feat(helm): Remove duplicate medcat-trainer string in created resources

.github/workflows/kubernetes-charts-build.yaml

@@ -47,6 +47,20 @@ jobs:
             echo "changed=true" >> "$GITHUB_OUTPUT"
           fi
 
+      - name: Recursive dependency update
+        if: steps.list-changed.outputs.changed == 'true'
+        working-directory: .
+        run: |
+          # Run twice so subcharts get their deps first, then umbrella gets updated copies (with nested deps)
+          for _ in 1 2; do
+            for chart in deployment/kubernetes/charts/*/; do
+              if [[ -f "${chart}Chart.yaml" ]] && grep -q "^dependencies:" "${chart}Chart.yaml" 2>/dev/null; then
+                echo "Updating dependencies for $chart"
+                helm dependency update "$chart"
+              fi
+            done
+          done
+
       - name: Run chart-testing (lint)
         if: steps.list-changed.outputs.changed == 'true'
         working-directory: .

deployment/kubernetes/charts/cogstack-helm-ce/Chart.lock

@@ -8,5 +8,5 @@ dependencies:
 - name: medcat-trainer-helm
   repository: file://../medcat-trainer-helm
   version: 0.0.1
-digest: sha256:ed3f7c95117421145affc912bbec79151b7dd55062c7358b837074f0e0bf4641
-generated: "2026-02-26T12:55:11.318221565Z"
+digest: sha256:08371a768a9f330606777903fab163ca84918222bbe3f516fab2772f5563d390
+generated: "2026-02-26T15:00:09.073243923Z"

deployment/kubernetes/charts/cogstack-helm-ce/Chart.yaml

@@ -27,6 +27,8 @@ maintainers:
   - name: alhendrickson
     email: alistair@cogstack.org
 
+icon: "https://avatars.githubusercontent.com/u/28688163"
+
 dependencies:
   - name: medcat-service-helm
     alias: medcat-service
@@ -37,5 +39,6 @@ dependencies:
     version: "0.0.1"
     repository: "file://../medcat-service-helm"
   - name: medcat-trainer-helm
+    alias: medcat-trainer
     version: "0.0.1"
     repository: "file://../medcat-trainer-helm"

deployment/kubernetes/charts/cogstack-helm-ce/README.md

@@ -15,23 +15,12 @@ This chart is an umbrella chart that deploys:
 ## Prerequisites
 
 - Kubernetes cluster
-- Helm 3
+- Helm 3+
 
 ## Installation
 
-From the chart directory (or repo root), update dependencies and install:
-
-```bash
-cd deployment/kubernetes/charts/cogstack-helm-ce
-helm dependency update
-helm install cogstack-ce . --namespace cogstack --create-namespace
-```
-
-Or from the repo root:
-
-```bash
-helm dependency update deployment/kubernetes/charts/cogstack-helm-ce
-helm install cogstack-ce deployment/kubernetes/charts/cogstack-helm-ce --namespace cogstack --create-namespace
+```sh
+helm install cogstack oci://registry-1.docker.io/cogstacksystems/cogstack-helm-ce
 ```
 
 ## Configuration
@@ -67,7 +56,7 @@ anoncat-service:
 Install with overrides:
 
 ```bash
-helm install cogstack-ce . -f my-values.yaml --namespace cogstack --create-namespace
+helm install cogstack . -f my-values.yaml --namespace cogstack --create-namespace
 ```
 
 ## Dependencies

deployment/kubernetes/charts/cogstack-helm-ce/templates/NOTES.txt

@@ -0,0 +1,21 @@
+# CogStack Community Edition is installed
+
+# 1. AnonCAT Service port forward
+export ANONCAT_POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name=anoncat-service,app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $ANONCAT_POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+kubectl --namespace {{ .Release.Namespace }} port-forward $ANONCAT_POD_NAME 5001:$CONTAINER_PORT --pod-running-timeout=5m0s & 
+
+# 2.Medcat service port forward
+export MEDCAT_POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name=anoncat-service,app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $MEDCAT_POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+kubectl --namespace {{ .Release.Namespace }} port-forward $MEDCAT_POD_NAME 5000:$CONTAINER_PORT --pod-running-timeout=5m0s &
+
+# 3. MedCAT Trainer Port forward
+export TRAINER_POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name=medcat-trainer,app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $TRAINER_POD_NAME -o jsonpath="{.spec.containers[?(@.name==\"nginx\")].ports[0].containerPort}")
+export CONTAINER_PORT_API=$(kubectl get pod --namespace {{ .Release.Namespace }} $TRAINER_POD_NAME -o jsonpath="{.spec.containers[?(@.name==\"medcat-trainer\")].ports[0].containerPort}")
+kubectl --namespace {{ .Release.Namespace }} port-forward $TRAINER_POD_NAME 8000:$CONTAINER_PORT 8001:$CONTAINER_PORT_API &
+
+echo "Visit http://127.0.0.1:5000 to use MedCAT Service"
+echo "Visit http://127.0.0.1:5001 to use AnonCAT"
+echo "Visit http://127.0.0.1:8000 to use MedCAT Trainer"

deployment/kubernetes/charts/medcat-service-helm/templates/tests/test-acceptance.yaml

@@ -14,6 +14,17 @@ spec:
       securityContext:
         runAsUser: 0
       command: ["/bin/sh", "-c"]
+      env:
+        # Only assert the payload if we are using the default model packs. This is to avoid testing a model that doesnt have the concepts set.
+        - name: SHOULD_ASSERT_PAYLOAD
+          value: {{- if and (not .Values.model.downloadUrl)
+              (or
+                (eq .Values.env.APP_MEDCAT_MODEL_PACK "/cat/models/examples/example-medcat-v2-model-pack.zip")
+                (eq .Values.env.APP_MEDCAT_MODEL_PACK "/cat/models/examples/example-deid-model-pack.zip")
+              )
+            }} "true"{{- else }} "false"{{- end }}
+        - name: EXPECTED_ANNOTATION
+          value: "{{- if .Values.env.DEID_MODE -}}PATIENT{{- else -}}Kidney Failure{{- end -}}"
       args:
         - |
           set -e
@@ -23,24 +34,35 @@ spec:
           api="{{ include "medcat-service.fullname" . }}:{{ .Values.service.port }}/api/process"
           input_text="The patient was diagnosed with Kidney Failure"
           input_payload="{\"content\":{\"text\":\"${input_text}\"}}"
-          expected_annotation="Kidney Failure"
 
           echo "Calling POST $api with payload '$input_payload'"
-          actual=$(curl -s -X POST "$api" \
+          http_code=$(curl -s -w "%{http_code}" -o /tmp/response_body -X POST "$api" \
             -H 'Content-Type: application/json' \
             --user-agent 'helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}' \
             -d "$input_payload")
+          actual=$(cat /tmp/response_body)
+
+          if [ "$http_code" != "200" ]; then
+            echo "Expected HTTP 200 OK, got $http_code"
+            echo "Response body: $actual"
+            exit 1
+          fi
+          echo "Response status: $http_code OK"
 
           echo "Received result '$actual'"
 
           actual_annotation=$(echo "$actual" | jq -r '.result.annotations[0]["0"].pretty_name')
-          echo "Expected Annotation is '${expected_annotation}'. Actual Annotation is '${actual_annotation}'"
-
-          if [ "$actual_annotation" = "$expected_annotation" ]; then
-            echo "Service working and extracting annotations"
-          else
-            echo "Expected: $expected_annotation, Got: $actual_annotation"
-            echo -e "Actual response was:\n${actual}"
-            exit 1
+
+          if [ "$SHOULD_ASSERT_PAYLOAD" = "true" ]; then
+            echo "Expected Annotation is '${EXPECTED_ANNOTATION}'"
+
+            if [ "$actual_annotation" = "$EXPECTED_ANNOTATION" ]; then
+              echo "Service working and extracting annotations"
+            else
+              echo "Expected: $EXPECTED_ANNOTATION, Got: $actual_annotation"
+              echo -e "Actual response was:\n${actual}"
+              exit 1
+            fi
           fi
+          echo "Passed acceptance test for medcat service"
   restartPolicy: Never

deployment/kubernetes/charts/medcat-service-helm/values.yaml

@@ -60,7 +60,7 @@ env:
   OTEL_EXPERIMENTAL_RESOURCE_DETECTORS: "containerid,os"
   OTEL_RESOURCE_ATTRIBUTES: "k8s.pod.uid=$(K8S_POD_UID),k8s.pod.name=$(K8S_POD_NAME),k8s.namespace.name=$(K8S_POD_NAMESPACE),k8s.node.name=$(K8S_NODE_NAME)"
   OTEL_METRICS_EXPORTER: "none"
-  OTEL_LOGS_EXPORTER: "none"  
+  OTEL_LOGS_EXPORTER: "none"
   OTEL_PYTHON_FASTAPI_EXCLUDED_URLS: "/api/health,/metrics"
 
 # Enable downloading of public models using wget on startup. Model will be downloaded to /models/<name> and used for APP_MEDCAT_MODEL_PACK
@@ -70,7 +70,6 @@ model: {}
   # Name of the model pack to save to. Will be stored at /models/<name>
   # name: my-model.zip
 
-
 # Allow setting env values from field/configmap/secret references. Defaults to include k8s details f
 envValueFrom:
   K8S_NODE_NAME:
@@ -86,7 +85,6 @@ envValueFrom:
     fieldRef:
       fieldPath: metadata.namespace
 
-
 # This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
 imagePullSecrets: []
 # This is to override the chart name.
@@ -150,7 +148,7 @@ ingress:
       paths:
         - path: /
           pathType: ImplementationSpecific
-  # - Optional alternative to hosts: allows for global ingress without hostname. Overrides hosts if both are set. 
+  # - Optional alternative to hosts: allows for global ingress without hostname. Overrides hosts if both are set.
   # http:
   #   - paths:
   #       - path: /medcat-service

deployment/kubernetes/charts/medcat-trainer-helm/Chart.yaml

@@ -27,6 +27,8 @@ maintainers:
   - name: alhendrickson
     email: alistair@cogstack.org
 
+icon: "https://avatars.githubusercontent.com/u/28688163"
+
 # Chart.yaml
 dependencies:
   - name: solr

deployment/kubernetes/charts/medcat-trainer-helm/templates/ingress.yaml

@@ -35,7 +35,7 @@ spec:
             {{- end }}
             backend:
               service:
-                name: {{ include "medcat-trainer-helm.fullname" $ }}-medcat-trainer
+                name: {{ include "medcat-trainer-helm.fullname" $ }}
                 port:
                   number: {{ $.Values.service.port }}
           {{- end }}

deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-configmap.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 kind: ConfigMap
 metadata:
-  name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer-config
+  name: {{ include "medcat-trainer-helm.fullname" . }}-config
   labels:
     {{- include "medcat-trainer-helm.labels" . | nindent 4 }}
     app.kubernetes.io/component: medcat-trainer

deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-deployment.yaml

@@ -1,7 +1,7 @@
 apiVersion: apps/v1
 kind: Deployment
 metadata:
-  name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer
+  name: {{ include "medcat-trainer-helm.fullname" . }}
   labels:
     {{- include "medcat-trainer-helm.labels" . | nindent 4 }}
 spec:
@@ -55,7 +55,7 @@ spec:
             - /etc/supervisord.conf
           envFrom:
             - configMapRef:
-                name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer-env
+                name: {{ include "medcat-trainer-helm.fullname" . }}-env
             - secretRef:
                 name: {{ include "medcat-trainer-helm.fullname" . }}-secret
           {{- with .Values.livenessProbe }}
@@ -134,7 +134,7 @@ spec:
       volumes:
         - name: medcat-trainer-config
           configMap:
-            name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer-config
+            name: {{ include "medcat-trainer-helm.fullname" . }}-config
         - name: api-media
           persistentVolumeClaim:
             claimName: {{ include "medcat-trainer-helm.fullname" . }}-api-media

deployment/kubernetes/charts/medcat-trainer-helm/templates/medcat-trainer-env-configmap.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 kind: ConfigMap
 metadata:
-  name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer-env
+  name: {{ include "medcat-trainer-helm.fullname" . }}-env
   labels:
     {{- include "medcat-trainer-helm.labels" . | nindent 4 }}
     app.kubernetes.io/component: medcat-trainer

deployment/kubernetes/charts/medcat-trainer-helm/templates/service.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 kind: Service
 metadata:
-  name: {{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer
+  name: {{ include "medcat-trainer-helm.fullname" . }}
   labels:
     {{- include "medcat-trainer-helm.labels" . | nindent 4 }}
 spec:

deployment/kubernetes/charts/medcat-trainer-helm/templates/tests/test-connection.yaml

@@ -11,5 +11,5 @@ spec:
     - name: wget
       image: busybox
       command: ['wget']
-      args: ['{{ include "medcat-trainer-helm.fullname" . }}-medcat-trainer:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
+      args: ['{{ include "medcat-trainer-helm.fullname" . }}:{{ .Values.service.port }}/nginx/health/live', '-U helm-test {{ .Chart.Name }}-v{{ .Chart.Version }}']
   restartPolicy: Never