split VCellClientTest into admin and prod, set Guice DI on all services

Dockerfile

@@ -2,7 +2,7 @@ FROM eclipse-temurin:17 as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
-         --add-modules java.base \
+         --add-modules ALL-MODULE-PATH \
          --strip-debug \
          --no-man-pages \
          --no-header-files \
@@ -60,17 +60,7 @@ RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
 ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
 
 # Copy JAR files
-COPY ./vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
-     ./vcell-client/target/maven-jars/*.jar \
- 	 ./vcell-core/target/vcell-core-0.0.1-SNAPSHOT.jar \
-     ./vcell-core/target/maven-jars/*.jar \
- 	 ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
-     ./vcell-server/target/maven-jars/*.jar \
- 	 ./vcell-vmicro/target/vcell-vmicro-0.0.1-SNAPSHOT.jar \
-     ./vcell-vmicro/target/maven-jars/*.jar \
-     ./vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT.jar \
-     ./vcell-admin/target/maven-jars/*.jar \
-     ./vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
+COPY ./vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
      ./vcell-cli/target/maven-jars/*.jar \
      ./non-maven-java-libs/org/sbml/libcombine/libCombineLinux64/0.2.7/libCombineLinux64-0.2.7.jar \
      /usr/local/app/vcell/lib/

README.md

@@ -69,7 +69,7 @@ Requirements:  Eclipse IDE for Java Developers and Java JDK 1.8 or later
      * Name: VCellClient
      * Main: 
          * Project: `vcell-client`
-         * Main Class: `cbit.vcell.client.test.VCellClientTest`
+         * Main Class: `cbit.vcell.client.test.VCellClientMain`
      * Arguments:
          * Program arguments: `vcellapi-beta.cam.uchc.edu:8080`
          * VM arguments are:
@@ -111,7 +111,7 @@ VCell Server Installation General Requirements
 
 
 ### Other Details
-1. Creating certs [details](README_certs.md)  
+1. Creating certs [details](docs-misc/README_certs.md)  
     1.1. (TLS/SSL website for (vcellapi.cam.uchc.edu,vcell-api.cam.uchc.edu)  
     1.2. Microsoft authenticode codesigning (to prevent install4j from being rejected on windows clients)  
     1.3. Apple codesigning for macos (prevents from mac refusing install4j install))  
@@ -122,9 +122,9 @@ VCell Server Installation General Requirements
 4. Building VCell Client/Server [Software detailed instructions](docker/build/README.md)  
     4.1.  Github/Travis/Appveyor/Dockerhub [Instructions](README_git_trav_appv_dhub.md)  
 5. Deploying VCell Client/Server software [detailed instructions](docker/swarm/README.md)  
-    5.1. VCell System [Flow-Control](README_flow_control.md)  
+    5.1. VCell System [Flow-Control](docs-misc/README_flow_control.md)  
 6. Server Administration [detailed instructions](docker/swarm/README_admin.md) (.e.g restarting VCell services)  
-7.  [Debugging detailed instructions](README_Debugging.md) (.e.g debug vcell client/server)  
+7.  [Debugging detailed instructions](docs-misc/README_Debugging.md) (.e.g debug vcell client/server)  
 8. serverconfig.sh file must be customized for your configuration (see vcell/docker/swarm/serverconfig-uch.sh).  
 
 

docker/build/Dockerfile-api-dev

@@ -1,34 +1,44 @@
 FROM eclipse-temurin:17 as jre-build
 
 # Create a custom Java runtime
-#   java.beans.PropertyChangeEvent requires java.desktop
-#   org.apache.logging.log4j.core.util.DefaultShutdownCallbackRegistry requires java.management (MBeanRegistrationException)
 RUN $JAVA_HOME/bin/jlink \
-         --add-modules java.base,java.instrument,java.logging,java.management,java.desktop,java.naming,java.sql,java.xml,jdk.jdwp.agent,jdk.httpserver \
+         --add-modules ALL-MODULE-PATH \
          --strip-debug \
          --no-man-pages \
          --no-header-files \
          --compress=2 \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM python:3.9.7-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
+# now we have Java 17 and Python 3.9
+
 RUN apt-get -y update && \
-    apt-get install -y curl dnsutils && \
+    apt-get install -y --no-install-recommends curl dnsutils && \
     mkdir -p /usr/local/app/lib 
-
+
+RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
+ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
+
 WORKDIR /usr/local/app
 
-COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
-     ./vcell-server/target/maven-jars/*.jar \
-     ./vcell-api/target/vcell-api-0.0.1-SNAPSHOT.jar \
+# Copy JAR files
+COPY ./vcell-api/target/vcell-api-0.0.1-SNAPSHOT.jar \
      ./vcell-api/target/maven-jars/*.jar \
      ./lib/
 
+# Copy and install vcell-cli-utils
+COPY ./vcell-cli-utils/ /usr/local/app/python/vcell_cli_utils/
+RUN cd /usr/local/app/python/vcell_cli_utils/ && \
+    poetry config cache-dir "/poetry/.cache" --local && \
+    chmod 755 poetry.toml && \
+    poetry install
+
+# copy API resources
 COPY ./vcell-api/docroot ./docroot
 COPY ./vcell-api/webapp ./webapp
 COPY ./vcell-api/keystore_macbook.jks .
@@ -53,6 +63,7 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
 	ssl_ignoreHostMismatch=true \
 	ssl_ignoreCertProblems=false \
 	submit_service_host="submit" \
+	workingDir="/usr/local/app" \
 	userTimezone="-05:00"
 
 ENV dbpswdfile=/run/secrets/dbpswd \
@@ -71,6 +82,7 @@ ENTRYPOINT java \
 	-Dlog4j.configurationFile=/usr/local/app/vcell-api.log4j.xml \
 	-Dvcell.server.id="${serverid}" \
 	-Dvcell.installDir=/usr/local/app \
+	-Dcli.workingDir="${workingDir}" \
 	-Dvcell.server.dbConnectURL="${dburl}" \
 	-Dvcell.server.dbDriverName="${dbdriver}" \
 	-Dvcell.server.dbUserid="${dbuser}" \

docker/build/Dockerfile-clientgen-dev

@@ -1,4 +1,23 @@
-FROM openjdk:17-jdk-slim
+FROM eclipse-temurin:17 as jre-build
+
+# Create a custom Java runtime
+RUN $JAVA_HOME/bin/jlink \
+         --add-modules java.base,java.instrument,java.logging,java.management,java.desktop,java.naming,java.transaction.xa,java.xml,jdk.jdwp.agent \
+         --strip-debug \
+         --no-man-pages \
+         --no-header-files \
+         --compress=2 \
+         --output /javaruntime
+
+# Define base image and copy in jlink created minimal Java 17 environment
+FROM debian:buster-slim
+ENV JAVA_HOME=/opt/java/openjdk
+ENV PATH "${JAVA_HOME}/bin:${PATH}"
+COPY --from=jre-build /javaruntime $JAVA_HOME
+
+RUN mkdir -p /usr/local/app && \
+	apt-get -y update && \
+    apt-get -y install wget
 
 RUN mkdir /installer && cd /installer && \
     wget --quiet -O install4j_unix_10_0_4.tar.gz \

docker/build/Dockerfile-data-dev

@@ -1,62 +1,8 @@
-# VTK and OpenJDK n Alpine Linux
-#FROM alpine:3.7
-# Install some Alpine packages
-#RUN apk add --no-cache \
-#    bash \
-#    build-base \
-#    cmake \
-#    wget \
-#    mesa-dev \
-#    mesa-osmesa \
-#    python2-dev
-# Download and extract VTK source, then configure and build VTK
-#RUN wget -nv -O- http://www.vtk.org/files/release/7.1/VTK-7.1.0.tar.gz | \
-#    tar xz && \
-#    cd VTK-7.1.0 && \
-#    cmake \
-#    -D CMAKE_BUILD_TYPE:STRING=Release \
-#    -D CMAKE_INSTALL_PREFIX:STRING=/usr \
-#    -D BUILD_DOCUMENTATION:BOOL=OFF \
-#    -D BUILD_EXAMPLES:BOOL=OFF \
-#    -D BUILD_TESTING:BOOL=OFF \
-#    -D BUILD_SHARED_LIBS:BOOL=ON \
-#    -D VTK_USE_X:BOOL=OFF \
-#    -D VTK_OPENGL_HAS_OSMESA:BOOL=ON \
-#    -D OSMESA_LIBRARY=/usr/lib/libOSMesa.so.8 \
-#    -D OSMESA_INCLUDE_DIR=/usr/include/GL/ \
-#    -D VTK_RENDERING_BACKEND:STRING=OpenGL \
-#    -D VTK_Group_MPI:BOOL=OFF \
-#    -D VTK_Group_StandAlone:BOOL=OFF \
-#    -D VTK_Group_Rendering:BOOL=ON \
-#    -D VTK_WRAP_PYTHON=ON \
-#    -D VTK_PYTHON_VERSION:STRING=2 \
-#    . && \
-#    make -j 2 && \
-#    make install && \
-#    cd .. && rm -rf VTK-7.1.0
-# install thrift python package
-#RUN wget https://bootstrap.pypa.io/get-pip.py \
-#    && python get-pip.py \
-#    && pip install thrift
-#RUN apk update && apk upgrade && \
-#    apk add openjdk8 && \
-#    mkdir /tmp/tmprt && \
-#    cd /tmp/tmprt && \
-#    apk add zip && \
-#    unzip -q /usr/lib/jvm/default-jvm/jre/lib/rt.jar && \
-#    apk add zip && \
-#    zip -q -r /tmp/rt.zip . && \
-#    apk del zip && \
-#    cd /tmp && \
-#    mv rt.zip /usr/lib/jvm/default-jvm/jre/lib/rt.jar && \
-#    rm -rf /tmp/tmprt /var/cache/apk/* bin/jjs bin/keytool bin/orbd bin/pack200 bin/policytool \
-#    bin/rmid bin/rmiregistry bin/servertool bin/tnameserv bin/unpack200 
-
 FROM eclipse-temurin:17 as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
-         --add-modules java.base,java.instrument,java.logging,java.management,java.desktop,java.naming,java.sql,java.xml,jdk.jdwp.agent \
+         --add-modules ALL-MODULE-PATH \
          --strip-debug \
          --no-man-pages \
          --no-header-files \
@@ -71,9 +17,9 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
 
-RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-	apt-get -y install openssh-client screen
+RUN apt-get -y update && \
+	apt-get -y install openssh-client screen && \
+    mkdir -p /usr/local/app
 
 RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
 ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
@@ -157,5 +103,5 @@ ENTRYPOINT java \
 	-Dvcell.mongodb.port.internal=${mongodb_port_internal} \
 	-Dvcell.mongodb.database=${mongodb_database} \
 	-Dvcelldata.web.server.port=${webDataPort} \
-	-cp "./lib/*" cbit.vcell.message.server.data.SimDataServer \
+	-cp "./lib/*" cbit.vcell.message.server.data.SimDataServerMain \
 	"${servertype}"

docker/build/Dockerfile-sched-dev

@@ -2,7 +2,7 @@ FROM eclipse-temurin:17 as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
-         --add-modules java.base,java.instrument,java.logging,java.management,java.desktop,java.naming,java.sql,java.transaction.xa,java.xml,jdk.jdwp.agent \
+         --add-modules ALL-MODULE-PATH \
          --strip-debug \
          --no-man-pages \
          --no-header-files \

docker/build/Dockerfile-web-dev

@@ -2,7 +2,7 @@ FROM eclipse-temurin:17 as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
-         --add-modules java.base,java.instrument,java.logging,java.management,java.desktop,java.naming,java.sql,java.xml,jdk.jdwp.agent,jdk.httpserver \
+         --add-modules ALL-MODULE-PATH \
          --strip-debug \
          --no-man-pages \
          --no-header-files \

docker/build/installers/VCell.install4j

@@ -120,7 +120,7 @@
     <launcher name="VCell-${compiler:Site}-MacOSX" id="102" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.test.VCellClientTest" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <scanDirectory location="lib" failOnError="false" />
         </classPath>
@@ -156,7 +156,7 @@
     <launcher name="VCell-${compiler:Site}-Windows64" id="345" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.test.VCellClientTest" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.test.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <scanDirectory location="lib" failOnError="false" />
         </classPath>
@@ -186,7 +186,7 @@
     <launcher name="VCell-${compiler:Site}-Windows32" id="447" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
-      <java mainClass="cbit.vcell.client.test.VCellClientTest" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.test.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <scanDirectory location="lib" failOnError="false" />
         </classPath>
@@ -217,7 +217,7 @@
     <launcher name="VCell-${compiler:Site}-Linux32" id="534" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
-      <java mainClass="cbit.vcell.client.test.VCellClientTest" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.test.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <scanDirectory location="lib" failOnError="false" />
         </classPath>
@@ -244,7 +244,7 @@
     <launcher name="VCell-${compiler:Site}-Linux64" id="627" icnsFile="${compiler:vcellIcnsFile}">
       <executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
       <splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
-      <java mainClass="cbit.vcell.client.test.VCellClientTest" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
+      <java mainClass="cbit.vcell.client.test.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
         <classPath>
           <scanDirectory location="lib" failOnError="false" />
         </classPath>

docker/swarm/README_admin.md

@@ -8,6 +8,7 @@ sudo docker service update --force --detach=false vcellrel_data
 sudo docker service update --force --detach=false vcellrel_sched  
 sudo docker service update --force --detach=false vcellrel_submit  
 sudo docker service update --force --detach=false vcellrel_api  
+sudo docker service update --force --detach=false vcellrel_web  
 (not used) sudo docker service update --force --detach=false vcellrel_opt  
 
 ### Restart Alpha Site (from development swarm cluster, e.g. vcellapi-beta.cam.uchc.edu or vcell-node3 or vcell-node4)  
@@ -20,4 +21,5 @@ sudo docker service update --force --detach=false vcellalpha_data
 sudo docker service update --force --detach=false vcellalpha_sched  
 sudo docker service update --force --detach=false vcellalpha_submit  
 sudo docker service update --force --detach=false vcellalpha_api  
+sudo docker service update --force --detach=false vcellalpha_web  
 (not used) sudo docker service update --force --detach=false vcellalpha_opt  

docker/swarm/localconfig_realslurm_oracle.sh

@@ -182,13 +182,10 @@ VCELL_SECRETS_DIR=${HOME}/vcellkeys_oracle
 VCELL_SIMDATADIR_ARCHIVE_EXTERNAL=/share/apps/vcell12/users
 VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
 VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-1/users
-VCELL_SIMDATADIR_ARCHIVE_HOST_ORIG=/Volumes/vcell-2/users
 VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
 VCELL_SIMDATADIR_HOST=/Volumes/vcell/users
 VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell3/users
 VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell/users
-VCELL_SIMDATADIR_SECONDARY_EXTERNAL_ORIG=/share/apps/vcell7/users
-VCELL_SIMDATADIR_SECONDARY_HOST_ORIG=/Volumes/vcell-1/users
 VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE

docker/swarm/localconfig_realslurm_postgres.sh

@@ -181,11 +181,11 @@ VCELL_REPO_NAMESPACE=$VCELL_REPO_NAMESPACE
 VCELL_SECRETS_DIR=${HOME}/vcellkeys_postgres
 VCELL_SIMDATADIR_ARCHIVE_EXTERNAL=/share/apps/vcell12/users
 VCELL_SIMDATADIR_ARCHIVE_INTERNAL=/share/apps/vcell12/users
-VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-2/users
+VCELL_SIMDATADIR_ARCHIVE_HOST=/Volumes/vcell-1/users
 VCELL_SIMDATADIR_EXTERNAL=/share/apps/vcell3/users
 VCELL_SIMDATADIR_HOST=/Volumes/vcell/users
-VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell10/users
-VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell-1/users
+VCELL_SIMDATADIR_SECONDARY_EXTERNAL=/share/apps/vcell3/users
+VCELL_SIMDATADIR_SECONDARY_HOST=/Volumes/vcell/users
 VCELL_SIMDATADIR_PARALLEL_EXTERNAL=/share/apps/vcell3parallel
 VCELL_SITE_CAMEL=${_site_camel}
 VCELL_SITE=$VCELL_SITE

pom.xml

@@ -124,6 +124,7 @@
 		<imagej.version>${imagej2.version}</imagej.version>
 		<!-- JFreeChart - http://www.jfree.org/jfreechart/ -->
 		<jfreechart.version>1.5.0</jfreechart.version>
+		<picocli.version>4.6.3</picocli.version>
 
 	</properties>
 

vcell-admin/pom.xml

@@ -125,7 +125,7 @@
 		<dependency>
 			<groupId>info.picocli</groupId>
 			<artifactId>picocli</artifactId>
-			<version>4.6.3</version>
+			<version>${picocli.version}</version>
 		</dependency>
 	</dependencies>