Vibhav dev

.env.example

@@ -1,15 +1,48 @@
 # TableScanner Environment Variables
 # Copy this file to .env and fill in your actual values
 
+# =============================================================================
+# AUTHENTICATION
+# =============================================================================
 # KBase Service Authentication Token
-KB_SERVICE_AUTH_TOKEN=your_kbase_token_here
+# For development testing, use your personal token from KBase
+KB_SERVICE_AUTH_TOKEN=YOUR_KBASE_TOKEN_HERE
 
-# Cache directory for storing downloaded files and SQLite databases
+# =============================================================================
+# CACHE SETTINGS
+# =============================================================================
+# Cache directory for storing downloaded SQLite databases
 CACHE_DIR=/tmp/tablescanner_cache
 
+# Maximum age of cached files in hours (default: 24)
+CACHE_MAX_AGE_HOURS=24
+
+# =============================================================================
+# KBASE SERVICE URLS
+# =============================================================================
 # KBase Workspace Service URL
+WORKSPACE_URL=https://appdev.kbase.us/services/ws
+
+# Base URL for KBase services
+KBASE_ENDPOINT=https://appdev.kbase.us/services
+
+# KBase Blobstore/Shock service URL
+BLOBSTORE_URL=https://appdev.kbase.us/services/shock-api
+
+# =============================================================================
+# APPLICATION SETTINGS
+# =============================================================================
+# Enable debug mode (true/false)
+DEBUG=false
+
+# =============================================================================
+# TEST DATA (AppDev)
+# =============================================================================
+# Test BERDLTable object: 76990/ADP1Test
+# Test pangenome: GCF_000368685.1
+# Narrative: https://appdev.kbase.us/narrative/76990
 WORKSPACE_URL=https://kbase.us/services/ws
 
 # Root path for proxy deployment (e.g., "/services/berdl_table_scanner")
 # Leave empty if running at root path (i.e., "/") for local dev
-ROOT_PATH=/services/berdl_table_scanner
+ROOT_PATH=/services/berdl_table_scanner

.gitignore

@@ -1,3 +1,5 @@
+trash/
+
 .DS_Store
 .idea
 test/test.cfg
@@ -20,3 +22,9 @@ venv/
 
 # Environment variables
 .env
+
+# External libraries (cloned)
+lib/
+
+# Cache directory
+cache/

app/config.py

@@ -1,18 +1,64 @@
 """
 Configuration settings for TableScanner application.
+
+Loads configuration from environment variables and .env file.
+All KBase service URLs and authentication settings are managed here.
 """
 
 from pydantic_settings import BaseSettings
+from pydantic import Field
 
 
 class Settings(BaseSettings):
-    """Application settings."""
+    """
+    Application settings loaded from environment variables.
+
+    Create a .env file based on .env.example to configure locally.
+    """
+
+    # ==========================================================================
+    # AUTHENTICATION
+    # ==========================================================================
+    KB_SERVICE_AUTH_TOKEN: str = Field(
+        ...,
+        description="KBase authentication token for API access"
+    )
+
+    # ==========================================================================
+    # CACHE SETTINGS
+    # ==========================================================================
+    CACHE_DIR: str = Field(
+        default="/tmp/tablescanner_cache",
+        description="Directory for caching downloaded files and SQLite databases"
+    )
+    CACHE_MAX_AGE_HOURS: int = Field(
+        default=24,
+        description="Maximum age of cached files in hours before re-download"
+    )
 
-    KB_SERVICE_AUTH_TOKEN: str
-    CACHE_DIR: str
+    # ==========================================================================
+    # KBASE SERVICE URLS
+    # ==========================================================================
+    WORKSPACE_URL: str = Field(
+        default="https://kbase.us/services/ws",
+        description="KBase Workspace service URL"
+    )
+    KBASE_ENDPOINT: str = Field(
+        default="https://kbase.us/services",
+        description="Base URL for KBase services"
+    )
+    BLOBSTORE_URL: str = Field(
+        default="https://kbase.us/services/shock-api",
+        description="KBase blobstore/shock service URL"
+    )
 
-    # KBase Workspace settings
-    WORKSPACE_URL: str
+    # ==========================================================================
+    # APPLICATION SETTINGS
+    # ==========================================================================
+    DEBUG: bool = Field(
+        default=False,
+        description="Enable debug mode with verbose logging"
+    )
 
     # Root path for proxy deployment (e.g., "/services/berdl_table_scanner")
     ROOT_PATH: str = ""
@@ -23,5 +69,5 @@ class Config:
         case_sensitive = True
 
 
-# Global settings instance
+# Global settings instance - loaded at module import
 settings = Settings()

app/main.py

@@ -1,10 +1,17 @@
 """
 TableScanner FastAPI Application
 
-Main application factory module.
+Main application factory module for the TableScanner service.
+Provides REST API endpoints for querying BERDL table data.
+
+Run with: uv run fastapi dev app/main.py
 """
 
+from pathlib import Path
 from fastapi import FastAPI
+from fastapi.staticfiles import StaticFiles
+from fastapi.middleware.cors import CORSMiddleware
+
 from app.routes import router
 from app.config import settings
 
@@ -13,22 +20,55 @@ def create_app() -> FastAPI:
     """
     Application factory function.
 
+    Creates and configures the FastAPI application with:
+    - Static file serving for viewer.html
+    - API routes
+
     Returns:
         FastAPI: Configured FastAPI application instance
     """
+    # Configure root_path for KBase dynamic services
+    # KBase services are often deployed at /services/service_name
+    # Pydantic Settings management or manual environ check can handle this.
+    import os
+    root_path = os.environ.get("KB_SERVICE_ROOT_PATH", "")
+
+
+    description = """
+    ## TableScanner API
+
+    A FastAPI service for querying BERDL table data from KBase.
+
+    ### Features
+    - List pangenomes from BERDLTables objects
+    - List tables within a pangenome
+    - Query table data with filtering, sorting, and pagination
+    - Local caching for performance
+
+    ### Authentication
+    Pass your KBase auth token in the `Authorization` header.
+    """
+
     app = FastAPI(
         title="TableScanner",
-        description="API for table scanning operations",
+        root_path=root_path,
+        description=description,
         version="1.0.0",
-        root_path=settings.ROOT_PATH
+        docs_url="/docs",
+        redoc_url="/redoc",
     )
 
     # Store settings in app state for access throughout the application
     app.state.settings = settings
 
-    # Include routes
+    # Include API routes
     app.include_router(router)
 
+    # Mount static files directory for viewer.html
+    static_dir = Path(__file__).parent.parent / "static"
+    if static_dir.exists():
+        app.mount("/static", StaticFiles(directory=static_dir), name="static")
+
     return app