Help generate docs

.github/workflows/site_deploy.yml

@@ -39,7 +39,6 @@ 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;\
@@ -182,30 +181,16 @@ jobs:
         ssh-keyscan $VCELL_MANAGER_NODE >> ~/.ssh/known_hosts
         cd docker/swarm
         scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/${VCELL_CONFIG_FILE_NAME} .
-    - name: setup java 17 with maven cache (for documentation build)
-      uses: actions/setup-java@v4
-      with:
-        distribution: 'temurin'
-        java-version: '17'
-        cache: 'maven'
-    - name: build documentation for web help
-      if: ${{ github.event.inputs.server_only != 'true' }}
-      run: |
-        set -ux
-        mvn clean install -DskipTests
-    - name: deploy installers and web help to vcell.org
+    - name: deploy installers to vcell.org
       run: |
         set -ux
         cd docker/swarm
         ssh -t ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE} sudo docker login -u ${{ github.actor }} -p "${{ secrets.GITHUB_TOKEN }}" ghcr.io
         if ${{ github.event.inputs.server_only != 'true' }}; then
-          # build and install the client installers, and the web help (kubernetes cluster deployments are separate)
-          ./deploy-action-kubernetes.sh \
+          # build and install the client installers (kubernetes cluster deployments are separate)
+          ./deploy-installers.sh \
               --ssh-user ${{ secrets.CD_FULL_USER }} \
-              --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`

.github/workflows/webhelp-deploy.yml

@@ -0,0 +1,60 @@
+name: webhelp-deploy.yml
+on:
+  workflow_dispatch:
+jobs:
+  deploy:
+    name: Deploy Web Help Documentation
+    runs-on: ubuntu-20.04
+    steps:
+      - name: checkout tag
+        uses: actions/checkout@v4
+
+      - name: setup global environment variables
+        run: |
+          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
+          echo "VCELL_MANAGER_NODE=vcellapi.cam.uchc.edu" >> $GITHUB_ENV
+
+      - name: setup ssh-agent
+        uses: webfactory/ssh-agent@v0.8.0
+        with:
+          ssh-private-key: ${{ secrets.VC_KEY }}
+
+      - name: setup java 17 with maven cache (for documentation build)
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+          cache: 'maven'
+
+      - name: build documentation for web help
+        run: |
+          mvn clean install -DskipTests
+
+      - name: Deploy Web Help
+        run: |
+          set -ux
+          webhelp_local_dir="~/work/vcell/vcell/vcell-client/target/classes/vcellDoc"
+          ssh_user=${{ secrets.CD_FULL_USER }}
+          webhelp_deploy_dir="${VCELL_WEBHELP_REMOTE_DIR}"
+          manager_node="${VCELL_MANAGER_NODE}"
+          if [[ -z "${webhelp_deploy_dir}" || -z "${manager_node}" ]]; then
+            echo "Error: VCELL_WEBHELP_REMOTE_DIR or manager_node is not set."
+            exit 1;
+          fi
+          if ! rsync -a -vvv "${webhelp_local_dir}/topics" "$ssh_user@$manager_node:${webhelp_deploy_dir}";
+          then
+            echo "failed to copy html files in topic directory to webhelp deploy directory";
+          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";
+          fi
+
+      - name: Setup tmate session 3
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
+        with:
+          limit-access-to-actor: false
+

docker/swarm/deploy-installers.sh

@@ -0,0 +1,113 @@
+#!/usr/bin/env bash
+
+set -ux
+
+show_help() {
+	echo "Deploys vcell client installers."
+	echo ""
+	echo "usage: deploy-installers.sh [OPTIONS] REQUIRED-ARGUMENTS"
+	echo ""
+	echo "  REQUIRED-ARGUMENTS"
+	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 ""
+	echo "  [OPTIONS]"
+	echo "    -h | --help           show this message"
+	echo ""
+	echo "    --ssh-user user       user for ssh to node [defaults to current user id using whoami]"
+	echo "                          (user must have passwordless sudo for docker commands on manager-node)"
+	echo ""
+	echo "    --installer-deploy-dir /path/to/installer/dir"
+	echo "                          directory for installers accessible to users"
+	echo "                          typically a web-accessible location to download the client installers for each platform"
+	echo ""
+	echo ""
+	echo ""
+	echo "example:"
+	echo ""
+	echo "deploy-installers.sh \\"
+	echo "   --ssh-user vcell \\"
+	echo "   --installer_deploy_dir /share/apps/vcell3/apache_webroot/htdocs/webstart/Alpha \\"
+	echo "   vcellapi.cam.uchc.edu \\"
+	echo "   ./server.config"
+	exit 1
+}
+
+if [[ $# -lt 2 ]]; then
+    show_help
+fi
+
+ssh_user=$(whoami)
+installer_deploy_dir=
+while :; do
+	case $1 in
+		-h|--help)
+			show_help
+			exit
+			;;
+		--ssh-user)
+			shift
+			ssh_user=$1
+			;;
+		--installer-deploy-dir)
+			shift
+			installer_deploy_dir=$1
+			;;
+		-?*)
+			printf 'ERROR: Unknown option: %s\n' "$1" >&2
+			echo ""
+			show_help
+			;;
+		*)               # Default case: No more options, so break out of the loop.
+			break
+	esac
+	shift
+done
+
+if [[ $# -ne 2 ]] ; then
+    show_help
+fi
+
+manager_node=$1
+local_config_file=$2
+
+# get settings from config file
+vcell_siteCamel=$(grep VCELL_SITE_CAMEL "$local_config_file" | cut -d"=" -f2)
+vcell_version=$(grep VCELL_VERSION_NUMBER "$local_config_file" | cut -d"=" -f2)
+vcell_build=$(grep VCELL_BUILD_NUMBER "$local_config_file" | cut -d"=" -f2)
+
+
+#
+# if --installer-deploy-dir, then copy the installers from ./generated_installers directory to the installer deploy directory
+#
+if [ ! -z "$installer_deploy_dir" ]; then
+  # vcell_siteCamel=Alpha
+  # vcell_version=7.0.0
+  # vcell_build=19
+  # version=7_0_0_19
+  version=$(echo "${vcell_version}_${vcell_build}" | tr '.' _)
+  if ! scp "./generated_installers/VCell_${vcell_siteCamel}_windows-x64_${version}_64bit.exe" \
+    "./generated_installers/VCell_${vcell_siteCamel}_unix_${version}_32bit.sh" \
+    "./generated_installers/VCell_${vcell_siteCamel}_macos_${version}_64bit.dmg" \
+    "./generated_installers/VCell_${vcell_siteCamel}_windows-x32_${version}_32bit.exe" \
+    "./generated_installers/VCell_${vcell_siteCamel}_unix_${version}_64bit.sh" \
+    "./generated_installers/updates.xml" \
+    "./generated_installers/updates_linux32.xml" \
+    "./generated_installers/updates_linux64.xml" \
+    "./generated_installers/updates_mac64.xml" \
+    "./generated_installers/updates_win32.xml" \
+    "./generated_installers/updates_win64.xml" \
+    "./generated_installers/output.txt" \
+    "./generated_installers/md5sums" \
+    "./generated_installers/sha256sums" \
+      "$ssh_user@$manager_node:${installer_deploy_dir}";
+  then
+    echo "failed to copy installers";
+    exit 1;
+  fi
+fi
+
+echo "exited normally"
+
+exit 0

docker/swarm/serverconfig-uch.sh

@@ -115,7 +115,7 @@ VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
 #
 # write out the environment file to be for:
-# 1. deployment actions (e.g. deploy-action-kubernetes.sh)
+# 1. deployment actions (e.g. deploy-installers.sh)
 # 2. runtime environment for the docker stack run command (kubernetes uses ConfigMaps in vcell-fluxcd repo), what about VCell Installers?
 #
 cat <<EOF >"$_outputfile"