue where the progress of an ongoing file download was not shown correctly. [#3614](https://github.com/JabRef/jabref/issues/3614)
 - We fixed an issue where odd linked files could not be selected in the entry editor. [#3639](https://github.com/JabRef/jabref/issues/3639)
 - We fixed and extended the RIS import functionality to cover more fields. [#3634](https://github.com/JabRef/jabref/issues/3634) [#2607](https://github.com/JabRef/jabref/issues/2607)
 - Chaining modifiers in BibTeX key pattern now works as described in the documentation. [#3648](https://github.com/JabRef/jabref/issues/3648)
 - We fixed an issue where not all bibtex/biblatex fields would be exported as latex-free to MS-Office XML [koppor#284](https://github.com/koppor/jabref/issues/284)
 - We fixed an issue where linked files would be deleted from bibliography entries despite choosing the "Cancel" option in the dialog menu.
 - We fixed the name of the group editing window to "Add group" instead of "Edit Group" when adding a new group. [koppor#277](https://github.com/koppor/jabref/issues/277)
+- We fixed an issue where the "Copy linked files" dialog produced an error when the entry had no file [#3818](https://github.com/JabRef/jabref/issues/3818)
 
 ### Removed
 - We removed the [Look and Feels from JGoodies](http://www.jgoodies.com/freeware/libraries/looks/), because the open source version is not compatible with Java 9.

build.gradle

@@ -85,6 +85,7 @@ configurations {
 }
 
 dependencies {
+    // Include all jar-files in the 'lib' folder as dependencies
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
     compile 'com.jgoodies:jgoodies-common:1.8.1'
@@ -105,7 +106,7 @@ dependencies {
     compile "org.libreoffice:unoil:5.4.2"
 
     compile 'com.github.bkromhout:java-diff-utils:2.1.1'
-    compile 'info.debatty:java-string-similarity:1.0.1'
+    compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -114,24 +115,24 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.7.1'
 
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.45'
+    compile 'mysql:mysql-connector-java:5.1.46'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:24.0-jre'
+    compile 'com.google.guava:guava:24.1-jre'
 
     // JavaFX stuff
-    compile 'com.airhacks:afterburner.fx:1.7.0'
-    compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
+    compile 'de.codecentric.centerdevice:javafxsvg:1.3.0'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6'
     compile 'org.fxmisc.richtext:richtextfx:0.8.2'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
+    compile 'javax.inject:javax.inject:1'
 
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
@@ -141,11 +142,11 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility
-    compile 'org.slf4j:slf4j-api:1.8.0-beta1'
-    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.10.0'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.10.0'
-    compile 'org.apache.logging.log4j:log4j-api:2.10.0'
-    compile 'org.apache.logging.log4j:log4j-core:2.10.0'
+    compile 'org.slf4j:slf4j-api:1.8.0-beta2'
+    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.0'
 
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
@@ -154,17 +155,17 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.9'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.9'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.0.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.0.1'
 
     testCompile 'org.junit.jupiter:junit-jupiter-api:5.1.0'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.1.0'
     testRuntime 'org.junit.jupiter:junit-jupiter-engine:5.1.0'
     testRuntime 'org.junit.vintage:junit-vintage-engine:5.1.0'
     testCompile 'org.junit.platform:junit-platform-launcher:1.1.0'
-    testRuntime 'org.apache.logging.log4j:log4j-core:2.10.0'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.10.0'
-    testCompile 'org.mockito:mockito-core:2.15.0'
+    testRuntime 'org.apache.logging.log4j:log4j-core:2.11.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
+    testCompile 'org.mockito:mockito-core:2.16.0'
     testCompile 'com.github.tomakehurst:wiremock:2.15.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
@@ -193,26 +194,6 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
             }
         }
-        withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("1.0.10")) {
-                selection.reject("Version 1.0.10 is broken... waiting for 1.0.11")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("1.0.10")) {
-                selection.reject("Version 1.0.10 is broken... waiting for 1.0.11")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("2.0.0-BETA")) {
-                selection.reject("Version 2.0.0-BETA is broken... waiting for a working version... see #3561")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("2.0.0-BETA")) {
-                selection.reject("Version 2.0.0-BETA is broken... waiting for a working version... see #3561")
-            }
-        }
         withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /2.*/) {
                 selection.reject("Cannot be upgraded to version 2")