diff --git a/.gitignore b/.gitignore index c06e054944e..c99265d8037 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,25 @@ src/main/webapp/node doc/swagger-ui/open-api.json /.theia/launch.json /yarn.lock + +.gradle +**/build/ +!src/**/build/ + +# Ignore Gradle GUI config +gradle-app.setting + +# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored) +!gradle-wrapper.jar + +# Avoid ignore Gradle wrappper properties +!gradle-wrapper.properties + +# Cache of project +.gradletasknamecache + +# Eclipse Gradle plugin generated files +# Eclipse Core +.project +# JDT-specific (Eclipse Java Development Tools) +.classpath diff --git a/build.gradle.kts b/build.gradle.kts new file mode 100644 index 00000000000..53bf451cf12 --- /dev/null +++ b/build.gradle.kts @@ -0,0 +1,232 @@ +plugins { + id("org.gradle.test-retry") version "1.4.0" + id("org.springframework.boot") version "2.6.6" + id("io.spring.dependency-management") version "1.0.11.RELEASE" + id("org.siouan.frontend-jdk11") version "6.0.0" + id("com.github.johnrengelman.processes") version "0.5.0" + id("org.springdoc.openapi-gradle-plugin") version "1.3.4" + java + war +} + +group = "ca.corefacility.bioinformatics" +version = "22.07-SNAPSHOT" +description = "irida" + +java { + sourceCompatibility = JavaVersion.VERSION_11 + targetCompatibility = JavaVersion.VERSION_11 +} + +repositories { + mavenLocal() + mavenCentral() + maven { + url = uri("https://clojars.org/repo") + } +} + +dependencies { + implementation("org.springframework.boot:spring-boot-starter") { + exclude(group = "org.apache.logging.log4j", module = "log4j-to-slf4j") + } + implementation("org.springframework.boot:spring-boot-starter-validation") + implementation("org.springframework.boot:spring-boot-starter-security") + implementation("org.apache.oltu.oauth2:org.apache.oltu.oauth2.client:1.0.0") { + exclude(group = "org.slf4j") + } + implementation("org.springframework.boot:spring-boot-starter-data-jpa") + implementation("org.springframework.data:spring-data-envers") { + exclude(group = "org.slf4j") + } + implementation("org.liquibase:liquibase-core") + implementation("org.hibernate:hibernate-envers") + implementation("org.apache.commons:commons-dbcp2") { + exclude(group = "commons-logging", module = "commons-logging") + } + implementation("commons-net:commons-net:3.8.0") + implementation("org.apache.jena:jena-tdb:4.3.2") { + exclude(group = "xml-apis") + exclude(group = "org.slf4j") + } + implementation("org.apache.jena:jena-text:4.3.2") { + exclude(group = "xml-apis") + exclude(group = "org.slf4j") + exclude(group = "log4j") + } + implementation("org.springframework.boot:spring-boot-starter-web") + implementation("org.springframework.boot:spring-boot-starter-web-services") + implementation("org.springframework.boot:spring-boot-starter-hateoas") + implementation("org.springframework.security.oauth:spring-security-oauth2:2.3.6.RELEASE") { + exclude(group = "org.codehaus.jackson", module = "jackson-mapper-asl") + } + implementation("commons-io:commons-io:2.11.0") + implementation("commons-fileupload:commons-fileupload:1.4") + implementation("org.apache.poi:poi-ooxml:5.2.2") { + exclude(group = "stax", module = "stax-api") + exclude(group = "org.apache.logging.log4j", module = "log4j-api") + } + implementation("org.thymeleaf:thymeleaf-spring5") + implementation("org.thymeleaf.extras:thymeleaf-extras-springsecurity5") + implementation("com.github.mxab.thymeleaf.extras:thymeleaf-extras-data-attribute") + implementation("nz.net.ultraq.thymeleaf:thymeleaf-layout-dialect") + implementation("commons-beanutils:commons-beanutils:1.9.4") + implementation("org.springframework.boot:spring-boot-starter-mail") + implementation("org.apache.logging.log4j:log4j-api") + implementation("org.apache.logging.log4j:log4j-to-slf4j") + implementation("com.google.guava:guava:31.0.1-jre") + implementation("commons-cli:commons-cli:1.2") + implementation("uk.ac.babraham:fastqc:0.11.9-nml-custom") + implementation("org.aspectj:aspectjweaver") + implementation("org.biojava:biojava3-core:3.0") + implementation("org.apache.commons:commons-csv:1.8") + implementation("com.sksamuel.diff:diff:1.1.11") + implementation("org.pf4j:pf4j:2.4.0") + implementation("com.github.jmchilton.blend4j:blend4j:0.2.1-2201df9") { + exclude(group = "javax.xml.stream") + exclude(group = "com.sun.xml.bind") + } + implementation("net.matlux:jvm-breakglass:0.0.8") + implementation("com.google.code.gson:gson") + implementation("com.github.pjfanning:excel-streaming-reader:3.6.1") + implementation("org.springdoc:springdoc-openapi-webmvc-core:1.5.6") { + exclude(group = "jakarta.xml.bind", module = "jakarta.xml.bind-api") + exclude(group = "jakarta.validation", module = "jakarta.validation-api") + } + runtimeOnly("mysql:mysql-connector-java") + testImplementation("org.springframework.boot:spring-boot-starter-test") { + exclude(group = "org.springframework.boot", module = "spring-boot-test-autoconfigure") + } + testImplementation("org.junit.platform:junit-platform-launcher") + testImplementation("org.springframework.security:spring-security-test") + testImplementation("org.mockito:mockito-core") + testImplementation("io.rest-assured:rest-assured") + testImplementation("io.rest-assured:json-path") + testImplementation("com.github.springtestdbunit:spring-test-dbunit:1.3.0") + testImplementation("org.dbunit:dbunit:2.7.2") { + exclude(group = "org.slf4j") + } + testImplementation("org.seleniumhq.selenium:selenium-support:3.141.59") + testImplementation("org.seleniumhq.selenium:selenium-chrome-driver:3.141.59") + testImplementation("org.mockftpserver:MockFtpServer:2.6") + providedCompile("org.springframework.boot:spring-boot-starter-tomcat") +} + +tasks.bootRun { + dependsOn(":assembleFrontend") + systemProperties(System.getProperties().mapKeys { it.key as String }) +} + +frontend { + nodeVersion.set("16.15.0") + nodeInstallDirectory.set(file("${projectDir}/src/main/webapp/node")) + yarnEnabled.set(true) + yarnVersion.set("3.1.1") + assembleScript.set("build") + installScript.set("install") + packageJsonDirectory.set(file("${projectDir}/src/main/webapp")) +} + +tasks.withType { + systemProperties(mapOf("junit.platform.execution.listeners.deactivate" to "ca.corefacility.bioinformatics.irida.junit5.listeners.Integration*")) + useJUnitPlatform { + excludeTags("IntegrationTest") + } + testLogging { + events("passed", "skipped", "failed") + showStandardStreams = true + } +} + +fun createIntegrationTestTask(name: String, tags: String?, excludeListeners: String?): TaskProvider { + return tasks.register("${name}ITest") { + val defaultSystemProperties = mapOf( + "junit.platform.execution.listeners.deactivate" to excludeListeners, + "spring.datasource.url" to "jdbc:mysql://localhost:3306/irida_integration_test", + "irida.db.profile" to "it", + "irida.it.nosandbox" to "true", + "irida.it.headless" to "true", + "spring.profiles.active" to "test", + "irida.it.rootdirectory" to temporaryDir, + "sequence.file.base.directory" to "${temporaryDir}/sequence-file-base", + "reference.file.base.directory" to "${temporaryDir}/reference-file-base", + "output.file.base.directory" to "${temporaryDir}/output-file-base" + ) + val providedSystemProperties = System.getProperties().mapKeys { it.key as String } + systemProperties(defaultSystemProperties + providedSystemProperties) + + useJUnitPlatform { + includeTags(tags) + } + testLogging { + events("passed", "skipped", "failed") + showStandardStreams = true + } + retry { + maxRetries.set(5) + } + } +} + +val integrationTestsMap = mapOf( + "ui" to mapOf( + "tags" to "IntegrationTest & UI", + "excludeListeners" to "ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener" + ), + "service" to mapOf( + "tags" to "IntegrationTest & Service", + "excludeListeners" to "ca.corefacility.bioinformatics.irida.junit5.listeners.*" + ), + "rest" to mapOf( + "tags" to "IntegrationTest & Rest", + "excludeListeners" to "ca.corefacility.bioinformatics.irida.junit5.listeners.*" + ), + "galaxy" to mapOf( + "tags" to "IntegrationTest & Galaxy & !Pipeline", + "excludeListeners" to "ca.corefacility.bioinformatics.irida.junit5.listeners.*" + ), + "galaxyPipeline" to mapOf( + "tags" to "IntegrationTest & Galaxy & Pipeline", + "excludeListeners" to "ca.corefacility.bioinformatics.irida.junit5.listeners.*" + ), +) + +integrationTestsMap.forEach { + createIntegrationTestTask(it.key, it.value.get("tags"), it.value.get("excludeListeners")) +} + +// we do not want to build an executable war so skip this task +tasks.bootWar { enabled = false } + +tasks.war { + //dependsOn(":toolsListExport") + //archiveClassifier.set("") + exclude("node") + exclude("node_modules/") + exclude(".yarn/") + exclude("resources/css/") + exclude("resources/js/") + exclude("webpack*") + exclude(".yarn*") + exclude("package.json") + exclude("styles.js") + exclude("entries.js") + exclude(".eslintrc.js") + exclude("postcss.config.js") +} + +task("toolsListExport") { + classpath = java.sourceSets["main"].runtimeClasspath + mainClass.set("ca.corefacility.bioinformatics.irida.util.ToolsListExporter") + args("${buildDir}/tools-list.yml") +} + +openApi { + outputDir.set(file("${buildDir}/doc")) + outputFileName.set("open-api.json") + //forkProperties.set("-Dspring.profiles.active=dev,swagger -Dirida.db.profile=it -Dspring.datasource.url=jdbc:mysql://localhost:3306/irida_integration_test") +} + +tasks.named("processResources") { + dependsOn(":assembleFrontend") +} diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 00000000000..41d9927a4d4 Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 00000000000..aa991fceae6 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 00000000000..1b6c787337f --- /dev/null +++ b/gradlew @@ -0,0 +1,234 @@ +#!/bin/sh + +# +# Copyright © 2015-2021 the original authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +############################################################################## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# +############################################################################## + +# Attempt to set APP_HOME + +# Resolve links: $0 may be a link +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac +done + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit + +APP_NAME="Gradle" +APP_BASE_NAME=${0##*/} + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&2 + +die () { + echo + echo "$*" + echo + exit 1 +} >&2 + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; +esac + +CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD=$JAVA_HOME/jre/sh/java + else + JAVACMD=$JAVA_HOME/bin/java + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac +fi + +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + + # Now convert the arguments - kludge to limit ourselves to /bin/sh + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) + fi + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg + done +fi + +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 00000000000..107acd32c4e --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,89 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%" == "" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%" == "" set DIRNAME=. +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if "%ERRORLEVEL%" == "0" goto execute + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* + +:end +@rem End local scope for the variables with windows NT shell +if "%ERRORLEVEL%"=="0" goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/settings.gradle b/settings.gradle new file mode 100644 index 00000000000..b44242a8fdf --- /dev/null +++ b/settings.gradle @@ -0,0 +1,5 @@ +/* + * This file was generated by the Gradle 'init' task. + */ + +rootProject.name = 'irida' \ No newline at end of file