Stop tracking .DS_Store

add trigger to is-collector too

.gitignore

@@ -1,3 +1,8 @@
 # ---> Ansible
 *.retry
+.DS_Store
+
+src/java-7-oracle.tar.gz
+Dockerfile.almalinux8-java7
+Dockerfile.ubuntu14-java7
 

Dockerfile

@@ -7,6 +7,8 @@ ENV J2REDIR=/usr/lib/jvm/zulu7/jre
 ENV JAVA_HOME=/usr/lib/jvm/zulu7
 ENV PATH=$JAVA_HOME/bin:$JAVA_HOME/db/bin:$JAVA_HOME/jre/bin:$PATH
 
+ENV TZ="Europe/Rome"
+
 # ENV DERBY_HOME=/docker-java-home/db
 ENV USER=gcube
 ENV GLOBUS_LOCATION=/home/gcube/gCore
@@ -15,23 +17,69 @@ ENV PATH=$GLOBUS_LOCATION/bin:$PATH
 #ENV EXIST_HOME=
 #ENV GLOBUS_OPTIONS="-Dexist.home=$EXIST_HOME"
 ENV GLOBUS_OPTIONS=""
-ENV USER=$LOGNAME
+ENV LOGNAME=$USER
 ENV GCORE_START_OPTIONS="-DX509_USER_PROXY=$X509_USER_PROXY -Xms2800M -Xmx4800M"
 
-RUN adduser --system --gecos "Gcube service user" --disabled-password --disabled-login --uid 333 --shell /usr/sbin/nologin gcube 
+RUN addgroup --system --gid 333 gcube
+RUN adduser --system --gecos "Gcube service user" --disabled-password --disabled-login --uid 333 --ingroup gcube --shell /usr/sbin/nologin gcube 
 RUN apt-get update
-RUN apt-get install -y wget
+RUN apt-get install -y wget nano less
+
 WORKDIR /home/gcube
-RUN cd /home/gcube && wget https://nexus.d4science.org/nexus/content/repositories/gcube-staging-gcore/org/gcube/distribution/ghn-distribution/7.0.1-4.16.0-144317/ghn-distribution-7.0.1-4.16.0-144317.tar.gz && tar zxf ghn-distribution-7.0.1-4.16.0-144317.tar.gz && rm -f ghn-distribution-7.0.1-4.16.0-144317.tar.gz && mkdir -p /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc && chown gcube /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc
+
+RUN cd /home/gcube && wget https://nexus.d4science.org/nexus/content/repositories/gcube-releases/org/gcube/distribution/ghn-distribution/7.0.0-4.2.0-132545/ghn-distribution-7.0.0-4.2.0-132545.tar.gz && tar zxf ghn-distribution-7.0.0-4.2.0-132545.tar.gz && rm -f ghn-distribution-7.0.0-4.2.0-132545.tar.gz && mkdir -p /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc && chown -R gcube:gcube /home/gcube/gCore
+#chown gcube:gcube /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc 
+RUN chmod -R u=rwX,g=rX,o-rwx /home/gcube
+
+RUN rm /home/gcube/gCore/lib/accounting-lib-2.3.0-4.2.0-132276.jar 
+RUN rm /home/gcube/gCore/lib/document-store-lib-1.4.0-4.2.0-135110.jar
+RUN rm /home/gcube/gCore/lib/document-store-lib-couchbase-1.2.0-4.2.0-131889.jar
+# RUN cd /home/gcube && wget https://nexus.d4science.org/nexus/content/repositories/gcube-staging-gcore/org/gcube/distribution/ghn-distribution/7.0.1-4.16.0-144317/ghn-distribution-7.0.1-4.16.0-144317.tar.gz && tar zxf ghn-distribution-7.0.1-4.16.0-144317.tar.gz && rm -f ghn-distribution-7.0.1-4.16.0-144317.tar.gz && mkdir -p /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc && chown gcube /home/gcube/gCore/logs /home/gcube/gCore/tmp /home/gcube/gCore/config /home/gcube/gCore/etc
+# add fake-accounting-lib
+
+# RUN rm /home/gcube/gCore/lib/accounting-lib-3.5.0.jar
+# RUN rm /home/gcube/gCore/lib/document-store-lib-2.5.0.jar
+# RUN rm /home/gcube/gCore/lib/document-store-lib-couchbase-1.6.0-4.16.0-171307.jar
+RUN wget -P /home/gcube/gCore/lib https://nexus.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/accounting/fake-accounting-lib/3.2.0-SNAPSHOT/fake-accounting-lib-3.2.0-20190311.105710-2.jar
+
+RUN rm /home/gcube/gCore/lib/is-publisher-2.2.0-4.2.0-126946.jar
+RUN wget -P /home/gcube/gCore/lib https://nexus.d4science.org/nexus/content/repositories/gcube-releases-gcore/org/gcube/informationsystem/is-publisher/2.2.1-4.15.0-181697/is-publisher-2.2.1-4.15.0-181697.jar
+
 COPY src/gcube-start-container.sh /home/gcube/gCore/bin/gcore-start-container
+COPY src/gcore-start-container-daemon /home/gcube/gCore/bin/gcore-start-container-daemon
 COPY src/GHNConfig.xml /home/gcube/gCore/config/GHNConfig.xml
+RUN rm /home/gcube/gCore/lib/common-authorization-2.0.1-4.2.0-139995.jar
+COPY src/common-authorization-2.0.2-4.3.0.jar /home/gcube/gCore/lib/
+RUN rm /home/gcube/gCore/lib/common-scope-maps-1.0.5-4.2.0-134574.jar
+COPY src/common-scope-maps-1.1.0-4.15.0-178670.jar /home/gcube/gCore/lib/
+COPY src/ServiceMaps.tar.gz /home/gcube/
+
+RUN tar xzvf /home/gcube/ServiceMaps.tar.gz -C /home/gcube/gCore/config/
+RUN chmod 750 /home/gcube/gCore/config/ServiceMap_*.xml
+
+# Update loggin settings
+# Log with debug
+# COPY src/container-log4j.properties.stdout.debug /home/gcube/gCore/container-log4j.properties
+COPY src/container-log4j.properties /home/gcube/gCore/
+COPY src/logging.jul.properties /home/gcube/gCore/
+RUN chown -R gcube:gcube /home/gcube/gCore
+
+# COPY src/log4j-stdout-appender.patch /home/gcube/gCore/
+# RUN cat /home/gcube/gCore/log4j-stdout-appender.patch >> /home/gcube/gCore/container-log4j.properties
+# RUN sed -i 's/log4j.rootLogger=ERROR,FULL,LITE/log4j.rootLogger=ERROR,stdout/' /home/gcube/gCore/container-log4j.properties
 RUN $GLOBUS_LOCATION/bin/gcore-load-env
 RUN chmod 755 /home/gcube/gCore/bin/gcore-start-container
 # Remove Resultset from distribution
 # RUN /home/gcube/gCore/bin/gcore-undeploy-service org.gcube.common.searchservice.resultsetservice
-RUN /home/gcube/gCore/bin/gcore-undeploy-service resultsetservice-3.1.0-4.16.0-126939
-EXPOSE 8080
+# RUN /home/gcube/gCore/bin/gcore-undeploy-service resultsetservice-3.1.0-4.16.0-126939
+RUN /home/gcube/gCore/bin/gcore-undeploy-service resultsetservice-3.1.0-4.2.0-126939
+RUN mkdir /gcube-data && chown gcube.nogroup /gcube-data
+
+
 USER gcube
-ENTRYPOINT exec /home/gcube/gCore/bin/gcore-start-container
+EXPOSE 8080
+CMD /home/gcube/gCore/bin/gcore-start-container
+# ENTRYPOINT exec /home/gcube/gCore/bin/gcore-start-container
+# ENTRYPOINT ["tail", "-f", "/dev/null"]
 # For Spring-Boot project, use the entrypoint below to reduce Tomcat startup time.
 #ENTRYPOINT exec java $JAVA_OPTS -Djava.security.egd=file:/dev/./urandom -jar ansibleplaybookisregistryservice.jar

JenkinsFile

@@ -48,5 +48,26 @@ pipeline {
             }
         }
     }
+    stage('trigger IS-collector image job') {
+        steps {
+            script {
+                build(job: 'is-collector-service-image', wait: false, propagate: false);
+            }
+        }
+    }
+    stage('trigger Resource Manager image job') {
+        steps {
+            script {
+                build(job: 'resource-manager-service-image', wait: false, propagate: false);
+            }
+        }
+    }
+    stage('trigger VRE Modeler image job') {
+        steps {
+            script {
+                build(job: 'vremodeler-image', wait: false, propagate: false);
+            }
+        }
+    }    
   }
 }

README.md

@@ -5,11 +5,11 @@ The included Docker file will build a default image for the gHN distribution
 ## Build the image
 
 ```shell
-$ docker build -t ghn-distribution .
+$ docker build -t gcore-distribution .
 ```
 
 ## Run the image
 
 ```shell
-$ docker container run --name gcore-hosting-node -p 8080:8080 ghn-distribution 
+$ docker container run --name gcore-hosting-node -p 8080:8080 gcore-distribution 
 ```

src/container-log4j.properties

@@ -0,0 +1,47 @@
+
+# Base logger shows ERRORs only by default and sends them to 2 appenders
+log4j.rootLogger=INFO,FULL
+
+log4j.appender.FULL=org.apache.log4j.ConsoleAppender
+log4j.appender.FULL.layout=org.apache.log4j.PatternLayout
+log4j.appender.FULL.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.FULL.threshold=INFO
+
+#system-loggers, overwrite default priority of root logger
+log4j.logger.org.gcube=INFO
+#globus logger with dedicated appender and no propagation to root logger
+log4j.logger.org.globus.wsrf=WARN,GLOBUS
+log4j.appender.GLOBUS=org.apache.log4j.ConsoleAppender
+log4j.appender.GLOBUS.layout=org.apache.log4j.PatternLayout
+log4j.appender.GLOBUS.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.delegation=ERROR, DELEGATION
+log4j.appender.DELEGATION=org.apache.log4j.ConsoleAppender
+log4j.appender.DELEGATION.layout=org.apache.log4j.PatternLayout
+log4j.appender.DELEGATION.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.DELEGATION.threshold=INFO
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.vremanagement.ghnmanager=ERROR, MANAGER
+log4j.appender.MANAGER=org.apache.log4j.ConsoleAppender
+log4j.appender.MANAGER.layout=org.apache.log4j.PatternLayout
+log4j.appender.MANAGER.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.MANAGER.threshold=INFO
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.vremanagement.deployer=ERROR, DEPLOYER
+log4j.appender.DEPLOYER.layout=org.apache.log4j.PatternLayout
+log4j.appender.DEPLOYER=org.apache.log4j.ConsoleAppender
+log4j.appender.DEPLOYER.threshold=INFO
+
+
+#GCUBEHandler logger 
+log4j.logger.org.gcube.common.handlers=TRACE, ACCESS
+log4j.appender.ACCESS=org.apache.log4j.ConsoleAppender
+log4j.appender.ACCESS.layout=org.apache.log4j.PatternLayout
+log4j.appender.ACCESS.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.ACCESS.threshold=INFO
+
+

src/container-log4j.properties.stdout.debug

@@ -0,0 +1,47 @@
+
+# Base logger shows ERRORs only by default and sends them to 2 appenders
+log4j.rootLogger=DEBUG,FULL
+
+log4j.appender.FULL=org.apache.log4j.ConsoleAppender
+log4j.appender.FULL.layout=org.apache.log4j.PatternLayout
+log4j.appender.FULL.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.FULL.threshold=DEBUG
+
+#system-loggers, overwrite default priority of root logger
+log4j.logger.org.gcube=DEBUG
+#globus logger with dedicated appender and no propagation to root logger
+log4j.logger.org.globus.wsrf=WARN,GLOBUS
+log4j.appender.GLOBUS=org.apache.log4j.ConsoleAppender
+log4j.appender.GLOBUS.layout=org.apache.log4j.PatternLayout
+log4j.appender.GLOBUS.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.delegation=ERROR, DELEGATION
+log4j.appender.DELEGATION=org.apache.log4j.ConsoleAppender
+log4j.appender.DELEGATION.layout=org.apache.log4j.PatternLayout
+log4j.appender.DELEGATION.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.DELEGATION.threshold=INFO
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.vremanagement.ghnmanager=ERROR, MANAGER
+log4j.appender.MANAGER=org.apache.log4j.ConsoleAppender
+log4j.appender.MANAGER.layout=org.apache.log4j.PatternLayout
+log4j.appender.MANAGER.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.MANAGER.threshold=INFO
+
+#service-specific logger with dedicated appender
+log4j.logger.org.gcube.common.vremanagement.deployer=ERROR, DEPLOYER
+log4j.appender.DEPLOYER.layout=org.apache.log4j.PatternLayout
+log4j.appender.DEPLOYER=org.apache.log4j.ConsoleAppender
+log4j.appender.DEPLOYER.threshold=INFO
+
+
+#GCUBEHandler logger 
+log4j.logger.org.gcube.common.handlers=TRACE, ACCESS
+log4j.appender.ACCESS=org.apache.log4j.ConsoleAppender
+log4j.appender.ACCESS.layout=org.apache.log4j.PatternLayout
+log4j.appender.ACCESS.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n
+log4j.appender.ACCESS.threshold=INFO
+
+

src/gcore-start-container-daemon

@@ -0,0 +1,49 @@
+#! /bin/sh
+#
+# Portions of this file Copyright 1999-2005 University of Chicago
+# Portions of this file Copyright 1999-2005 The University of Southern California.
+#
+# This file or a portion of this file is licensed under the
+# terms of the Globus Toolkit Public License, found at
+# http://www.globus.org/toolkit/download/license.html.
+# If you redistribute this file, with or without
+# modifications, you must include this notice in the file.
+#
+RESTART_DELAY=20
+RESTART_FILE=$GLOBUS_LOCATION/config/.restart
+RESTART_AND_CLEAN_FILE=$GLOBUS_LOCATION/config/.restartAndClean
+
+#kill the running daemons (if any)
+rm -rf nohup.out 1>/dev/null 2>&1
+
+ps -fwww -u $LOGNAME | grep "org.globus.wsrf.container.ServiceContainer" | grep -v grep | grep -v $$ |  awk '{print $2}' | xargs -n1 kill -9 1>/dev/null 2>&1
+
+#give the time to close the socket correctly
+sleep 1
+
+
+$GLOBUS_LOCATION/bin/gcore-start-container-reboot "$@"  
+
+
+while [  1 ]; do
+	sleep 10
+	if [ -e $RESTART_FILE ]; then
+		rm -rf $RESTART_FILE
+		sleep $RESTART_DELAY
+		$GLOBUS_LOCATION/bin/gcore-start-container-reboot "$@" 
+	fi
+	
+	if [ -e $RESTART_AND_CLEAN_FILE ]; then
+		rm -rf $RESTART_AND_CLEAN_FILE
+		sleep $RESTART_DELAY
+		#clean up the state
+		rm -f $GLOBUS_LOCATION/config/GHNProfile.xml* 2>&1 1>/dev/null
+   		rm -f $GLOBUS_LOCATION/etc/*/RIProfile.xml* 2>&1 1>/dev/null
+   		rm -rf $HOME/.gcore/ 2>&1 1>/dev/null
+   		#restart
+		$GLOBUS_LOCATION/bin/gcore-start-container-reboot "$@" 
+	fi
+done
+
+
+

src/gcube-start-container.sh

@@ -1,4 +1,32 @@
-#! /bin/sh
+#! /bin/bash
+
+
+# if [ -n "$EXIST_HOME" ]; then
+#   # our container is running a IS Collector
+#   if [ -L "$EXIST_HOME/webapp/WEB-INF/data" ] ; then
+#       # exist data has been already mounted on NFS
+#       echo "eXist data should be already in place on NFS"
+#   elif [ -d "$EXIST_HOME/webapp/WEB-INF/data" ] ; then
+#       echo "First run: set up our directory structure on the NFS mountpoint"
+#       mkdir -p /gcube-data/{db,backup} && mv $EXIST_HOME/webapp/WEB-INF/{data,logs,attachments} /gcube-data/db/
+#       if [ $? -eq 0 ]; then
+#         for dir in {data,logs,attachments}; do
+#           ln -s /gcube-data/db/${dir} $EXIST_HOME/webapp/WEB-INF/${dir}
+#         done
+#       else
+#         echo "Move failed: data already exists on NFS"
+#         exit 1
+#       fi
+#   else
+#       echo "Not a link, not a directory: a pony :-)?"
+#   fi
+# fi
+
+# mkdir -p /gcube-data/db/{data,logs,attachments}
+# mkdir -p $NFS_GCORE_PATH/persisted
+# mkdir $HOME/.gcore && chown gcube:gcube $HOME/.gcore
+# ln -s $NFS_GCORE_PATH/persisted $HOME/.gcore/
+
 
 if [ -z "$GLOBUS_LOCATION"  ]
 then
@@ -45,7 +73,7 @@ newargs="$mode $newargs"
 [ -e "$GLOBUS_LOCATION/tmp" ] ||  mkdir -p $GLOBUS_LOCATION/tmp
 
 #clean up the services' state if needed
-[ -f "$GLOBUS_LOCATION/config/GHNProfile.xml" ] ||  rm -rf ~/.gcore
+#[ -f "$GLOBUS_LOCATION/config/GHNProfile.xml" ] ||  rm -rf ~/.gcore
 
 cd $GLOBUS_LOCATION
 echo "gCore is running with ($newargs) and logging into logs/container.log..."

src/logging.jul.properties

@@ -0,0 +1,20 @@
+# Log levels in descending order OFF,SEVERE,WARNING,INFO,CONFIG,FINE,FINER,FINEST,ALL
+handlers = java.util.logging.FileHandler
+
+# Set the default logging level for the root logger
+.level = OFF
+
+# Set the default logging level for new FileHandler instances
+java.util.logging.FileHandler.level = OFF
+
+# Set the default formatter for new FileHandler instances
+java.util.logging.FileHandler.formatter = java.util.logging.SimpleFormatter
+java.util.logging.FileHandler.pattern = logs/jul.%g.log
+java.util.logging.FileHandler.limit = 2000000
+java.util.logging.FileHandler.count = 10
+
+
+# Set the default logging level for the logger named ...
+gr.uoa.level =  OFF
+org.gcube.level = OFF
+com.sun = OFF