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Commit 0995ccf6 authored by felmer's avatar felmer
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LMS-768 rename 'etlserver' project to 'datastore_server' 

SVN: 9972
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datastore_server/.checkstyle 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<fileset-config file-format-version="1.2.0" simple-config="false">
<local-check-config name="CISD Checks" location="/build_resources/checkstyle/cisd_checkstyle.xml" type="project" description="">
<additional-data name="protect-config-file" value="false"/>
</local-check-config>
<fileset name="all" enabled="true" check-config-name="CISD Checks" local="true">
<file-match-pattern match-pattern=".+ch/systemsx/cisd.+" include-pattern="true"/>
</fileset>
</fileset-config>
datastore_server/.classpath 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="source/java"/>
<classpathentry kind="src" path="sourceTest/java"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry combineaccessrules="false" kind="src" path="/common"/>
<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
<classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
<classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
<classpathentry combineaccessrules="false" kind="src" path="/bds"/>
<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
<classpathentry combineaccessrules="false" kind="src" path="/args4j"/>
<classpathentry kind="lib" path="/libraries/cglib/cglib-nodep.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
<classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
<classpathentry combineaccessrules="false" kind="src" path="/server-common"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
datastore_server/.project 0 → 100644
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>datastore_server</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.atlassw.tools.eclipse.checkstyle.CheckstyleBuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>com.atlassw.tools.eclipse.checkstyle.CheckstyleNature</nature>
</natures>
</projectDescription>
datastore_server/build/antrun.sh 0 → 100755
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#! /bin/bash
ME="$0"
MYDIR=${ME%/*}
cd $MYDIR
ant -lib ../../build_resources/lib/ecj.jar "$@"
datastore_server/build/build.xml 0 → 100644
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<project name="etlserver" default="dist" basedir="..">
<import file="../../build_resources/ant/build-common.xml" />
<project-classpath name="ecp" classes="${classes}" />
<property name="original.dist" value="dist" />
<property name="mainfolder" value="etlserver" />
<property name="dist.etlserver" value="${dist}/${mainfolder}" />
<property name="dist.etlserver.lib" value="${dist.etlserver}/lib" />
<property name="jar.file" value="${dist.etlserver.lib}/etlserver.jar" />
<property name="dist.file.prefix" value="${dist}/etlserver" />
<property name="nativesrc" value="${lib}/unix/native" />
<property name="nativeroot" value="${targets}/ant" />
<property name="native" value="${nativeroot}/native" />
<target name="clean">
<delete dir="${dist}" />
</target>
<target name="compile" depends="build-common.compile, clean" />
<target name="run-tests">
<antcall target="build-common.run-tests">
<param name="test.suite" value="tests_fast.xml" />
</antcall>
</target>
<target name="jar" depends="compile">
<mkdir dir="${dist.etlserver.lib}" />
<build-info revision="revision.number" version="version.number" clean="clean.flag" />
<echo file="${build.info.file}">${version.number}:${revision.number}:${clean.flag}</echo>
<copy todir="${native}">
<fileset dir="${nativesrc}">
<include name="**/unix.so" />
</fileset>
</copy>
<recursive-jar destfile="${jar.file}">
<fileset dir="${classes}">
<include name="**/*.class" />
<include name="${build.info.filename}" />
</fileset>
<fileset dir="${nativeroot}">
<include name="**/unix.so"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="ch.systemsx.cisd.etlserver.Main" />
<attribute name="Class-Path"
value="etlserver-plugins.jar log4j.jar activation.jar mail.jar spring.jar fast-md5.jar
commons-codec.jar commons-lang.jar commons-io.jar commons-logging.jar commons-httpclient.jar" />
<attribute name="Version" value="${version.number}" />
<attribute name="Build-Number"
value="${version.number} (r${revision.number},${clean.flag})" />
</manifest>
</recursive-jar>
</target>
<target name="dist" depends="jar">
<copy file="${lib}/activation/activation.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/mail/mail.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/log4j/log4j.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/commons-codec/commons-codec.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/commons-io/commons-io.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/commons-lang/commons-lang.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/commons-logging/commons-logging.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/commons-httpclient/commons-httpclient.jar"
todir="${dist.etlserver.lib}" />
<copy file="${lib}/spring/spring.jar" todir="${dist.etlserver.lib}" />
<copy file="${lib}/fast-md5/fast-md5.jar" todir="${dist.etlserver.lib}" />
<property name="dist.file"
value="${dist.file.prefix}-${version.number}-r${revision.number}.zip" />
<zip basedir="${dist}" destfile="${dist.file}">
<zipfileset dir="${original.dist}" excludes="**/etlserver.sh" prefix="${mainfolder}" />
<zipfileset file="${original.dist}/etlserver.sh"
filemode="755"
prefix="${mainfolder}" />
</zip>
<delete dir="${dist.etlserver}" />
</target>
<target name="ci" depends="run-tests, check-dependencies, dist">
</target>
</project>
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datastore_server/dist/data/incoming/.gitignore 0 → 100644
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datastore_server/dist/data/store/.gitignore 0 → 100644
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datastore_server/dist/etc/etlserver.conf 0 → 100644
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#
# ETL Server configuration file
#
#
# Home directory of the JRE that should be used
#
#JAVA_HOME=${JAVA_HOME:=/usr/java/latest}
#
# Options to the JRE
#
JAVA_OPTS=${JAVA_OPTS:=-server}
#
# Maximal number of log files to keep
#
MAXLOGS=5
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datastore_server/dist/etc/log.xml 0 → 100644
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<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
<appender name="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender">
<param name="File" value="log/etlserver_log.txt"/>
<param name="DatePattern" value="'.'yyyy-MM-dd"/>
<layout class="org.apache.log4j.PatternLayout">
<param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
</layout>
</appender>
<appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
<layout class="org.apache.log4j.PatternLayout">
<param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
</layout>
</appender>
<appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
<appender name="EMAIL" class="org.apache.log4j.net.SMTPAppender">
<param name="BufferSize" value="512" />
<param name="SMTPHost" value="localhost" />
<param name="From" value="etlserver@localhost" />
<param name="To" value="root@localhost" />
<param name="Subject" value="ATTENTION: etl server" />
<param name="EvaluatorClass" value="ch.systemsx.cisd.common.logging.AlwaysTrueTriggeringEventEvaluator" />
<layout class="org.apache.log4j.PatternLayout">
<param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
</layout>
<!--filter class="org.apache.log4j.varia.LevelRangeFilter">
<param name="LevelMin" value="ERROR"/>
<param name="LevelMax" value="FATAL"/>
</filter-->
</appender>
<category name="NOTIFY">
<priority value="info" />
<appender-ref ref="EMAIL" />
</category>
<root>
<priority value="info" />
<appender-ref ref="DEFAULT" />
</root>
</log4j:configuration>
datastore_server/dist/etc/openBIS.keystore 0 → 100644
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datastore_server/dist/etc/service.properties 0 → 100644
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# The root directory of the data store
storeroot-dir = data/store
# The check interval (in seconds)
check-interval = 60
# The time-out for clean up work in the shutdown sequence (in seconds).
# Note that that the maximal time for the shutdown sequence to complete can be as large
# as twice this time.
# Remark: On a network file system, it is not recommended to turn this value to something
# lower than 180.
shutdown-timeout = 180
# If free disk space goes below value defined here, a notification email will be sent.
# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
# specified or if value is negative, the system will not be watching.
highwater-mark = 1048576
# If a data set is successfully registered it sends out an email to the registrator.
# If this property is not specified, no email is sent to the registrator. This property
# does not affect the mails which are sent, when the data set could not be registered.
notify-successful-registration = false
# The URL of the openBIS server
server-url = https://localhost:8443/openbis
# The username to use when contacting the openBIS server
username = etlserver
# The password to use when contacting the openBIS server
password = <change this>
# SMTP properties (must start with 'mail' to be considered).
# mail.smtp.host = localhost
# mail.from = etlserver@localhost
# ---------------- Timing parameters for file system operations on remote shares.
# Time (in seconds) to wait for any file system operation to finish. Operations exceeding this
# timeout will be terminated.
timeout = 60
# Number of times that a timed out operation will be tried again (0 means: every file system
# operation will only ever be performed once).
max-retries = 11
# Time (in seconds) to wait after an operation has been timed out before re-trying.
failure-interval = 10
# Globally used separator character which separates entities in a data set file name
data-set-file-name-entity-separator = _
# Prefixes for processing paths for all procedure types.
# default-prefix-for-absolute-paths is the key for paths starting with '/'.
# default-prefix-for-relative-paths is the key for paths not starting with '/'.
#
default-prefix-for-absolute-paths =
# Processors of processing instructions.
#
# processors: comma separated list of procedure type codes
# processor.<procedure type code>.prefix-for-absolute-paths: Key for a processing path starting with '/'.
# processor.<procedure type code>.prefix-for-relative-paths: Key for a processing path not starting with '/'.
# processor.<procedure type code>.parameters-file: Name of the file containing the processing parameters.
# processor.<procedure type code>.finished-file-template: Name of the marker file which finishes processing.
processors = DATA_ACQUISITION
processor.DATA_ACQUISITION.prefix-for-absolute-paths = ${default-prefix-for-absolute-paths}
processor.DATA_ACQUISITION.prefix-for-relative-paths = targets/processing
processor.DATA_ACQUISITION.parameters-file = parameters
processor.DATA_ACQUISITION.data-set-code-prefix-glue = ${data-set-file-name-entity-separator}
processor.DATA_ACQUISITION.finished-file-template = .MARKER_is_finished_{0}
# Can be one of PROPRIETARY (the data as acquired from the measurement device)
# or BDS_DIRECTORY (the data in BDS format in a directory container).
processor.DATA_ACQUISITION.input-storage-format = PROPRIETARY
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
inputs=main-thread
# ---------------------------------------------------------------------------
# 'main-thread' thread configuration
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
main-thread.incoming-dir = data/incoming
# The group the samples extracted by this thread belong to. If commented out or empty, then samples
# are considered associated to a database instance (not group private).
# main-thread.group-code = <change this>
# ---------------- Plugin properties
# The extractor class to use for code extraction
main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
# The extractor class to use for type extraction
main-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
main-thread.type-extractor.file-format-type = TIFF
main-thread.type-extractor.locator-type = RELATIVE_LOCATION
main-thread.type-extractor.data-set-type = HCS_IMAGE
main-thread.type-extractor.procedure-type = DATA_ACQUISITION
# The storage processor (IStorageProcessor implementation)
main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
# main-thread.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
# main-thread.storage-processor.version = 1.1
# main-thread.storage-processor.sampleTypeCode = CELL_PLATE
# main-thread.storage-processor.sampleTypeDescription = Screening Plate
# main-thread.storage-processor.format = UNKNOWN V1.0
datastore_server/dist/etlserver.bat 0 → 100755
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@echo off
java -Djavax.net.ssl.trustStore=etc\openBIS.keystore -jar lib\etlserver.jar %1 %2 %3 %4 %5 %6 %7
datastore_server/dist/etlserver.sh 0 → 100755
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#!/bin/bash
#
# Control script for CISD openBIS ETL Server on Unix / Linux systems
# -------------------------------------------------------------------------
awkBin()
{
# We need a awk that accepts variable assignments with '-v'
case `uname -s` in
"SunOS")
echo "nawk"
return
;;
esac
# default
echo "awk"
}
isPIDRunning()
{
if [ "$1" = "" ]; then
return 1
fi
if [ "$1" = "fake" ]; then # for unit tests
return 0
fi
# This will have a return value of 0 on BSDish systems
isBSD="`ps aux > /dev/null 2>&1; echo $?`"
AWK=`awkBin`
if [ "$isBSD" = "0" ]; then
if [ "`ps aux | $AWK -v PID=$1 '{if ($2==PID) {print "FOUND"}}'`" = "FOUND" ]; then
return 0
else
return 1
fi
else
if [ "`ps -ef | $AWK -v PID=$1 '{if ($2==PID) {print "FOUND"}}'`" = "FOUND" ]; then
return 0
else
return 1
fi
fi
}
rotateLogFiles()
{
logfile=$1
max=$2
if [ -z "$logfile" ]; then
echo "Error: rotateLogFiles: logfile argument missing"
return 1
fi
if [ -z "$max" ]; then
echo "Error: rotateLogFiles: max argument missing"
return 1
fi
test -f $logfile.$max && rm $logfile.$max
n=$max
while [ $n -gt 1 ]; do
nnew=$(($n-1))
test -f $logfile.$nnew && mv $logfile.$nnew $logfile.$n
n=$nnew
done
test -f $logfile && mv $logfile $logfile.1
}
getStatus()
{
if [ -f $PIDFILE ]; then
PID=`cat $PIDFILE`
isPIDRunning $PID
if [ $? -eq 0 ]; then
return 0
else
return 1
fi
else
return 2
fi
}
printStatus()
{
if [ -f $PIDFILE ]; then
PID=`cat $PIDFILE`
isPIDRunning $PID
if [ $? -eq 0 ]; then
echo "ETL Server is running (pid $PID)"
return 0
else
echo "ETL Server is dead (stale pid $PID)"
return 1
fi
else
echo "ETL Server is not running."
return 2
fi
}
#
# definitions
#
PIDFILE=${ETLSERVER_PID:-etlserver.pid}
CONFFILE=etc/etlserver.conf
LOGFILE=log/etlserver_log.txt
STARTUPLOG=log/startup_log.txt
SUCCESS_MSG="etlserver ready and waiting for data"
JAR_FILE=lib/etlserver.jar
MAX_LOOPS=10
#
# change to installation directory
#
bin=$0
if [ -L $bin ]; then
bin=`dirname $bin`/`readlink $bin`
fi
WD=`dirname $bin`
cd $WD
SCRIPT=./`basename $0`
#
# source configuration script, if any
#
test -f $CONFFILE && source $CONFFILE
if [ "$JAVA_HOME" != "" ]; then
JAVA_BIN="$JAVA_HOME/bin/java"
else
JAVA_BIN="java"
fi
command=$1
ALL_JAVA_OPTS="-Djavax.net.ssl.trustStore=etc/openBIS.keystore $JAVA_OPTS"
# ensure that we ignore a possible prefix "--" for any command
command="${command#--*}"
case "$command" in
start)
getStatus
EXIT_STATUS=$?
if [ $EXIT_STATUS -eq 0 ]; then
echo "Cannot start ETL Server: already running."
exit 100
fi
echo -n "Starting ETL Server "
rotateLogFiles $LOGFILE $MAXLOGS
shift 1
${JAVA_BIN} ${ALL_JAVA_OPTS} -jar $JAR_FILE "$@" > $STARTUPLOG 2>&1 & echo $! > $PIDFILE
if [ $? -eq 0 ]; then
# wait for initial self-test to finish
n=0
while [ $n -lt $MAX_LOOPS ]; do
sleep 1
if [ ! -f $PIDFILE ]; then
break
fi
if [ -s $STARTUPLOG ]; then
PID=`cat $PIDFILE 2> /dev/null`
isPIDRunning $PID
if [ $? -ne 0 ]; then
break
fi
fi
grep "$SUCCESS_MSG" $LOGFILE > /dev/null 2>&1
if [ $? -eq 0 ]; then
break
fi
n=$(($n+1))
done
PID=`cat $PIDFILE 2> /dev/null`
isPIDRunning $PID
if [ $? -eq 0 ]; then
grep "$SUCCESS_MSG" $LOGFILE > /dev/null 2>&1
if [ $? -ne 0 ]; then
echo "(pid $PID - WARNING: SelfTest not yet finished)"
else
echo "(pid $PID)"
fi
else
echo "FAILED"
if [ -s $STARTUPLOG ]; then
echo "startup log says:"
cat $STARTUPLOG
else
echo "log file says:"
tail $LOGFILE
fi
fi
else
echo "FAILED"
fi
;;
stop)
echo -n "Stopping ETL Server "
if [ -f $PIDFILE ]; then
PID=`cat $PIDFILE 2> /dev/null`
isPIDRunning $PID
if [ $? -eq 0 ]; then
kill $PID
n=0
while [ $n -lt $MAX_LOOPS ]; do
isPIDRunning $PID
if [ $? -ne 0 ]; then
break
fi
sleep 1
n=$(($n+1))
done
isPIDRunning $PID
if [ $? -ne 0 ]; then
echo "(pid $PID)"
test -f $PIDFILE && rm $PIDFILE 2> /dev/null
else
echo "FAILED"
fi
else
if [ -f $PIDFILE ]; then
rm $PIDFILE 2> /dev/null
echo "(was dead - cleaned up pid file)"
fi
fi
else
echo "(not running - nothing to do)"
fi
;;
status)
printStatus
EXIT_STATUS=$?
exit $EXIT_STATUS
;;
restart)
$SCRIPT stop
$SCRIPT start
;;
help)
${JAVA_BIN} ${ALL_JAVA_OPTS} -jar $JAR_FILE --help
;;
version)
${JAVA_BIN} ${ALL_JAVA_OPTS} -jar $JAR_FILE --version
;;
show-shredder)
${JAVA_BIN} ${ALL_JAVA_OPTS} -jar $JAR_FILE --show-shredder
;;
*)
echo $"Usage: $0 {start|stop|restart|status|help|version|show-shredder}"
exit 200
;;
esac
exit 0
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<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
<appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
<layout class="org.apache.log4j.PatternLayout">
<param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
</layout>
</appender>
<appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
<root>
<priority value ="info" />
<appender-ref ref="STDOUT" />
</root>
</log4j:configuration>
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# The root directory of the data store
storeroot-dir = targets/store
# The check interval (in seconds)
check-interval = 5
# The time-out for clean up work in the shutdown sequence (in seconds).
# Note that that the maximal time for the shutdown sequence to complete can be as large
# as twice this time.
shutdown-timeout = 2
# If free disk space goes below value defined here, a notification email will be sent.
# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
# specified or if value is negative, the system will not be watching.
highwater-mark = 1048576
# If a data set is successfully registered it sends out an email to the registrator.
# If this property is not specified, no email is sent to the registrator. This property
# does not affect the mails which are sent, when the data set could not be registered.
notify-successful-registration = false
# The URL of the openBIS server
server-url = http://localhost:8080/openbis
# The username to use when contacting the openBIS server
username = etlserver
# The password to use when contacting the openBIS server
password = doesnotmatter
# SMTP properties (must start with 'mail' to be considered).
# mail.smtp.host = localhost
# mail.from = etlserver@localhost
# mail.smtp.user =
# mail.smtp.password =
# Maximum number of retries if renaming failed.
# renaming.failure.max-retries = 12
# The number of milliseconds to wait before retrying to execute the renaming process.
# renaming.failure.millis-to-sleep = 5000
# Globally used separator character which separates entities in a data set file name
data-set-file-name-entity-separator = _
# Prefixes for processing paths for all procedure types.
# default-prefix-for-absolute-paths is the key for paths starting with '/'.
# default-prefix-for-relative-paths is the key for paths not starting with '/'.
#
default-prefix-for-absolute-paths =
# Processors of processing instructions.
#
# processors: comma separated list of procedure type codes
# processor.<procedure type code>.prefix-for-absolute-paths: Key for a processing path starting with '/'.
# processor.<procedure type code>.prefix-for-relative-paths: Key for a processing path not starting with '/'.
# processor.<procedure type code>.parameters-file: Name of the file containing the processing parameters.
# processor.<procedure type code>.finished-file-template: Name of the marker file which finishes processing.
processors = DATA_ACQUISITION
processor.DATA_ACQUISITION.prefix-for-absolute-paths = ${default-prefix-for-absolute-paths}
processor.DATA_ACQUISITION.prefix-for-relative-paths = targets/processing
processor.DATA_ACQUISITION.parameters-file = parameters
processor.DATA_ACQUISITION.data-set-code-prefix-glue = ${data-set-file-name-entity-separator}
processor.DATA_ACQUISITION.finished-file-template = .MARKER_is_finished_{0}
processor.DATA_ACQUISITION.input-storage-format = BDS_DIRECTORY
# time after which the copy of a single file for processing should complete.
# If that will not happen, operation will be terminated and relaunched.
processor.DATA_ACQUISITION.data-copy-timeout = 10
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
inputs=main-thread
# ---------------------------------------------------------------------------
# 'main-thread' thread configuration
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
main-thread.incoming-dir = targets/incoming
# The group the samples extracted by this thread belong to. If commented out or empty, then samples
# are considered associated to a database instance (not group private).
# main-thread.group-code = CISD
# The store format that should be applied in the incoming directory.
main-thread.incoming-dir.format =
# ---------------- Plugin properties
# The extractor plugin class to use for code extraction
main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
main-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
main-thread.type-extractor.file-format-type = TIFF
main-thread.type-extractor.locator-type = RELATIVE_LOCATION
main-thread.type-extractor.data-set-type = HCS_IMAGE
main-thread.type-extractor.procedure-type = DATA_ACQUISITION
# The storage processor (IStorageProcessor implementation)
#main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
main-thread.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
main-thread.storage-processor.version = 1.1
main-thread.storage-processor.sampleTypeCode = CELL_PLATE
main-thread.storage-processor.sampleTypeDescription = Screening Plate
main-thread.storage-processor.format = HCS_IMAGE V1.0
main-thread.storage-processor.number_of_channels = 2
main-thread.storage-processor.contains_original_data = TRUE
main-thread.storage-processor.well_geometry = 3x3
main-thread.storage-processor.file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSImageFileExtractor
datastore_server/resource/dependency-structure.ddf 0 → 100644
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#
#
#
#show allResults
{root} = ch.systemsx.cisd
{etlserver} = ${root}.etlserver
######################################################################
# Check dependencies to openbis
{openbis} = ${root}.openbis
[etlserver] = ${etlserver}.*
[private_openbis] = ${openbis}.* excluding ${openbis}.generic.shared.dto.* ${openbis}.generic.shared.IETLLIMSService
check sets [etlserver]
check [etlserver] independentOf [private_openbis]
datastore_server/resource/eclipse/ETL Server Fast Suite.launch 0 → 100644
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− 0
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.testng.eclipse.launchconfig">
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
<listEntry value="/libraries/testng/testng-jdk15.jar"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="1"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.testng.remote.RemoteTestNG"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="datastore_server"/>
<mapAttribute key="org.testng.eclipse.ALL_CLASS_METHODS"/>
<listAttribute key="org.testng.eclipse.CLASS_TEST_LIST"/>
<stringAttribute key="org.testng.eclipse.COMPLIANCE_LEVEL" value="JDK"/>
<listAttribute key="org.testng.eclipse.GROUP_LIST"/>
<listAttribute key="org.testng.eclipse.GROUP_LIST_CLASS"/>
<stringAttribute key="org.testng.eclipse.LOG_LEVEL" value="2"/>
<listAttribute key="org.testng.eclipse.SUITE_TEST_LIST">
<listEntry value="sourceTest/java/tests_fast.xml"/>
</listAttribute>
<intAttribute key="org.testng.eclipse.TYPE" value="3"/>
</launchConfiguration>
datastore_server/resource/eclipse/ETL Server.launch 0 → 100644
+ 13
− 0
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
<listEntry value="/datastore_server/source/java/ch/systemsx/cisd/etlserver/Main.java"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="1"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="ch.systemsx.cisd.etlserver.Main"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="datastore_server"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-ea"/>
</launchConfiguration>
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