Merge pull request #1239 from virtualcell/1225-update-help

update vcell help

.github/workflows/site_deploy.yml

@@ -43,6 +43,7 @@ jobs:
         echo "VCELL_TAG=`git rev-parse --short HEAD`" >> $GITHUB_ENV
         echo "VCELL_REPO_NAMESPACE=ghcr.io/virtualcell" >> $GITHUB_ENV
         echo "VCELL_DEPLOY_REMOTE_DIR=/share/apps/vcell3/deployed_github" >> $GITHUB_ENV
+        echo "VCELL_WEBHELP_REMOTE_DIR=/share/apps/vcell3/apache_webroot/htdocs/webstart/VCell_Tutorials/VCell_Help" >> $GITHUB_ENV
         if [ "${{ github.event.inputs.vcell_site }}" == "rel" ]; then\
         	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;\
@@ -199,19 +200,33 @@ jobs:
         singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io
         singularity pull $BATCH_SINGULARITY_FILENAME oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
         singularity pull $OPT_SINGULARITY_FILENAME   oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ github.event.inputs.vcell_version }}.${{ github.event.inputs.vcell_build }}
-    - name: deploy installers and singularity to kubernetes site
+    - name: setup java 17 with maven cache (for documentation build)
+      uses: actions/setup-java@v3
+      with:
+        distribution: 'temurin'
+        java-version: '17'
+        cache: 'maven'
+    - name: build documentation for web help
+      if: ${{ github.event.inputs.server_only != 'true' }}
+      run: |
+        set -ux
+        cd vcell-client
+        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' }}
       run: |
         set -ux
         cd docker/swarm
         ssh -t ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
         if ${{ github.event.inputs.server_only != 'true' }}; then
-          # build and install the client installers and the singularity images (kubernetes cluster deployments are separate)
+          # build and install the client installers, the singularity images, and the web help (kubernetes cluster deployments are separate)
           ./deploy-action-kubernetes.sh \
               --ssh-user ${{ secrets.CD_FULL_USER }} \
               --install-singularity \
               --build-installers \
               --installer-deploy-dir $VCELL_INSTALLER_REMOTE_DIR \
+              --webhelp-local-dir ../../vcell-client/target/classes/vcellDoc \
+              --webhelp-deploy-dir $VCELL_WEBHELP_REMOTE_DIR \
               ${VCELL_MANAGER_NODE} \
               ./${VCELL_CONFIG_FILE_NAME}
           export VCELL_SITE_CAMEL=`cat $VCELL_CONFIG_FILE_NAME | grep VCELL_SITE_CAMEL | cut -d"=" -f2`

docker/swarm/deploy-action-kubernetes.sh

@@ -24,6 +24,12 @@ show_help() {
 	echo "                          directory for installers accessible to users"
 	echo "                          typically a web-accessible location to download the client installers for each platform"
 	echo ""
+	echo "    --webhelp-local-dir  /local/path/to/vcellDoc"
+	echo "                          directory for VCell java help including html files"
+	echo ""
+	echo "    --webhelp-deploy-dir /remote/path/to/web/VCell_Help"
+	echo "                          directory for deployed html webhelp published on web server"
+	echo ""
 	echo "    --install-singularity  optionally install batch and opt singularity images on each compute node in 'vcell' SLURM partition"
 	echo ""
 	echo ""
@@ -33,6 +39,8 @@ show_help() {
 	echo "   --ssh-user vcell \\"
 	echo "   --install_singularity \\"
 	echo "   --build_installers --installer_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/Test \\"
+	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 "   ./server.config"
 	exit 1
@@ -44,6 +52,8 @@ fi
 
 ssh_user=$(whoami)
 installer_deploy_dir=
+webhelp_local_dir=
+webhelp_deploy_dir=
 build_installers=false
 install_singularity=false
 while :; do
@@ -60,6 +70,14 @@ while :; do
 			shift
 			installer_deploy_dir=$1
 			;;
+		--webhelp-local-dir)
+			shift
+			webhelp_local_dir=$1
+			;;
+		--webhelp-deploy-dir)
+			shift
+			webhelp_deploy_dir=$1
+			;;
 		--install-singularity)
 			install_singularity=true
 			;;
@@ -167,10 +185,24 @@ if [ "$build_installers" == "true" ]; then
 			echo "failed to copy installers"; 
 			exit 1;
 		fi
-
 	fi
 fi
 
+#
+# if --webhelp_deploy_dir, then copy the help html files from vcell-client/target/classes/vcellDoc/topics to the webhelp deploy directory
+#
+if [ ! -z "$webhelp_deploy_dir" ]; then
+  if ! scp -r "${webhelp_local_dir}/topics" "$ssh_user@$manager_node:${webhelp_deploy_dir}/topics";
+  then
+    echo "failed to copy html files in topic directory to webhelp deploy directory";
+    exit 1;
+  fi
+  if ! scp "${webhelp_local_dir}/VCellHelpTOC.html" "$ssh_user@$manager_node:${webhelp_deploy_dir}/index.html";
+  then
+    echo "failed to index.html to webhelp deploy directory";
+    exit 1;
+  fi
+fi
 
 echo "exited normally"
 

vcell-client/src/main/java/org/vcell/documentation/DocImageReference.java

@@ -18,7 +18,6 @@ public DocImageReference(String imageTarget, boolean bInline) {
 		super();
 		this.imageTarget = imageTarget;
 		this.bInline = bInline;
-		DocumentCompiler.referencedImageFiles.add(imageTarget);
 	}
 
 	public String getImageTarget() {

vcell-client/src/main/java/org/vcell/documentation/DocReferenceTarget.java

@@ -0,0 +1,4 @@
+package org.vcell.documentation;
+
+public interface DocReferenceTarget {
+}