Merge branch 'master' of https://github.com/Siedlerchr/jabref into co…

…ntentSelector

* 'master' of https://github.com/Siedlerchr/jabref:
  Rework DBLPFetcher to new structure (#2314)
  Consider dev tag in version comparison (#2312)
  Update diffutils from 1.3.0 to 2.1.1
  Replace usages of Throwable with Exception (#2310)
  Add missing srcDir statement
  improve documentation of save order limitation - see #2305
  Adapt CSL tests to CRLF and LF (#2306)
  Use SPDX license identifiers
  Add key format of #2275 as requirement to CONTRIBUTING.md
  Add fallback exception handler (#2287)
  Update citeproc dependency to 1.0.1 (#2303)
  Remove duplicate code getResolvedFieldOrAlias (#2296)
  Update testCompile dependencies (mockito-core, wiremock)
  Change execution order (#2302)
  Use https for files.jabref.org
  Use compileJava instead of getdeps to decrease build time even more
  Update install4j from 6.1.1 to 6.1.3
  Fix local metadata synchronization

CHANGELOG.md

@@ -15,10 +15,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - URLs can now be passed as arguments to the `-import` and `-importToOpen` command line options. The referenced file is downloaded and then imported as usual.
 
 ### Fixed
+- We fixed an issue which caused a metadata loss on reconnection to shared database. [#2219](https://github.com/JabRef/jabref/issues/2219)
 - We fixed an issue which caused an internal error when leaving the file path field empty and connecting to a shared database.
 - We fixed an issue where the file permissions of the .bib-file were changed upon saving [#2279](https://github.com/JabRef/jabref/issues/2279).
 - We fixed an issue which prevented that a database was saved successfully if JabRef failed to generate new BibTeX-keys [#2285](https://github.com/JabRef/jabref/issues/2285).
 - We fixed an issue when JabRef restores its session and a shared database was used: The error message "No suitable driver found" will not appear.
+- Update check now correctly notifies about new release if development version is used. [#2298](https://github.com/JabRef/jabref/issues/2298)
+- Fixed [#2311](https://github.com/JabRef/jabref/issues/2311): The DBLP fetcher has been rewritten and is working again.
 
 ### Removed
 

CONTRIBUTING.md

@@ -29,6 +29,17 @@ Add a line with your changes in the appropriate section.
 If you did internal refactorings or improvements not visible to the user (e.g., UI, .bib file), then you don't need to put an entry there.
 
 
+#### Key format
+Example: `<kbd>Ctrl</kbd> + <kbd>Enter</kbd>`
+
+In case you add keys to the changelog, please follow these rules:
+
+- `<kbd>` tag for each key
+- First letter of key capitalized
+- Combined keys separated by `+`
+- Spaces before and after separator `+`
+
+
 ### Author credits
 You will be given credit in the `AUTHORS` file in the root of the repository and the 'About' pages inside the main application.
 We will periodically update the contributors list inside `AUTHORS`.

build.gradle

@@ -87,7 +87,7 @@ dependencies {
     compile 'org.openoffice:ridl:4.1.2'
     compile 'org.openoffice:unoil:4.1.2'
 
-    compile 'com.googlecode.java-diff-utils:diffutils:1.3.0'
+    compile 'com.github.bkromhout:java-diff-utils:2.1.1'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -122,11 +122,11 @@ dependencies {
     // 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'
     compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
-    compile 'de.undercouch:citeproc-java:1.0.0-SNAPSHOT'
+    compile 'de.undercouch:citeproc-java:1.0.1'
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.2.9'
-    testCompile 'com.github.tomakehurst:wiremock:2.2.2'
+    testCompile 'org.mockito:mockito-core:2.2.15'
+    testCompile 'com.github.tomakehurst:wiremock:2.3.1'
     testCompile 'org.assertj:assertj-swing-junit:3.4.0'
 }
 
@@ -141,6 +141,7 @@ sourceSets {
         java {
             compileClasspath += main.output + test.output
             runtimeClasspath += main.output + test.output
+            srcDir file('src/databaseTest/java')
         }
     }
     integrationTest {
@@ -382,17 +383,6 @@ task releaseJar(dependsOn: "shadowJar") {
     }
 }
 
-// fetch all dependencies to speedup CircleCI build
-// this is necessary until https://discuss.circleci.com/t/effective-caching-for-gradle/540 is resolved
-// see http://stackoverflow.com/a/27455099/873282 for an inspiration of this task
-// better solution: https://discuss.gradle.org/t/how-to-download-maven-dependencies-into-project-local-directory-and-set-eclipse-classpath/9851
-task getdeps(type: Copy) {
-    from(configurations.compile + configurations.antlr3 + configurations.antlr4 + configurations.testCompile) {
-        include "*.jar"
-    }
-    into 'build/tmp/alldeps/'
-}
-
 jmh {
     warmupIterations = 5
     iterations = 10

circle.yml

@@ -10,7 +10,7 @@ dependencies:
     - install4j6/bin/install4jc --verbose --license=$INSTALL4J_KEY
   override:
     # We do this to decrease build time by using CircleCI's cache. See https://discuss.circleci.com/t/effective-caching-for-gradle/540 for a longer motivation.
-    - ./gradlew getdeps
+    - ./gradlew compileJava
   cache_directories:
     - "~/.install4j6"
     - "~/downloads"

external-libraries.txt

@@ -5,11 +5,9 @@ This file is manually kept in sync with build.gradle and the binary jars contain
 
 ## License
 
- * GPLv2+ means "GPLv2 or later"
- * GPLv2! means "exactly version 2.0 of GPL"
- * GPLv2  means, we haven't checked whether later options are allowed
- * similar for LGPL and other version of GPL
-
+We follow the [SPDX license identifiers](https://spdx.org/licenses/).
+In case you add a library, please use these identifiers.
+For instance, "BSD" is not exactg enough, there are numerous variants out there: BSD-2-Clouse,  	BSD-3-Clause-No-Nuclear-Warranty, ...
 
 # Fonts and Icons
 
@@ -40,17 +38,17 @@ License: BSD
 Id:      commons-cli:commons-cli
 Project: Apache Commons CLI
 URL:     http://commons.apache.org/cli/
-License: Apache 2.0
+License: Apache-2.0
 
 Id:      commons-logging:commons-logging
 Project: Apache Commons Logging
 URL:     http://commons.apache.org/logging/
-License: Apache 2.0
+License: Apache-2.0
 
-Id:      com.googlecode.java-diff-utils
+Id:      com.github.bkromhout:java-diff-utils
 Project: java-diff-utils
-URL:     http://code.google.com/p/java-diff-utils/
-License: Apache 2.0
+URL:     https://github.com/bkromhout/java-diff-utils
+License: Apache-2.0
 
 Id:      com.impossibl.pgjdbc-ng:pgjdbc-ng
 Project: pgjdbc-ng
@@ -85,32 +83,32 @@ License: MIT
 Id:      mysql:mysql-connector-java
 Project: MySQL Connector/J
 URL:     http://www.mysql.de/downloads/connector/j/
-License: GPLv2! and Oracle's FOSS License Exception (http://www.mysql.com/about/legal/licensing/foss-exception/) allowing GPLv3
+License: GPL-2.0 and Oracle's FOSS License Exception (http://www.mysql.com/about/legal/licensing/foss-exception/) allowing GPLv3
 
 Id:      net.java.dev.glazedlists:glazedlists_java15
 Project: Glazed Lists
 URL:     http://www.glazedlists.com/
-License: LPGL 2.1! (not explicitly, but no comments in the source header) and MPL
+License: LGPL-2.1 (not explicitly, but no comments in the source header) and MPL-2.0
 
 Id:      org.apache.logging.log4j
 Project: Apache Log2j 2
 URL:     http://logging.apache.org/log4j/2.x/
-License: Apache 2.0
+License: Apache-2.0
 
 Id:      org.apache.pdfbox:fontbox
 Project: Apache PDFBox
 URL:     http://pdfbox.apache.org
-License: Apache 2.0
+License: Apache-2.0
 
 Id:      org.apache.pdfbox:jempbox
 Project: Apache PDFBox
 URL:     http://pdfbox.apache.org
-License: Apache 2.0
+License: Apache-2.0
 
 Id:      org.apache.pdfbox:pdfbox
 Project: Apache PDFBox
 URL:     http://pdfbox.apache.org
-License: Apache 2.0
+License: Apache-2.0
 
 Id:      org.bouncycastle:bcprov-jdk15on
 Project: The Legion of the Bouncy Castle
@@ -130,22 +128,22 @@ License: LGPL 3.0
 Id:      org.openoffice:jurt
 Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK
-License: LGPL 3.0
+License: Apache-2.0
 
 Id:      org.openoffice:ridl
 Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK
-License: LGPL 3.0
+License: Apache-2.0
 
 Id:      org.openoffice:unoil
 Project: OpenOffice.org
 URL:     http://www.openoffice.org/api/SDK
-License: LGPL 3.0
+License: Apache-2.0
 
 Id:      org.swinglabs.swingx:swingx-core
 Project: SwingX
 URL:     https://swingx.java.net/
-License: LGPL 3.0
+License: LGPL-3.0
 
 Id:      microba
 Path:    lib/microba.jar
@@ -157,7 +155,7 @@ Id:      spin
 Path:    lib/spin.jar
 Project: Spin
 URL:     http://spin.sourceforge.net/
-License: LGPL 2.1+
+License: LGPL-2.1+
 
 Id:      org.citationstyles.styles
 Project: CSL Styles
@@ -167,11 +165,11 @@ Licence: Creative Commons Attribution-ShareAlike 3.0 Unported license
 Id:      org.citationstyles.locales
 Project: CSL Locales
 URL:     https://github.com/citation-style-language/locales
-Licence: Creative Commons Attribution-ShareAlike 3.0 Unported license
+Licence: CC-BY-SA-3.0
 
 Id:      de.undercouch.citeproc-java
 Project: Citeproc-Java
 URL:     http://michel-kraemer.github.io/citeproc-java/
-Licence: Apache License, Version 2.0
+Licence: Apache-2.0
 
 The last entry has to end with an empty line. Otherwise the entry is not present in About.html.

jabref.install4j

@@ -708,7 +708,7 @@ return true;</string>
     </applications>
   </installerGui>
   <mediaSets>
-    <windows name="Windows 32bit JRE" id="73" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="32" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-x86-1.8.0_112" manualJREEntry="false" bundleType="2" jreURL="http://files.jabref.org/jres/windows-x86-1.8.0_112.tar.gz" jreShared="true" directDownload="false" installOnlyIfNecessary="true" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Windows 32bit JRE" id="73" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="32" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-x86-1.8.0_112" manualJREEntry="false" bundleType="2" jreURL="https://files.jabref.org/jres/windows-x86-1.8.0_112.tar.gz" jreShared="true" directDownload="false" installOnlyIfNecessary="true" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedLaunchers />
@@ -721,7 +721,7 @@ return true;</string>
         <customAttributes />
       </autoUpdate>
     </windows>
-    <windows name="Windows 64bit JRE" id="74" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_112" manualJREEntry="false" bundleType="2" jreURL="http://files.jabref.org/jres/windows-amd64-1.8.0_112.tar.gz" jreShared="true" directDownload="false" installOnlyIfNecessary="true" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Windows 64bit JRE" id="74" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_112" manualJREEntry="false" bundleType="2" jreURL="https://files.jabref.org/jres/windows-amd64-1.8.0_112.tar.gz" jreShared="true" directDownload="false" installOnlyIfNecessary="true" customInstallBaseDir="" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedLaunchers />
@@ -734,7 +734,7 @@ return true;</string>
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macos name="Mac OS X Single Bundle JRE" id="77" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.fullName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="macosx-amd64-1.8.0_112_unpacked" manualJREEntry="false" bundleType="2" jreURL="http://files.jabref.org/jres/macosx-amd64-1.8.0_112_unpacked.tar.gz" jreShared="false" directDownload="false" installOnlyIfNecessary="false" appleJre="false" requiredVmIdPrefix="" customInstallBaseDir="" contentFilesType="1" installerName="${i18n:InstallerName(${compiler:sys.fullName})}" volumeName="${compiler:sys.shortName}" compressDmg="false" launcherId="23">
+    <macos name="Mac OS X Single Bundle JRE" id="77" customizedId="" mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:version}" installDir="${compiler:sys.fullName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="macosx-amd64-1.8.0_112_unpacked" manualJREEntry="false" bundleType="2" jreURL="https://files.jabref.org/jres/macosx-amd64-1.8.0_112_unpacked.tar.gz" jreShared="false" directDownload="false" installOnlyIfNecessary="false" appleJre="false" requiredVmIdPrefix="" customInstallBaseDir="" contentFilesType="1" installerName="${i18n:InstallerName(${compiler:sys.fullName})}" volumeName="${compiler:sys.shortName}" compressDmg="false" launcherId="23">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedBeans />

scripts/prepare-install4j.sh

@@ -7,19 +7,17 @@ fi
 
 # ensure that tar archive of install4j exists
 cd ~/downloads
-if [ ! -f install4j_unix_6_1_1.tar.gz ]; then
-  wget --quiet http://download-aws.ej-technologies.com/install4j/install4j_unix_6_1_1.tar.gz
-fi;
+wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_6_1_3.tar.gz
 
 # extract tar archive of install4j into the source directory of JabRef
 cd ~/jabref
-tar -xzf ~/downloads/install4j_unix_6_1_1.tar.gz
+tar -xzf ~/downloads/install4j_unix_6_1_3.tar.gz
 
 # fetch JREs
 if [ ! -d ~/.install4j6/jres/ ]; then
   mkdir -p ~/.install4j6/jres/
 fi
 cd ~/.install4j6/jres/
-wget --quiet -nc http://files.jabref.org/jres/windows-x86-1.8.0_112.tar.gz
-wget --quiet -nc http://files.jabref.org/jres/windows-amd64-1.8.0_112.tar.gz
-wget --quiet -nc http://files.jabref.org/jres/macosx-amd64-1.8.0_112_unpacked.tar.gz
+wget --quiet -nc https://files.jabref.org/jres/windows-x86-1.8.0_112.tar.gz
+wget --quiet -nc https://files.jabref.org/jres/windows-amd64-1.8.0_112.tar.gz
+wget --quiet -nc https://files.jabref.org/jres/macosx-amd64-1.8.0_112_unpacked.tar.gz

src/main/java/net/sf/jabref/FallbackExceptionHandler.java

@@ -0,0 +1,24 @@
+package net.sf.jabref;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.Marker;
+import org.apache.logging.log4j.MarkerManager;
+
+/**
+ * Catch and log any unhandled exceptions.
+ */
+public class FallbackExceptionHandler implements Thread.UncaughtExceptionHandler {
+
+    private static final Marker UncaughtException_MARKER = MarkerManager.getMarker("UncaughtException");
+
+    public static void installExceptionHandler() {
+        Thread.setDefaultUncaughtExceptionHandler(new FallbackExceptionHandler());
+    }
+
+    @Override
+    public void uncaughtException(Thread thread, Throwable exception) {
+        Logger logger = LogManager.getLogger(FallbackExceptionHandler.class);
+        logger.error(UncaughtException_MARKER, "Uncaught exception Occurred in " + thread, exception);
+    }
+}

src/main/java/net/sf/jabref/JabRefExecutorService.java

@@ -26,6 +26,7 @@ public class JabRefExecutorService implements Executor {
     private final ExecutorService executorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef CachedThreadPool");
+        thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         return thread;
     });
     private final ConcurrentLinkedQueue<Thread> startedThreads = new ConcurrentLinkedQueue<>();
@@ -90,6 +91,7 @@ public void executeWithLowPriorityInOwnThread(final Runnable runnable, String na
         final Thread thread = new Thread(target);
         target.thread = thread;
         thread.setName("JabRef - " + name + " - low prio");
+        thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         startedThreads.add(thread);
         thread.setPriority(Thread.MIN_PRIORITY);
         thread.start();
@@ -106,6 +108,7 @@ public void executeInOwnThread(Thread thread) {
     public void executeWithLowPriorityInOwnThreadAndWait(Runnable runnable) {
         Thread thread = new Thread(runnable);
         thread.setName("JabRef low prio");
+        thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         startedThreads.add(thread);
         thread.setPriority(Thread.MIN_PRIORITY);
         thread.start();

src/main/java/net/sf/jabref/JabRefMain.java

@@ -40,6 +40,8 @@ public static void main(String[] args) {
     }
 
     private static void start(String[] args) {
+        FallbackExceptionHandler.installExceptionHandler();
+
         JabRefPreferences preferences = JabRefPreferences.getInstance();
 
         ProxyPreferences proxyPreferences = preferences.getProxyPreferences();

src/main/java/net/sf/jabref/gui/actions/BaseAction.java

@@ -8,5 +8,5 @@
 @FunctionalInterface
 public interface BaseAction {
 
-    void action() throws Throwable;
+    void action() throws Exception;
 }

src/main/java/net/sf/jabref/gui/actions/CopyBibTeXKeyAndLinkAction.java

@@ -25,7 +25,7 @@ public CopyBibTeXKeyAndLinkAction(MainTable mainTable) {
     }
 
     @Override
-    public void action() throws Throwable {
+    public void action() throws Exception {
         List<BibEntry> entries = mainTable.getSelectedEntries();
         if (!entries.isEmpty()) {
             StringBuilder sb = new StringBuilder();

src/main/java/net/sf/jabref/gui/bibtexkeypattern/SearchFixDuplicateLabels.java

@@ -64,7 +64,7 @@ public void run() {
     }
 
     @Override
-    public void init() throws Throwable {
+    public void init() throws Exception {
         panel.output(Localization.lang("Resolving duplicate BibTeX keys..."));
 
     }

src/main/java/net/sf/jabref/gui/exporter/SaveDatabaseAction.java

@@ -81,7 +81,7 @@ public SaveDatabaseAction(BasePanel panel, Path filePath) {
     }
 
     @Override
-    public void init() throws Throwable {
+    public void init() throws Exception {
         success = false;
         canceled = false;
         fileLockedError = false;
@@ -280,7 +280,7 @@ private boolean saveDatabase(File file, boolean selectedOnly, Charset encoding)
      * Run the "Save" operation. This method offloads the actual save operation to a background thread, but
      * still runs synchronously using Spin (the method returns only after completing the operation).
      */
-    public void runCommand() throws Throwable {
+    public void runCommand() throws Exception {
         // This part uses Spin's features:
         Worker worker = getWorker();
         // The Worker returned by getWorker() has been wrapped
@@ -300,12 +300,12 @@ public void runCommand() throws Throwable {
         callback.update(); // Runs the update() method on the EDT.
     }
 
-    public void save() throws Throwable {
+    public void save() throws Exception {
         runCommand();
         frame.updateEnabledState();
     }
 
-    public void saveAs() throws Throwable {
+    public void saveAs() throws Exception {
         // configure file dialog
         FileDialog dialog = new FileDialog(frame);
         dialog.withExtension(FileExtensions.BIBTEX_DB);
@@ -324,7 +324,7 @@ public void saveAs() throws Throwable {
      * Run the "Save as" operation. This method offloads the actual save operation to a background thread, but
      * still runs synchronously using Spin (the method returns only after completing the operation).
      */
-    public void saveAs(File file) throws Throwable {
+    public void saveAs(File file) throws Exception {
         BibDatabaseContext context = panel.getBibDatabaseContext();
 
         if (context.getLocation() == DatabaseLocation.SHARED) {