[pull] main from Australian-Imaging-Service:main

.github/workflows/packer-build-ci.yml

@@ -3,39 +3,45 @@ name: Packer build
 
 on:
   push:
-    branches:
-      - v1.7
-      - v1.8
-    paths:
-      - "**.pkr.hcl"
-  pull_request:
-    branches:
-      - v1.7
-      - v1.8
-    paths:
-      - "**.pkr.hcl"
+    tags:
+      - "v*"
   workflow_dispatch:
 
 env:
   REGISTRY: ghcr.io
 
+permissions:
+  contents: read
+  packages: write
+
 jobs:
   packer:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-
     name: packer
 
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
+          - 32000:5000
+
     steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v2
+      - name: Docker metadata
+        id: meta
+        uses: docker/metadata-action@v3
         with:
-          fetch-depth: 0
+          images: ${{ env.REGISTRY }}/${{ github.repository_owner }}/xnat-web
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}},enable=${{ !startsWith(github.ref, 'refs/tags/v0.') }}
+            type=sha
 
       - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v1
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -53,13 +59,25 @@ jobs:
           sudo apt-add-repository "deb [arch=amd64] https://apt.releases.hashicorp.com $(lsb_release -cs) main"
           sudo apt-get -q update && sudo apt-get -yq install packer
 
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
       - name: Build Artifacts
         run: |
+          # run make instructions if file exists
           [[ -f Makefile ]] && make
-          CHANGED_FILES=$(git diff --name-only ${{github.event.before}}..${{github.event.after}} |grep '\.pkr\.hcl$')
-          for FILE in "${CHANGED_FILES[@]}"; do
-          packer validate -syntax-only "${FILE}"
-          [[ $? -eq 0 ]] && packer build -color=false -on-error=abort -only=docker.* "${FILE}"
-          done
+          if packer validate "./"; then
+            packer build -color=false -on-error=abort -only=docker.xnat-web "./"
+          fi
         env:
           PACKER_LOG: 1
+
+      # Push docker image produced by packer with tags
+      - name: Push docker image
+        uses: akhilerm/tag-push-action@v2.0.0
+        with:
+          src: localhost:32000/xnat-web:ci
+          dst: |
+            ${{ steps.meta.outputs.tags }}

Makefile

@@ -1,33 +1,33 @@
-xnat_version = 1.8.2.2
-plugin_container_service_ver = 3.0.0
+xnat_version = 1.8.4.1
+plugin_container_service_ver = 3.1.1
 plugin_ldap_auth_ver = 1.1.0
-plugin_ohif-viewer_ver = 3.0.1
-plugin_openid_auth_ver = 1.0.2
+plugin_ohif_viewer_ver = 3.2.0
+plugin_openid_auth_ver = 1.2.0-SNAPSHOT
 plugin_xsync_ver = 1.4.0.1
-plugin_batch-launch_ver = 0.4.0
+plugin_batch_launch_ver = 0.5.0
 
 xnat_war = xnat-web-$(xnat_version).war
-xnat_url = https://github.com/Australian-Imaging-Service/xnat-web/releases/download/release-$(xnat_version)-ais/$(xnat_war)
+xnat_url = https://bitbucket.org/xnatdev/xnat-web/downloads/$(xnat_war)
 
 plugin_container_service_jar = container-service-$(plugin_container_service_ver).jar
 plugin_container_service_url = https://bitbucket.org/xnatdev/container-service/downloads/container-service-$(plugin_container_service_ver)-fat.jar
 
 plugin_ldap_auth_jar = ldap-auth-plugin-$(plugin_ldap_auth_ver).jar
 plugin_ldap_auth_url = https://bitbucket.org/xnatx/ldap-auth-plugin/downloads/$(plugin_ldap_auth_jar)
 
-plugin_ohif-viewer_jar = ohif-viewer-$(plugin_ohif-viewer_ver).jar
-plugin_ohif-viewer_url = https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin/downloads/ohif-viewer-$(plugin_ohif-viewer_ver)-XNAT-1.8.0.jar
+plugin_ohif_viewer_jar = ohif-viewer-$(plugin_ohif_viewer_ver).jar
+plugin_ohif_viewer_url = https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin/downloads/ohif-viewer-$(plugin_ohif_viewer_ver)-XNAT-1.8.0.jar
 
 plugin_openid_auth_jar = openid-auth-plugin-$(plugin_openid_auth_ver).jar
-plugin_openid_auth_url = https://github.com/Australian-Imaging-Service/xnat-openid-auth-plugin/releases/download/$(plugin_openid_auth_ver)/xnat-openid-auth-plugin-all-$(plugin_openid_auth_ver).jar
+plugin_openid_auth_url = https://github.com/Australian-Imaging-Service/openid-auth-plugin/releases/download/$(plugin_openid_auth_ver)/openid-auth-plugin-$(plugin_openid_auth_ver).jar
 
 plugin_xsync_jar = xsync-plugin-all-$(plugin_xsync_ver).jar
 plugin_xsync_url = https://bitbucket.org/xnatdev/xsync/downloads/$(plugin_xsync_jar)
 
-plugin_batch-launch_jar = batch-launch-plugin-$(plugin_batch-launch_ver).jar
-plugin_batch-launch_url = https://bitbucket.org/xnatx/xnatx-batch-launch-plugin/downloads/$(plugin_batch_launch_jar)
+plugin_batch_launch_jar = batch-launch-plugin-$(plugin_batch_launch_ver).jar
+plugin_batch_launch_url = https://bitbucket.org/xnatx/xnatx-batch-launch-plugin/downloads/$(plugin_batch_launch_jar)
 
-plugins = $(plugin_container_service_jar) $(plugin_ldap_auth_jar) $(plugin_openid_auth_jar) $(plugin_ohif-viewer_jar) $(plugin_xsync_jar) $(plugin_batch-launch_jar)
+plugins = $(plugin_container_service_jar) $(plugin_ldap_auth_jar) $(plugin_openid_auth_jar) $(plugin_ohif_viewer_jar) $(plugin_xsync_jar) $(plugin_batch_launch_jar)
 
 $(xnat_war) : $(plugins)
 	wget --no-verbose -O $(xnat_war) $(xnat_url)
@@ -41,14 +41,14 @@ $(plugin_ldap_auth_jar) :
 $(plugin_openid_auth_jar) :
 	wget --no-verbose -O $(plugin_openid_auth_jar) $(plugin_openid_auth_url)
 
-$(plugin_ohif-viewer_jar) :
-	wget --no-verbose -O $(plugin_ohif-viewer_jar) $(plugin_ohif-viewer_url)
+$(plugin_ohif_viewer_jar) :
+	wget --no-verbose -O $(plugin_ohif_viewer_jar) $(plugin_ohif_viewer_url)
 
 $(plugin_xsync_jar) :
 	wget --no-verbose -O $(plugin_xsync_jar) $(plugin_xsync_url)
 
-$(plugin_batch-launch_jar) : 
-	wget --no-verbose -O ${plugin_batch-launch_jar} $(plugin_batch-launch_url)
+$(plugin_batch_launch_jar) :
+	wget --no-verbose -O $(plugin_batch_launch_jar) $(plugin_batch_launch_url)
 
 .PHONY : clean
 clean :

README.md

@@ -5,14 +5,14 @@
 $ make
 
 # Build all images
-$ packer build xnat-web.pkr.hcl
+$ packer build .
 
 # Build an individual image
-$ packer build -only docker.xnat17 xnat-web.pkr.hcl
+$ packer build -only docker.xnat-web .
 
 # Build all docker images
-$ packer build -only docker.* xnat-web.pkr.hcl
-```
+$ packer build -only docker.* .
 
-Reference:
-* https://bitbucket.org/xnatdev/container-service/downloads/
+# Build the xnat-web docker image with an overridden uid
+$ packer build -var "run_as_uid=997" -only docker.xnat-web .
+```

xnat-web-variables.pkr.hcl

@@ -0,0 +1,40 @@
+variable "xnat_version" {
+  default = "1.8.4.1"
+  type = string
+}
+variable "xnat_root" {
+  default = "/data/xnat"
+  type = string
+}
+variable "xnat_home" {
+  default = "/data/xnat/home"
+  type = string
+}
+variable "xnat_plugins" {
+  default = "/data/xnat/home/plugins"
+  type = string
+}
+variable "xnat_plugins_list" {
+  default = [
+    "container-service-3.1.1.jar",
+    "ldap-auth-plugin-1.1.0.jar",
+    "ohif-viewer-3.2.0.jar",
+    "openid-auth-plugin-1.2.0-SNAPSHOT.jar",
+    "xsync-plugin-all-1.4.0.1.jar",
+    "batch-launch-plugin-0.5.0.jar"
+  ]
+  type = list(string)
+}
+variable "run_as_uid" {
+  default = "0"
+  type = string
+}
+variable "docker_image" {
+  default = "tomcat:9.0.62-jdk8-openjdk-bullseye"
+  type = string
+}
+variable "repository" {
+  # Do not change default - required for CI/CD pipeline
+  default = "localhost:32000"
+  type = string
+}

xnat-web.pkr.hcl

@@ -1,39 +1,7 @@
-variable "xnat_version" {
-  default = "1.8.2.2"
-  type = string
-}
-variable "xnat_root" {
-  default = "/data/xnat"
-  type = string
-}
-variable "xnat_home" {
-  default = "/data/xnat/home"
-  type = string
-}
-variable "xnat_plugins" {
-  default = "/data/xnat/home/plugins"
-  type = string
-}
-variable "xnat_plugins_list" {
-  default = [
-    "container-service-3.0.0.jar",
-    "ldap-auth-plugin-1.1.0.jar",
-    "ohif-viewer-3.0.1.jar",
-    "openid-auth-plugin-1.0.2.jar",
-    "xsync-plugin-all-1.4.0.1.jar",
-    "batch-launch-plugin-0.4.0.jar"
-  ]
-  type = list(string)
-}
-variable "run_as_uid" {
-  default = "0"
-  type = string
-}
-variable "docker_image" {
-  default = "tomcat:9.0.46-jdk8-openjdk-buster"
-  type = string
-}
-
+# xnat-build/xnat-web.pkr.hcl
+# variables: xnat-build/xnat-web-variables.pkr.hcl
+# pre-req.: make
+#
 build {
   provisioner "shell" {
     inline = [
@@ -77,7 +45,6 @@ build {
   provisioner "shell" {
     inline = [
       "apt-get update",
-      "apt-get -y install postgresql-client",
       "rm -rf $${CATALINA_HOME}/webapps/*",
       "unzip -o -d $${CATALINA_HOME}/webapps/ROOT /tmp/xnat-web-*.war",
       "sed -i 's/ch.qos.logback.core.rolling.RollingFileAppender/ch.qos.logback.core.ConsoleAppender/' $${CATALINA_HOME}/webapps/ROOT/WEB-INF/classes/logback.xml",
@@ -93,17 +60,14 @@ build {
   }
 
   post-processors {
+    # Do not remove ci tag - required for CICD pipeline
+    # used for development; microk8s registry
     post-processor "docker-tag" {
-      repository =  "ghcr.io/australian-imaging-service/${source.name}"
-      tags = ["${var.xnat_version}"]
+      repository =  "${var.repository}/${source.name}"
+      tags = ["${var.xnat_version}","ci"]
       only = ["docker.xnat-web"]
     }
-    #post-processor "docker-push" { only = ["docker.xnat-web"]}
-  }
-  post-processors {
-    post-processor "docker-tag" {
-      repository =  "localhost:32000/${source.name}"
-      tags = ["${var.xnat_version}"]
+    post-processor "docker-push" {
       only = ["docker.xnat-web"]
     }
   }
@@ -120,8 +84,7 @@ source "docker" "xnat-web" {
     "ENV XNAT_HOME=${var.xnat_home}",
     "LABEL maintainer=\"Dean Taylor <dean.taylor@uwa.edu.au>\"",
     "LABEL org.opencontainers.image.source https://github.com/australian-imaging-service/xnat-build",
-    "USER ${var.run_as_uid}",
-    "VOLUME ${var.xnat_root}/archive ${var.xnat_root}/cache ${var.xnat_root}/prearchive ${var.xnat_home}/work"
+    "USER ${var.run_as_uid}"
   ]
   commit = true
   image = var.docker_image