Merge pull request #9 from seqeralabs/groundswell-regex

fix: fixes a regex problem on groundswell manifest
seqeralabs · Oct 15, 2024 · bded849 · bded849
2 parents 9426b6e + a77a645
commit bded849
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diff --git a/platform_versioned_docs/version-23.3/enterprise_templates/k8s/groundswell.yml b/platform_versioned_docs/version-23.3/enterprise_templates/k8s/groundswell.yml
@@ -0,0 +1,137 @@
+---
+kind: ConfigMap
+apiVersion: v1
+metadata:
+  name: tower-groundswell-cfg
+data:
+  # Server settings
+  SWELL_SERVER_HOST: "0.0.0.0"
+  SWELL_SERVER_PORT: "8090"
+
+  # API settings
+  SWELL_API_TRAIN_TIMEOUT: "60"
+  SWELL_API_TRAIN_BATCH_SIZE: "1000"
+  SWELL_API_PREDICT_FRACTIONAL_CPUS: "false"
+
+  # Database settings, different from the Tower DB credentials.
+  # If using Amazon RDS or similar managed database services, `SWELL_DB_URL` will have the form 
+  # SWELL_DB_URL=mysql://db1.abcdefghijkl.us-east-1.rds.amazonaws.com:3306/swell or similar
+  SWELL_DB_URL: mysql://<ANOTHER_DB_AND_PORT>/swell
+  SWELL_DB_USER: swell
+  SWELL_DB_PASSWORD: <YOUR GROUNDSWELL DATABASE PASSWORD>
+  SWELL_DB_DIALECT: mysql
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: groundswell
+  labels:
+    app: groundswell
+spec:
+  selector:
+    app: groundswell
+  ports:
+    - name: http
+      port: 8090
+      # targetPort must match with the SWELL_SERVER_PORT in the ConfigMap above.
+      targetPort: 8090
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: groundswell
+  labels:
+    app: groundswell
+spec:
+  selector:
+    matchLabels:
+      app: groundswell
+  strategy:
+    type: Recreate
+
+  template:
+    metadata:
+      labels:
+        app: groundswell
+    spec:
+      imagePullSecrets:
+        - name: "cr.seqera.io"
+      securityContext:
+        fsGroup: 101
+
+      initContainers:
+        - name: wait-for-tower-db
+          image: "mysql:8.0"
+          command:
+            - 'bash'
+            - '-c'
+            - |
+              echo "$(date): starting check for db $TOWER_DB_URL"
+              # Strip initial Java connection string and options after '?' from URI
+              until mysqlsh --uri "$(echo $TOWER_DB_URL |cut -d'?' -f1 |sed -e 's@jdbc:\(.*\)@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
+                echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
+                sleep $SLEEP_PERIOD_SECONDS
+              done
+              echo "$(date): db server ready"
+          env:
+            - name: SLEEP_PERIOD_SECONDS
+              value: "5"
+          envFrom:
+            - configMapRef:
+                name: tower-backend-cfg
+
+        - name: wait-for-swell-db
+          image: "mysql:8.0"
+          command:
+            - 'bash'
+            - '-c'
+            - |
+              echo "$(date): starting check for db $SWELL_DB_URL"
+              # Strip initial Java connection string and options after '?' from URI 
+              until mysqlsh --uri "$SWELL_DB_URL" -u"$SWELL_DB_USER" -p"$SWELL_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
+                echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
+                sleep $SLEEP_PERIOD_SECONDS
+              done
+              echo "$(date): db server ready"
+          env:
+            - name: SLEEP_PERIOD_SECONDS
+              value: "5"
+          envFrom:
+            - configMapRef:
+                name: tower-groundswell-cfg
+
+        - name: migrate-db
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
+          command: ['/opt/groundswell/bin/migrate-db.sh']
+          envFrom:
+            - configMapRef:
+                name: tower-groundswell-cfg
+            - configMapRef:
+                name: tower-backend-cfg
+
+      containers:
+        - name: groundswell
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
+          env:
+            - name: MPLCONFIGDIR
+              value: "/tmp"
+          envFrom:
+            - configMapRef:
+                name: tower-backend-cfg
+            - configMapRef:
+                name: tower-groundswell-cfg
+          volumeMounts:
+            - name: tmp-volume
+              mountPath: /tmp/
+          securityContext:
+            capabilities:
+              drop:
+              - ALL
+            readOnlyRootFilesystem: true
+            runAsNonRoot: true
+            runAsUser: 101
+
+      volumes:
+        - name: tmp-volume
+          emptyDir:
+            sizeLimit: "1Gi"
diff --git a/platform_versioned_docs/version-23.4/enterprise_templates/k8s/groundswell.yml b/platform_versioned_docs/version-23.4/enterprise_templates/k8s/groundswell.yml
@@ -0,0 +1,137 @@
+---
+kind: ConfigMap
+apiVersion: v1
+metadata:
+  name: tower-groundswell-cfg
+data:
+  # Server settings
+  SWELL_SERVER_HOST: "0.0.0.0"
+  SWELL_SERVER_PORT: "8090"
+
+  # API settings
+  SWELL_API_TRAIN_TIMEOUT: "60"
+  SWELL_API_TRAIN_BATCH_SIZE: "1000"
+  SWELL_API_PREDICT_FRACTIONAL_CPUS: "false"
+
+  # Database settings, different from the tower DB credentials.
+  # If using Amazon RDS or similar managed database services, `SWELL_DB_URL` will have the form 
+  # SWELL_DB_URL=mysql://db1.abcdefghijkl.us-east-1.rds.amazonaws.com:3306/swell or similar
+  SWELL_DB_URL: mysql://<DB_AND_PORT>/swell
+  SWELL_DB_USER: swell
+  SWELL_DB_PASSWORD: <YOUR DATABASE PASSWORD>
+  SWELL_DB_DIALECT: mysql
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: groundswell
+  labels:
+    app: groundswell
+spec:
+  selector:
+    app: groundswell
+  ports:
+    - name: http
+      port: 8090
+      # targetPort must match with the SWELL_SERVER_PORT in the ConfigMap above.
+      targetPort: 8090
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: groundswell
+  labels:
+    app: groundswell
+spec:
+  selector:
+    matchLabels:
+      app: groundswell
+  strategy:
+    type: Recreate
+
+  template:
+    metadata:
+      labels:
+        app: groundswell
+    spec:
+      imagePullSecrets:
+        - name: "cr.seqera.io"
+      securityContext:
+        fsGroup: 101
+
+      initContainers:
+        - name: wait-for-tower-db
+          image: "mysql:8.0"
+          command:
+            - 'bash'
+            - '-c'
+            - |
+              echo "$(date): starting check for db $TOWER_DB_URL"
+              # Strip initial Java connection string and options after '?' from URI
+              until mysqlsh --uri "$(echo $TOWER_DB_URL |cut -d'?' -f1 |sed -e 's@jdbc:\(.*\)@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
+                echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
+                sleep $SLEEP_PERIOD_SECONDS
+              done
+              echo "$(date): db server ready"
+          env:
+            - name: SLEEP_PERIOD_SECONDS
+              value: "5"
+          envFrom:
+            - configMapRef:
+                name: tower-backend-cfg
+
+        - name: wait-for-swell-db
+          image: "mysql:8.0"
+          command:
+            - 'bash'
+            - '-c'
+            - |
+              echo "$(date): starting check for db $SWELL_DB_URL"
+              # Strip initial Java connection string and options after '?' from URI 
+              until mysqlsh --uri "$SWELL_DB_URL" -u"$SWELL_DB_USER" -p"$SWELL_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
+                echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
+                sleep $SLEEP_PERIOD_SECONDS
+              done
+              echo "$(date): db server ready"
+          env:
+            - name: SLEEP_PERIOD_SECONDS
+              value: "5"
+          envFrom:
+            - configMapRef:
+                name: tower-groundswell-cfg
+
+        - name: migrate-db
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
+          command: ['/opt/groundswell/bin/migrate-db.sh']
+          envFrom:
+            - configMapRef:
+                name: tower-groundswell-cfg
+            - configMapRef:
+                name: tower-backend-cfg
+
+      containers:
+        - name: groundswell
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
+          env:
+            - name: MPLCONFIGDIR
+              value: "/tmp"
+          envFrom:
+            - configMapRef:
+                name: tower-backend-cfg
+            - configMapRef:
+                name: tower-groundswell-cfg
+          volumeMounts:
+            - name: tmp-volume
+              mountPath: /tmp/
+          securityContext:
+            capabilities:
+              drop:
+              - ALL
+            readOnlyRootFilesystem: true
+            runAsNonRoot: true
+            runAsUser: 101
+
+      volumes:
+        - name: tmp-volume
+          emptyDir:
+            sizeLimit: "1Gi"
diff --git a/platform_versioned_docs/version-24.1/enterprise/_templates/k8s/groundswell.yml b/platform_versioned_docs/version-24.1/enterprise/_templates/k8s/groundswell.yml
@@ -68,7 +68,7 @@ spec:
             - |
               echo "$(date): starting check for db $TOWER_DB_URL"
               # Strip initial Java connection string and options after '?' from URI
-              until mysqlsh --uri "$(echo $TOWER_DB_URL |sed -e 's@jdbc:\(.*\)?.*@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
+              until mysqlsh --uri "$(echo $TOWER_DB_URL |cut -d'?' -f1 |sed -e 's@jdbc:\(.*\)@\1@')" -u"$TOWER_DB_USER" -p"$TOWER_DB_PASSWORD" --sql -e "SELECT VERSION()"; do
                 echo "$(date): see you in $SLEEP_PERIOD_SECONDS seconds"
                 sleep $SLEEP_PERIOD_SECONDS
               done
@@ -101,7 +101,7 @@ spec:
                 name: tower-groundswell-cfg
 
         - name: migrate-db
-          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
           command: ['/opt/groundswell/bin/migrate-db.sh']
           envFrom:
             - configMapRef:
@@ -111,7 +111,7 @@ spec:
 
       containers:
         - name: groundswell
-          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.3.3"
+          image: "cr.seqera.io/private/nf-tower-enterprise/groundswell:0.4.0"
           env:
             - name: MPLCONFIGDIR
               value: "/tmp"