Refactor configuration management; update S3 integration, add new migration scripts, and implement pre-flight checks

example.config.yaml

@@ -1,50 +1,51 @@
-# System Configuration
-mongo_uri: "mongodb://localhost:27017"
-database_name: "helia"
+# Helia Application Configuration
+# Copy this file to config.yaml and adjust values as needed.
 
-# S3 Configuration (MinIO or AWS)
-s3_endpoint: "https://s3.amazonaws.com"
-s3_access_key: "your_access_key"
-s3_secret_key: "your_secret_key"
-s3_bucket: "your-bucket-name"
-s3_prefix: ""
-s3_region: "us-east-1"
+patient_limit: 5
 
-# Run Configuration
-limit: 5
+mongo:
+  uri: "mongodb://localhost:27017"
+  db_name: "helia"
+
+s3:
+  endpoint: "http://localhost:9000"
+  access_key_id: ""
+  secret_access_key: ""
+  bucket: "helia"
+  prefix: "daic-woz"
+  region: "eu-west-1"
 
 providers:
   openai:
-    # Set api_key here or export OPENAI_API_KEY
     api_base: "https://api.openai.com/v1"
-    api_format: "openai"
+    api_key: "sk-xxx"
+    api_spec: "openai"
 
   anthropic:
-    # Set api_key here or export ANTHROPIC_API_KEY
     api_base: "https://api.anthropic.com/v1"
-    api_format: "anthropic"
+    api_key: "sk-xxx"
+    api_spec: "anthropic"
 
   openrouter:
-    # Set api_key here or export OPENROUTER_API_KEY
     api_base: "https://openrouter.ai/api/v1"
-    api_format: "openai"
+    api_key: "sk-xxx"
+    api_spec: "openai"
 
   local_ollama:
-    # API key optional for local_* providers
     api_base: "http://localhost:11434/v1"
-    api_format: "ollama"
+    api_spec: "ollama"
 
 runs:
-  - run_name: "baseline_gpt4"
+  baseline_gpt4:
     model:
-      provider: openai
+      provider: "openai"
       model_name: "gpt-4o"
-      temperature: 0.0
+      temperature: 1.0
     prompt_id: "default"
 
-  - run_name: "test_llama3"
+  test_llama3:
     model:
-      provider: local_ollama
+      provider: "local_ollama"
       model_name: "llama3"
       temperature: 0.7
     prompt_id: "default"