-
-
-So how does the app know where to find this file and **load the messages content**?
-
-We have configured it as a **external property** in a file `application.properties` and load the
-configuration on application startup! Cool eh?
-
-
-This is how the file content looks like:
+### Dropbox Process
-```
-messages.file=messages.txt
-```
-
-So how do we access the value of the `messages.file` property in our application with Spring?
-
-Have a look in the class `AppConfig`, there the magic happens:
+The dropbox processes the data before moving it into OpenBiS. A successful processing is shown
+below.
-```groovy
-@Configuration
-@PropertySource("application.properties")
-class AppConfig {
+The process is triggered when a marker filed called `MARKER_is_finished_
-
-You might have already spotted the interface `NewsMedia` and its implementing class `DeveloperNews`
-in the app's source code. Here you can see an example for the magic of inversion of control.
-
-The `NewsMedia` interface is just an abstraction that we will later use, because we don't care about
-the actual implementation details. By this, we also do not create any dependencies to concrete
-implementation details but on actual behaviour. Concrete implementations can then later be exchanged
-without causing any breaking changes in the client code base.
-
-The interface has only one method: `String getNews()`. Now let's have a closer look into the
-class `DeveloperNews` that implements this interface:
-
-```java
-class DeveloperNews implements NewsMedia{
-
- private MessageService service
-
- DeveloperNews(MessageService service) {
- this.service = service
- }
-
- @Override
- String getNews() {
- return service.collectMessage()
- }
-}
-```
-
-When you check the constructor signature, you see that this method has only one argument, which is a
-reference to an object of type `MessageService`. And when the `getNews()` method is called by the
-client, the class delegates this request to the message service. Since we have stored the reference
-in a private field, that is super easy, we known how to call the service.
-
-So why is this inversion of control?
-
-Because the `DeveloperNews` class does not manage the instantiation of a concrete message service.
-The configuration happened outside of the class, therefore the DeveloperNews class has no direct
-control over the instantiation. If it had, it would look like this:
-
-```java
-DeveloperNews(String filePathToMessages) {
- this.service = new CodingPrayersMessageService(filePathToMessages)
-}
-```
-
-That doesn't look good, does it? In order to create an instance of a message service, we would need
-to know the conrete implementation and its required properties (here it is the file path to
-the `messages.txt`). So the `DeveloperNews` class has the control over the message service.
-
-Instead, we would like to not take care about these details, so we invert the control and inject the
-dependency via the constructor.
-
-Please find more in depth documentation on the
-official [Spring website](https://spring.io/projects/spring-framework).
-
-
-
-
-
+!!! info
+Ususally you only need to adapt the `incoming-dir` and `program-class` when setting up a new dropbox.
+For more configuration options please see the [OpenBiS documentation](https://openbis.readthedocs.io/en/20.10.x/software-developer-documentation/server-side-extensions/dss-dropboxes.html#configuration).
diff --git a/mvnw b/mvnw
deleted file mode 100755
index a16b543..0000000
--- a/mvnw
+++ /dev/null
@@ -1,310 +0,0 @@
-#!/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} $MAVEN_CONFIG "$@"
diff --git a/mvnw.cmd b/mvnw.cmd
deleted file mode 100644
index c8d4337..0000000
--- a/mvnw.cmd
+++ /dev/null
@@ -1,182 +0,0 @@
-@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; $webclient.DownloadFile('%DOWNLOAD_URL%', '%WRAPPER_JAR%')"^
- "}"
- if "%MVNW_VERBOSE%" == "true" (
- echo Finished downloading %WRAPPER_JAR%
- )
-)
-@REM End of extension
-
-@REM Provide a "standardized" way to retrieve the CLI args that will
-@REM work with both Windows and non-Windows executions.
-set MAVEN_CMD_LINE_ARGS=%*
-
-%MAVEN_JAVA_EXE% %JVM_CONFIG_MAVEN_PROPS% %MAVEN_OPTS% %MAVEN_DEBUG_OPTS% -classpath %WRAPPER_JAR% "-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" %WRAPPER_LAUNCHER% %MAVEN_CONFIG% %*
-if ERRORLEVEL 1 goto error
-goto end
-
-:error
-set ERROR_CODE=1
-
-:end
-@endlocal & set ERROR_CODE=%ERROR_CODE%
-
-if not "%MAVEN_SKIP_RC%" == "" goto skipRcPost
-@REM check for post script, once with legacy .bat ending and once with .cmd ending
-if exist "%HOME%\mavenrc_post.bat" call "%HOME%\mavenrc_post.bat"
-if exist "%HOME%\mavenrc_post.cmd" call "%HOME%\mavenrc_post.cmd"
-:skipRcPost
-
-@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on'
-if "%MAVEN_BATCH_PAUSE%" == "on" pause
-
-if "%MAVEN_TERMINATE_CMD%" == "on" exit %ERROR_CODE%
-
-exit /B %ERROR_CODE%
diff --git a/pom.xml b/pom.xml
index 7f819b9..7717d9b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,97 +1,151 @@
-Reads properties from a properties file and creates beans for the application.
- * - * @since 0.1.0 - */ -@Configuration -@PropertySource("application.properties") -class AppConfig { - - @Value('${messages.file}') - public String messagesFile - - @Bean - MessageService messageService() { - return new CodingPrayersMessageService(messagesFile) - } - - @Bean - NewsMedia newsMedia() { - return new DeveloperNews(messageService()) - } - -} diff --git a/src/main/groovy/life/qbic/springminimaltemplate/CodingPrayersMessageService.groovy b/src/main/groovy/life/qbic/springminimaltemplate/CodingPrayersMessageService.groovy deleted file mode 100644 index 54c29f1..0000000 --- a/src/main/groovy/life/qbic/springminimaltemplate/CodingPrayersMessageService.groovy +++ /dev/null @@ -1,29 +0,0 @@ -package life.qbic.springminimaltemplate - -/** - * Example implementation of a {@link MessageService} - * - * @since 0.1.0 - */ -class CodingPrayersMessageService implements MessageService { - - private ListMessage services shall provide access to received messages.
- * - * @since 0.1.0 - */ -interface MessageService { - - /** - * Collects the latest message - * @return the latest message - * @since 0.1.0 - */ - String collectMessage() -} diff --git a/src/main/groovy/life/qbic/springminimaltemplate/NewsMedia.groovy b/src/main/groovy/life/qbic/springminimaltemplate/NewsMedia.groovy deleted file mode 100644 index d335196..0000000 --- a/src/main/groovy/life/qbic/springminimaltemplate/NewsMedia.groovy +++ /dev/null @@ -1,17 +0,0 @@ -package life.qbic.springminimaltemplate - -/** - * Example interface for a news media - * - * @since 0.1.0 - */ -interface NewsMedia { - - /** - * Returns latest news - * @return news stuff! - * @since 0.1.0 - */ - String getNews() - -} \ No newline at end of file diff --git a/src/main/groovy/life/qbic/springminimaltemplate/SpringMinimalTemplateApplication.groovy b/src/main/groovy/life/qbic/springminimaltemplate/SpringMinimalTemplateApplication.groovy deleted file mode 100644 index e9ba274..0000000 --- a/src/main/groovy/life/qbic/springminimaltemplate/SpringMinimalTemplateApplication.groovy +++ /dev/null @@ -1,23 +0,0 @@ -package life.qbic.springminimaltemplate - -import org.springframework.boot.SpringApplication -import org.springframework.boot.autoconfigure.SpringBootApplication -import org.springframework.context.annotation.AnnotationConfigApplicationContext - -@SpringBootApplication -class SpringMinimalTemplateApplication { - - static void main(String[] args) { - SpringApplication.run(SpringMinimalTemplateApplication, args) - - AnnotationConfigApplicationContext context = new AnnotationConfigApplicationContext(AppConfig.class) - - NewsMedia media = context.getBean("newsMedia", NewsMedia.class) - println "####################### Message of the day ##################" - println media.getNews() - println "##############################################################" - - context.close() - } - -} diff --git a/src/main/java/life/qbic/registration/openbis/DataSetProvenance.java b/src/main/java/life/qbic/registration/openbis/DataSetProvenance.java new file mode 100644 index 0000000..aa82b8b --- /dev/null +++ b/src/main/java/life/qbic/registration/openbis/DataSetProvenance.java @@ -0,0 +1,94 @@ +package life.qbic.registration.openbis; + +import com.fasterxml.jackson.annotation.JsonProperty; +import java.io.Serializable; +import java.util.Arrays; +import java.util.Objects; + +/** + * Class holding provenance information provided by the user. This is a record of immutable data. + * + * @since 1.0.0 + */ +public class DataSetProvenance implements Serializable { + + private static final long serialVersionUID = -1597156104025439195L; + + @JsonProperty("origin") + private String origin; + @JsonProperty("user") + private String user; + @JsonProperty("measurementId") + private String measurementId; + @JsonProperty("datasetFiles") + private String[] datasetFiles; + @JsonProperty("taskId") + private String taskId; + @JsonProperty("history") + private String[] history; + + + private DataSetProvenance() { + + } + public DataSetProvenance(String origin, String user, String measurementId, String[] datasetFiles, + String taskId, String[] history) { + this.origin = origin; + this.user = user; + this.measurementId = measurementId; + this.datasetFiles = datasetFiles; + this.taskId = taskId; + this.history = history; + } + + public String origin() { + return origin; + } + + public String user() { + return user; + } + + public String measurementId() { + return measurementId; + } + + public String[] datasetFiles() { + return datasetFiles; + } + + public String taskId() { + return taskId; + } + + public String[] history() { + return history; + } + + @Override + public final boolean equals(Object o) { + if (this == o) { + return true; + } + if (!(o instanceof DataSetProvenance)) { + return false; + } + + DataSetProvenance that = (DataSetProvenance) o; + return Objects.equals(origin, that.origin) && Objects.equals(user, that.user) + && Objects.equals(measurementId, that.measurementId) && Arrays.equals( + datasetFiles, that.datasetFiles) && Objects.equals(taskId, that.taskId) + && Arrays.equals(history, that.history); + } + + @Override + public int hashCode() { + int result = Objects.hashCode(origin); + result = 31 * result + Objects.hashCode(user); + result = 31 * result + Objects.hashCode(measurementId); + result = 31 * result + Arrays.hashCode(datasetFiles); + result = 31 * result + Objects.hashCode(taskId); + result = 31 * result + Arrays.hashCode(history); + return result; + } +} diff --git a/src/main/java/life/qbic/registration/openbis/OpenBisDropboxETL.java b/src/main/java/life/qbic/registration/openbis/OpenBisDropboxETL.java new file mode 100644 index 0000000..be29f86 --- /dev/null +++ b/src/main/java/life/qbic/registration/openbis/OpenBisDropboxETL.java @@ -0,0 +1,81 @@ +package life.qbic.registration.openbis; + +import ch.systemsx.cisd.common.exceptions.NotImplementedException; +import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext; +import ch.systemsx.cisd.etlserver.registrator.api.v2.AbstractJavaDataSetRegistrationDropboxV2; +import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet; +import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2; +import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable; +import java.io.File; +import life.qbic.registration.openbis.exceptions.fail.MeasurementHasDataException; +import life.qbic.registration.openbis.exceptions.fail.UnknownSampleTypeException; +import life.qbic.registration.openbis.types.QDatasetType; +import life.qbic.registration.openbis.types.QPropertyType; +import life.qbic.registration.openbis.types.QSampleType; + +/** + * The Dropbox ETL process. + *+ * This process is responsible for + *
-
+ *
- fetching the measurement sample from openbis + *
- creating a data set linked to the sample + *
- moving files into the dataset + *
-
+ *
- the measurement sample already exists in openbis + *
- only one measurement sample exists with the provided identifier + *
- the measurement sample has no data set linked as one measurement can only have one dataset. + *