CogStack Cohorter Helm Chart

CogStack Cohorter — cohort identification powered by Ollama and MedCAT

Architecture

Component	Image	Description
WebApp	cogstacksystems/cogstack-cohorter-webapp	React + Node.js frontend and API
NL2DSL	cogstacksystems/cogstack-cohorter-nl2dsl	Natural language → cohort DSL compiler
MedCAT	cogstacksystems/medcat-service	Clinical NER and concept normalisation (subchart)
Ollama	ollama/ollama	LLM serving backend (subchart)

MedCAT and Ollama are deployed as subcharts: - MedCAT: cogstacksystems/medcat-service-helm (OCI) - Ollama: otwld/ollama

Prerequisites

• Kubernetes 1.21+
• Helm 3.10+
• A storage class that supports ReadWriteOnce PVCs
• Sufficient node resources for the Ollama model (the default gpt-oss:20b requires ~14 GB of memory/VRAM)

Installation

From Docker Hub OCI (published chart):

helm install cogstack-cohorter oci://registry-1.docker.io/cogstacksystems/cogstack-cohorter-helm

Configuration

All configurable values are in values.yaml. Key sections:

Ollama

ollama:
  enabled: true
  ollama:
    models:
      pull:
        - gpt-oss:20b   # pulled automatically on first startup
  persistentVolume:
    enabled: true
    size: 10Gi

Models are pulled automatically by the otwld subchart's built-in init container. Change ollama.ollama.models.pull to use a different model — make sure nl2dsl.env.OLLAMA_MODEL matches.

MedCAT

medcat:
  enabled: true
  env:
    APP_MEDCAT_MODEL_PACK: "/cat/models/examples/example-medcat-v2-model-pack.zip"

To use a custom model pack, provide a download URL:

medcat:
  model:
    downloadUrl: "https://your-host/medcat_model_pack.zip"
    name: "medcat_model_pack.zip"

WebApp data volume

The WebApp requires a SNOMED data directory mounted at /usr/src/app/server/data. A PVC is provisioned automatically:

webapp:
  persistence:
    enabled: true
    size: 5Gi

Populate the PVC with either: - snomed_terms_data.tar.gz — auto-extracted by the entrypoint on first startup, or - Pre-extracted files: snomed_terms.json, cui_pt2ch.json, and patient data files

To generate synthetic patient data on first startup (demo mode):

webapp:
  env:
    RANDOM_DATA: "true"

Ingress

ingress:
  enabled: true
  className: nginx
  hosts:
    - host: cohorter.example.com
      paths:
        - path: /
          pathType: ImplementationSpecific
  tls:
    - secretName: cohorter-tls
      hosts:
        - cohorter.example.com

Autoscaling (webapp only)

autoscaling:
  enabled: true
  minReplicas: 1
  maxReplicas: 3
  targetCPUUtilizationPercentage: 80

Uninstallation

helm uninstall cogstack-cohorter

Support

For issues and questions, please visit the CogStack GitHub repository.

Requirements

Repository	Name	Version
https://otwld.github.io/ollama-helm/	ollama(ollama)	>=0.1.0
oci://registry-1.docker.io/cogstacksystems	medcat(medcat-service-helm)	0.0.1

Values

Key	Type	Default	Description
autoscaling	object	{"enabled":false,"maxReplicas":3,"minReplicas":1,"targetCPUUtilizationPercentage":80}	-------------------------------------------------------------------------
fullnameOverride	string	""
global	object	{"imagePullSecrets":[]}	-------------------------------------------------------------------------
httpRoute	object	{"annotations":{},"enabled":false,"hostnames":["chart-example.local"],"parentRefs":[{"name":"gateway","sectionName":"http"}],"rules":[{"matches":[{"path":{"type":"PathPrefix","value":"/"}}]}]}	-------------------------------------------------------------------------
ingress	object	{"annotations":{},"className":"","enabled":false,"hosts":[{"host":"cogstack-cohort.local","paths":[{"path":"/","pathType":"ImplementationSpecific"}]}],"tls":[]}	-------------------------------------------------------------------------
medcat	object	{"enabled":true,"env":{"APP_ENABLE_METRICS":"true","APP_MEDCAT_MODEL_PACK":"/cat/models/examples/example-medcat-v2-model-pack.zip"},"image":{"tag":"latest"},"resources":{},"service":{"port":5000}}	-------------------------------------------------------------------------
medcat.enabled	bool	true	Enable the MedCAT subchart.
nameOverride	string	"cogstack-cohorter"	-------------------------------------------------------------------------
nl2dsl	object	{"affinity":{},"enabled":true,"env":{"ALLOW_ORIGINS":"*","OLLAMA_MODEL":"llama3.2:3b"},"image":{"pullPolicy":"Always","repository":"cogstacksystems/cogstack-cohorter-nl2dsl","tag":"latest"},"livenessProbe":{"httpGet":{"path":"/","port":"http"},"initialDelaySeconds":30,"periodSeconds":10},"nodeSelector":{},"readinessProbe":{"httpGet":{"path":"/","port":"http"},"initialDelaySeconds":10,"periodSeconds":5},"replicaCount":1,"resources":{},"service":{"port":3002,"type":"ClusterIP"},"tolerations":[]}	-------------------------------------------------------------------------
nl2dsl.enabled	bool	true	Enable the NL2DSL deployment and service.
ollama	object	{"enabled":true,"ollama":{"models":{"pull":["llama3.2:3b"]}},"persistentVolume":{"enabled":true,"size":"10Gi","storageClass":""},"resources":{},"service":{"port":11434,"type":"ClusterIP"}}	-------------------------------------------------------------------------
ollama.enabled	bool	true	Enable the Ollama subchart.
podAnnotations	object	{}	-------------------------------------------------------------------------
podLabels	object	{}
podSecurityContext	object	{}
securityContext	object	{}
serviceAccount	object	{"annotations":{},"automount":true,"create":true,"name":""}	-------------------------------------------------------------------------
webapp	object	{"affinity":{},"data":{"downloadUrl":""},"enabled":true,"env":{"RANDOM_DATA":"true"},"image":{"pullPolicy":"Always","repository":"cogstacksystems/cogstack-cohorter-webapp","tag":"latest"},"initContainers":[],"livenessProbe":{"httpGet":{"path":"/","port":"http"},"initialDelaySeconds":60,"periodSeconds":15},"nodeSelector":{},"persistence":{"accessMode":"ReadWriteOnce","enabled":true,"existingClaim":"","size":"5Gi","storageClass":""},"readinessProbe":{"httpGet":{"path":"/","port":"http"},"initialDelaySeconds":30,"periodSeconds":10},"replicaCount":1,"resources":{},"service":{"port":3000,"type":"ClusterIP"},"tolerations":[]}	-------------------------------------------------------------------------
webapp.enabled	bool	true	Enable the WebApp deployment and service.

---

Autogenerated from chart metadata using helm-docs v1.14.2