Merge pull request #1248 from virtualcell/alpha-to-vxrails-k8s

Github CD action to deploy vcell alpha to kubernetes
virtualcell · May 16, 2024 · c870030 · c870030
2 parents f710641 + 4b4cbfa
commit c870030
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Showing 17 changed files with 190 additions and 200 deletions.
diff --git a/.github/workflows/site_deploy.yml b/.github/workflows/site_deploy.yml
@@ -13,19 +13,15 @@ on:
       vcell_build:
         description: 'build number'
         required: true
-        default: '23'
+        default: '148'
       vcell_site:
-        description: 'rel or alpha or test'
+        description: 'rel or alpha or test (note rel is Swarm, alpha and test are Kubernetes)'
         required: true
         default: 'alpha'
       server_only:
         description: 'Deploy only the server components?'
         required: true
         default: 'false'
-      deployment_type:
-        description: 'swarm or kubernetes (choose kubernetes for vcell_site="test")'
-        required: true
-        default: 'swarm'
 jobs:
   build:
     name: Build client installers
@@ -48,7 +44,7 @@ jobs:
         	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
         	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Rel"" >> $GITHUB_ENV;\
         else if [ "${{ github.event.inputs.vcell_site }}" == "alpha" ]; then\
-         	echo "VCELL_MANAGER_NODE=vcellapi-beta.cam.uchc.edu" >> $GITHUB_ENV;\
+         	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
         	echo "VCELL_INSTALLER_REMOTE_DIR="/share/apps/vcell3/apache_webroot/htdocs/webstart/Alpha"" >> $GITHUB_ENV;\
         else if [ "${{ github.event.inputs.vcell_site }}" == "test" ]; then\
          	echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV;\
@@ -212,7 +208,7 @@ jobs:
         set -ux
         mvn clean install -DskipTests
     - name: deploy installers and singularity to kubernetes site and web help to vcell.org
-      if: ${{ github.event.inputs.deployment_type == 'kubernetes' }}
+      if: ${{ github.event.inputs.vcell_site != 'rel' }}
       run: |
         set -ux
         cd docker/swarm
@@ -237,7 +233,7 @@ jobs:
           ./deploy-action-kubernetes.sh \
               --ssh-user ${{ secrets.CD_FULL_USER }} \
               --install-singularity  \
-              ${VCELL_MANAGER_NODE} \
+              ${VCELL_MANAGER_NODE} \ 
               ./${VCELL_CONFIG_FILE_NAME}
         fi
     - name: Capitalize first character of site name
@@ -246,13 +242,16 @@ jobs:
         SITE="${{ github.event.inputs.vcell_site }}"
         SITE_CAPITALIZED="$(tr '[:lower:]' '[:upper:]' <<< ${SITE:0:1})${SITE:1}"
         VCELL_SWVERSION="${SITE_CAPITALIZED}_Version_${{ github.event.inputs.vcell_version }}_build_${{ github.event.inputs.vcell_build}}"
-        KUSTOMIZE_OVERLAY="stage"
+        KUSTOMIZE_OVERLAY='not-specified'
+        if [ "${{ github.event.inputs.vcell_site }}" == "rel" ]; then KUSTOMIZE_OVERLAY="prod"; fi
+        if [ "${{ github.event.inputs.vcell_site }}" == "alpha" ]; then KUSTOMIZE_OVERLAY="dev"; fi
+        if [ "${{ github.event.inputs.vcell_site }}" == "test" ]; then KUSTOMIZE_OVERLAY="stage"; fi
         CONTAINER_IMAGE_TAG="${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build}}"
         echo "VCELL_SWVERSION=${VCELL_SWVERSION}" >> $GITHUB_ENV
         echo "KUSTOMIZE_OVERLAY=${KUSTOMIZE_OVERLAY}" >> $GITHUB_ENV
         echo "CONTAINER_IMAGE_TAG=${CONTAINER_IMAGE_TAG}" >> $GITHUB_ENV
-    - name: Call webhook to deploy to kubernetes cluster (overlay 'stage')
-      if: ${{ github.event.inputs.deployment_type == 'kubernetes' }}
+    - name: Call webhook to deploy to kubernetes cluster (overlay 'prod', 'dev' or 'stage')
+      if: ${{ github.event.inputs.vcell_site != 'rel' }}
       run: |
         git_sha=$(git rev-parse --short "$GITHUB_SHA")
         echo '{"ref": "main","inputs":{"overlay": "'${KUSTOMIZE_OVERLAY}'","tag":"'${CONTAINER_IMAGE_TAG}'","swversion": "'${VCELL_SWVERSION}'"}}' >body
@@ -261,7 +260,7 @@ jobs:
           -H 'Content-Type: application/json' \
           --data "@body"
     - name: deploy to swarm site
-      if: ${{ github.event.inputs.deployment_type == 'swarm' }}
+      if: ${{ github.event.inputs.vcell_site == 'rel' }}
       run: |
         set -ux
         cd docker/swarm

diff --git a/docker/swarm/deploy-action-kubernetes.sh b/docker/swarm/deploy-action-kubernetes.sh
@@ -3,12 +3,12 @@
 set -ux
 
 show_help() {
-	echo "Deploys or updates a deployment of VCell on remote Kubernetes cluster"
+	echo "Deploys vcell client installers, webhelp and singularity images for a Kubernetes deploy"
 	echo ""
 	echo "usage: deploy-action-kubernetes.sh [OPTIONS] REQUIRED-ARGUMENTS"
 	echo ""
 	echo "  REQUIRED-ARGUMENTS"
-	echo "    manager-node          any node for ssh access ( vcellapi-test.cam.uchc.edu )"
+	echo "    manager-node          any node for ssh access (e.g. vcellapi.cam.uchc.edu)"
 	echo ""
 	echo "    local-config-file     local config file for setting environment"
 	echo ""
@@ -38,10 +38,10 @@ show_help() {
 	echo "deploy-action-kubernetes.sh \\"
 	echo "   --ssh-user vcell \\"
 	echo "   --install_singularity \\"
-	echo "   --build_installers --installer_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/Test \\"
+	echo "   --build_installers --installer_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/Alpha \\"
 	echo "   --webhelp_local_dir ../../vcell-client/target/classes/vcellDoc \\"
 	echo "   --webhelp_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/VCell_Tutorials/VCell_Help \\"
-	echo "   vcellapi-test.cam.uchc.edu \\"
+	echo "   vcellapi.cam.uchc.edu \\"
 	echo "   ./server.config"
 	exit 1
 }

diff --git a/docker/swarm/serverconfig-uch.sh b/docker/swarm/serverconfig-uch.sh
@@ -43,76 +43,27 @@ case $VCELL_SITE in
 		VCELL_API_PORT_EXTERNAL=443
 		VCELL_API_PREFIX_V0=""
 		VCELL_API_PREFIX_V1=""
-		VCELL_DEBUG_PORT_BASE=5000
 		_applicationId="1471-8022-1038-5553"
 		;;
-	BETA)
-		_site_port_offset=1
-		VCELL_API_HOST_EXTERNAL=vcellapi.cam.uchc.edu
-		VCELL_S3_EXPORT_BASEURL=https://vcellapi.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=443
-		VCELL_API_PREFIX_V0="/api/v0"
-		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5010
-		_applicationId="1471-8022-1038-5552"
-		;;
 	ALPHA)
 		_site_port_offset=2
-		VCELL_API_HOST_EXTERNAL=vcellapi-beta.cam.uchc.edu
-		VCELL_S3_EXPORT_BASEURL=https://vcellapi-beta.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=8080
+		VCELL_API_HOST_EXTERNAL=vcell-dev.cam.uchc.edu
+		VCELL_S3_EXPORT_BASEURL=https://vcell-dev.cam.uchc.edu
+		VCELL_API_PORT_EXTERNAL=443
 		VCELL_API_PREFIX_V0="/api/v0"
 		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5020
 		_applicationId="1471-8022-1038-5554"
 		;;
 	TEST)
 		_site_port_offset=3
 		# VCELL_API_PORT_EXTERNAL=8081
-		VCELL_API_HOST_EXTERNAL=vcellapi-test.cam.uchc.edu
-		VCELL_S3_EXPORT_BASEURL=https://vcellapi-test.cam.uchc.edu
+		VCELL_API_HOST_EXTERNAL=vcell-stage.cam.uchc.edu
+		VCELL_S3_EXPORT_BASEURL=https://vcell-stage.cam.uchc.edu
 		VCELL_API_PORT_EXTERNAL=443
 		VCELL_API_PREFIX_V0="/api/v0"
 		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5030
 		_applicationId="1471-8022-1038-5555"
 		;;
-	TEST2)
-		_site_port_offset=4
-		VCELL_API_HOST_EXTERNAL=vcellapi-beta.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=8082
-		VCELL_API_PREFIX_V0="/api/v0"
-		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5040
-		_applicationId="1471-8022-1038-5556"
-		;;
-	TEST3)
-		_site_port_offset=5
-		VCELL_API_HOST_EXTERNAL=vcellapi-beta.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=8083
-		VCELL_API_PREFIX_V0="/api/v0"
-		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5050
-		_applicationId="1471-8022-1038-5557"
-		;;
-	TEST4)
-		_site_port_offset=6
-		VCELL_API_HOST_EXTERNAL=vcellapi-beta.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=8084
-		VCELL_API_PREFIX_V0="/api/v0"
-		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5060
-		_applicationId="1471-8022-1038-5558"
-		;;
-	TEST5)
-		_site_port_offset=7
-		VCELL_API_HOST_EXTERNAL=vcellapi-beta.cam.uchc.edu
-		VCELL_API_PORT_EXTERNAL=8085
-		VCELL_API_PREFIX_V0="/api/v0"
-		VCELL_API_PREFIX_V1="/api/v1"
-		VCELL_DEBUG_PORT_BASE=5070
-		_applicationId="1471-8022-1038-5559"
-		;;
 	*)
 		printf 'ERROR: Unknown site: %s\n' "$1" >&2
 		;;
@@ -141,13 +92,6 @@ VCELL_SLURM_LOCAL_SINGULARITY_DIR=/local/singularityImages
 VCELL_SLURM_CENTRAL_SINGULARITY_DIR=/share/apps/vcell3/singularityImages
 VCELL_SLURM_SINGULARITY_MODULE_NAME=singularity/vcell-3.10.0
 
-#
-# VCELL_API_PORT_EXTERNAL uses 443 for Beta and Rel (but on different machines/swarm clusters)
-#     ALPHA, TEST, TEST2, TEST3, etc. uses ports starting with 8080
-#     Note: port 8080 is currently needed by vcell.org website.
-#
-
-
 VCELL_JMS_SIM_PORT_EXTERNAL=$((61616 + _site_port_offset))
 VCELL_JMS_SIM_RESTPORT_EXTERNAL=$((8161 + _site_port_offset))
 VCELL_MONGO_PORT_EXTERNAL=$((27017 + _site_port_offset))
@@ -173,7 +117,7 @@ VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 #
 # write out the environment file to be for:
 # 1. deployment actions (e.g. deploy-action-swarm.sh or deploy-action-kubernetes.sh)
-# 2. runtime environment for the docker stack run command
+# 2. runtime environment for the docker stack run command (Docker swarm mode only, kubernetes uses ConfigMaps in vcell-fluxcd repo)
 #
 cat <<EOF >"$_outputfile"
 VCELL_API_HOST_EXTERNAL=$VCELL_API_HOST_EXTERNAL

diff --git a/pom.xml b/pom.xml
@@ -97,6 +97,8 @@
 		<activemq-client.version>5.18.3</activemq-client.version>
 		<axis.version>1.4</axis.version>
 		<axis-wsdl4j.version>1.2</axis-wsdl4j.version>
+		<bcprov-jdk15on.version>1.70</bcprov-jdk15on.version>
+		<bcpkix-jdk15on.version>1.70</bcpkix-jdk15on.version>
 		<bio-formats.version>6.7.0</bio-formats.version>
 		<bio-formats_plugins.version>${bio-formats.version}</bio-formats_plugins.version>
 		<biojava.version>6.0.4</biojava.version>
@@ -123,6 +125,7 @@
 		<imagej2.version>2.3.0</imagej2.version>
 		<imagej.version>${imagej2.version}</imagej.version>
 		<itext.version>2.1.7</itext.version>
+		<quarkus-itext.version>3.0.5</quarkus-itext.version>
 		<jackson-annotations.version>2.15.2</jackson-annotations.version>
 		<jackson-core.version>2.15.2</jackson-core.version>
 		<jackson-databind.version>2.15.2</jackson-databind.version>
@@ -172,7 +175,7 @@
 		<sesame-rio-rdfxml.version>2.9.0</sesame-rio-rdfxml.version>
 		<sesame-rio-n3.version>2.9.0</sesame-rio-n3.version>
 		<slf4j-api.version>2.0.9</slf4j-api.version>
-		<sshj.version>0.38.0</sshj.version>
+		<sshj.version>0.35.0</sshj.version>
 		<xercesImpl.version>2.8.0</xercesImpl.version>
 		<xstream.version>1.4.20</xstream.version>
 		<xom.version>1.2.5</xom.version>

diff --git a/vcell-core/pom.xml b/vcell-core/pom.xml
@@ -243,7 +243,34 @@
 			<groupId>com.lowagie</groupId>
 			<artifactId>itext</artifactId>
 			<version>${itext.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.bouncycastle</groupId>
+					<artifactId>bcmail-jdk14</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.bouncycastle</groupId>
+					<artifactId>bcprov-jdk14</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.bouncycastle</groupId>
+					<artifactId>bctsp-jdk14</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/org.bouncycastle/bcprov-jdk15on -->
+		<dependency>
+			<groupId>org.bouncycastle</groupId>
+			<artifactId>bcprov-jdk15on</artifactId>
+			<version>${bcprov-jdk15on.version}</version>
 		</dependency>
+		<!-- https://mvnrepository.com/artifact/org.bouncycastle/bcpkix-jdk15on -->
+		<dependency>
+			<groupId>org.bouncycastle</groupId>
+			<artifactId>bcpkix-jdk15on</artifactId>
+			<version>${bcpkix-jdk15on.version}</version>
+		</dependency>
+
 		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-lang3 -->
 		<dependency>
 			<groupId>org.apache.commons</groupId>

diff --git a/vcell-core/src/main/java/cbit/vcell/solvers/mb/MovingBoundaryReader.java b/vcell-core/src/main/java/cbit/vcell/solvers/mb/MovingBoundaryReader.java
@@ -141,40 +141,40 @@ void testquery(){
     }
 
     private double[] getDoubleArray(String... names){
-        MovingBoundardyVH5TypedPath<double[]> dpath = new MovingBoundardyVH5TypedPath<double[]>(root, double[].class, names);
+        MovingBoundaryVH5TypedPath<double[]> dpath = new MovingBoundaryVH5TypedPath<double[]>(root, double[].class, names);
         return dpath.get();
     }
 
     private double singleDouble(String... names){
         double[] a = getDoubleArray(names);
         if(a.length != 1){
-            throw new MovingBoundaryResultException(MovingBoundardyVH5Path.concat(names) + " is not single element array");
+            throw new MovingBoundaryResultException(MovingBoundaryVH5Path.concat(names) + " is not single element array");
         }
         return a[0];
     }
 
     private long[] getLongArray(String... names){
-        MovingBoundardyVH5TypedPath<long[]> dpath = new MovingBoundardyVH5TypedPath<long[]>(root, long[].class, names);
+        MovingBoundaryVH5TypedPath<long[]> dpath = new MovingBoundaryVH5TypedPath<long[]>(root, long[].class, names);
         return dpath.get();
     }
 
     private long singleLong(String... names){
         long[] a = getLongArray(names);
         if(a.length != 1){
-            throw new MovingBoundaryResultException(MovingBoundardyVH5Path.concat(names) + " is not single element array");
+            throw new MovingBoundaryResultException(MovingBoundaryVH5Path.concat(names) + " is not single element array");
         }
         return a[0];
     }
 
     private int[] getIntArray(String... names){
-        MovingBoundardyVH5TypedPath<int[]> dpath = new MovingBoundardyVH5TypedPath<int[]>(root, int[].class, names);
+        MovingBoundaryVH5TypedPath<int[]> dpath = new MovingBoundaryVH5TypedPath<int[]>(root, int[].class, names);
         return dpath.get();
     }
 
     private int singleInt(String... names){
         int[] a = getIntArray(names);
         if(a.length != 1){
-            throw new MovingBoundaryResultException(MovingBoundardyVH5Path.concat(names) + " is not single element array");
+            throw new MovingBoundaryResultException(MovingBoundaryVH5Path.concat(names) + " is not single element array");
         }
         return a[0];
     }
@@ -400,10 +400,10 @@ private class PlaneNodes {
         final H5CompoundDS species;
 
         PlaneNodes() throws Exception{
-            MovingBoundardyVH5TypedPath<H5CompoundDS> dpath = new MovingBoundardyVH5TypedPath<H5CompoundDS>(root, H5CompoundDS.class, "elements");
+            MovingBoundaryVH5TypedPath<H5CompoundDS> dpath = new MovingBoundaryVH5TypedPath<H5CompoundDS>(root, H5CompoundDS.class, "elements");
             elements = dpath.get();
             elements.read();
-            dpath = new MovingBoundardyVH5TypedPath<H5CompoundDS>(root, H5CompoundDS.class, "species");
+            dpath = new MovingBoundaryVH5TypedPath<H5CompoundDS>(root, H5CompoundDS.class, "species");
             species = dpath.get();
             species.read();
         }
@@ -441,7 +441,7 @@ public int[] getBoundaryIndexes(int timeIndex){
 
             VCAssert.assertTrue(timeIndex >= 0, "negative time index");
             validateTimeIndex(timeIndex);
-            MovingBoundardyVH5TypedPath<H5ScalarDS> path = new MovingBoundardyVH5TypedPath<>(root, H5ScalarDS.class, "boundaries");
+            MovingBoundaryVH5TypedPath<H5ScalarDS> path = new MovingBoundaryVH5TypedPath<>(root, H5ScalarDS.class, "boundaries");
             H5ScalarDS hsd = path.get();
             hsd.init();
             long[] start = hsd.getStartDims();

diff --git a/...ll/solvers/mb/MovingBoundardyVH5Path.java → ...ell/solvers/mb/MovingBoundaryVH5Path.java b/...ll/solvers/mb/MovingBoundardyVH5Path.java → ...ell/solvers/mb/MovingBoundaryVH5Path.java
@@ -24,18 +24,18 @@
  *
  * @author GWeatherby
  */
-public class MovingBoundardyVH5Path {
+public class MovingBoundaryVH5Path {
 
     protected Object target;
     protected Exception exc;
-    protected static final Logger lg = LogManager.getLogger(MovingBoundardyVH5Path.class);
+    protected static final Logger lg = LogManager.getLogger(MovingBoundaryVH5Path.class);
 
 
     /**
      * @param g     staring point, not null
      * @param names path to search
      */
-    public MovingBoundardyVH5Path(Group g, String... names){
+    public MovingBoundaryVH5Path(Group g, String... names){
         target = null;
         exc = null;
         try {

diff --git a/...lvers/mb/MovingBoundardyVH5TypedPath.java → ...olvers/mb/MovingBoundaryVH5TypedPath.java b/...lvers/mb/MovingBoundardyVH5TypedPath.java → ...olvers/mb/MovingBoundaryVH5TypedPath.java
@@ -17,9 +17,9 @@
  * @param <T> type of returned data. primitives not supported, autoboxing not supported
  * @author GWeatherby
  */
-public class MovingBoundardyVH5TypedPath<T> extends MovingBoundardyVH5Path {
+public class MovingBoundaryVH5TypedPath<T> extends MovingBoundaryVH5Path {
 
-    public MovingBoundardyVH5TypedPath(Group g, Class<T> clzz, String... names){
+    public MovingBoundaryVH5TypedPath(Group g, Class<T> clzz, String... names){
         super(g, names);
         Objects.requireNonNull(clzz);
         if(clzz.isPrimitive()){