Java 17 htsjdk

.appveyor.yml

@@ -8,7 +8,7 @@ branches:
 skip_tags: true
 max_jobs: 1
 image: Previous Ubuntu1604
-stack: jdk 8, python 3.9, node 14
+stack: jdk 17, python 3.9, node 14
 
 build_script:
   - python3 -m pip install mkdocs mkdocs-material

README.md

@@ -96,7 +96,7 @@ NGB binaries can be retrieved from the following locations:
 
 ## Requirements
 
-* **[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+* **[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
 * **[Node.js = 6.9.5](https://nodejs.org/en/download/package-manager/)** 
 * **[Docker engine](https://docs.docker.com/engine/installation/)** *used to build docker images, if it is not a case - then could not be installed*
 * **[MkDocs >= 0.16.0](http://www.mkdocs.org/#installation)** and **[mkdocs-material](http://squidfunk.github.io/mkdocs-material/getting-started/#installing-mkdocs)** *used to build documentation, if it is not a case - then could not be installed*

build.gradle

@@ -31,10 +31,6 @@ class Version {
     }
 }
 
-task wrapper(type: Wrapper) {
-    gradleVersion = '3.3'
-}
-
 task ui(type: Copy) {
     dependsOn ':client:buildUI'
     doFirst {
@@ -79,9 +75,9 @@ task buildDoc(type: Tar) {
     dependsOn runMkdocs
     from("$rootDir/docs/site") {
     }
-    archiveName = "ngb-docs.tar.gz"
-    destinationDir file(distDir)
-    extension = 'tar.gz'
+    archiveBaseName = "ngb-docs"
+    getDestinationDirectory().set(file(distDir))
+    archiveExtension = 'tar.gz'
     compression = Compression.GZIP
 }
 
@@ -125,7 +121,7 @@ task buildJar(type: GradleBuild) {
     if (runTests) {
         tasks = ['clean', 'build']
     } else {
-        tasks = ['clean', 'bootRepackage']
+        tasks = ['clean', 'bootJar']
     }
     startParameter.projectProperties = [profile    : 'jar',
                                         database   : database,
@@ -147,10 +143,10 @@ task buildCli(type: GradleBuild) {
         tasks = ['clean', 'assemble']
     }
     buildFile = "$rootDir/server/ngb-cli/build.gradle"
-    dir = "$rootDir/ngb-cli/catgenome"
+    dir = "$rootDir/ngb-cli"
     doLast {
         copy {
-            from "$cliBuilds/ngb-cli.tar.gz"
+            from "$cliBuilds/ngb-cli.tgz"
             into distDir
         }
     }
@@ -222,7 +218,7 @@ task buildDesktopJar(type: GradleBuild) {
     if (runTests) {
         tasks = ['clean', 'build']
     } else {
-        tasks = ['clean', 'bootRepackage']
+        tasks = ['clean', 'bootWar']
     }
     startParameter.projectProperties = [profile    : 'jar',
                                         database   : database,

client/build.gradle

@@ -1,7 +1,7 @@
-import com.moowork.gradle.node.npm.NpmInstallTask
+import com.github.gradle.node.npm.task.NpmInstallTask
 
 plugins {
-    id "com.moowork.node" version "1.1.1"
+    id "com.github.node-gradle.node" version "7.1.0"
 }
 
 def desktop = hasProperty("desktop")

config/checkstyle/checkstyle.xml

@@ -0,0 +1,120 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE module PUBLIC "-//Puppy Crawl//DTD Check Configuration 1.3//EN" "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
+<!--
+    Checkstyle-Configuration: checkstyle for CatGenome
+    Description: none
+-->
+<module name="Checker">
+  <property name="severity" value="warning"/>
+  <module name="TreeWalker">
+    <property name="tabWidth" value="4"/>
+    <module name="ConstantName">
+      <!-- This changes the default check for static finals by allowing "logger" as an exception. -->
+      <property name="format" value="^([A-Z][A-Z0-9]*(_[A-Z0-9]+)*|logger|log)$"/>
+    </module>
+    <module name="LocalFinalVariableName"/>
+    <module name="LocalVariableName"/>
+    <module name="MemberName"/>
+    <module name="MethodName"/>
+    <module name="PackageName"/>
+    <module name="ParameterName"/>
+    <module name="StaticVariableName"/>
+    <module name="TypeName"/>
+    <module name="AvoidStarImport">
+        <property name="severity" value="ignore"/>
+    </module>
+    <module name="IllegalImport"/>
+    <module name="RedundantImport"/>
+    <module name="UnusedImports"/>
+    <module name="LineLength">
+      <property name="max" value="120"/>
+      <property name="tabWidth" value="4"/>
+    </module>
+    <module name="MethodLength">
+      <property name="max" value="150"/>
+    </module>
+    <module name="ParameterNumber">
+      <property name="severity" value="ignore"/>
+      <metadata name="net.sf.eclipsecs.core.lastEnabledSeverity" value="inherit"/>
+    </module>
+    <module name="EmptyForIteratorPad"/>
+    <module name="MethodParamPad"/>
+    <module name="NoWhitespaceAfter">
+      <property name="tokens" value="BNOT,DEC,DOT,INC,LNOT,UNARY_MINUS,UNARY_PLUS"/>
+    </module>
+    <module name="NoWhitespaceBefore"/>
+    <module name="OperatorWrap">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="ParenPad"/>
+    <module name="TypecastParenPad"/>
+    <module name="WhitespaceAfter">
+        <property name="tokens" value="COMMA, SEMI"/>
+    </module>
+    <module name="WhitespaceAround">
+      <property name="severity" value="ignore"/>
+      <property name="tokens" value="ASSIGN,BAND,BAND_ASSIGN,BOR,BOR_ASSIGN,BSR,BSR_ASSIGN,BXOR,BXOR_ASSIGN,COLON,DIV,DIV_ASSIGN,EQUAL,GE,GT,LAND,LCURLY,LE,LITERAL_ASSERT,LITERAL_CATCH,LITERAL_DO,LITERAL_ELSE,LITERAL_FINALLY,LITERAL_FOR,LITERAL_IF,LITERAL_RETURN,LITERAL_SYNCHRONIZED,LITERAL_TRY,LITERAL_WHILE,LOR,LT,MINUS,MINUS_ASSIGN,MOD,MOD_ASSIGN,NOT_EQUAL,PLUS,PLUS_ASSIGN,QUESTION,RCURLY,SL,SLIST,SL_ASSIGN,SR,SR_ASSIGN,STAR,STAR_ASSIGN,LITERAL_ASSERT,TYPE_EXTENSION_AND,WILDCARD_TYPE"/>
+    </module>
+    <module name="ModifierOrder"/>
+    <module name="RedundantModifier"/>
+    <module name="AvoidNestedBlocks">
+        <property name="allowInSwitchCase" value="true"/>
+    </module>
+    <module name="EmptyBlock"/>
+    <module name="LeftCurly">
+      <property name="maxLineLength" value="120"/>
+    </module>
+    <module name="NeedBraces"/>
+    <module name="RightCurly"/>
+    <module name="AvoidInlineConditionals">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="EmptyStatement"/>
+    <module name="EqualsHashCode"/>
+    <module name="HiddenField">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="IllegalInstantiation"/>
+    <module name="InnerAssignment"/>
+    <module name="MagicNumber">
+      <property name="ignoreNumbers" value="-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 256, 1024, 65535"/>
+      <property name="ignoreHashCodeMethod" value="true"/>
+    </module>
+    <module name="MissingSwitchDefault"/>
+    <!--<module name="RedundantThrows">  Removed in Checkstyle 6.2
+      <property name="allowUnchecked" value="true"/>
+      <property name="suppressLoadErrors" value="true"/>
+    </module>-->
+    <module name="SimplifyBooleanExpression">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="SimplifyBooleanReturn">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="DesignForExtension">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="FinalClass"/>
+    <module name="HideUtilityClassConstructor"/>
+    <module name="InterfaceIsType"/>
+    <module name="VisibilityModifier">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="ArrayTypeStyle"/>
+    <module name="FinalParameters">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="TodoComment">
+      <property name="severity" value="ignore"/>
+    </module>
+    <module name="UpperEll"/>
+    <module name="Indentation"/>
+    <module name="ParameterNumber">
+      <property name="max" value="20"/>
+    </module>
+  </module>
+  <module name="NewlineAtEndOfFile">
+    <property name="severity" value="ignore"/>
+  </module>
+  <module name="FileTabCharacter"/>
+</module>

desktop/README.md

@@ -1,6 +1,6 @@
 # Requirements
 
-**[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+**[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
 **[Node.js = 6.9.5](https://nodejs.org/en/download/package-manager/)** 
 
 # How to build NGB desktop application

docker/README.md

@@ -1,7 +1,7 @@
 # Requirements
 
 * **[Docker engine](https://docs.docker.com/engine/installation/)**
-* **[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+* **[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
 
 # How to build NGB docker image
 

docker/core/Dockerfile

@@ -6,19 +6,19 @@ ENV CLI_HOME $INSTALL_DIR/ngb-cli/bin/
 ENV NGS_DATA_DIR /ngs/
 ENV PATH $PATH:$CLI_HOME
 
-#Install OpenJDK 8
+#Install OpenJDK 17
 RUN apt-get -y update && \
-    apt-get -y install wget openjdk-8-jre nginx
+    apt-get -y install wget openjdk-17-jre nginx
 
 #Install NGB server binaries
 RUN mkdir ${NGB_HOME}
 COPY catgenome.jar ${NGB_HOME}
 
 #Install NGB CLI
-COPY ngb-cli.tar.gz ${INSTALL_DIR}
+COPY ngb-cli.tgz ${INSTALL_DIR}
 RUN cd ${INSTALL_DIR} && \
-    tar -zxvf ngb-cli.tar.gz && \
-    rm ngb-cli.tar.gz
+    tar -zxvf ngb-cli.tgz && \
+    rm ngb-cli.tgz
 
 
 # Configure "Open from NGB server"

docs/md/installation/binaries.md

@@ -15,8 +15,8 @@ Verify that your system meets or exceeds the following hardware/software require
   * Ubuntu >= 14.04
   * CentOS >= 6
   * RedHat >= 6
-  * **[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
-  * **[Tomcat 8](https://tomcat.apache.org/tomcat-8.0-doc/setup.html)**
+  * **[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
+  * **[Tomcat 9](https://tomcat.apache.org/tomcat-9.0-doc/setup.html)**
 * Client web-browser requirements
   * Chrome (>= 56)
   * Firefox (>= 51)

docs/md/installation/desktop.md

@@ -10,7 +10,7 @@ Verify that your system meets or exceeds the following hardware/software require
     * CPU: 2 cores
     * RAM: 4Gb
     * HDD: 20 Gb free space
-    * **[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+    * **[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
     * GIT
 
 ## Get Source Code

docs/md/installation/standalone.md

@@ -10,7 +10,7 @@ Verify that your system meets or exceeds the following hardware/software require
     * CPU: 2 cores
     * RAM: 4Gb
     * HDD: 20 Gb free space
-    * **[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+    * **[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
     * GIT
 
 * Client web-browser requirements

export-templates/target-identification/build.gradle

@@ -1,7 +1,7 @@
-import com.moowork.gradle.node.npm.NpmInstallTask
+import com.github.gradle.node.npm.task.NpmInstallTask
 
 plugins {
-    id "com.moowork.node" version "1.1.1"
+  id "com.github.node-gradle.node" version "7.1.0"
 }
 
 def nodeVersion = "14.17.5"

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Mon Jan 30 16:40:20 MSK 2017
+#Fri Mar 14 11:56:52 TRT 2025
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.3-bin.zip

server/README.md

@@ -1,6 +1,6 @@
 # Requirements
 
-**[Oracle JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 8](http://openjdk.java.net/install/)**
+**[Oracle JDK 17](https://docs.oracle.com/javase/17/docs/technotes/guides/install/install_overview.html)** or **[Open JDK 17](http://openjdk.java.net/install/)**
 
 # How to build NGB server