fix(helm): Fix jupyter examples in cogstack-helm-ce

helm-charts/cogstack-ce-helm/templates/_helpers.tpl

@@ -65,6 +65,47 @@ Create the name of the service account to use
 Dependency URLs
 */}}
 
+
+{{- define "medcat-service.service-name" -}}
+{{ include "medcat-service.fullname" (dict "Values" .Values "Chart" (dict "Name" "medcat-service") "Release" .Release ) }}
+{{- end -}}
+
+{{- define "medcat-service.port" -}}
+{{ index .Values "medcat-service" "service" "port" }}
+{{- end -}}
+
+{{- define "medcat-service.url" -}}
+{{- $url := (index .Values "medcat-service" "url") | default "" -}}
+{{- if $url -}}
+{{ $url }}
+{{- else if not (index .Values "medcat-service" "enabled") -}}
+"unset"
+{{- else -}}
+http://{{ include "medcat-service.service-name" . }}:{{ include "medcat-service.port" . }}
+{{- end -}}
+{{- end -}}
+
+{{- define "anoncat-service.service-name" -}}
+{{ include "medcat-service.fullname" (dict "Values" (index .Values "anoncat-service") "Chart" (dict "Name" "anoncat-service") "Release" .Release ) }}
+{{- end -}}
+
+{{- define "anoncat-service.port" -}}
+{{ index .Values "anoncat-service" "service" "port" }}
+{{- end -}}
+
+{{- define "anoncat-service.url" -}}
+{{- $url := (index .Values "anoncat-service" "url") | default "" -}}
+{{- if $url -}}
+{{ $url }}
+{{- else if not (index .Values "anoncat-service" "enabled") -}}
+"unset"
+{{- else -}}
+http://{{ include "anoncat-service.service-name" . }}:{{ include "anoncat-service.port" . }}
+{{- end -}}
+{{- end -}}
+
+
+
 {{- define "opensearch.url" -}}
 {{- if .Values.opensearch.enabled }}
 {{- $serviceName := include "opensearch.serviceName" (index .Subcharts "opensearch") -}}

helm-charts/cogstack-ce-helm/templates/jupyterhub-configmap.yaml

@@ -0,0 +1,7 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: cogstack-ce-helm-jupyterhub-config
+data:
+  MEDCAT_SERVICE_URL: {{ include "medcat-service.url" . }}
+  ANONCAT_SERVICE_URL: {{ include "anoncat-service.url" . }}

helm-charts/cogstack-ce-helm/templates/medcat-trainer-provisioining.yaml

@@ -15,7 +15,7 @@ data:
           description: "Example project for medcat trainer using MedCAT Service"
           annotationGuidelineLink: "https://docs.google.com/document/d/1xxelBOYbyVzJ7vLlztP2q1Kw9F5Vr1pRwblgrXPS7QM/edit?usp=sharing"
           useModelService: true
-          modelServiceUrl: "http://{{ include "cogstack-ce-helm.fullname" . }}-medcat-service:5000"
+          modelServiceUrl: {{ include "medcat-service.url" . }}
       - dataset:
           name: "Example Dataset - psych.csv - deid"
           url: "https://raw.githubusercontent.com/CogStack/cogstack-nlp/be9825f151da2d3b6faac80d49e5be91a1629c68/medcat-trainer/notebook_docs/example_data/psych.csv"
@@ -25,5 +25,5 @@ data:
           description: "Example project for medcat trainer using AnonCAT Service"
           annotationGuidelineLink: "https://docs.google.com/document/d/1xxelBOYbyVzJ7vLlztP2q1Kw9F5Vr1pRwblgrXPS7QM/edit?usp=sharing"
           useModelService: true
-          modelServiceUrl: "http://{{ include "cogstack-ce-helm.fullname" . }}-anoncat-service:5000"
+          modelServiceUrl: {{ include "anoncat-service.url" . }}
 {{- end }}

helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-config-map.yaml

@@ -1,6 +1,6 @@
 apiVersion: v1
 kind: ConfigMap
 metadata:
-  name: opensearch-provisioning-config
+  name: {{ include "cogstack-ce-helm.fullname" . }}-opensearch-provisioning-config
 data:
 {{ (.Files.Glob "provisioning/*").AsConfig | indent 2 }}

helm-charts/cogstack-ce-helm/templates/opensearch-provisioning-post-install.yaml

@@ -39,5 +39,5 @@ spec:
   volumes:
     - name: opensearch-provisioning-config
       configMap:
-        name: opensearch-provisioning-config
+        name: {{ include "cogstack-ce-helm.fullname" . }}-opensearch-provisioning-config
 {{- end }}

helm-charts/cogstack-ce-helm/values.yaml

@@ -114,3 +114,15 @@ cogstack-jupyterhub:
         tag: "2.2.2"
         # -- JupyterHub singleuser image pull policy.
         pullPolicy: IfNotPresent
+      extraEnv:
+        MEDCAT_SERVICE_URL:
+          valueFrom:
+            configMapKeyRef:
+              name: cogstack-ce-helm-jupyterhub-config
+              key: MEDCAT_SERVICE_URL
+        ANONCAT_SERVICE_URL:
+          name: ANONCAT_SERVICE_URL
+          valueFrom:
+            configMapKeyRef:
+              name: cogstack-ce-helm-jupyterhub-config
+              key: ANONCAT_SERVICE_URL

helm-charts/cogstack-jupyterhub-helm/examples/medcat-opensearch-e2e.ipynb

@@ -49,7 +49,7 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 67,
+      "execution_count": null,
       "id": "17deaa5c",
       "metadata": {},
       "outputs": [
@@ -77,7 +77,7 @@
         "sample_text = \"John was diagnosed with Kidney Failure\"\n",
         "\n",
         "# Service URLs from environment variables\n",
-        "medcat_base_url = os.getenv(\"MEDCAT_URL\", \"http://cogstack-medcat-service:5000\").rstrip(\"/\")\n",
+        "medcat_base_url = os.getenv(\"MEDCAT_SERVICE_URL\", \"http://cogstack-medcat-service:5000\").rstrip(\"/\")\n",
         "medcat_url = medcat_base_url + \"/api/process\"\n",
         "\n",
         "opensearch_url = os.getenv(\"OPENSEARCH_URL\", \"https://opensearch-cluster-master:9200\")\n",
@@ -107,7 +107,8 @@
         "annotations_index = \"discharge_annotations\"\n",
         "\n",
         "# Static demo note id used across all steps\n",
-        "note_id = \"demo-note-kidney-failure-001\""
+        "note_id = \"demo-note-kidney-failure-001\"\n",
+        "subject_id = 1"
       ]
     },
     {

helm-charts/cogstack-jupyterhub-helm/examples/medcat-service-tutorial.ipynb

@@ -54,11 +54,11 @@
                 "sample_text = \"John was diagnosed with Kidney Failure\"\n",
                 "\n",
                 "medcat_base_url = os.getenv(\n",
-                "    \"MEDCAT_URL\", \"http://cogstack-medcat-service:5000\"\n",
+                "    \"MEDCAT_SERVICE_URL\", \"http://cogstack-medcat-service:5000\"\n",
                 ").rstrip(\"/\")\n",
                 "\n",
                 "anoncat_base_url = os.getenv(\n",
-                "    \"ANONCAT_URL\", \"http://cogstack-ce-anoncat-service:5000\"\n",
+                "    \"ANONCAT_SERVICE_URL\", \"http://cogstack-ce-anoncat-service:5000\"\n",
                 ").rstrip(\"/\")\n",
                 "\n",
                 "medcat_url = medcat_base_url + \"/api/process\"\n",

helm-charts/cogstack-jupyterhub-helm/values.yaml

@@ -35,11 +35,12 @@ jupyterhub:
         c.Application.log_level = 'DEBUG'
       00-custom-spawner: |
         # Custom environment variables for user pods
-        c.KubeSpawner.environment = {
-            'GRANT_SUDO': '1',
-            'CHOWN_HOME': 'yes',
-            'CHOWN_HOME_OPTS': '-R',
-        }
+        c.KubeSpawner.environment = c.KubeSpawner.environment or {}
+        c.KubeSpawner.environment.update({
+          'GRANT_SUDO': '1',
+          'CHOWN_HOME': 'yes',
+          'CHOWN_HOME_OPTS': '-R',
+        })
         # Allow root in notebooks
         c.KubeSpawner.args = ['--allow-root']
   proxy:

helm-charts/local_dev_startup.sh

@@ -25,7 +25,14 @@ helm test medcat-service --logs
 
 ## helm install trainer-registry oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm --wait --timeout 5m0s
 
-helm upgrade cogstack-ce-helm ./cogstack-ce-helm --install
+# Run cogstack-ce-helm
+
+helm repo add opensearch https://opensearch-project.github.io/helm-charts/
+helm dependency update ./medcat-trainer-helm
+helm dependency update ./cogstack-jupyterhub-helm
+helm dependency update ./cogstack-ce-helm
+
+helm upgrade cogstack-ce-helm ./cogstack-ce-helm --install --dependency-update --wait --timeout 30m0s
 
 # Stop any running port forwards
 # ps -ef | grep '[p]ort-forward' | awk '{print $2}' | xargs -r kill