Merge branch 'develop' into releases/Release_2_11_1_Branch

diff --git a/build.gradle b/build.gradle
index 5d2aba7..58d2764 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1389,6 +1389,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'GETDOWN_INSTALL_DIR': getdown_install_dir,
     'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
     'BUILD_DIR': install4jBuildDir,
+    'UNIX_DESKTOP_ADDITIONS': install4j_unix_desktop_additions,
   ]
 
   destination = "${jalviewDir}/${install4jBuildDir}"

diff --git a/getdown/lib/FJVL_VERSION b/getdown/lib/FJVL_VERSION
new file mode 100644 (file)
index 0000000..e7a1de7
--- /dev/null
+++ b/getdown/lib/FJVL_VERSION
@@ -0,0 +1 @@
+1.8.3-1.2.4_FJVL

diff --git a/getdown/lib/JVL_VERSION b/getdown/lib/JVL_VERSION
new file mode 100644 (file)
index 0000000..756f4bd
--- /dev/null
+++ b/getdown/lib/JVL_VERSION
@@ -0,0 +1 @@
+1.8.3-1.2.4_JVL

diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar
index 13ff1ea..9c0f96e 100644 (file)
Binary files a/getdown/lib/getdown-core.jar and b/getdown/lib/getdown-core.jar differ

diff --git a/getdown/lib/getdown-launcher-local.jar b/getdown/lib/getdown-launcher-local.jar
index 568cf07..cfa96f3 100644 (file)
Binary files a/getdown/lib/getdown-launcher-local.jar and b/getdown/lib/getdown-launcher-local.jar differ

diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index c353e9b..2f8baa7 100644 (file)
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ

diff --git a/getdown/src/getdown/ant/pom.xml b/getdown/src/getdown/ant/pom.xml
index ff1c73a..8dcef42 100644 (file)
--- a/getdown/src/getdown/ant/pom.xml
+++ b/getdown/src/getdown/ant/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.3_FJVL</version>
+    <version>1.8.3-1.2.4_FJVL</version>
   </parent>
 
   <artifactId>getdown-ant</artifactId>

diff --git a/getdown/src/getdown/core/pom.xml b/getdown/src/getdown/core/pom.xml
index 7eb03a8..2d0e89a 100644 (file)
--- a/getdown/src/getdown/core/pom.xml
+++ b/getdown/src/getdown/core/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.3_FJVL</version>
+    <version>1.8.3-1.2.4_FJVL</version>
   </parent>
 
   <artifactId>getdown-core</artifactId>
@@ -132,6 +132,20 @@
           <useFile>false</useFile>
         </configuration>
       </plugin>
+
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-jar-plugin</artifactId>
+        <version>3.1.0</version>
+        <configuration>
+          <archive>
+            <manifest>
+              <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+            </manifest>
+          </archive>
+        </configuration>
+      </plugin>
+
     </plugins>
   </build>
 

diff --git a/getdown/src/getdown/launcher/pom.xml b/getdown/src/getdown/launcher/pom.xml
index dc2e676..ad87541 100644 (file)
--- a/getdown/src/getdown/launcher/pom.xml
+++ b/getdown/src/getdown/launcher/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.threerings.getdown</groupId>
     <artifactId>getdown</artifactId>
-    <version>1.8.3-1.2.3_FJVL</version>
+    <version>1.8.3-1.2.4_FJVL</version>
   </parent>
 
   <artifactId>getdown-launcher</artifactId>
@@ -118,6 +118,7 @@
           <archive>
             <manifest>
               <mainClass>com.threerings.getdown.launcher.GetdownApp</mainClass>
+              <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
             </manifest>
             <manifestEntries>
               <Permissions>all-permissions</Permissions>

diff --git a/getdown/src/getdown/mvn_cmd b/getdown/src/getdown/mvn_cmd
index 0d2315d..3f9b4a2 100755 (executable)
--- a/getdown/src/getdown/mvn_cmd
+++ b/getdown/src/getdown/mvn_cmd
@@ -3,7 +3,7 @@
 if [ x$JVLVERSION != x ]; then
   export VERSION=$JVLVERSION
 else
-  export VERSION=1.8.3-1.2.3_JVL
+  export VERSION=1.8.3-1.2.4_JVL
 fi
 
 if [ x${VERSION%_JVL} = x$VERSION ]; then
@@ -19,6 +19,7 @@ if [ x$RET = x0 ]; then
   cp core/target/getdown-core-$VERSION.jar ../../../getdown/lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to getdown/lib"
   cp core/target/getdown-core-$VERSION.jar ../../../j8lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j8lib"
   cp core/target/getdown-core-$VERSION.jar ../../../j11lib/getdown-core.jar && echo "Copied getdown-core-$VERSION.jar to j11lib"
+  echo "$VERSION" > ../../../getdown/lib/JVL_VERSION
 fi
 
 VERSION=${VERSION/JVL/FJVL}
@@ -28,4 +29,5 @@ mvn package -Dgetdown.host.whitelist="jalview.org,*.jalview.org" -Dallow_file_pr
 RET=$?
 if [ x$RET = x0 ]; then
   cp launcher/target/getdown-launcher-$VERSION.jar ../../../getdown/lib/getdown-launcher-local.jar && echo "Copied getdown-launcher-$VERSION.jar to getdown/lib/getdown-launcher-local.jar"
+  echo "$VERSION" > ../../../getdown/lib/FJVL_VERSION
 fi

diff --git a/getdown/src/getdown/pom.xml b/getdown/src/getdown/pom.xml
index 0299940..2ca4aa1 100644 (file)
--- a/getdown/src/getdown/pom.xml
+++ b/getdown/src/getdown/pom.xml
@@ -10,7 +10,7 @@
   <groupId>com.threerings.getdown</groupId>
   <artifactId>getdown</artifactId>
   <packaging>pom</packaging>
-  <version>1.8.3-1.2.3_FJVL</version>
+  <version>1.8.3-1.2.4_FJVL</version>
 
   <name>getdown</name>
   <description>An application installer and updater.</description>

diff --git a/gradle.properties b/gradle.properties
index ace0303..9c6832a 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -122,9 +122,10 @@ install4j_info_plist_file_associations = file_associations_auto-Info_plist.xml
 install4j_installer_file_associations = file_associations_auto-install4j8.xml
 #install4j_DMG_uninstaller_app_files = uninstall_old_jalview_files.xml
 install4j_build_dir = build/install4j
-install4j_media_types = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
+install4j_media_types = windows,macosArchive,unixArchive,unixInstaller
 install4j_faster = false
 install4j_installer_name = Jalview Installer
+install4j_unix_desktop_additions = Categories=Science;Biology;Java;
 
 OSX_KEYSTORE =
 OSX_KEYPASS =

diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index 13ff1ea..9c0f96e 100644 (file)
Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ

diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index 13ff1ea..9c0f96e 100644 (file)
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ

diff --git a/utils/download_jres.sh b/utils/download_jres.sh
index 5bfc26d..89ed8fc 100755 (executable)
--- a/utils/download_jres.sh
+++ b/utils/download_jres.sh
@@ -18,6 +18,9 @@ JVM_IMPL=hotspot
 HEAP_SIZE=normal
 VENDOR=adoptopenjdk
 IMAGE_TYPE=jre
+TAR=tar
+ZIP=zip
+UNZIP=unzip
 
 STRIP_MAC_APP_BUNDLING=false
 CREATE_ARCHIVES="zip tgz"
@@ -29,7 +32,7 @@ RM=/bin/rm
 unzip-strip() (
   local zip=$1
   local dest=${2:-.}
-  local temp=$(mktemp -d) && unzip -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
+  local temp=$(mktemp -d) && $UNZIP -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
   shopt -s dotglob && local f=("$temp"/*) &&
   if (( ${#f[@]} == 1 )) && [[ -d "${f[0]}" ]] ; then
     mv "$temp"/*/* "$dest"
@@ -63,10 +66,10 @@ for FEATURE_VERSION in 8 11; do
       else
         echo "using tar"
         if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
-          tar --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
+          $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
           RET=$?
         else
-          tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+          $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
           RET=$?
         fi
       fi
@@ -87,14 +90,14 @@ for FEATURE_VERSION in 8 11; do
               ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
               [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
               cd ${NAME}
-              zip -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
+              $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
               cd -
               ;;
             tgz)
               EXT=tar.gz
               echo "Creating ${NAME}.${EXT} for install4j bundling"
               [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
-              tar -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
+              $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
               ;;
             *)
               echo "Archiving as '${CREATEARCHIVE}' file not supported"

diff --git a/utils/install4j/install4j8_template.install4j b/utils/install4j/install4j8_template.install4j
index 4f37185..961c5c0 100644 (file)
--- a/utils/install4j/install4j8_template.install4j
+++ b/utils/install4j/install4j8_template.install4j
@@ -38,6 +38,7 @@
       <variable name="GETDOWN_ALT_DIR" value="alt" />
       <variable name="GETDOWN_INSTALL_DIR" value="install" />
       <variable name="INFO_PLIST_FILE_ASSOCIATIONS_FILE" value="file_associations_auto-Info_plist.xml" />
+      <variable name="UNIX_DESKTOP_ADDITIONS" value="Categories=Science;Biology;Java;" />
     </variables>
     <codeSigning macEnabled="true" macPkcs12File="${compiler:OSX_KEYSTORE}" />
   </application>
@@ -126,22 +127,7 @@
         <id>2350</id>
         <id>2450</id>
       </macStaticAssociationActions>
-      <infoPlist>${compiler:file("${compiler:INFO_PLIST_FILE_ASSOCIATIONS_FILE}")}</infoPlist>
-      <iconImageFiles>
-        <file path="${compiler:JALVIEW_DIR}/resources/images/JalviewLogo_Huge.png" />
-      </iconImageFiles>
-    </launcher>
-    <launcher name="${compiler:JALVIEW_NAME} package" id="1876" menuName="${compiler:sys.shortName} ${compiler:JALVIEW_VERSION}" fileset="1873">
-      <executable name="${compiler:sys.shortName}" iconSet="true" redirectStderr="false" failOnStderrOutput="false" executableMode="gui" changeWorkingDirectory="false" singleInstance="true" />
-      <java mainClass="jalview.bin.Launcher" vmParameters="-Dinstaller_template_version=${compiler:INSTALLER_TEMPLATE_VERSION}">
-        <classPath>
-          <scanDirectory location="${compiler:GETDOWN_DIST_DIR}" failOnError="false" />
-        </classPath>
-      </java>
-      <macStaticAssociationActions mode="selected">
-        <id>2350</id>
-        <id>2450</id>
-      </macStaticAssociationActions>
+      <desktopFile>${compiler:UNIX_DESKTOP_ADDITIONS}</desktopFile>
       <infoPlist>${compiler:file("${compiler:INFO_PLIST_FILE_ASSOCIATIONS_FILE}")}</infoPlist>
       <iconImageFiles>
         <file path="${compiler:JALVIEW_DIR}/resources/images/JalviewLogo_Huge.png" />
@@ -1076,42 +1062,6 @@ return console.askYesNo(message, true);
     </styles>
   </installerGui>
   <mediaSets>
-    <linuxDeb name="Jalview .deb Package" id="153" mediaFileName="jalview-${compiler:JALVIEW_VERSION}" dependencies="openjdk-8-jre" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org">
-      <excludedComponents>
-        <component id="1031" />
-        <component id="1155" />
-        <component id="1156" />
-        <component id="1276" />
-        <component id="2110" />
-      </excludedComponents>
-      <excludedLaunchers>
-        <launcher id="737" />
-      </excludedLaunchers>
-      <exclude>
-        <entry defaultFileset="true" />
-        <entry filesetId="734" />
-        <entry filesetId="880" />
-        <entry filesetId="882" />
-      </exclude>
-    </linuxDeb>
-    <linuxRPM name="Jalview RPM Package" id="570" mediaFileName="jalview-${compiler:JALVIEW_VERSION}" dependencies="java-1.8.0-openjdk" arch="noarch">
-      <excludedComponents>
-        <component id="1031" />
-        <component id="1155" />
-        <component id="1156" />
-        <component id="1276" />
-        <component id="2110" />
-      </excludedComponents>
-      <excludedLaunchers>
-        <launcher id="737" />
-      </excludedLaunchers>
-      <exclude>
-        <entry defaultFileset="true" />
-        <entry filesetId="734" />
-        <entry filesetId="880" />
-        <entry filesetId="882" />
-      </exclude>
-    </linuxRPM>
     <windows name="Windows x64 EXE Installer" id="743" mediaFileName="${compiler:sys.shortName}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" customInstallBaseDir="~/AppData/Local">
       <excludedComponents>
         <component id="1155" />
@@ -1166,7 +1116,7 @@ return console.askYesNo(message, true);
         <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
-    <unixInstaller name="Unix Shell Installer" id="1595" mediaFileName="${compiler:sys.shortName}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" customInstallBaseDir="~/opt/">
+    <unixInstaller name="Linux x64 Shell Installer" id="1595" mediaFileName="${compiler:sys.shortName}-${compiler:JALVIEW_VERSION}-linux_x64-java_${compiler:JAVA_INTEGER_VERSION}" customInstallBaseDir="~/opt/">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
@@ -1196,9 +1146,27 @@ return console.askYesNo(message, true);
         <entry filesetId="880" />
         <entry filesetId="882" />
         <entry filesetId="1873" />
+        <entry filesetId="2105" />
       </exclude>
-      <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
+      <jreBundle includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
     </unixArchive>
+    <unixInstaller name="Unix Shell Installer" id="2639" mediaFileName="${compiler:sys.shortName}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" customInstallBaseDir="~/opt/">
+      <excludedComponents>
+        <component id="1155" />
+        <component id="1156" />
+        <component id="1276" />
+        <component id="1881" />
+        <component id="2110" />
+      </excludedComponents>
+      <exclude>
+        <entry defaultFileset="true" />
+        <entry filesetId="880" />
+        <entry filesetId="882" />
+        <entry filesetId="1873" />
+        <entry filesetId="2105" />
+      </exclude>
+      <jreBundle includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
+    </unixInstaller>
   </mediaSets>
   <buildIds>
     <mediaSet refId="153" />
@@ -1208,5 +1176,6 @@ return console.askYesNo(message, true);
     <mediaSet refId="878" />
     <mediaSet refId="1595" />
     <mediaSet refId="1596" />
+    <mediaSet refId="2639" />
   </buildIds>
 </install4j>