Merge pull request #33 from rafiattrach/rename-download-dir

Rename data/ to m3_data/ to avoid user directory conflicts

Author: MoreiraP12

.gitignore

@@ -79,3 +79,4 @@ Desktop.ini
 
 # Datasets and other large files
 data/
+m3_data/

src/m3/cli.py

@@ -90,9 +90,9 @@ def dataset_init_cmd(
     """
     Download a supported dataset (e.g., 'mimic-iv-demo') and load it into a local SQLite
 
-    Raw downloaded files are stored in a `data/raw_files/<dataset_name>/` subdirectory
+    Raw downloaded files are stored in a `m3_data/raw_files/<dataset_name>/` subdirectory
     and are **not** deleted after processing.
-    The SQLite database is stored in `data/databases/` or path specified by `--db-path`.
+    The SQLite database is stored in `m3_data/databases/` or path specified by `--db-path`.
     """
     logger.info(f"CLI 'init' called for dataset: '{dataset_name}'")
 

src/m3/config.py

@@ -32,7 +32,7 @@ def _get_project_root() -> Path:
 
 
 _PROJECT_ROOT = _get_project_root()
-_PROJECT_DATA_DIR = _PROJECT_ROOT / "data"
+_PROJECT_DATA_DIR = _PROJECT_ROOT / "m3_data"
 
 DEFAULT_DATABASES_DIR = _PROJECT_DATA_DIR / "databases"
 DEFAULT_RAW_FILES_DIR = _PROJECT_DATA_DIR / "raw_files"
@@ -63,7 +63,7 @@ def get_dataset_config(dataset_name: str) -> dict | None:
 def get_default_database_path(dataset_name: str) -> Path | None:
     """
     Return the default SQLite DB path for a given dataset,
-    under <project_root>/data/databases/.
+    under <project_root>/m3_data/databases/.
     """
     cfg = get_dataset_config(dataset_name)
     if cfg and "default_db_filename" in cfg:
@@ -77,7 +77,7 @@ def get_default_database_path(dataset_name: str) -> Path | None:
 def get_dataset_raw_files_path(dataset_name: str) -> Path | None:
     """
     Return the raw-file storage path for a dataset,
-    under <project_root>/data/raw_files/<dataset_name>/.
+    under <project_root>/m3_data/raw_files/<dataset_name>/.
     """
     cfg = get_dataset_config(dataset_name)
     if cfg:

src/m3/mcp_client_configs/dynamic_mcp_config.py

@@ -10,6 +10,12 @@
 from pathlib import Path
 from typing import Any
 
+# Error messages
+_DATABASE_PATH_ERROR_MSG = (
+    "Could not determine default database path for mimic-iv-demo.\n"
+    "Please run 'm3 init mimic-iv-demo' first."
+)
+
 
 class MCPConfigGenerator:
     """Generator for MCP server configurations."""
@@ -165,16 +171,19 @@ def interactive_config(self) -> dict[str, Any]:
 
         if backend == "sqlite":
             print("\n📁 SQLite Configuration:")
+            from m3.config import get_default_database_path
+
+            default_db_path = get_default_database_path("mimic-iv-demo")
+            if default_db_path is None:
+                raise ValueError(_DATABASE_PATH_ERROR_MSG)
+            print(f"Default database path: {default_db_path}")
+
             db_path = (
                 input(
                     "SQLite database path (optional, press Enter to use default): "
                 ).strip()
                 or None
             )
-            if db_path:
-                print(f"✅ Will use database: {db_path}")
-            else:
-                print("✅ Will use default database path")
 
         elif backend == "bigquery":
             print("\n☁️  BigQuery Configuration:")
@@ -269,6 +278,15 @@ def print_config_info(config: dict[str, Any]):
 
     if "M3_DB_PATH" in server_config["env"]:
         print(f"💾 Database path: {server_config['env']['M3_DB_PATH']}")
+    elif server_config["env"].get("M3_BACKEND") == "sqlite":
+        # Show the default path when using SQLite backend
+        from m3.config import get_default_database_path
+
+        default_path = get_default_database_path("mimic-iv-demo")
+        if default_path is None:
+            raise ValueError(_DATABASE_PATH_ERROR_MSG)
+        print(f"💾 Database path: {default_path}")
+
     if "M3_PROJECT_ID" in server_config["env"]:
         print(f"☁️  Project ID: {server_config['env']['M3_PROJECT_ID']}")
 

src/m3/mcp_client_configs/setup_claude_desktop.py

@@ -160,7 +160,7 @@ def setup_claude_desktop(
         print(f"🔧 Backend: {backend}")
 
         if backend == "sqlite":
-            db_path_display = db_path or "default (data/databases/mimic_iv_demo.db)"
+            db_path_display = db_path or "default (m3_data/databases/mimic_iv_demo.db)"
             print(f"💾 Database: {db_path_display}")
         elif backend == "bigquery":
             project_display = project_id or "physionet-data"