fix: siibra-api parcellation map to use siibra-python v2

.helm/siibra-api/Chart.yaml

@@ -15,10 +15,10 @@ 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: 0.1.3
+version: 0.1.4
 
 # 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: "0.3.17"
+appVersion: "0.3.18"

.helm/siibra-api/templates/deployment-worker-v4.yaml

@@ -0,0 +1,91 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "siibra-api.fullname" $ }}-worker-v4
+  labels:
+    queuename: {{ . }}
+    {{- include "siibra-api.labels" $ | nindent 4 }}
+spec:
+  strategy:
+    type: RollingUpdate
+    # This rolling update setup allow k8s to scale down before bringing up new pods.
+    # This should be more resource conservative, whilst sacrificing some availability during update.
+    rollingUpdate:
+      maxSurge: 0
+      maxUnavailable: 1
+
+  {{- if not $.Values.autoscaling.enabled }}
+  replicas: {{ $.Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      role: worker
+      queuename: v4-all
+      sapiFlavor: {{ $.Values.sapiFlavor }}
+      {{- include "siibra-api.selectorLabels" $ | nindent 6 }}
+  template:
+    metadata:
+      {{- with $.Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        role: worker
+        queuename: v4-all
+        sapiFlavor: {{ $.Values.sapiFlavor }}
+        {{- include "siibra-api.labels" $ | nindent 8 }}
+	{{- with $.Values.podLabels }}
+        {{- toYaml . | nindent 8 }}
+        {{- end }}
+    spec:
+      {{- with $.Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "siibra-api.serviceAccountName" $ }}
+      securityContext:
+        {{- toYaml $.Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: {{ $.Chart.Name }}
+          securityContext:
+            {{- toYaml $.Values.securityContext | nindent 12 }}
+          image: "{{ $.Values.image.repository }}:{{ include "siibra-api.root-img" $ }}-worker-v4"
+          imagePullPolicy: {{ $.Values.image.pullPolicy }}
+          livenessProbe:
+            # each pod has 20 seconds to become lively (which by definition is ready)
+            initialDelaySeconds: 2
+            periodSeconds: 10
+            timeoutSeconds: 4
+            failureThreshold: 12
+            exec:
+              command: ["/bin/bash", "-c", "cd /worker && python worker_health_v4.py"]
+          envFrom:
+            - configMapRef:
+                name: siibra-api-common
+          env:
+            - name: SIIBRA_CACHEDIR
+              value: "/siibra-api-volume/{{- include "siibra-api.cache-dir" $ -}}"
+            - name: SIIBRA_API_NAMESPACE
+              value: {{ $.Values.sapiFlavor }}
+          resources:
+            {{- toYaml $.Values.resourcesWorkerPod | nindent 12 }}
+          {{- with $.Values.volumeMounts }}
+          volumeMounts:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+      {{- with $.Values.volumes }}
+      volumes:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- 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/siibra-api/values.yaml

@@ -4,8 +4,8 @@
 
 replicaCount: 1
 
-sapiVersion: "0.3.15" # "latest" or "0.3.15"
-sapiWorkerQueues: ["core", "features", "volumes", "compounds", "vocabularies"]
+sapiVersion: "0.3.18" # "latest" or "0.3.15"
+sapiWorkerQueues: ["core", "features", "compounds", "vocabularies"]
 sapiFlavor: "prod" # could be prod, rc, latest, etc
 
 image:

api/common/data_handlers/__init__.py

@@ -1,6 +1,5 @@
 from . import core
 from . import features
-from . import volumes
 from . import compounds
 
 from ...siibra_api_config import ROLE