Merge pull request #7 from TheJacksonLaboratory/G3-205-add-redis-to-w…

…ebsite

G3 205 Add redis to legacy website

deploy/k8s/base/configmap.yaml

@@ -4,4 +4,7 @@ metadata:
   name: geneweaver-legacy-config
 data:
   AUTH_CLIENTID: "wMjx3nGV24qneBjXqz52IhEpq6AU7reo"
-  APPLICATION_RESULTS: "/var/geneweaver/results"
+  APPLICATION_RESULTS: "/var/geneweaver/results"
+  CELERY_HOST: "redis-master"
+  CELERY_PORT: "6379"
+  CELERY_BACKEND: "redis"

deploy/k8s/base/deployment.yaml

@@ -13,18 +13,27 @@ spec:
     metadata:
       labels:
         app: geneweaver-legacy
+      annotations:
+        gke-gcsfuse/volumes: "true"
     spec:
       serviceAccountName: workload-identity-geneweaver
       volumes:
         - name: geneweaver-legacy
-          emptyDir: { }
+          persistentVolumeClaim:
+            claimName: geneweaver-pvc
       containers:
         - name: geneweaver-legacy
           image: geneweaver-legacy
           imagePullPolicy: Always
           volumeMounts:
             - name: geneweaver-legacy
               mountPath: /var/geneweaver/results
+          env:
+            - name: CELERY_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: redis
+                  key: redis-password
           envFrom:
             - configMapRef:
                 name: geneweaver-legacy-config

deploy/k8s/base/kustomization.yaml

@@ -7,3 +7,4 @@ resources:
   - deployment.yaml
   - service.yaml
   - external-secrets.yaml
+  - persistent-volume-claim.yaml

deploy/k8s/base/persistent-volume-claim.yaml

@@ -0,0 +1,11 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: geneweaver-pvc
+spec:
+  accessModes:
+  - ReadWriteMany
+  resources:
+    requests:
+      storage: 100Gi
+  storageClassName: cloud-storage-rwm

deploy/k8s/overlays/jax-cluster-dev-10--dev/kustomization.yaml

@@ -4,3 +4,5 @@ namespace: dev
 resources:
   - ../../base
   - ingress.yaml
+patchesStrategicMerge:
+  - persistent-volume-claim.yaml

deploy/k8s/overlays/jax-cluster-dev-10--dev/persistent-volume-claim.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: geneweaver-pvc
+spec:
+  volumeName: geneweaver-pv-dev

deploy/k8s/overlays/jax-cluster-dev-10--sqa/kustomization.yaml

@@ -4,3 +4,5 @@ namespace: sqa
 resources:
   - ../../base
   - ingress.yaml
+patchesStrategicMerge:
+  - persistent-volume-claim.yaml

deploy/k8s/overlays/jax-cluster-dev-10--sqa/persistent-volume-claim.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: geneweaver-pvc
+spec:
+  volumeName: geneweaver-pv-sqa

deploy/k8s/overlays/jax-cluster-prod-10--prod/kustomization.yaml

@@ -4,3 +4,5 @@ namespace: prod
 resources:
   - ../../base
   - ingress.yaml
+patchesStrategicMerge:
+  - persistent-volume-claim.yaml

deploy/k8s/overlays/jax-cluster-prod-10--prod/persistent-volume-claim.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: geneweaver-pvc
+spec:
+  volumeName: geneweaver-pv-prod

deploy/k8s/overlays/jax-cluster-prod-10--stage/kustomization.yaml

@@ -4,3 +4,5 @@ namespace: stage
 resources:
   - ../../base
   - ingress.yaml
+patchesStrategicMerge:
+  - persistent-volume-claim.yaml

deploy/k8s/overlays/jax-cluster-prod-10--stage/persistent-volume-claim.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: geneweaver-pvc
+spec:
+  volumeName: geneweaver-pv-stage

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.2.0"
+version = "1.3.0"
 description = ""
 authors = ["Alexander Berger <[email protected]>"]
 readme = "README.md"
@@ -27,6 +27,7 @@ pandas = "^2.2.2"
 pydantic = "^2.7.3"
 pydantic-settings = "^2.3.0"
 authlib = "^1.3.1"
+redis = "^5.0.6"
 
 [build-system]
 requires = ["poetry-core"]

src/config.py

@@ -1,8 +1,8 @@
 import os
 import binascii
-from typing import Any
+from typing import Any, Optional
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, model_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
@@ -23,8 +23,26 @@ class ApplicationConfig(BaseModel):
 
 class Celery(BaseModel):
 
-    url: str = "amqp://geneweaver:geneweaver@localhost:5672/geneweaver"
     backend: str = "amqp"
+    host: str = "localhost"
+    port: int = 5672
+    user: str = ""
+    password: str = ""
+    db: int = 1
+    url: Optional[str] = Field(None, validate_default=True)
+
+    @model_validator(mode='after')
+    def url_validator(self):
+        if self.url is None:
+            if self.password:
+                credentials = f"{self.user}:{self.password}@"
+            elif self.user:
+                credentials = f"{self.user}@"
+            else:
+                credentials = ""
+            db = f"/{self.db}" if self.db else ""
+            self.url = f"{self.backend}://{credentials}{self.host}:{self.port}{db}"
+        return self
 
 
 class DB(BaseModel):

src/tools/toolcommon.py

@@ -12,7 +12,7 @@
     #broker=BROKER_URL,
     #backend=CELERY_RESULT_BACKEND,
     broker=config.get('celery', 'url'),
-    backend=config.get('celery', 'backend'),
+    backend=config.get('celery', 'url'),
 )
 
 # Optional configuration, see the application user guide.