diff --git a/build.gradle b/build.gradle deleted file mode 100644 index 29dc879..0000000 --- a/build.gradle +++ /dev/null @@ -1,67 +0,0 @@ -plugins { - id("com.github.johnrengelman.shadow") version "8.1.1" - id("io.micronaut.application") version "4.0.3" - id("io.micronaut.aot") version "4.0.3" -} - -version = "0.1" -group = "org.jacksonlaboratory" - -repositories { - mavenCentral() -} - -dependencies { - annotationProcessor("io.micronaut:micronaut-http-validation") - annotationProcessor("io.micronaut.openapi:micronaut-openapi") - annotationProcessor("io.micronaut.serde:micronaut-serde-processor") - implementation("io.micronaut.neo4j:micronaut-neo4j-bolt") - implementation("io.micronaut.serde:micronaut-serde-jackson") - implementation("io.swagger.core.v3:swagger-annotations") - implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - implementation("org.monarchinitiative.phenol:phenol-io:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - implementation("org.monarchinitiative.phenol:phenol-annotations:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - compileOnly("org.graalvm.nativeimage:svm") - runtimeOnly("ch.qos.logback:logback-classic") - testImplementation("io.micronaut:micronaut-http-client") - testRuntimeOnly("org.neo4j.test:neo4j-harness") -} - - -application { - mainClass.set("org.jacksonlaboratory.Application") -} -java { - sourceCompatibility = JavaVersion.toVersion("17") - targetCompatibility = JavaVersion.toVersion("17") -} - -graalvmNative.toolchainDetection = false -micronaut { - runtime("netty") - testRuntime("junit5") - processing { - incremental(true) - annotations("org.jacksonlaboratory.*") - } - aot { - // Please review carefully the optimizations enabled below - // Check https://micronaut-projects.github.io/micronaut-aot/latest/guide/ for more details - optimizeServiceLoading = false - convertYamlToJava = false - precomputeOperations = true - cacheEnvironment = true - optimizeClassLoading = true - deduceEnvironment = true - optimizeNetty = true - } -} - - - diff --git a/gradle.properties b/gradle.properties deleted file mode 100644 index 65630f2..0000000 --- a/gradle.properties +++ /dev/null @@ -1 +0,0 @@ -micronautVersion=4.1.2 diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar deleted file mode 100644 index 033e24c..0000000 Binary files a/gradle/wrapper/gradle-wrapper.jar and /dev/null differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties deleted file mode 100644 index 9f4197d..0000000 --- a/gradle/wrapper/gradle-wrapper.properties +++ /dev/null @@ -1,7 +0,0 @@ -distributionBase=GRADLE_USER_HOME -distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip -networkTimeout=10000 -validateDistributionUrl=true -zipStoreBase=GRADLE_USER_HOME -zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew deleted file mode 100755 index fcb6fca..0000000 --- a/gradlew +++ /dev/null @@ -1,248 +0,0 @@ -#!/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/HEAD/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 - -# This is normally unused -# shellcheck disable=SC2034 -APP_BASE_NAME=${0##*/} -APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit - -# Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD=maximum - -warn () { - echo "$*" -} >&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: $JAVA_HOME - -Please set the JAVA_HOME variable in your environment to match the -location of your Java installation." - fi -else - JAVACMD=java - if ! command -v java >/dev/null 2>&1 - then - die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. - -Please set the JAVA_HOME variable in your environment to match the -location of your Java installation." - fi -fi - -# Increase the maximum file descriptors if we can. -if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then - case $MAX_FD in #( - max*) - # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. - # shellcheck disable=SC3045 - MAX_FD=$( ulimit -H -n ) || - warn "Could not query maximum file descriptor limit" - esac - case $MAX_FD in #( - '' | soft) :;; #( - *) - # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. - # shellcheck disable=SC3045 - ulimit -n "$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 - - -# 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"' - -# 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 "$CLASSPATH" \ - org.gradle.wrapper.GradleWrapperMain \ - "$@" - -# Stop when "xargs" is not available. -if ! command -v xargs >/dev/null 2>&1 -then - die "xargs is not available" -fi - -# 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 deleted file mode 100644 index 6689b85..0000000 --- a/gradlew.bat +++ /dev/null @@ -1,92 +0,0 @@ -@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=. -@rem This is normally unused -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% equ 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% equ 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! -set EXIT_CODE=%ERRORLEVEL% -if %EXIT_CODE% equ 0 set EXIT_CODE=1 -if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% -exit /b %EXIT_CODE% - -:mainEnd -if "%OS%"=="Windows_NT" endlocal - -:omega diff --git a/micronaut-cli.yml b/micronaut-cli.yml deleted file mode 100644 index 5d5eceb..0000000 --- a/micronaut-cli.yml +++ /dev/null @@ -1,6 +0,0 @@ -applicationType: default -defaultPackage: org.jacksonlaboratory -testFramework: junit -sourceLanguage: java -buildTool: gradle -features: [app-name, github-workflow-ci, graalvm, gradle, http-client-test, java, java-application, junit, logback, micronaut-aot, micronaut-build, micronaut-http-validation, neo4j-bolt, netty-server, openapi, properties, readme, serialization-jackson, shade] diff --git a/mvnw b/mvnw new file mode 100755 index 0000000..8d937f4 --- /dev/null +++ b/mvnw @@ -0,0 +1,308 @@ +#!/bin/sh +# ---------------------------------------------------------------------------- +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you 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 +# +# http://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. +# ---------------------------------------------------------------------------- + +# ---------------------------------------------------------------------------- +# Apache Maven Wrapper startup batch script, version 3.2.0 +# +# Required ENV vars: +# ------------------ +# JAVA_HOME - location of a JDK home dir +# +# Optional ENV vars +# ----------------- +# MAVEN_OPTS - parameters passed to the Java VM when running Maven +# e.g. to debug Maven itself, use +# set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000 +# MAVEN_SKIP_RC - flag to disable loading of mavenrc files +# ---------------------------------------------------------------------------- + +if [ -z "$MAVEN_SKIP_RC" ] ; then + + if [ -f /usr/local/etc/mavenrc ] ; then + . /usr/local/etc/mavenrc + fi + + if [ -f /etc/mavenrc ] ; then + . /etc/mavenrc + fi + + if [ -f "$HOME/.mavenrc" ] ; then + . "$HOME/.mavenrc" + fi + +fi + +# OS specific support. $var _must_ be set to either true or false. +cygwin=false; +darwin=false; +mingw=false +case "$(uname)" in + CYGWIN*) cygwin=true ;; + MINGW*) mingw=true;; + Darwin*) darwin=true + # Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home + # See https://developer.apple.com/library/mac/qa/qa1170/_index.html + if [ -z "$JAVA_HOME" ]; then + if [ -x "/usr/libexec/java_home" ]; then + JAVA_HOME="$(/usr/libexec/java_home)"; export JAVA_HOME + else + JAVA_HOME="/Library/Java/Home"; export JAVA_HOME + fi + fi + ;; +esac + +if [ -z "$JAVA_HOME" ] ; then + if [ -r /etc/gentoo-release ] ; then + JAVA_HOME=$(java-config --jre-home) + fi +fi + +# For Cygwin, ensure paths are in UNIX format before anything is touched +if $cygwin ; then + [ -n "$JAVA_HOME" ] && + JAVA_HOME=$(cygpath --unix "$JAVA_HOME") + [ -n "$CLASSPATH" ] && + CLASSPATH=$(cygpath --path --unix "$CLASSPATH") +fi + +# For Mingw, ensure paths are in UNIX format before anything is touched +if $mingw ; then + [ -n "$JAVA_HOME" ] && [ -d "$JAVA_HOME" ] && + JAVA_HOME="$(cd "$JAVA_HOME" || (echo "cannot cd into $JAVA_HOME."; exit 1); pwd)" +fi + +if [ -z "$JAVA_HOME" ]; then + javaExecutable="$(which javac)" + if [ -n "$javaExecutable" ] && ! [ "$(expr "\"$javaExecutable\"" : '\([^ ]*\)')" = "no" ]; then + # readlink(1) is not available as standard on Solaris 10. + readLink=$(which readlink) + if [ ! "$(expr "$readLink" : '\([^ ]*\)')" = "no" ]; then + if $darwin ; then + javaHome="$(dirname "\"$javaExecutable\"")" + javaExecutable="$(cd "\"$javaHome\"" && pwd -P)/javac" + else + javaExecutable="$(readlink -f "\"$javaExecutable\"")" + fi + javaHome="$(dirname "\"$javaExecutable\"")" + javaHome=$(expr "$javaHome" : '\(.*\)/bin') + JAVA_HOME="$javaHome" + export JAVA_HOME + fi + fi +fi + +if [ -z "$JAVACMD" ] ; then + 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 + else + JAVACMD="$(\unset -f command 2>/dev/null; \command -v java)" + fi +fi + +if [ ! -x "$JAVACMD" ] ; then + echo "Error: JAVA_HOME is not defined correctly." >&2 + echo " We cannot execute $JAVACMD" >&2 + exit 1 +fi + +if [ -z "$JAVA_HOME" ] ; then + echo "Warning: JAVA_HOME environment variable is not set." +fi + +# traverses directory structure from process work directory to filesystem root +# first directory with .mvn subdirectory is considered project base directory +find_maven_basedir() { + if [ -z "$1" ] + then + echo "Path not specified to find_maven_basedir" + return 1 + fi + + basedir="$1" + wdir="$1" + while [ "$wdir" != '/' ] ; do + if [ -d "$wdir"/.mvn ] ; then + basedir=$wdir + break + fi + # workaround for JBEAP-8937 (on Solaris 10/Sparc) + if [ -d "${wdir}" ]; then + wdir=$(cd "$wdir/.." || exit 1; pwd) + fi + # end of workaround + done + printf '%s' "$(cd "$basedir" || exit 1; pwd)" +} + +# concatenates all lines of a file +concat_lines() { + if [ -f "$1" ]; then + # Remove \r in case we run on Windows within Git Bash + # and check out the repository with auto CRLF management + # enabled. Otherwise, we may read lines that are delimited with + # \r\n and produce $'-Xarg\r' rather than -Xarg due to word + # splitting rules. + tr -s '\r\n' ' ' < "$1" + fi +} + +log() { + if [ "$MVNW_VERBOSE" = true ]; then + printf '%s\n' "$1" + fi +} + +BASE_DIR=$(find_maven_basedir "$(dirname "$0")") +if [ -z "$BASE_DIR" ]; then + exit 1; +fi + +MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}; export MAVEN_PROJECTBASEDIR +log "$MAVEN_PROJECTBASEDIR" + +########################################################################################## +# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central +# This allows using the maven wrapper in projects that prohibit checking in binary data. +########################################################################################## +wrapperJarPath="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" +if [ -r "$wrapperJarPath" ]; then + log "Found $wrapperJarPath" +else + log "Couldn't find $wrapperJarPath, downloading it ..." + + if [ -n "$MVNW_REPOURL" ]; then + wrapperUrl="$MVNW_REPOURL/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar" + else + wrapperUrl="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar" + fi + while IFS="=" read -r key value; do + # Remove '\r' from value to allow usage on windows as IFS does not consider '\r' as a separator ( considers space, tab, new line ('\n'), and custom '=' ) + safeValue=$(echo "$value" | tr -d '\r') + case "$key" in (wrapperUrl) wrapperUrl="$safeValue"; break ;; + esac + done < "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.properties" + log "Downloading from: $wrapperUrl" + + if $cygwin; then + wrapperJarPath=$(cygpath --path --windows "$wrapperJarPath") + fi + + if command -v wget > /dev/null; then + log "Found wget ... using wget" + [ "$MVNW_VERBOSE" = true ] && QUIET="" || QUIET="--quiet" + if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then + wget $QUIET "$wrapperUrl" -O "$wrapperJarPath" || rm -f "$wrapperJarPath" + else + wget $QUIET --http-user="$MVNW_USERNAME" --http-password="$MVNW_PASSWORD" "$wrapperUrl" -O "$wrapperJarPath" || rm -f "$wrapperJarPath" + fi + elif command -v curl > /dev/null; then + log "Found curl ... using curl" + [ "$MVNW_VERBOSE" = true ] && QUIET="" || QUIET="--silent" + if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then + curl $QUIET -o "$wrapperJarPath" "$wrapperUrl" -f -L || rm -f "$wrapperJarPath" + else + curl $QUIET --user "$MVNW_USERNAME:$MVNW_PASSWORD" -o "$wrapperJarPath" "$wrapperUrl" -f -L || rm -f "$wrapperJarPath" + fi + else + log "Falling back to using Java to download" + javaSource="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/MavenWrapperDownloader.java" + javaClass="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/MavenWrapperDownloader.class" + # For Cygwin, switch paths to Windows format before running javac + if $cygwin; then + javaSource=$(cygpath --path --windows "$javaSource") + javaClass=$(cygpath --path --windows "$javaClass") + fi + if [ -e "$javaSource" ]; then + if [ ! -e "$javaClass" ]; then + log " - Compiling MavenWrapperDownloader.java ..." + ("$JAVA_HOME/bin/javac" "$javaSource") + fi + if [ -e "$javaClass" ]; then + log " - Running MavenWrapperDownloader.java ..." + ("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$wrapperUrl" "$wrapperJarPath") || rm -f "$wrapperJarPath" + fi + fi + fi +fi +########################################################################################## +# End of extension +########################################################################################## + +# If specified, validate the SHA-256 sum of the Maven wrapper jar file +wrapperSha256Sum="" +while IFS="=" read -r key value; do + case "$key" in (wrapperSha256Sum) wrapperSha256Sum=$value; break ;; + esac +done < "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.properties" +if [ -n "$wrapperSha256Sum" ]; then + wrapperSha256Result=false + if command -v sha256sum > /dev/null; then + if echo "$wrapperSha256Sum $wrapperJarPath" | sha256sum -c > /dev/null 2>&1; then + wrapperSha256Result=true + fi + elif command -v shasum > /dev/null; then + if echo "$wrapperSha256Sum $wrapperJarPath" | shasum -a 256 -c > /dev/null 2>&1; then + wrapperSha256Result=true + fi + else + echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available." + echo "Please install either command, or disable validation by removing 'wrapperSha256Sum' from your maven-wrapper.properties." + exit 1 + fi + if [ $wrapperSha256Result = false ]; then + echo "Error: Failed to validate Maven wrapper SHA-256, your Maven wrapper might be compromised." >&2 + echo "Investigate or delete $wrapperJarPath to attempt a clean download." >&2 + echo "If you updated your Maven version, you need to update the specified wrapperSha256Sum property." >&2 + exit 1 + fi +fi + +MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS" + +# For Cygwin, switch paths to Windows format before running java +if $cygwin; then + [ -n "$JAVA_HOME" ] && + JAVA_HOME=$(cygpath --path --windows "$JAVA_HOME") + [ -n "$CLASSPATH" ] && + CLASSPATH=$(cygpath --path --windows "$CLASSPATH") + [ -n "$MAVEN_PROJECTBASEDIR" ] && + MAVEN_PROJECTBASEDIR=$(cygpath --path --windows "$MAVEN_PROJECTBASEDIR") +fi + +# Provide a "standardized" way to retrieve the CLI args that will +# work with both Windows and non-Windows executions. +MAVEN_CMD_LINE_ARGS="$MAVEN_CONFIG $*" +export MAVEN_CMD_LINE_ARGS + +WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain + +# shellcheck disable=SC2086 # safe args +exec "$JAVACMD" \ + $MAVEN_OPTS \ + $MAVEN_DEBUG_OPTS \ + -classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \ + "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \ + ${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@" diff --git a/mvnw.cmd b/mvnw.cmd new file mode 100644 index 0000000..f80fbad --- /dev/null +++ b/mvnw.cmd @@ -0,0 +1,205 @@ +@REM ---------------------------------------------------------------------------- +@REM Licensed to the Apache Software Foundation (ASF) under one +@REM or more contributor license agreements. See the NOTICE file +@REM distributed with this work for additional information +@REM regarding copyright ownership. The ASF licenses this file +@REM to you under the Apache License, Version 2.0 (the +@REM "License"); you may not use this file except in compliance +@REM with the License. You may obtain a copy of the License at +@REM +@REM http://www.apache.org/licenses/LICENSE-2.0 +@REM +@REM Unless required by applicable law or agreed to in writing, +@REM software distributed under the License is distributed on an +@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +@REM KIND, either express or implied. See the License for the +@REM specific language governing permissions and limitations +@REM under the License. +@REM ---------------------------------------------------------------------------- + +@REM ---------------------------------------------------------------------------- +@REM Apache Maven Wrapper startup batch script, version 3.2.0 +@REM +@REM Required ENV vars: +@REM JAVA_HOME - location of a JDK home dir +@REM +@REM Optional ENV vars +@REM MAVEN_BATCH_ECHO - set to 'on' to enable the echoing of the batch commands +@REM MAVEN_BATCH_PAUSE - set to 'on' to wait for a keystroke before ending +@REM MAVEN_OPTS - parameters passed to the Java VM when running Maven +@REM e.g. to debug Maven itself, use +@REM set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000 +@REM MAVEN_SKIP_RC - flag to disable loading of mavenrc files +@REM ---------------------------------------------------------------------------- + +@REM Begin all REM lines with '@' in case MAVEN_BATCH_ECHO is 'on' +@echo off +@REM set title of command window +title %0 +@REM enable echoing by setting MAVEN_BATCH_ECHO to 'on' +@if "%MAVEN_BATCH_ECHO%" == "on" echo %MAVEN_BATCH_ECHO% + +@REM set %HOME% to equivalent of $HOME +if "%HOME%" == "" (set "HOME=%HOMEDRIVE%%HOMEPATH%") + +@REM Execute a user defined script before this one +if not "%MAVEN_SKIP_RC%" == "" goto skipRcPre +@REM check for pre script, once with legacy .bat ending and once with .cmd ending +if exist "%USERPROFILE%\mavenrc_pre.bat" call "%USERPROFILE%\mavenrc_pre.bat" %* +if exist "%USERPROFILE%\mavenrc_pre.cmd" call "%USERPROFILE%\mavenrc_pre.cmd" %* +:skipRcPre + +@setlocal + +set ERROR_CODE=0 + +@REM To isolate internal variables from possible post scripts, we use another setlocal +@setlocal + +@REM ==== START VALIDATION ==== +if not "%JAVA_HOME%" == "" goto OkJHome + +echo. +echo Error: JAVA_HOME not found in your environment. >&2 +echo Please set the JAVA_HOME variable in your environment to match the >&2 +echo location of your Java installation. >&2 +echo. +goto error + +:OkJHome +if exist "%JAVA_HOME%\bin\java.exe" goto init + +echo. +echo Error: JAVA_HOME is set to an invalid directory. >&2 +echo JAVA_HOME = "%JAVA_HOME%" >&2 +echo Please set the JAVA_HOME variable in your environment to match the >&2 +echo location of your Java installation. >&2 +echo. +goto error + +@REM ==== END VALIDATION ==== + +:init + +@REM Find the project base dir, i.e. the directory that contains the folder ".mvn". +@REM Fallback to current working directory if not found. + +set MAVEN_PROJECTBASEDIR=%MAVEN_BASEDIR% +IF NOT "%MAVEN_PROJECTBASEDIR%"=="" goto endDetectBaseDir + +set EXEC_DIR=%CD% +set WDIR=%EXEC_DIR% +:findBaseDir +IF EXIST "%WDIR%"\.mvn goto baseDirFound +cd .. +IF "%WDIR%"=="%CD%" goto baseDirNotFound +set WDIR=%CD% +goto findBaseDir + +:baseDirFound +set MAVEN_PROJECTBASEDIR=%WDIR% +cd "%EXEC_DIR%" +goto endDetectBaseDir + +:baseDirNotFound +set MAVEN_PROJECTBASEDIR=%EXEC_DIR% +cd "%EXEC_DIR%" + +:endDetectBaseDir + +IF NOT EXIST "%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config" goto endReadAdditionalConfig + +@setlocal EnableExtensions EnableDelayedExpansion +for /F "usebackq delims=" %%a in ("%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config") do set JVM_CONFIG_MAVEN_PROPS=!JVM_CONFIG_MAVEN_PROPS! %%a +@endlocal & set JVM_CONFIG_MAVEN_PROPS=%JVM_CONFIG_MAVEN_PROPS% + +:endReadAdditionalConfig + +SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe" +set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar" +set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain + +set WRAPPER_URL="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar" + +FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO ( + IF "%%A"=="wrapperUrl" SET WRAPPER_URL=%%B +) + +@REM Extension to allow automatically downloading the maven-wrapper.jar from Maven-central +@REM This allows using the maven wrapper in projects that prohibit checking in binary data. +if exist %WRAPPER_JAR% ( + if "%MVNW_VERBOSE%" == "true" ( + echo Found %WRAPPER_JAR% + ) +) else ( + if not "%MVNW_REPOURL%" == "" ( + SET WRAPPER_URL="%MVNW_REPOURL%/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar" + ) + if "%MVNW_VERBOSE%" == "true" ( + echo Couldn't find %WRAPPER_JAR%, downloading it ... + echo Downloading from: %WRAPPER_URL% + ) + + powershell -Command "&{"^ + "$webclient = new-object System.Net.WebClient;"^ + "if (-not ([string]::IsNullOrEmpty('%MVNW_USERNAME%') -and [string]::IsNullOrEmpty('%MVNW_PASSWORD%'))) {"^ + "$webclient.Credentials = new-object System.Net.NetworkCredential('%MVNW_USERNAME%', '%MVNW_PASSWORD%');"^ + "}"^ + "[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12; $webclient.DownloadFile('%WRAPPER_URL%', '%WRAPPER_JAR%')"^ + "}" + if "%MVNW_VERBOSE%" == "true" ( + echo Finished downloading %WRAPPER_JAR% + ) +) +@REM End of extension + +@REM If specified, validate the SHA-256 sum of the Maven wrapper jar file +SET WRAPPER_SHA_256_SUM="" +FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO ( + IF "%%A"=="wrapperSha256Sum" SET WRAPPER_SHA_256_SUM=%%B +) +IF NOT %WRAPPER_SHA_256_SUM%=="" ( + powershell -Command "&{"^ + "$hash = (Get-FileHash \"%WRAPPER_JAR%\" -Algorithm SHA256).Hash.ToLower();"^ + "If('%WRAPPER_SHA_256_SUM%' -ne $hash){"^ + " Write-Output 'Error: Failed to validate Maven wrapper SHA-256, your Maven wrapper might be compromised.';"^ + " Write-Output 'Investigate or delete %WRAPPER_JAR% to attempt a clean download.';"^ + " Write-Output 'If you updated your Maven version, you need to update the specified wrapperSha256Sum property.';"^ + " exit 1;"^ + "}"^ + "}" + if ERRORLEVEL 1 goto error +) + +@REM Provide a "standardized" way to retrieve the CLI args that will +@REM work with both Windows and non-Windows executions. +set MAVEN_CMD_LINE_ARGS=%* + +%MAVEN_JAVA_EXE% ^ + %JVM_CONFIG_MAVEN_PROPS% ^ + %MAVEN_OPTS% ^ + %MAVEN_DEBUG_OPTS% ^ + -classpath %WRAPPER_JAR% ^ + "-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" ^ + %WRAPPER_LAUNCHER% %MAVEN_CONFIG% %* +if ERRORLEVEL 1 goto error +goto end + +:error +set ERROR_CODE=1 + +:end +@endlocal & set ERROR_CODE=%ERROR_CODE% + +if not "%MAVEN_SKIP_RC%"=="" goto skipRcPost +@REM check for post script, once with legacy .bat ending and once with .cmd ending +if exist "%USERPROFILE%\mavenrc_post.bat" call "%USERPROFILE%\mavenrc_post.bat" +if exist "%USERPROFILE%\mavenrc_post.cmd" call "%USERPROFILE%\mavenrc_post.cmd" +:skipRcPost + +@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on' +if "%MAVEN_BATCH_PAUSE%"=="on" pause + +if "%MAVEN_TERMINATE_CMD%"=="on" exit %ERROR_CODE% + +cmd /C exit /B %ERROR_CODE% diff --git a/oan-etl/build.gradle b/oan-etl/build.gradle deleted file mode 100644 index 5f77fcb..0000000 --- a/oan-etl/build.gradle +++ /dev/null @@ -1,67 +0,0 @@ -plugins { - id("com.github.johnrengelman.shadow") version "8.1.1" - id("io.micronaut.application") version "4.0.3" - id('jacoco') -} - -group = 'org.jax' -version = '0.0.2-alpha' - -repositories { - mavenCentral() -} - -dependencies { - implementation project(':oan-model') - annotationProcessor("info.picocli:picocli-codegen") - annotationProcessor("io.micronaut.serde:micronaut-serde-processor") - testAnnotationProcessor("io.micronaut:micronaut-inject-java") - implementation("info.picocli:picocli") - implementation("io.micronaut.picocli:micronaut-picocli") - implementation("io.micronaut.serde:micronaut-serde-jackson") - implementation("io.micronaut.neo4j:micronaut-neo4j-bolt") - implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - implementation("org.monarchinitiative.phenol:phenol-io:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - implementation("org.monarchinitiative.phenol:phenol-annotations:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - runtimeOnly("ch.qos.logback:logback-classic") - testImplementation("io.micronaut.test:micronaut-test-junit5") - testImplementation("org.neo4j.test:neo4j-harness") - testRuntimeOnly("javax.validation:validation-api:2.0.1.Final") - testRuntimeOnly("javax.annotation:javax.annotation-api:1.3.2") - testRuntimeOnly('javax.ws.rs:javax.ws.rs-api:2.1.1') - testImplementation platform('org.junit:junit-bom:5.9.1') - testImplementation('org.junit.jupiter:junit-jupiter') -} - -application { - mainClass.set("org.jax.oan.GraphCommand") -} -java { - sourceCompatibility = JavaVersion.toVersion("17") - targetCompatibility = JavaVersion.toVersion("17") -} - -micronaut { - testRuntime("junit5") - processing { - incremental(true) - annotations("org.jacksonlaboratory.*") - } -} - -test { - finalizedBy jacocoTestReport // report is always generated after tests run -} -jacocoTestReport { - dependsOn test // tests are required to run before generating the report - reports { - xml.required = false - csv.required = false - } -} diff --git a/oan-etl/pom.xml b/oan-etl/pom.xml new file mode 100644 index 0000000..ae8acc2 --- /dev/null +++ b/oan-etl/pom.xml @@ -0,0 +1,157 @@ + + 4.0.0 + + + netty + + + org.jax.oan + ontology-annotation-network + 1.0-SNAPSHOT + + + oan-etl + oan-etl + + oan-etl is a micronaut cli application for loading ontology annotation to neo4j + + + + org.jax.oan + oan-model + ${project.parent.version} + + + info.picocli + picocli + + + io.micronaut.picocli + micronaut-picocli + + + io.micronaut.serde + micronaut-serde-jackson + + + io.micronaut.neo4j + micronaut-neo4j-bolt + + + org.monarchinitiative.phenol + phenol-io + + + org.monarchinitiative.phenol + phenol-core + + + org.monarchinitiative.phenol + phenol-annotations + + + + javax.validation + validation-api + test + + + javax.annotation + javax.annotation-api + test + + + javax.ws.rs + javax.ws.rs-api + test + + + io.micronaut + micronaut-http-client + test + + + io.micronaut.test + micronaut-test-junit5 + test + + + io.micronaut + micronaut-inject-java + test + + + org.neo4j.test + neo4j-harness + test + + + + + + + + org.jacoco + jacoco-maven-plugin + + + jacoco-report + verify + + report + + + + + + + + + + release + + + + src/main/resources + true + + + + + org.apache.maven.plugins + maven-dependency-plugin + 3.1.2 + + + copy-dependencies + package + + copy-dependencies + + + compile + ${project.build.directory}/lib + + + + + + + org.apache.maven.plugins + maven-jar-plugin + + + + true + lib/ + org.jax.oan.GraphCommand + + + + + + + + + + diff --git a/oan-etl/src/main/java/org/jax/oan/ontology/HpoGraphLoader.java b/oan-etl/src/main/java/org/jax/oan/ontology/HpoGraphLoader.java index 2ff8fb3..6625089 100644 --- a/oan-etl/src/main/java/org/jax/oan/ontology/HpoGraphLoader.java +++ b/oan-etl/src/main/java/org/jax/oan/ontology/HpoGraphLoader.java @@ -9,14 +9,11 @@ import org.monarchinitiative.phenol.annotations.formats.hpo.HpoAssociationData; import org.monarchinitiative.phenol.annotations.formats.hpo.HpoGeneAnnotation; import org.monarchinitiative.phenol.annotations.formats.hpo.HpoOnset; -import org.monarchinitiative.phenol.annotations.formats.hpo.category.HpoCategory; import org.monarchinitiative.phenol.annotations.formats.hpo.category.HpoCategoryMap; import org.monarchinitiative.phenol.annotations.io.hpo.DiseaseDatabase; -import org.monarchinitiative.phenol.annotations.io.hpo.HpoAnnotationLine; import org.monarchinitiative.phenol.annotations.io.hpo.HpoaDiseaseDataContainer; import org.monarchinitiative.phenol.annotations.io.hpo.HpoaDiseaseDataLoader; import org.monarchinitiative.phenol.io.OntologyLoader; -import org.monarchinitiative.phenol.ontology.algo.OntologyTerms; import org.monarchinitiative.phenol.ontology.data.Ontology; import org.monarchinitiative.phenol.ontology.data.Term; import org.monarchinitiative.phenol.ontology.data.TermId; diff --git a/oan-etl/src/main/resources/application-test.properties b/oan-etl/src/main/resources/application-test.properties new file mode 100644 index 0000000..ab3327a --- /dev/null +++ b/oan-etl/src/main/resources/application-test.properties @@ -0,0 +1 @@ +neo4j.embedded.ephemeral=true diff --git a/oan-etl/src/main/resources/application-test.yml b/oan-etl/src/main/resources/application-test.yml deleted file mode 100644 index b9846ee..0000000 --- a/oan-etl/src/main/resources/application-test.yml +++ /dev/null @@ -1,3 +0,0 @@ -neo4j: - embedded: - ephemeral: true diff --git a/oan-etl/src/main/resources/application.properties b/oan-etl/src/main/resources/application.properties new file mode 100644 index 0000000..f544bea --- /dev/null +++ b/oan-etl/src/main/resources/application.properties @@ -0,0 +1,4 @@ +neo4j.uri= bolt://localhost:7687 +neo4j.username=neo4j +neo4j.password=password + diff --git a/oan-etl/src/main/resources/application.yml b/oan-etl/src/main/resources/application.yml deleted file mode 100644 index 634af47..0000000 --- a/oan-etl/src/main/resources/application.yml +++ /dev/null @@ -1,4 +0,0 @@ -neo4j: - uri: bolt://localhost:7687 - username: neo4j - password: password diff --git a/oan-etl/src/test/java/org/jax/oan/ontology/HpoGraphLoaderTest.java b/oan-etl/src/test/java/org/jax/oan/ontology/HpoGraphLoaderTest.java index 2ed321f..96f71a1 100644 --- a/oan-etl/src/test/java/org/jax/oan/ontology/HpoGraphLoaderTest.java +++ b/oan-etl/src/test/java/org/jax/oan/ontology/HpoGraphLoaderTest.java @@ -50,7 +50,6 @@ public HpoGraphLoaderTest(Driver driver, HpoGraphLoader graphLoader, Operations void configureGraph(HpoAssociationData associations, HpoaDiseaseDataContainer container, Ontology ontology, Path loincPath){ - List termIds = ontology.getTerms().stream().map(Term::id).toList(); operations.truncate(); graphLoader.phenotypes(session, ontology.getTerms(), Map.of()); graphLoader.diseases(session, container); diff --git a/oan-model/build.gradle b/oan-model/build.gradle deleted file mode 100644 index 36d9007..0000000 --- a/oan-model/build.gradle +++ /dev/null @@ -1,34 +0,0 @@ -plugins { - id 'java-library' - id('jacoco') -} - -group = 'org.jax' -version = '0.1' - -repositories { - mavenCentral() -} - -dependencies { - testImplementation platform('org.junit:junit-bom:5.9.1') - implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - testImplementation 'org.junit.jupiter:junit-jupiter' -} - -test { - useJUnitPlatform() -} - -test { - finalizedBy jacocoTestReport // report is always generated after tests run -} -jacocoTestReport { - dependsOn test // tests are required to run before generating the report - reports { - xml.required = false - csv.required = false - } -} diff --git a/oan-model/pom.xml b/oan-model/pom.xml new file mode 100644 index 0000000..8946200 --- /dev/null +++ b/oan-model/pom.xml @@ -0,0 +1,38 @@ + + 4.0.0 + + + org.jax.oan + ontology-annotation-network + 1.0-SNAPSHOT + + + oan-model + oan-model + + oan-model contains the common models + + + + org.monarchinitiative.phenol + phenol-core + + + + + + org.jacoco + jacoco-maven-plugin + + + report + test + + report + + + + + + + diff --git a/oan-rest/build.gradle b/oan-rest/build.gradle deleted file mode 100644 index f74fe54..0000000 --- a/oan-rest/build.gradle +++ /dev/null @@ -1,85 +0,0 @@ -plugins { - id("com.github.johnrengelman.shadow") version "8.1.1" - id("io.micronaut.application") version "4.0.3" - id("io.micronaut.aot") version "4.0.3" - id('jacoco') -} - -version = "0.1" -group = "org.jax" - -repositories { - mavenCentral() -} - -dependencies { - implementation project(":oan-model") - implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){ - exclude group: 'org.slf4j', module: 'slf4j-api' - } - annotationProcessor("io.micronaut:micronaut-http-validation") - annotationProcessor("io.micronaut.openapi:micronaut-openapi") - annotationProcessor("io.micronaut.serde:micronaut-serde-processor") - implementation("io.micronaut.neo4j:micronaut-neo4j-bolt") - implementation("io.micronaut.serde:micronaut-serde-jackson") - implementation("io.swagger.core.v3:swagger-annotations") - compileOnly("org.graalvm.nativeimage:svm") - runtimeOnly("ch.qos.logback:logback-classic") - - testImplementation("io.micronaut:micronaut-http-client") - testImplementation("io.micronaut.test:micronaut-test-rest-assured") - testRuntimeOnly("org.neo4j.test:neo4j-harness") - testImplementation('org.hamcrest:hamcrest-all:1.3') - testImplementation('org.junit.jupiter:junit-jupiter') - testImplementation("io.micronaut.test:micronaut-test-junit5") - testImplementation("org.mockito:mockito-junit-jupiter") - testRuntimeOnly('javax.ws.rs:javax.ws.rs-api:2.1.1') - testRuntimeOnly("javax.validation:validation-api:2.0.1.Final") - testRuntimeOnly("javax.annotation:javax.annotation-api:1.3.2") - testRuntimeOnly("org.neo4j.test:neo4j-harness") - -} - - -application { - mainClass.set("org.jax.oan.Application") -} -java { - sourceCompatibility = JavaVersion.toVersion("17") - targetCompatibility = JavaVersion.toVersion("17") -} - -graalvmNative.toolchainDetection = false -micronaut { - runtime("netty") - testRuntime("junit5") - processing { - incremental(true) - annotations("org.jax.oan.*") - } - aot { - // Please review carefully the optimizations enabled below - // Check https://micronaut-projects.github.io/micronaut-aot/latest/guide/ for more details - optimizeServiceLoading = false - convertYamlToJava = false - precomputeOperations = true - cacheEnvironment = true - optimizeClassLoading = true - deduceEnvironment = true - optimizeNetty = true - } -} - - -test { - finalizedBy jacocoTestReport // report is always generated after tests run -} - -jacocoTestReport { - dependsOn test // tests are required to run before generating the report - reports { - xml.required = false - csv.required = false - } -} - diff --git a/oan-rest/pom.xml b/oan-rest/pom.xml new file mode 100644 index 0000000..37bbf2f --- /dev/null +++ b/oan-rest/pom.xml @@ -0,0 +1,104 @@ + + 4.0.0 + + + org.jax.oan + ontology-annotation-network + 1.0-SNAPSHOT + + + oan-rest + oan-rest + + oan-rest is the micronaut rest-api + + + + org.jax.oan + oan-model + ${project.parent.version} + + + io.micronaut + micronaut-inject-java + + + org.monarchinitiative.phenol + phenol-core + + + io.micronaut.neo4j + micronaut-neo4j-bolt + + + io.micronaut.serde + micronaut-serde-jackson + + + io.micronaut + micronaut-http-server-netty + + + io.swagger.core.v3 + swagger-annotations + + + javax.validation + validation-api + test + + + javax.annotation + javax.annotation-api + test + + + javax.ws.rs + javax.ws.rs-api + test + + + io.micronaut + micronaut-http-client + test + + + io.micronaut.test + micronaut-test-junit5 + test + + + io.micronaut + micronaut-inject-java + test + + + org.neo4j.test + neo4j-harness + test + + + io.micronaut.test + micronaut-test-rest-assured + + + + + + + org.jacoco + jacoco-maven-plugin + + + report + test + + report + + + + + + + + diff --git a/oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java b/oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java index 76d9a85..3cfa169 100644 --- a/oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java +++ b/oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java @@ -20,7 +20,6 @@ import java.io.IOException; import java.io.PrintWriter; import java.nio.file.Files; -import java.util.List; import java.util.Map; import static org.jax.oan.TestData.*; diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000..6fb0112 --- /dev/null +++ b/pom.xml @@ -0,0 +1,309 @@ + + + + 4.0.0 + + org.jax.oan + ontology-annotation-network + pom + 1.0-SNAPSHOT + + ontology-annotation-network + https://github.com/TheJacksonLaboratory/ontology-annotation-network + + + UTF-8 + UTF-8 + 17 + ${java.version} + ${java.version} + + 4.1.0 + 2.0.3 + 2.2 + 5.10.0 + 5.3.1 + 2.1.1 + 5.13.0 + 6.2.0 + 2.2.0 + 2.2.19 + 4.7.5 + 1.4.11 + + + + oan-model + oan-etl + oan-rest + + + + + Michael Gargano + michael.gargano@jax.org + The Jackson Laboratory + https://www.jax.org + + + + + + + io.micronaut.picocli + micronaut-picocli + 5.0.1 + + + org.monarchinitiative.phenol + phenol-io + ${phenol.version} + + + org.slf4j + slf4j-api + + + + + org.monarchinitiative.phenol + phenol-core + ${phenol.version} + + + org.slf4j + slf4j-api + + + + + org.monarchinitiative.phenol + phenol-annotations + ${phenol.version} + + + org.slf4j + slf4j-api + + + + + io.micronaut + micronaut-inject-java + ${micronaut.version} + compile + + + io.micronaut.serde + micronaut-serde-jackson + ${micronaut-serde.version} + + + io.micronaut.serde + micronaut-serde-processor + ${micronaut-serde.version} + + + io.micronaut.neo4j + micronaut-neo4j-bolt + ${micronaut-neo4j.version} + + + ch.qos.logback + logback-classic + 1.4.8 + + + io.swagger.core.v3 + swagger-annotations + ${swagger.version} + + + info.picocli + picocli + ${picocli.version} + + + io.micronaut + micronaut-inject-java + ${micronaut.version} + test + + + io.micronaut.test + micronaut-test-rest-assured + ${micronaut.version} + test + + + io.micronaut.test + micronaut-test-junit5 + ${micronaut.version} + test + + + io.micronaut + micronaut-http-server-netty + ${micronaut.version} + compile + + + io.micronaut + micronaut-http-client + ${micronaut.version} + test + + + org.neo4j.test + neo4j-harness + ${neo4j.version} + test + + + org.junit.jupiter + junit-jupiter + ${junit-jupiter.version} + test + + + org.mockito + mockito-junit-jupiter + ${mockito.version} + test + + + org.hamcrest + hamcrest + ${hamcrest.version} + test + + + javax.ws.rs + javax.ws.rs-api + ${javars.version} + test + + + javax.annotation + javax.annotation-api + 1.3.2 + test + + + javax.validation + validation-api + 2.0.1.Final + test + + + + + + + org.junit.jupiter + junit-jupiter + + + ch.qos.logback + logback-classic + + + + + + ossrh + https://s01.oss.sonatype.org/content/repositories/snapshots + + true + + + + + + + + org.jacoco + jacoco-maven-plugin + 0.8.11 + + + prepare-agent + + prepare-agent + + + + + + + + + io.micronaut.maven + micronaut-maven-plugin + + + + maven-clean-plugin + 3.1.0 + + + + maven-resources-plugin + 3.0.2 + + + maven-compiler-plugin + 3.8.0 + + + + + + + io.micronaut.serde + micronaut-serde-processor + ${micronaut-serde.version} + + + io.micronaut + micronaut-inject-java + ${micronaut.version} + + + info.picocli + picocli-codegen + ${picocli.version} + + + + + + maven-surefire-plugin + 2.22.1 + + + maven-jar-plugin + 3.0.2 + + + maven-install-plugin + 2.5.2 + + + maven-deploy-plugin + 2.8.2 + + + + maven-site-plugin + 3.7.1 + + + maven-project-info-reports-plugin + 3.0.0 + + + + + diff --git a/settings.gradle b/settings.gradle deleted file mode 100644 index 7c6de27..0000000 --- a/settings.gradle +++ /dev/null @@ -1,6 +0,0 @@ - -rootProject.name="ontology-annotation-network" -include 'oan-rest' -include 'oan-etl' -include 'oan-model' -