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Unverified Commit 0436d74d authored by Martin Weise's avatar Martin Weise
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Added Invenio Support for deposit a draft

parent f8c58ea7
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2 merge requests!81New stable release,!80Multiple features connected with user management and ownership of databases
This commit is part of merge request !81. Comments created here will be created in the context of that merge request.
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......@@ -122,6 +122,25 @@ services:
logging:
driver: json-file
fda-document-service:
restart: on-failure
container_name: fda-document-service
hostname: fda-document-service
build: ./fda-document-service
image: fda-document-service
networks:
fda-public:
environment:
SPRING_PROFILES_ACTIVE: docker
TZ: Europe/Vienna
ports:
- "9099:9099"
depends_on:
fda-discovery-service:
condition: service_healthy
logging:
driver: json-file
fda-authentication-service:
restart: on-failure
container_name: fda-authentication-service
......
HELP.md
target/
!.mvn/wrapper/maven-wrapper.jar
!**/src/main/**/target/
!**/src/test/**/target/
### Generated ###
ready
service_ready
### STS ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache
### IntelliJ IDEA ###
.idea/
*.iws
*.iml
*.ipr
### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
build/
!**/src/main/**/build/
!**/src/test/**/build/
### VS Code ###
.vscode/
###### FIRST STAGE ######
FROM fda-metadata-db:latest as dependency
MAINTAINER Martin Weise <martin.weise@tuwien.ac.at>
###### SECOND STAGE ######
FROM maven:slim as build
COPY ./pom.xml ./
RUN mvn -fn -B dependency:go-offline > /dev/null
COPY --from=dependency /root/.m2/repository/at/tuwien /root/.m2/repository/at/tuwien
COPY ./rest-service ./rest-service
COPY ./services ./services
COPY ./report ./report
# Make sure it compiles
RUN mvn -q clean package -DskipTests > /dev/null
###### THIRD STAGE ######
FROM openjdk:11-jre-slim as runtime
COPY ./service_ready /usr/bin
RUN chmod +x /usr/bin/service_ready
HEALTHCHECK --interval=10s --timeout=5s --retries=12 CMD service_ready
COPY --from=build ./rest-service/target/rest-service-*.jar ./rest-service.jar
EXPOSE 9099
ENTRYPOINT ["java", "-Dlog4j2.formatMsgNoLookups=true", "-jar", "./rest-service.jar"]
# FDA Document Service
## Documentation
- OpenAPI v3: http://localhost:9099/swagger-ui/index.html
- OpenAPI v3 endpoint: http://localhost:9099/v3/api-docs/
- OpenAPI v3 YAML: http://localhost:9099/v3/api-docs.yaml
\ No newline at end of file
#!/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
#
# 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.
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
# Maven Start Up Batch script
#
# Required ENV vars:
# ------------------
# JAVA_HOME - location of a JDK home dir
#
# Optional ENV vars
# -----------------
# M2_HOME - location of maven2's installed home dir
# 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 "$MAVEN_SKIP_RC" ] ; then
if [ -f /etc/mavenrc ] ; then
. /etc/mavenrc
fi
if [ -f "$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
export JAVA_HOME="`/usr/libexec/java_home`"
else
export JAVA_HOME="/Library/Java/Home"
fi
fi
;;
esac
if [ -z "$JAVA_HOME" ] ; then
if [ -r /etc/gentoo-release ] ; then
JAVA_HOME=`java-config --jre-home`
fi
fi
if [ -z "$M2_HOME" ] ; then
## resolve links - $0 may be a link to maven's home
PRG="$0"
# need this for relative symlinks
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname "$PRG"`/$link"
fi
done
saveddir=`pwd`
M2_HOME=`dirname "$PRG"`/..
# make it fully qualified
M2_HOME=`cd "$M2_HOME" && pwd`
cd "$saveddir"
# echo Using m2 at $M2_HOME
fi
# For Cygwin, ensure paths are in UNIX format before anything is touched
if $cygwin ; then
[ -n "$M2_HOME" ] &&
M2_HOME=`cygpath --unix "$M2_HOME"`
[ -n "$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 $mingw ; then
[ -n "$M2_HOME" ] &&
M2_HOME="`(cd "$M2_HOME"; pwd)`"
[ -n "$JAVA_HOME" ] &&
JAVA_HOME="`(cd "$JAVA_HOME"; pwd)`"
fi
if [ -z "$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="`which 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
CLASSWORLDS_LAUNCHER=org.codehaus.plexus.classworlds.launcher.Launcher
# 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/.."; pwd`
fi
# end of workaround
done
echo "${basedir}"
}
# concatenates all lines of a file
concat_lines() {
if [ -f "$1" ]; then
echo "$(tr -s '\n' ' ' < "$1")"
fi
}
BASE_DIR=`find_maven_basedir "$(pwd)"`
if [ -z "$BASE_DIR" ]; then
exit 1;
fi
##########################################################################################
# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
# This allows using the maven wrapper in projects that prohibit checking in binary data.
##########################################################################################
if [ -r "$BASE_DIR/.mvn/wrapper/maven-wrapper.jar" ]; then
if [ "$MVNW_VERBOSE" = true ]; then
echo "Found .mvn/wrapper/maven-wrapper.jar"
fi
else
if [ "$MVNW_VERBOSE" = true ]; then
echo "Couldn't find .mvn/wrapper/maven-wrapper.jar, downloading it ..."
fi
if [ -n "$MVNW_REPOURL" ]; then
jarUrl="$MVNW_REPOURL/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar"
else
jarUrl="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar"
fi
while IFS="=" read key value; do
case "$key" in (wrapperUrl) jarUrl="$value"; break ;;
esac
done < "$BASE_DIR/.mvn/wrapper/maven-wrapper.properties"
if [ "$MVNW_VERBOSE" = true ]; then
echo "Downloading from: $jarUrl"
fi
wrapperJarPath="$BASE_DIR/.mvn/wrapper/maven-wrapper.jar"
if $cygwin; then
wrapperJarPath=`cygpath --path --windows "$wrapperJarPath"`
fi
if command -v wget > /dev/null; then
if [ "$MVNW_VERBOSE" = true ]; then
echo "Found wget ... using wget"
fi
if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
wget "$jarUrl" -O "$wrapperJarPath"
else
wget --http-user=$MVNW_USERNAME --http-password=$MVNW_PASSWORD "$jarUrl" -O "$wrapperJarPath"
fi
elif command -v curl > /dev/null; then
if [ "$MVNW_VERBOSE" = true ]; then
echo "Found curl ... using curl"
fi
if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
curl -o "$wrapperJarPath" "$jarUrl" -f
else
curl --user $MVNW_USERNAME:$MVNW_PASSWORD -o "$wrapperJarPath" "$jarUrl" -f
fi
else
if [ "$MVNW_VERBOSE" = true ]; then
echo "Falling back to using Java to download"
fi
javaClass="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.java"
# For Cygwin, switch paths to Windows format before running javac
if $cygwin; then
javaClass=`cygpath --path --windows "$javaClass"`
fi
if [ -e "$javaClass" ]; then
if [ ! -e "$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class" ]; then
if [ "$MVNW_VERBOSE" = true ]; then
echo " - Compiling MavenWrapperDownloader.java ..."
fi
# Compiling the Java class
("$JAVA_HOME/bin/javac" "$javaClass")
fi
if [ -e "$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class" ]; then
# Running the downloader
if [ "$MVNW_VERBOSE" = true ]; then
echo " - Running MavenWrapperDownloader.java ..."
fi
("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$MAVEN_PROJECTBASEDIR")
fi
fi
fi
fi
##########################################################################################
# End of extension
##########################################################################################
export MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}
if [ "$MVNW_VERBOSE" = true ]; then
echo $MAVEN_PROJECTBASEDIR
fi
MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS"
# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
[ -n "$M2_HOME" ] &&
M2_HOME=`cygpath --path --windows "$M2_HOME"`
[ -n "$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 $@"
export MAVEN_CMD_LINE_ARGS
WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
exec "$JAVACMD" \
$MAVEN_OPTS \
-classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \
"-Dmaven.home=${M2_HOME}" "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \
${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@"
@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 https://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 Maven Start Up Batch script
@REM
@REM Required ENV vars:
@REM JAVA_HOME - location of a JDK home dir
@REM
@REM Optional ENV vars
@REM M2_HOME - location of maven2's installed home dir
@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 "%HOME%\mavenrc_pre.bat" call "%HOME%\mavenrc_pre.bat"
if exist "%HOME%\mavenrc_pre.cmd" call "%HOME%\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 DOWNLOAD_URL="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar"
FOR /F "tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO (
IF "%%A"=="wrapperUrl" SET DOWNLOAD_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 DOWNLOAD_URL="%MVNW_REPOURL%/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar"
)
if "%MVNW_VERBOSE%" == "true" (
echo Couldn't find %WRAPPER_JAR%, downloading it ...
echo Downloading from: %DOWNLOAD_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('%DOWNLOAD_URL%', '%WRAPPER_JAR%')"^
"}"
if "%MVNW_VERBOSE%" == "true" (
echo Finished downloading %WRAPPER_JAR%
)
)
@REM End of extension
@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 "%HOME%\mavenrc_post.bat" call "%HOME%\mavenrc_post.bat"
if exist "%HOME%\mavenrc_post.cmd" call "%HOME%\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%
exit /B %ERROR_CODE%
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.3.10.RELEASE</version>
</parent>
<groupId>at.tuwien</groupId>
<artifactId>fda-document-service</artifactId>
<version>1.1.0-alpha</version>
<name>fda-document-service</name>
<description>Demo project for Spring Boot</description>
<packaging>pom</packaging>
<modules>
<module>rest-service</module>
<module>services</module>
<module>report</module>
</modules>
<properties>
<java.version>11</java.version>
<spring-cloud.version>3.0.1</spring-cloud.version>
<mapstruct.version>1.4.2.Final</mapstruct.version>
<docker.version>3.2.7</docker.version>
<testcontainers.version>1.15.2</testcontainers.version>
<swagger.version>2.1.7</swagger.version>
<jacoco.version>0.8.7</jacoco.version>
<sqlserver.version>9.2.1.jre11</sqlserver.version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-webflux</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency><!-- https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.3-Release-Notes#validation-starter-no-longer-included-in-web-starters -->
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-validation</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.cloud</groupId>
<artifactId>spring-cloud-starter-bootstrap</artifactId>
<version>${spring-cloud.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-test</artifactId>
<scope>test</scope>
</dependency>
<!-- Data Source -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-elasticsearch</artifactId>
</dependency>
<!-- Entity and API -->
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>fda-metadata-db-api</artifactId>
<version>${project.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>fda-metadata-db-entites</artifactId>
<version>${project.version}</version>
<scope>compile</scope>
</dependency>
<!-- DataSource -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgresql.version}</version>
</dependency>
<dependency>
<groupId>org.mariadb.jdbc</groupId>
<artifactId>mariadb-java-client</artifactId>
<version>${mariadb.version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysql.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>${sqlserver.version}</version>
</dependency>
<!-- Testing -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-vintage-engine</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
</dependency>
<!-- IDE -->
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
</dependency>
<!-- Docker -->
<dependency>
<groupId>com.github.docker-java</groupId>
<artifactId>docker-java</artifactId>
<version>${docker.version}</version>
<exclusions>
<exclusion>
<groupId>javax.ws.rs</groupId>
<artifactId>jsr311-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.github.docker-java</groupId>
<artifactId>docker-java-transport-httpclient5</artifactId>
<version>${docker.version}</version>
</dependency>
<!-- Mapping -->
<dependency>
<groupId>org.mapstruct</groupId>
<artifactId>mapstruct-processor</artifactId>
<version>${mapstruct.version}</version>
<optional>true</optional><!-- IntelliJ -->
</dependency>
<dependency>
<groupId>org.mapstruct</groupId>
<artifactId>mapstruct</artifactId>
<version>${mapstruct.version}</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>${basedir}/src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/application*.yml</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<configuration>
<excludes>
<exclude>at/tuwien/utils/**/*</exclude>
<exclude>at/tuwien/handlers/**/*</exclude>
<exclude>at/tuwien/seeder/**/*</exclude>
<exclude>at/tuwien/mapper/**/*</exclude>
<exclude>at/tuwien/exception/**/*</exclude>
<exclude>at/tuwien/config/**/*</exclude>
<exclude>**/FdaContainerManagingApplication.class</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>verify</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>at.tuwien</groupId>
<artifactId>fda-document-service</artifactId>
<version>1.1.0-alpha</version>
</parent>
<artifactId>report</artifactId>
<version>1.1.0-alpha</version>
<name>fda-document-service-report</name>
<description>
This module is only intended for the pipeline coverage report. See the detailed report in the
respective modules
</description>
<properties>
<jacoco.version>0.8.7</jacoco.version>
</properties>
<dependencies>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>rest-service</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>services</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<id>report-aggregate</id>
<phase>verify</phase>
<goals>
<goal>report-aggregate</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>at.tuwien</groupId>
<artifactId>fda-document-service</artifactId>
<version>1.1.0-alpha</version>
</parent>
<artifactId>rest-service</artifactId>
<version>1.1.0-alpha</version>
<name>fda-document-service-rest-service</name>
<properties>
<jacoco.version>0.8.7</jacoco.version>
</properties>
<dependencies>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>services</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>repackage</goal><!-- to make it exuteable with $ java -jar ./app.jar -->
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
\ No newline at end of file
package at.tuwien;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.autoconfigure.domain.EntityScan;
import org.springframework.data.elasticsearch.repository.config.EnableElasticsearchRepositories;
import org.springframework.data.jpa.repository.config.EnableJpaAuditing;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.transaction.annotation.EnableTransactionManagement;
@SpringBootApplication
@EnableJpaAuditing
@EnableTransactionManagement
@EnableElasticsearchRepositories(basePackages = {"at.tuwien.repository.elastic"})
@EnableJpaRepositories(basePackages = {"at.tuwien.repository.jpa"})
@EntityScan(basePackages = {"at.tuwien.entities"})
public class FdaDocumentManagingApplication {
public static void main(String[] args) {
SpringApplication.run(FdaDocumentManagingApplication.class, args);
}
}
package at.tuwien.config;
import io.swagger.v3.oas.models.ExternalDocumentation;
import io.swagger.v3.oas.models.OpenAPI;
import io.swagger.v3.oas.models.info.Contact;
import io.swagger.v3.oas.models.info.Info;
import io.swagger.v3.oas.models.info.License;
import org.springdoc.core.GroupedOpenApi;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.info.BuildProperties;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class SwaggerConfig {
@Value("${app.version:unknown}")
private String version;
@Bean
public OpenAPI springShopOpenAPI() {
return new OpenAPI()
.info(new Info()
.title("Database Repository Document Service API")
.contact(new Contact()
.name("Prof. Andreas Rauber")
.email("andreas.rauber@tuwien.ac.at"))
.description("Service that manages the documents")
.version(version)
.license(new License()
.name("Apache 2.0")
.url("https://www.apache.org/licenses/LICENSE-2.0")))
.externalDocs(new ExternalDocumentation()
.description("Wiki Documentation")
.url("https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/wikis"));
}
@Bean
public GroupedOpenApi publicApi() {
return GroupedOpenApi.builder()
.group("document-service")
.pathsToMatch("/api/**")
.build();
}
}
package at.tuwien.endpoints;
import at.tuwien.api.document.record.CreateDraftDto;
import at.tuwien.api.document.record.DraftDto;
import at.tuwien.exception.DraftRecordCreateException;
import at.tuwien.service.DocumentService;
import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.security.SecurityRequirement;
import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
import javax.validation.Valid;
import javax.validation.constraints.NotNull;
import java.security.Principal;
@Log4j2
@RestController
@CrossOrigin(origins = "*")
@ControllerAdvice
@RequestMapping("/api/document")
public class DocumentEndpoint {
private final DocumentService documentService;
@Autowired
public DocumentEndpoint(DocumentService documentService) {
this.documentService = documentService;
}
@PostMapping
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Create a draft", security = @SecurityRequirement(name = "bearerAuth"))
public ResponseEntity<DraftDto> create(@NotNull @Valid @RequestBody CreateDraftDto data,
@NotNull Principal principal) throws DraftRecordCreateException {
final DraftDto document = documentService.create(data, principal);
return ResponseEntity.status(HttpStatus.CREATED)
.body(document);
}
@GetMapping("/{id}")
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Find a draft", security = @SecurityRequirement(name = "bearerAuth"))
public ResponseEntity<DraftDto> find(@NotNull @PathVariable("id") String documentId,
@NotNull Principal principal) throws DraftRecordCreateException {
final DraftDto document = documentService.findById(documentId, principal);
log.info("Found draft record with id {}", documentId);
log.debug("found draft record {}", document);
return ResponseEntity.status(HttpStatus.OK)
.body(document);
}
@PostMapping("/{id}")
@PreAuthorize("hasRole('ROLE_RESEARCHER')")
@Transactional(readOnly = true)
@Operation(summary = "Reserve draft DOI", security = @SecurityRequirement(name = "bearerAuth"))
public ResponseEntity<DraftDto> reserve(@NotNull @PathVariable("id") String documentId,
@NotNull Principal principal) throws DraftRecordCreateException {
final DraftDto document = documentService.reserveDoi(documentId, principal);
return ResponseEntity.status(HttpStatus.CREATED)
.body(document);
}
}
package at.tuwien.handlers;
import at.tuwien.api.error.ApiErrorDto;
import at.tuwien.exception.*;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.ControllerAdvice;
import org.springframework.web.bind.annotation.ExceptionHandler;
import org.springframework.web.bind.annotation.ResponseStatus;
import org.springframework.web.context.request.WebRequest;
import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
@ControllerAdvice
public class ApiExceptionHandler extends ResponseEntityExceptionHandler {
@ResponseStatus(HttpStatus.EXPECTATION_FAILED)
@ExceptionHandler(DraftRecordCreateException.class)
public ResponseEntity<ApiErrorDto> handle(DraftRecordCreateException e, WebRequest request) {
final ApiErrorDto response = ApiErrorDto.builder()
.status(HttpStatus.EXPECTATION_FAILED)
.message(e.getLocalizedMessage())
.code("error.document.create")
.build();
return new ResponseEntity<>(response, new HttpHeaders(), response.getStatus());
}
}
\ No newline at end of file
app.version: '@project.version@'
spring:
main.banner-mode: off
datasource:
url: jdbc:postgresql://fda-metadata-db:5432/fda
driver-class-name: org.postgresql.Driver
username: postgres
password: postgres
jpa:
show-sql: false
database-platform: org.hibernate.dialect.PostgreSQLDialect
hibernate:
ddl-auto: validate
open-in-view: false
application:
name: fda-document-service
cloud:
loadbalancer.ribbon.enabled: false
server.port: 9099
logging:
pattern.console: "%d %highlight(%-5level) %msg%n"
level:
root: warn
at.tuwien.: debug
at.tuwien.gateway.: trace
org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver: debug
eureka:
instance.hostname: fda-document-service
client.serviceUrl.defaultZone: http://fda-discovery-service:9090/eureka/
fda:
mount.path: /tmp
ready.path: /ready
document.endpoint: https://test.researchdata.tuwien.ac.at
dev.token: "${TOKEN}"
\ No newline at end of file
app.version: '@project.version@'
spring:
main.banner-mode: off
datasource:
url: jdbc:postgresql://localhost:5432/fda
driver-class-name: org.postgresql.Driver
username: postgres
password: postgres
jpa:
show-sql: false
database-platform: org.hibernate.dialect.PostgreSQLDialect
hibernate:
ddl-auto: validate
open-in-view: false
application:
name: fda-document-service
cloud:
loadbalancer.ribbon.enabled: false
springdoc.swagger-ui.enabled: true
server.port: 9099
logging:
pattern.console: "%d %highlight(%-5level) %msg%n"
level:
root: warn
at.tuwien.: debug
at.tuwien.gateway.: trace
org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver: debug
eureka:
instance.hostname: fda-document-service
client.serviceUrl.defaultZone: http://localhost:9090/eureka/
fda:
mount.path: /tmp
ready.path: ./ready
document.endpoint: https://test.researchdata.tuwien.ac.at
dev.token: "${TOKEN}"
\ No newline at end of file
# https://github.com/Netflix/Hystrix/issues/275
\ No newline at end of file
package at.tuwien;
import at.tuwien.api.document.metadata.*;
import at.tuwien.api.document.record.*;
import org.springframework.test.context.TestPropertySource;
import java.time.Instant;
import java.util.Date;
import java.util.List;
@TestPropertySource(locations = "classpath:application.properties")
public abstract class BaseUnitTest {
public final static String USER_1_USERNAME = "junit";
public final static AccessTypeDto DOCUMENT_1_RECORD_TYPE = AccessTypeDto.PUBLIC;
public final static FileTypeDto DOCUMENT_1_FILE_TYPE = FileTypeDto.PUBLIC;
public final static AccessOptionsDto DOCUMENT_1_ACCESS_OPTIONS = AccessOptionsDto.builder()
.record(DOCUMENT_1_RECORD_TYPE)
.files(DOCUMENT_1_FILE_TYPE)
.build();
public final static Boolean DOCUMENT_1_FILES_ENABLED = true;
public final static FilesOptionsDto DOCUMENT_1_FILES_OPTIONS = FilesOptionsDto.builder()
.enabled(DOCUMENT_1_FILES_ENABLED)
.build();
public final static String DOCUMENT_1_TITLE = "Test Draft";
public final static String DOCUMENT_1_RESOURCE_TYPE_TYPE = "other";
public final static Date DOCUMENT_1_PUBLICATION_DATE = Date.from(Instant.now());
public final static ResourceTypeDto DOCUMENT_1_RESOURCE_TYPE = ResourceTypeDto.builder()
.id(DOCUMENT_1_RESOURCE_TYPE_TYPE)
.build();
public final static String IDENTIFIER_1_IDENTIFIER = "0000-0003-4216-302X";
public final static IdentifierTypeDto IDENTIFIER_1_TYPE = IdentifierTypeDto.ORCID;
public final static IdentifierDto IDENTIFIER_1 = IdentifierDto.builder()
.identifier(IDENTIFIER_1_IDENTIFIER)
.scheme(IDENTIFIER_1_TYPE)
.build();
public final static String PERSON_1_GIVEN_NAME = "Martin";
public final static String PERSON_1_FAMILY_NAME = "Weise";
public final static String PERSON_1_NAME = "Weise, Martin";
public final static PersonOrOrgTypeDto PERSON_1_TYPE = PersonOrOrgTypeDto.PERSONAL;
public final static PersonOrOrganizationDto PERSON_1 = PersonOrOrganizationDto.builder()
.givenName(PERSON_1_GIVEN_NAME)
.familyName(PERSON_1_FAMILY_NAME)
.name(PERSON_1_NAME)
.type(PERSON_1_TYPE)
.identifiers(List.of(IDENTIFIER_1))
.build();
public final static AffiliationDto AFFILIATION_1 = AffiliationDto.builder()
.name("TU Wien")
.build();
public final static CreatorDto CREATOR_1 = CreatorDto.builder()
.personOrOrganization(PERSON_1)
.affiliations(List.of(AFFILIATION_1))
.build();
public final static MetadataDto DOCUMENT_1_METADATA = MetadataDto.builder()
.title(DOCUMENT_1_TITLE)
.resourceType(DOCUMENT_1_RESOURCE_TYPE)
.publicationDate(DOCUMENT_1_PUBLICATION_DATE)
.creators(List.of(CREATOR_1))
.build();
public final static CreateDraftDto DOCUMENT_1_CREATE_DRAFT = CreateDraftDto.builder()
.access(DOCUMENT_1_ACCESS_OPTIONS)
.files(DOCUMENT_1_FILES_OPTIONS)
.metadata(DOCUMENT_1_METADATA)
.build();
}
package at.tuwien.endpoint;
import at.tuwien.BaseUnitTest;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@ExtendWith(SpringExtension.class)
@SpringBootTest
public class DocumentEndpointUnitTest extends BaseUnitTest {
}
package at.tuwien.service;
import at.tuwien.BaseUnitTest;
import at.tuwien.api.document.record.CreateDraftDto;
import at.tuwien.api.document.record.DraftDto;
import at.tuwien.exception.DraftRecordCreateException;
import lombok.extern.log4j.Log4j2;
import org.apache.http.auth.BasicUserPrincipal;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.security.Principal;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@Log4j2
@DirtiesContext(classMode = DirtiesContext.ClassMode.BEFORE_EACH_TEST_METHOD)
@ExtendWith(SpringExtension.class)
@SpringBootTest
public class DocumentEndpointIntegrationTest extends BaseUnitTest {
@Autowired
private DocumentService documentService;
@Test
public void create_succeeds() throws DraftRecordCreateException {
final CreateDraftDto request = DOCUMENT_1_CREATE_DRAFT;
final Principal principal = new BasicUserPrincipal(USER_1_USERNAME);
/* mock */
/* test */
final DraftDto response = documentService.create(request, principal);
assertEquals(DOCUMENT_1_TITLE, response.getMetadata().getTitle());
}
@Test
public void reserve_succeeds() throws DraftRecordCreateException {
final CreateDraftDto request = DOCUMENT_1_CREATE_DRAFT;
final Principal principal = new BasicUserPrincipal(USER_1_USERNAME);
/* mock */
/* test */
final DraftDto document = documentService.create(request, principal);
final DraftDto response = documentService.reserveDoi(document.getId(), principal);
assertNotNull(response.getPids().getDoi());
}
}
# disable discovery
spring.cloud.discovery.enabled = false
# disable cloud config and config discovery
spring.cloud.config.discovery.enabled = false
spring.cloud.config.enabled = false
# disable datasource
spring.datasource.url=jdbc:h2:mem:testdb;DB_CLOSE_ON_EXIT=FALSE
spring.datasource.driverClassName=org.h2.Driver
spring.datasource.username=sa
spring.datasource.password=password
spring.jpa.database-platform=org.hibernate.dialect.H2Dialect
spring.jpa.hibernate.ddl-auto=create-drop
spring.jpa.show-sql=false
\ No newline at end of file
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