Update Helm Chart #190
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Update Helm Chart #190
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- Add resources - Add a key to change the storage mode - if RWO, the protes pods will be deployed on the same nodes - Update mongo to noble - Add init-script.js configMap - Update secrets - Update env - Update rabbitMQ to 4.1.4-management
Reviewer's GuideThis PR enhances the Helm chart by adding resource quotas, making PVC access modes configurable (with conditional pod affinity for RWO), upgrading MongoDB to the 'noble' image with revamped secret management and init scripting, bumping RabbitMQ and chart versions, and refactoring environment variable mappings across deployments. Entity relationship diagram for updated MongoDB secret and init scripterDiagram
MONGODB_SECRET {
string databaseRootUsername
string databaseRootPassword
string databaseUser
string databasePassword
string databaseName
}
CONFIGMAP_INIT_SCRIPT {
string init_script_js
}
MONGODB ||--|| MONGODB_SECRET : uses
MONGODB ||--|| CONFIGMAP_INIT_SCRIPT : uses
Class diagram for updated values.yaml resource and storage configurationclassDiagram
class Flower {
+string appName
+string basicAuth
+string image
+Resources resources
}
class ProTES {
+string appName
+string image
+Resources initResources
+Resources resources
}
class CeleryWorker {
+string appName
+string image
+Resources initResources
+Resources resources
}
class MongoDB {
+string appName
+Secret secret
+string volumeSize
+string image
+Resources resources
}
class RabbitMQ {
+string appName
+string volumeSize
+string image
+Resources resources
}
class Resources {
+map limits
+map requests
}
class Secret {
+string databaseRootUsername
+string databaseRootPassword
+string databaseUser
+string databasePassword
+string databaseName
}
Flower --> Resources
ProTES --> Resources
ProTES --> Resources : initResources
CeleryWorker --> Resources
CeleryWorker --> Resources : initResources
MongoDB --> Secret
MongoDB --> Resources
RabbitMQ --> Resources
Flow diagram for conditional pod affinity based on storage access modeflowchart TD
A["storageAccessMode = ReadWriteOnce?"] -->|Yes| B["Apply podAffinity: proTES pods scheduled with celery-worker on same node"]
A -->|No| C["No affinity: pods scheduled freely"]
File-Level Changes
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Hey there - I've reviewed your changes - here's some feedback:
- The mongo-init-script ConfigMap references dbproWES in the last section but earlier uses dbproTES—please correct the variable names for consistency.
- This PR doesn’t reference a GitHub issue as required by the contribution guidelines—please create or link the issue that tracks these Helm chart updates.
Prompt for AI Agents
Please address the comments from this code review:
## Overall Comments
- The mongo-init-script ConfigMap references dbproWES in the last section but earlier uses dbproTES—please correct the variable names for consistency.
- This PR doesn’t reference a GitHub issue as required by the contribution guidelines—please create or link the issue that tracks these Helm chart updates.
## Individual Comments
### Comment 1
<location> `deployment/templates/mongodb/mongo-init-script.yaml:7-8` </location>
<code_context>
+ name: mongo-init-script
+data:
+ init-script.js: |
+ db = db.getSiblingDB('taskStore');
+ dbproTES = db.getSiblingDB('{{ tpl .Values.mongodb.secret.databaseName . }}')
+
+ dbproTES.createUser({
</code_context>
<issue_to_address>
**issue (bug_risk):** Potential confusion with database variable assignments in init script.
Please ensure all database variables, such as 'dbproWES', are assigned before use to prevent runtime errors.
</issue_to_address>
### Comment 2
<location> `deployment/templates/mongodb/mongo-init-script.yaml:23-29` </location>
<code_context>
+
+ // Create the 'tasks' and 'service_info' collections
+ // Database configuration from https://github.com/elixir-cloud-aai/proTES/blob/2f2d88915d9948b0d2ffbe6799af01bbc413b00a/pro_tes/config.yaml#L30
+ db.createCollection('tasks');
+ db.runs.createIndex(
+ { task_id: 1, worker_id: 1 },
+ { unique: true, sparse: true }
+ );
+ db.createCollection('service_info');
+ db.service_info.createIndex(
+ { id: 1 }
+ );
</code_context>
<issue_to_address>
**issue (bug_risk):** Collections and indexes are created in both 'db' and 'dbproWES', but 'dbproWES' is not defined.
'dbproWES' must be defined before use to prevent a ReferenceError. Please assign it as done for 'dbproTES'.
</issue_to_address>Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
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Summary by Sourcery
Update Helm chart to version 2.0.0 with enhanced resource management, configurable storage modes, and updated database and message broker images
New Features:
Enhancements:
Build: