oxidicom version 2.0.0

charts/chris/Chart.yaml

@@ -17,7 +17,7 @@ keywords:
 icon: ./logo_chris.png
 
 type: application
-version: "0.13.0"
+version: "0.14.0"
 appVersion: "5.0.0"
 
 maintainers:

charts/chris/templates/heart.yml

@@ -106,20 +106,6 @@ spec:
             else:
                 created_user = User.objects.create_superuser(**superuser_config)
                 print(f'Created superuser "{created_user.username}"')
-
-            the_chris_user_config = {
-                'username': os.environ['CHRIS_USERNAME'],
-                'password': os.environ['CHRIS_PASSWORD'],
-                'email': os.environ['CHRIS_EMAIL']
-            }
-            if (existing_user := User.objects.filter(username=the_chris_user_config['username']).first()) is not None:
-                existing_user.set_password(the_chris_user_config['password'])
-                existing_user.save()
-                print(f'Updated password for user "{existing_user.username}"')
-            else:
-                created_user = User.objects.create_user(**the_chris_user_config)
-                print(f'Created user "{created_user.username}"')
-
           {{- include "cube.container" . | nindent 10 }}
             - name: CHRIS_SUPERUSER_USERNAME
               valueFrom:
@@ -136,21 +122,6 @@ spec:
                 secretKeyRef:
                   name: {{ .Release.Name }}-chris-superuser
                   key: email
-            - name: CHRIS_USERNAME
-              valueFrom:
-                secretKeyRef:
-                  name: {{ .Release.Name }}-the-chris-user
-                  key: CHRIS_USERNAME
-            - name: CHRIS_EMAIL
-              valueFrom:
-                secretKeyRef:
-                  name: {{ .Release.Name }}-the-chris-user
-                  key: CHRIS_EMAIL
-            - name: CHRIS_PASSWORD
-              valueFrom:
-                secretKeyRef:
-                  name: {{ .Release.Name }}-the-chris-user
-                  key: CHRIS_PASSWORD
 
         - name: wait-rabbitmq
           command:

charts/chris/templates/pfdcm/oxidicom-deployment.yml

@@ -1,12 +1,25 @@
+{{- define "orthanc.dicomService" -}}
+{{ .Release.Name }}-orthanc-dicom:{{ .Values.orthanc.dicomService.port }}
+{{- end -}}
+
 {{- define "oxidicom.pacsAddress" -}}
+{{- if (and .Values.orthanc.enabled (not .Values.orthanc.dicomService.enabled)) -}}
+{{- fail ".orthanc.dicomService.enabled must be true" -}}
+{{- end -}}
 {{- if .Values.pfdcm.listener.config.pacsAddress -}}
-{{- .Values.pfdcm.listener.config.pacsAddress -}},
+{{- if (and .Values.orthanc.enabled (not (contains (include "orthanc.dicomService" .) .Values.pfdcm.listener.config.pacsAddress))) -}}
+{{- fail (printf "pfdcm.listener.config.pacsAddress must be configured with %s=\"%s\"" .Values.orthanc.config.dicomAet (include "orthanc.dicomService" .)) -}}
+{{- end -}}
+{{- .Values.pfdcm.listener.config.pacsAddress -}}
+{{- else -}}
+{{ "{" }}{{ .Values.orthanc.config.dicomAet }}={{ include "orthanc.dicomService" . | quote }}{{ "}" }}
+{{- end -}}
 {{- end -}}
-{{- if .Values.orthanc.enabled -}}
-  {{- if not .Values.orthanc.dicomService.enabled -}}
-  {{- fail "Orthanc's .dicomService must be enabled" -}}
-  {{- end -}}
-{{ .Values.orthanc.config.dicomAet }}={{ .Release.Name }}-orthanc-dicom:{{ .Values.orthanc.dicomService.port }},
+{{- define "oxidicom.databasePoolSize" -}}
+{{- if .Values.pfdcm.listener.config.databasePool -}}
+{{- .Values.pfdcm.listener.config.databasePool -}}
+{{- else if .Values.postgresql.primary.resources.requests.cpu -}}
+{{- .Values.postgresql.primary.resources.requests.cpu -}}
 {{- end -}}
 {{- end -}}
 {{- if .Values.pfdcm.enabled -}}
@@ -53,52 +66,66 @@ spec:
           resources:
             {{- toYaml .Values.pfdcm.listener.resources | nindent 12 }}
           env:
-            - name: PORT
+            - name: OXIDICOM_DB_CONNECTION
+              valueFrom:
+                secretKeyRef:
+                  {{- if not .Values.postgresql.serviceBindings.enabled }}
+                  {{- fail "Oxidicom requires the value .postgresql.serviceBindings.enabled: true" }}
+                  {{- end }}
+                  name: {{ .Release.Name }}-postgresql-svcbind-custom-user
+                  key: uri
+            - name: OXIDICOM_LISTENER_PORT
               value: {{ .Values.pfdcm.listener.service.port | quote }}
-            - name: CHRIS_FILES_ROOT
+            - name: OXIDICOM_FILES_ROOT
               value: /data
-            - name: CHRIS_URL
-              value: "http://{{ .Release.Name }}-server:{{ .Values.cube.server.service.port }}/api/v1/"
-            - name: CHRIS_SCP_AET
+            - name: OXIDICOM_SCP_AET
               value: {{ .Values.pfdcm.aet | quote }}
-            - name: CHRIS_LISTENER_THREADS
+              {{- if (include "oxidicom.databasePoolSize" .) }}
+            - name: OXIDICOM_DB_POOL
+              value: {{ include "oxidicom.databasePoolSize" . | quote }}
+              {{- end }}
+              {{- if .Values.pfdcm.listener.config.batchSize }}
+            - name: OXIDICOM_DB_BATCH_SIZE
+              value: {{ .Values.pfdcm.listener.config.batchSize | quote }}
+              {{- end }}
+              {{- if .Values.pfdcm.listener.config.listenerThreads }}
+            - name: OXIDICOM_LISTENER_THREADS
               value: {{ .Values.pfdcm.listener.config.listenerThreads | quote }}
-            - name: CHRIS_PUSHER_THREADS
-              value: {{ .Values.pfdcm.listener.config.pusherThreads | quote }}
-
+              {{- end }}
               {{- if .Values.pfdcm.listener.config.verbose }}
-            - name: CHRIS_VERBOSE
+            - name: OXIDICOM_VERBOSE
               value: {{ .Values.pfdcm.listener.config.verbose | quote }}
               {{- end }}
-              {{- if .Values.pfdcm.listener.config.httpRetries }}
-            - name: CHRIS_HTTP_RETRIES
-              value: {{ .Values.pfdcm.listener.config.httpRetries | quote }}
+              {{- if .Values.pfdcm.listener.config.tokioThreads }}
+            - name: TOKIO_WORKER_THREADS
+              value: {{ .Values.pfdcm.listener.config.tokioThreads | quote }}
               {{- end }}
               {{- /* DICOM SCP Options */}}
               {{- if .Values.pfdcm.listener.config.strictPduLength }}
-            - name: CHRIS_SCP_STRICT
+            - name: OXIDICOM_SCP_STRICT
               value: {{ .Values.pfdcm.listener.config.strictPduLength | quote }}
               {{- end }}
               {{- if .Values.pfdcm.listener.config.maxPduLength }}
-            - name: CHRIS_SCP_MAX_PDU_LENGTH
+            - name: OXIDICOM_SCP_MAX_PDU_LENGTH
               value: {{ .Values.pfdcm.listener.config.maxPduLength | quote }}
               {{- end }}
               {{- if .Values.pfdcm.listener.config.uncompressedOnly }}
-            - name: CHRIS_SCP_UNCOMPRESSED_ONLY
+            - name: OXIDICOM_SCP_UNCOMPRESSED_ONLY
               value: {{ .Values.pfdcm.listener.config.uncompressedOnly | quote }}
               {{- end }}
+              {{- if .Values.pfdcm.listener.config.promiscuous }}
+            - name: OXIDICOM_SCP_PROMISCUOUS
+              value: {{ .Values.pfdcm.listener.config.promiscuous | quote }}
+              {{- end }}
               {{- if (include "oxidicom.pacsAddress" .) }}
-            - name: CHRIS_PACS_ADDRESS
+            - name: OXIDICOM_PACS_ADDRESS
               value: {{ include "oxidicom.pacsAddress" . | quote }}
               {{- end }}
 
               {{- /* Extra environment variables, manually specified */}}
               {{- if .Values.pfdcm.listener.env }}
               {{- .Values.pfdcm.listener.env | toYaml | nindent 12 }}
               {{- end }}
-          envFrom:
-            - secretRef:
-                name: {{ .Release.Name }}-the-chris-user
           volumeMounts:
             - mountPath: /data
               name: file-storage

charts/chris/values.yaml

@@ -186,6 +186,12 @@ postgresql:
     database: "chris"
     username: "chris"
 
+  # Create secret for service binding (Experimental)
+  # Ref: https://servicebinding.io/service-provider/
+  serviceBindings:
+    # required if pfdcm.listener.enabled: true
+    enabled: true
+
   # one of: [standalone, replication]
   # Replication is supported, see upstream README.md for configuration.
   architecture: standalone
@@ -336,14 +342,14 @@ pfdcm:
       insecureEdgeTerminationPolicy: Redirect
       destinationCACertificate: ''
   replicas: 1
-  maxWorkers: 1
+  maxWorkers: 8
   resources:
     limits:
       cpu: 1
-      memory: 1Gi
+      memory: 4Gi
     requests:
       cpu: 1
-      memory: 1Gi
+      memory: 4Gi
 
   # DICOM application entity title
   aet: "ChRIS"
@@ -377,7 +383,7 @@ pfdcm:
     image:
       repository: ghcr.io/fnndsc/oxidicom
       pullPolicy: IfNotPresent
-      tag: "1.0.2"
+      tag: "2.0.0"
     podAnnotations: {}
     # The PACS server must be configured to push to this service.
     # If using Orthanc, the Helm chart will help you validate your
@@ -393,16 +399,22 @@ pfdcm:
     #   - name: OTEL_RESOURCE_ATTRIBUTES
     #     value: service.name=oxidicom
     #   - name: OTEL_EXPORTER_OTLP_ENDPOINT
-    #     value: http://tempo:4318
+    #     value: http://tempo:4317
+
+    # Optional configurations of oxidicom.
     config:
-      ## number of times 
-      # httpRetries: 3
-
       ## number of DICOM listener threads
-      listenerThreads: 4
+      # listenerThreads: 8
+
+      ## number of Tokio runtime threads
+      ## ref: https://github.com/FNNDSC/oxidicom/tree/v2.0.0?tab=readme-ov-file#performance-tuning
+      # tokioThreads: 8
+
+      ## size of database connection pool
+      # databasePool: 10
 
-      ## number of threads to use for pushing files to CUBE
-      pusherThreads: 2
+      ## maximum number of PACS files to register per database command
+      # batchSize: 20
 
       ## verbose logging
       # verbose: true
@@ -412,19 +424,22 @@ pfdcm:
       # strictPduLength: true
       # uncompressedOnly: true
       # maxPduLength: 16384
+      ## Whether to accept unknown DICOM transfer syntaxes.
+      # promiscuous: true
 
       ## Addresses of the PACS pushing to us. Used for looking up the NumberOfSeriesRelatedInstances.
-      ## Do not specify a value for pacsAddress if you are using the Orthanc sub-chart.
-      # pacsAddress: pacs.server.local:4242
+      ## Do not specify a value for pacsAddress if you are using only the Orthanc sub-chart.
+      ## Value must be a string in the form `{AET="5.6.7.8:11111", MGH="9.10.11.12:33333"}`
+      # pacsAddress: '{HOSPITAL="pacs:4242"}'
     resources:
       # It's written in Rust!
-      # with 16 threads, CPU usage peaks at 120m and memory usage peaks at 1.3 GiB
+      # Memory usage typically stays under 20MiB, unless there is backpressure from slow disk or database write speed.
       limits:
-        cpu: 500m
-        memory: 1907Mi
+        cpu: 1
+        memory: 2Gi
       requests:
-        cpu: 500m
-        memory: 1907Mi
+        cpu: 1
+        memory: 2Gi
 
 # PACS server
 orthanc:

testing/default-values.yaml

@@ -44,14 +44,13 @@ pfdcm:
       type: NodePort
       nodePort: 32004
     config:
-      listenerThreads: 4
-      pusherThreads: 4
       verbose: true
+      promiscuous: true
     env:
       - name: OTEL_RESOURCE_ATTRIBUTES
         value: service.name=oxidicom
       - name: OTEL_EXPORTER_OTLP_ENDPOINT
-        value: http://otel-collector-opentelemetry-collector.observe.svc.cluster.local:4318
+        value: http://otel-collector-opentelemetry-collector.observe.svc.cluster.local:4317
     resources:
       limits:
         cpu: 500m

testing/observe/opentelemetry-collector.yaml

@@ -1,3 +1,6 @@
+image:
+  repository: "otel/opentelemetry-collector-contrib"
+
 # Valid values are "daemonset", "deployment", and "statefulset".
 mode: "daemonset"
 
@@ -58,8 +61,8 @@ config:
   receivers:
     otlp:
       protocols:
-        http:
-          endpoint: ${env:MY_POD_IP}:4318
+        grpc:
+          endpoint: ${env:MY_POD_IP}:4317
     kubeletstats:
       insecure_skip_verify: true
     # prometheus:
@@ -105,11 +108,11 @@ config:
 ports:
   otlp:
     enabled: false
-  otlp-http:
+  otlp-grpc:
     enabled: true
-    containerPort: 4318
-    servicePort: 4318
-    hostPort: 4318
+    containerPort: 4317
+    servicePort: 4317
+    hostPort: 4317
     protocol: TCP
   jaeger-compact:
     enabled: false