Added fixes

kube/services/fence/fence-deploy.yaml

@@ -195,8 +195,8 @@ spec:
 # DEPRECATED! Remove when all commons are no longer using local_settings.py
 #             for fence.
 # -----------------------------------------------------------------------------
-          - mountPath: /var/www/fence
-            name: "fence"
+          - name: "fence"
+            mountPath: "/var/www/fence"
           - name: "old-config-volume"
             readOnly: true
             mountPath: "/var/www/fence/local_settings.py"
@@ -271,13 +271,7 @@ spec:
           - |
             echo "${FENCE_PUBLIC_CONFIG:-""}" > "/var/www/fence/fence-config-public.yaml"
             python /var/www/fence/yaml_merge.py /var/www/fence/fence-config-public.yaml /var/www/fence/fence-config-secret.yaml > /var/www/fence/fence-config.yaml
-            cd /fence
-            tar xvf jwt-keys.tar
-            mkdir -p keys
-            mv jwt-keys/* keys/
-            rm -rf /fence/keys/key/
-            gunicorn -c deployment/wsgi/gunicorn.conf.py
-            #bash /fence/dockerrun.bash && if [[ -f /dockerrun.sh ]]; then bash /dockerrun.sh; fi
+            bash /fence/dockerrun.bash && if [[ -f /dockerrun.sh ]]; then bash /dockerrun.sh; fi
       - name: sidecar-nginx
         image: quay.io/cdis/nginx-sidecar:nginx-sidecar-feat_nginx-sidecar
         imagePullPolicy: IfNotPresent

kube/services/fence/fence-gunicorn.yaml

@@ -6,10 +6,8 @@ data:
   gunicorn.conf.py: |
     wsgi_app = "deployment.wsgi.wsgi:application"
     bind = "0.0.0.0:8000"
-    workers = 4
+    workers = 3
     preload_app = True    
     user = 'gen3'
     group = 'gen3'
     timeout = 300
-    keepalive = 2
-    keepalive_timeout = 5    

kube/services/peregrine/peregrine-deploy.yaml

@@ -90,6 +90,8 @@ spec:
         - name: nginx-main-config
           configMap:
             name: sidecar-nginx-main 
+        - name: peregrine
+          emptyDir: {}
       containers:
         - name: peregrine
           GEN3_PEREGRINE_IMAGE
@@ -196,6 +198,8 @@ spec:
             - name: "wsgi-config"
               mountPath: "/peregrine/deployment/wsgi/gunicorn.conf.py"
               subPath: gunicorn.conf.py
+            - name: "peregrine"
+              mountPat: "/var/www/peregrine"
           imagePullPolicy: Always
           resources:
             requests:
@@ -231,4 +235,4 @@ spec:
               subPath: "nginx.conf"
             - name: "nginx-config"
               mountPath: "/etc/nginx/conf.d/default.conf"
-              subPath: default.conf
+              subPath: default.conf

kube/services/peregrine/peregrine-gunicorn.yaml

@@ -10,4 +10,3 @@ data:
     user = 'gen3'
     group = 'gen3'
     timeout = 300
-    worker_class = "uvicorn.workers.UvicornWorker"

kube/services/presigned-url-fence/presigned-url-fence-deploy.yaml

@@ -106,6 +106,8 @@ spec:
         - name: privacy-policy
           configMap:
             name: "privacy-policy"
+        - name: fence
+          emptyDir: {}    
       securityContext:
         # nginx group in current images
         fsGroup: 101
@@ -175,6 +177,8 @@ spec:
 # DEPRECATED! Remove when all commons are no longer using local_settings.py
 #             for fence.
 # -----------------------------------------------------------------------------
+          - name: "fence"
+            mountPath: "/var/www/fence"
           - name: "old-config-volume"
             readOnly: true
             mountPath: "/var/www/fence/local_settings.py"

kube/services/sheepdog/sheepdog-deploy.yaml

@@ -86,6 +86,8 @@ spec:
         - name: nginx-main-config
           configMap:
             name: sidecar-nginx-main 
+        - name: sheepdog
+          emptyDir: {}
       # sheepdog transactions take forever -
       # try to let the complete before termination
       terminationGracePeriodSeconds: 50
@@ -211,6 +213,8 @@ spec:
             - name: "wsgi-config"
               mountPath: "/sheepdog/deployment/wsgi/gunicorn.conf.py"
               subPath: gunicorn.conf.py
+            - name: "sheepdog"
+              mountPath: "/var/www/sheepdog"
           imagePullPolicy: Always
           resources:
             requests:
@@ -234,4 +238,4 @@ spec:
               subPath: "nginx.conf"
             - name: "nginx-config"
               mountPath: "/etc/nginx/conf.d/default.conf"
-              subPath: default.conf
+              subPath: default.conf

kube/services/sheepdog/sheepdog-gunicorn.yaml

@@ -10,4 +10,3 @@ data:
     user = 'gen3'
     group = 'gen3'
     timeout = 300
-    worker_class = "uvicorn.workers.UvicornWorker"

kube/services/wts/wts-gunicorn.yaml

@@ -10,4 +10,3 @@ data:
     user = 'gen3'
     group = 'gen3'
     timeout = 300
-    worker_class = "uvicorn.workers.UvicornWorker"