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feat(helm): Add Medcat-trainer startup provisioning (#49)
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‎deployment/kubernetes/charts/medcat-trainer-helm/templates/NOTES.txt‎

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@@ -15,7 +15,7 @@
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export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "medcat-trainer-helm.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
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echo http://$SERVICE_IP:{{ .Values.service.port }}
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{{- else if contains "ClusterIP" .Values.service.type }}
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "medcat-trainer-helm.name" . }},app.kubernetes.io/instance={{ .Release.Name }},app.kubernetes.io/component=medcat-trainer" -o jsonpath="{.items[0].metadata.name}")
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export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "medcat-trainer-helm.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
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export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[?(@.name==\"nginx\")].ports[0].containerPort}")
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echo "Visit http://127.0.0.1:8080 to use your application"
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kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT

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

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@@ -38,4 +38,8 @@ data:
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stdout_logfile_maxbytes=0
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stderr_logfile=/dev/stderr
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stderr_logfile_maxbytes=0
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autorestart=true
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autorestart=true
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{{- if and .Values.provisioning .Values.provisioning.enabled }}
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provisioning.yaml: |
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{{ toYaml .Values.provisioning.config | indent 4 }}
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{{- end }}

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

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@@ -85,6 +85,11 @@ spec:
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name: api-media
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- mountPath: /home/api/static
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name: api-static
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{{- if and .Values.provisioning .Values.provisioning.enabled }}
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- mountPath: /home/configs/provisioning.yaml
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name: medcat-trainer-config
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subPath: provisioning.yaml
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{{- end }}
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{{- if eq .Values.DB_ENGINE "sqlite3" }}
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- mountPath: /home/api/db
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name: api-db

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

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@@ -14,6 +14,10 @@ data:
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DB_PATH: "/home/api/db/db.sqlite3"
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MCT_VERSION: {{ .Values.image.tag | default .Chart.AppVersion }}
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API_URL: http://localhost:{{ .Values.service.apiPort }}/api/
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{{- if and .Values.provisioning .Values.provisioning.enabled }}
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LOAD_EXAMPLES: "1"
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PROVISIONING_CONFIG_PATH: "/home/configs/provisioning.yaml"
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{{- end }}
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{{- range $key, $value := .Values.env }}
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{{ $key }}: {{ $value | quote }}
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{{- end }}

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

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@@ -26,7 +26,6 @@ env:
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EMAIL_PORT: "465"
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EMAIL_USER: "[email protected]"
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ENV: "non-prod"
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LOAD_EXAMPLES: "0"
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LOAD_NUM_DOC_PAGES: "10"
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MAX_DATASET_SIZE: "10000"
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MAX_MEDCAT_MODELS: "2"
@@ -40,6 +39,24 @@ env:
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DB_ENGINE: "postgresql"
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DB_PORT: "5432"
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provisioning:
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# -- Set to true to enable provisioning of projects and models on startup..
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enabled: false
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# -- Put yaml file contents here.See https://docs.cogstack.org/projects/medcat-trainer/en/latest/provisioning/
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config:
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projects:
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- dataset:
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name: "Example Dataset - psych.csv"
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url: "https://raw.githubusercontent.com/CogStack/cogstack-nlp/be9825f151da2d3b6faac80d49e5be91a1629c68/medcat-trainer/notebook_docs/example_data/psych.csv"
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description: "Dataset from https://raw.githubusercontent.com/CogStack/cogstack-nlp/be9825f151da2d3b6faac80d49e5be91a1629c68/medcat-trainer/notebook_docs/example_data/psych.csv"
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modelPack:
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name: "Example Model Pack"
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url: "https://github.com/CogStack/cogstack-nlp/raw/be9825f151da2d3b6faac80d49e5be91a1629c68/medcat-service/models/examples/example-medcat-v2-model-pack.zip"
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project:
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name: "Example Project"
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description: "Example project for medcat trainer"
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annotationGuidelineLink: "https://docs.google.com/document/d/1xxelBOYbyVzJ7vLlztP2q1Kw9F5Vr1pRwblgrXPS7QM/edit?usp=sharing"
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postgresql:
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enabled: true
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# TODO: Support custom DB overrides

‎deployment/kubernetes/local_dev_startup.sh‎

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@@ -20,7 +20,7 @@ helm test medcat-service --logs
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# Test medcat trainer
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# kubectl port-forward svc/nginx 8000:8000
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# helm upgrade x ./medcat-trainer-helm --install --wait --timeout 5m0s # Install if it doesnt already exist, else upgrade
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# helm upgrade medcat-trainer-helm ./medcat-trainer-helm --install --wait --timeout 5m0s # Install if it doesnt already exist, else upgrade
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# kubectl port-forward svc/medcat-trainer-solr 8983:8983
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## helm install trainer-registry oci://registry-1.docker.io/cogstacksystems/medcat-trainer-helm --wait --timeout 5m0s

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