Feat/ohdsi

.secrets.baseline

@@ -168,7 +168,7 @@
         "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 1784,
+        "line_number": 1796,
         "type": "Secret Keyword"
       }
     ],
@@ -186,7 +186,7 @@
         "hashed_secret": "9b5925ea817163740dfb287a9894e8ab3aba2c18",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 123,
+        "line_number": 128,
         "type": "Secret Keyword"
       }
     ],
@@ -249,7 +249,7 @@
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 38,
+        "line_number": 45,
         "type": "Basic Auth Credentials"
       }
     ],
@@ -267,7 +267,7 @@
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 161,
+        "line_number": 168,
         "type": "Secret Keyword"
       }
     ],

helm/ohdsi-atlas/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm/ohdsi-atlas/Chart.yaml

@@ -0,0 +1,24 @@
+apiVersion: v2
+name: ohdsi-atlas
+description: A Helm chart for Kubernetes
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "1.16.0"

helm/ohdsi-atlas/templates/NOTES.txt

@@ -0,0 +1,22 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "ohdsi-atlas.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "ohdsi-atlas.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "ohdsi-atlas.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "ohdsi-atlas.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}

helm/ohdsi-atlas/templates/_helpers.tpl

@@ -0,0 +1,64 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "ohdsi-atlas.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "ohdsi-atlas.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "ohdsi-atlas.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "ohdsi-atlas.labels" -}}
+helm.sh/chart: {{ include "ohdsi-atlas.chart" . }}
+{{ include "ohdsi-atlas.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "ohdsi-atlas.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "ohdsi-atlas.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+app: ohdsi-atlas
+public: "yes"
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "ohdsi-atlas.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "ohdsi-atlas.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

helm/ohdsi-atlas/templates/configmap.yaml

@@ -0,0 +1,38 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: ohdsi-atlas-config-local
+  annotations:
+    helm.sh/hook: pre-install
+    helm.sh/hook-weight: "0"
+data:
+  config-local.js: |
+    define([], function () {
+      var configLocal = {};
+      // WebAPI
+      configLocal.api = {
+        name: 'Gen3',
+        url: 'https://atlas.{{ .Values.atlas.hostname }}/WebAPI/'
+      };
+      configLocal.authProviders = [{
+        "name": "Fence",
+        "url": "user/login/openid",
+        "ajax": false,
+        "icon": "fa fa-openid"
+      }];
+      configLocal.cohortComparisonResultsEnabled = false;
+      configLocal.userAuthenticationEnabled = true;
+      configLocal.plpResultsEnabled = false;
+      return configLocal;
+    });
+    var parentOfThisIframe = window.parent;
+    var mouseoverCount = 0;
+    console.log("Adding activity event listener...");
+    window.addEventListener("mouseover", function(event) {
+        mouseoverCount++;
+        if (mouseoverCount % 20 == 0 && parentOfThisIframe) {
+            console.log("Activity detected. Atlas running in an iframe. Posting 'I'm alive' message...");
+            parentOfThisIframe.postMessage("refresh token!", "*");
+        mouseoverCount = 0;
+        }
+    });

helm/ohdsi-atlas/templates/deployment.yaml

@@ -0,0 +1,85 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: ohdsi-atlas-deployment
+  labels:
+    {{- include "ohdsi-atlas.labels" . | nindent 4 }}
+spec:
+  selector:
+    matchLabels:
+      {{- include "ohdsi-atlas.selectorLabels" . | nindent 6 }}
+  revisionHistoryLimit: 2
+  strategy:
+    type: RollingUpdate
+    rollingUpdate:
+      maxSurge: 1
+      maxUnavailable: 0
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "ohdsi-atlas.selectorLabels" . | nindent 8 }}
+    spec:
+      serviceAccountName: {{ include "ohdsi-atlas.serviceAccountName" . }}
+      affinity:
+        podAntiAffinity:
+          preferredDuringSchedulingIgnoredDuringExecution:
+          - weight: 100
+            podAffinityTerm:
+              labelSelector:
+                matchExpressions:
+                - key: app
+                  operator: In
+                  values:
+                  - ohdsi-atlas
+              topologyKey: "kubernetes.io/hostname"
+      automountServiceAccountToken: false
+
+      containers:
+        - name: ohdsi-atlas
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 8080
+            initialDelaySeconds: 30
+            periodSeconds: 60
+            timeoutSeconds: 30
+          readinessProbe:
+            httpGet:
+              path: /
+              port: 8080
+          volumeMounts:
+            - name: ohdsi-atlas-config-local
+              readOnly: false
+              mountPath: /usr/share/nginx/html/atlas/js/config-local.js
+              subPath: config-local.js
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          env: 
+      volumes:
+        - name: ohdsi-atlas-config-local
+          configMap:
+            name: ohdsi-atlas-config-local
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}

helm/ohdsi-atlas/templates/service.yaml

@@ -0,0 +1,13 @@
+kind: Service
+apiVersion: v1
+metadata:
+  name: ohdsi-atlas-service
+spec:
+  type: NodePort
+  selector:
+    app: ohdsi-atlas
+  ports:
+    - protocol: TCP
+      port: 80
+      targetPort: 8080
+      name: http

helm/ohdsi-atlas/templates/serviceaccount.yaml

@@ -0,0 +1,12 @@
+{{- if .Values.serviceAccount.create -}}
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: {{ include "ohdsi-atlas.serviceAccountName" . }}
+  labels:
+    {{- include "ohdsi-atlas.labels" . | nindent 4 }}
+  {{- with .Values.serviceAccount.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+{{- end }}

helm/ohdsi-atlas/templates/tests/test-connection.yaml

@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "ohdsi-atlas.fullname" . }}-test-connection"
+  labels:
+    {{- include "ohdsi-atlas.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": test
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args: ['{{ include "ohdsi-atlas.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never