|
-**SQLite:**
+**DuckDB (Local):**
```bash
git clone https://github.com/rafiattrach/m3.git && cd m3
docker build -t m3:lite --target lite .
@@ -205,7 +204,7 @@ pip install m3-mcp
"m3": {
"command": "m3-mcp-server",
"env": {
- "M3_BACKEND": "sqlite"
+ "M3_BACKEND": "duckdb"
}
}
}
@@ -233,14 +232,146 @@ pre-commit install
"args": ["-m", "m3.mcp_server"],
"cwd": "/path/to/m3",
"env": {
- "M3_BACKEND": "sqlite"
+ "M3_BACKEND": "duckdb"
}
}
}
}
```
-## Advanced Configuration
+#### Using `UV` (Recommended)
+Assuming you have [UV](https://docs.astral.sh/uv/getting-started/installation/) installed.
+
+**Step 1: Clone and Navigate**
+```bash
+# Clone the repository
+git clone https://github.com/rafiattrach/m3.git
+cd m3
+```
+
+**Step 2: Create `UV` Virtual Environment**
+```bash
+# Create virtual environment
+uv venv
+```
+
+**Step 3: Install M3**
+```bash
+uv sync
+# Do not forget to use `uv run` to any subsequent commands to ensure you're using the `uv` virtual environment
+```
+
+### šļø Database Configuration
+
+After installation, choose your data source:
+
+#### Option A: Local Demo (DuckDB + Parquet)
+
+**Perfect for learning and development - completely free!**
+
+1. **Initialize demo dataset**:
+ ```bash
+ m3 init mimic-iv-demo
+ ```
+
+2. **Setup MCP Client**:
+ ```bash
+ m3 config
+ ```
+
+ *Alternative: For Claude Desktop specifically:*
+ ```bash
+ m3 config claude --backend duckdb --db-path /Users/you/path/to/m3_data/databases/mimic_iv_demo.duckdb
+ ```
+
+5. **Restart your MCP client** and ask:
+
+ - "What tools do you have for MIMIC-IV data?"
+ - "Show me patient demographics from the ICU"
+
+#### Option B: Local Full Dataset (DuckDB + Parquet)
+
+**Run the entire MIMIC-IV dataset locally with DuckDB views over Parquet.**
+
+1. **Acquire CSVs** (requires PhysioNet credentials):
+ - Download the official MIMIC-IV CSVs from PhysioNet and place them under:
+ - `/Users/you/path/to/m3/m3_data/raw_files/mimic-iv-full/hosp/`
+ - `/Users/you/path/to/m3/m3_data/raw_files/mimic-iv-full/icu/`
+ - Note: `m3 init`'s auto-download function currently only supports the demo dataset. Use your browser or `wget` to obtain the full dataset.
+
+2. **Initialize full dataset**:
+ ```bash
+ m3 init mimic-iv-full
+ ```
+ - This may take up to 30 minutes, depending on your system (e.g. 10 minutes for MacBook Pro M3)
+ - Performance knobs (optional):
+ ```bash
+ export M3_CONVERT_MAX_WORKERS=6 # number of parallel files (default=4)
+ export M3_DUCKDB_MEM=4GB # DuckDB memory limit per worker (default=3GB)
+ export M3_DUCKDB_THREADS=4 # DuckDB threads per worker (default=2)
+ ```
+ Pay attention to your system specifications, especially if you have enough memory.
+
+3. **Select dataset and verify**:
+ ```bash
+ m3 use full # optional, as this automatically got set to full
+ m3 status
+ ```
+ - Status prints active dataset, local DB path, Parquet presence, quick row counts and total Parquet size.
+
+4. **Configure MCP client** (uses the full local DB):
+ ```bash
+ m3 config
+ # or
+ m3 config claude --backend duckdb --db-path /Users/you/path/to/m3/m3_data/databases/mimic_iv_full.duckdb
+ ```
+
+#### Option C: BigQuery (Full Dataset)
+
+**For researchers needing complete MIMIC-IV data**
+
+##### Prerequisites
+- Google Cloud account and project with billing enabled
+- Access to MIMIC-IV on BigQuery (requires PhysioNet credentialing)
+
+##### Setup Steps
+
+1. **Install Google Cloud CLI**:
+
+ **macOS (with Homebrew):**
+ ```bash
+ brew install google-cloud-sdk
+ ```
+
+ **Windows:** Download from https://cloud.google.com/sdk/docs/install
+
+ **Linux:**
+ ```bash
+ curl https://sdk.cloud.google.com | bash
+ ```
+
+2. **Authenticate**:
+ ```bash
+ gcloud auth application-default login
+ ```
+ *This will open your browser - choose the Google account that has access to your BigQuery project with MIMIC-IV data.*
+
+3. **Setup MCP Client for BigQuery**:
+ ```bash
+ m3 config
+ ```
+
+ *Alternative: For Claude Desktop specifically:*
+ ```bash
+ m3 config claude --backend bigquery --project-id YOUR_PROJECT_ID
+ ```
+
+4. **Test BigQuery Access** - Restart your MCP client and ask:
+ ```
+ Use the get_race_distribution function to show me the top 5 races in MIMIC-IV admissions.
+ ```
+
+## š§ Advanced Configuration
Need to configure other MCP clients or customize settings? Use these commands:
@@ -255,8 +386,8 @@ Generates configuration for any MCP client with step-by-step guidance.
# Quick universal config with defaults
m3 config --quick
-# Universal config with custom database
-m3 config --quick --backend sqlite --db-path /path/to/database.db
+# Universal config with custom DuckDB database
+m3 config --quick --backend duckdb --db-path /path/to/database.duckdb
# Save config to file for other MCP clients
m3 config --output my_config.json
@@ -291,7 +422,7 @@ m3 config # Choose OAuth2 option during setup
---
-## Available MCP Tools
+## š ļø Available MCP Tools
When your MCP client processes questions, it uses these tools automatically:
@@ -323,15 +454,17 @@ Try asking your MCP client these questions:
- `Prompt:` *What tables are available in the database?*
- `Prompt:` *What tools do you have for MIMIC-IV data?*
-## Troubleshooting
+## š© Pro Tips
+
+- Do you want to pre-approve the usage of all tools in Claude Desktop? Use the prompt below and then select **Always Allow**
+ - `Prompt:` *Can you please call all your tools in a logical sequence?*
+
+## š Troubleshooting
### Common Issues
-**SQLite "Database not found" errors:**
-```bash
-# Re-download demo database
-m3 init mimic-iv-demo
-```
+**Local "Parquet not found" or view errors:**
+Rerun the `m3 init` command for your chosen dataset.
**MCP client server not starting:**
1. Check your MCP client logs (for Claude Desktop: Help ā View Logs)
@@ -409,11 +542,11 @@ m3-mcp-server
## Roadmap
-- **Local Full Dataset**: Complete MIMIC-IV locally (no cloud costs)
-- **Advanced Tools**: More specialized medical data functions
-- **Visualization**: Built-in plotting and charting tools
-- **Enhanced Security**: Role-based access control, audit logging
-- **Multi-tenant Support**: Organization-level data isolation
+- š **Complete Local Full Dataset**: Complete the support for `mimic-iv-full` (Download CLI)
+- š§ **Advanced Tools**: More specialized medical data functions
+- š **Visualization**: Built-in plotting and charting tools
+- š **Enhanced Security**: Role-based access control, audit logging
+- š **Multi-tenant Support**: Organization-level data isolation
## Contributing
diff --git a/pyproject.toml b/pyproject.toml
index 66269dc..fb3d5b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ maintainers = [
]
readme = "README.md"
license = "MIT"
-keywords = ["mimic-iv", "clinical-data", "mcp", "llm", "medical", "healthcare", "sqlite", "bigquery"]
+keywords = ["mimic-iv", "clinical-data", "mcp", "llm", "medical", "healthcare", "duckdb", "bigquery"]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
@@ -50,14 +50,15 @@ dependencies = [
"cryptography>=41.0.0", # Cryptographic operations for JWT
"python-jose[cryptography]>=3.3.0", # Additional JWT support with crypto
"httpx>=0.24.0", # Modern HTTP client for OAuth2 token validation
+ "duckdb>=1.4.1",
]
-[project.dependency-groups]
+[dependency-groups]
dev = [
"ruff>=0.4.0",
"pre-commit>=3.0.0",
- "pytest>=7.4.0",
- "pytest-asyncio>=0.23.0",
+ "pytest>=8.0.0",
+ "pytest-asyncio>=0.24.0",
"pytest-mock>=3.10.0",
"aiohttp>=3.8.0", # For MCP client testing
]
diff --git a/src/m3/cli.py b/src/m3/cli.py
index 9198dfa..cc7a4dc 100644
--- a/src/m3/cli.py
+++ b/src/m3/cli.py
@@ -1,5 +1,4 @@
import logging
-import sqlite3
import subprocess
import sys
from pathlib import Path
@@ -10,12 +9,21 @@
from m3 import __version__
from m3.config import (
SUPPORTED_DATASETS,
+ detect_available_local_datasets,
+ get_active_dataset,
get_dataset_config,
- get_dataset_raw_files_path,
+ get_dataset_parquet_root,
get_default_database_path,
logger,
+ set_active_dataset,
+)
+from m3.data_io import (
+ compute_parquet_dir_size,
+ convert_csv_to_parquet,
+ download_dataset,
+ init_duckdb_from_parquet,
+ verify_table_rowcount,
)
-from m3.data_io import initialize_dataset
app = typer.Typer(
name="m3",
@@ -72,33 +80,45 @@ def dataset_init_cmd(
str,
typer.Argument(
help=(
- "Dataset to initialize. Default: 'mimic-iv-demo'. "
+ "Dataset to initialize (local). Default: 'mimic-iv-demo'. "
f"Supported: {', '.join(SUPPORTED_DATASETS.keys())}"
),
metavar="DATASET_NAME",
),
] = "mimic-iv-demo",
+ src: Annotated[
+ str | None,
+ typer.Option(
+ "--src",
+ help=(
+ "Path to existing raw CSV.gz root (hosp/, icu/). If provided, download is skipped."
+ ),
+ ),
+ ] = None,
db_path_str: Annotated[
str | None,
typer.Option(
"--db-path",
"-p",
- help="Custom path for the SQLite DB. Uses a default if not set.",
+ help="Custom path for the DuckDB file. Uses a default if not set.",
),
] = None,
):
"""
- Download a supported dataset (e.g., 'mimic-iv-demo') and load it into a local SQLite
-
- Raw downloaded files are stored in a `m3_data/raw_files//` subdirectory
- and are **not** deleted after processing.
- The SQLite database is stored in `m3_data/databases/` or path specified by `--db-path`.
+ Initialize a local dataset in one step by detecting what's already present:
+ - If Parquet exists: only initialize DuckDB views
+ - If raw CSV.gz exists but Parquet is missing: convert then initialize
+ - If neither exists: download (demo only), convert, then initialize
+
+ Notes:
+ - Auto-download currently supports only 'mimic-iv-demo'. For 'mimic-iv-full',
+ place the official raw CSV.gz files under /m3_data/raw_files//
+ with 'hosp/' and 'icu/' subdirectories, then re-run this command.
"""
logger.info(f"CLI 'init' called for dataset: '{dataset_name}'")
- dataset_key = dataset_name.lower() # Normalize for lookup
+ dataset_key = dataset_name.lower()
dataset_config = get_dataset_config(dataset_key)
-
if not dataset_config:
typer.secho(
f"Error: Dataset '{dataset_name}' is not supported or not configured.",
@@ -112,17 +132,82 @@ def dataset_init_cmd(
)
raise typer.Exit(code=1)
- # Currently, only mimic-iv-demo is fully wired up as an example.
- # This check can be removed or adapted as more datasets are supported.
- if dataset_key != "mimic-iv-demo":
+ # Resolve roots
+ pq_root = get_dataset_parquet_root(dataset_key)
+ if pq_root is None:
typer.secho(
- (
- f"Warning: While '{dataset_name}' is configured, only 'mimic-iv-demo' "
- "is fully implemented for initialization in this version."
- ),
- fg=typer.colors.YELLOW,
+ "Could not determine dataset directories.", fg=typer.colors.RED, err=True
)
+ raise typer.Exit(code=1)
+ csv_root_default = pq_root.parent.parent / "raw_files" / dataset_key
+ csv_root = Path(src).resolve() if src else csv_root_default
+
+ # Presence detection (check for any parquet or csv.gz files)
+ # NOTE: Checks need to be more robust as soon as we support the full dataset for download (don't just check for any file, but that no files are missing)
+ parquet_present = any(pq_root.rglob("*.parquet"))
+ raw_present = any(csv_root.rglob("*.csv.gz"))
+
+ typer.echo(f"Detected dataset: '{dataset_key}'")
+ typer.echo(f"Raw root: {csv_root} (present={raw_present})")
+ typer.echo(f"Parquet root: {pq_root} (present={parquet_present})")
+
+ # Step 1: Ensure raw dataset exists (download demo if missing; for full, inform and return)
+ if not raw_present and not parquet_present:
+ if dataset_key == "mimic-iv-demo":
+ out_dir = csv_root_default
+ out_dir.mkdir(parents=True, exist_ok=True)
+
+ typer.echo(f"Downloading dataset: '{dataset_key}'")
+ typer.echo(f"Listing URL: {dataset_config.get('file_listing_url')}")
+ typer.echo(f"Output directory: {out_dir}")
+
+ ok = download_dataset(dataset_key, out_dir)
+ if not ok:
+ typer.secho(
+ "Download failed. Please check logs for details.",
+ fg=typer.colors.RED,
+ err=True,
+ )
+ raise typer.Exit(code=1)
+ typer.secho("ā
Download complete.", fg=typer.colors.GREEN)
+
+ # Point csv_root to the downloaded location
+ csv_root = out_dir
+ raw_present = True
+ else:
+ typer.secho(
+ "Auto-download is only supported for 'mimic-iv-demo'.",
+ fg=typer.colors.YELLOW,
+ )
+ typer.secho(
+ (
+ "To initialize 'mimic-iv-full':\n"
+ "1) Download the official MIMIC-IV dataset from PhysioNet (this requires a PhysioNet account with dataset access)\n"
+ "2) Place the raw CSV.gz files under: {csv_root_default}\n"
+ " Ensure the structure includes 'hosp/' and 'icu/' subdirectories.\n"
+ "3) Then re-run: m3 init mimic-iv-full"
+ ),
+ fg=typer.colors.WHITE,
+ )
+ return
+
+ # Step 2: Ensure Parquet exists (convert if missing)
+ if not parquet_present:
+ typer.echo(f"Converting dataset: '{dataset_key}'")
+ typer.echo(f"CSV root: {csv_root}")
+ typer.echo(f"Parquet destination: {pq_root}")
+ ok = convert_csv_to_parquet(dataset_key, csv_root, pq_root)
+ if not ok:
+ typer.secho(
+ "Conversion failed. Please check logs for details.",
+ fg=typer.colors.RED,
+ err=True,
+ )
+ raise typer.Exit(code=1)
+ typer.secho("ā
Conversion complete.", fg=typer.colors.GREEN)
+
+ # Step 2: Initialize DuckDB over Parquet
final_db_path = (
Path(db_path_str).resolve()
if db_path_str
@@ -136,21 +221,23 @@ def dataset_init_cmd(
)
raise typer.Exit(code=1)
- # Ensure parent directory for the database exists
final_db_path.parent.mkdir(parents=True, exist_ok=True)
-
- raw_files_storage_path = get_dataset_raw_files_path(
- dataset_key
- ) # Will be created if doesn't exist
typer.echo(f"Initializing dataset: '{dataset_name}'")
- typer.echo(f"Target database path: {final_db_path}")
- typer.echo(f"Raw files will be stored at: {raw_files_storage_path.resolve()}")
+ typer.echo(f"DuckDB path: {final_db_path}")
+ typer.echo(f"Parquet root: {pq_root}")
+
+ if not pq_root or not pq_root.exists():
+ typer.secho(
+ f"Parquet directory not found at {pq_root}.",
+ fg=typer.colors.RED,
+ err=True,
+ )
+ raise typer.Exit(code=1)
- initialization_successful = initialize_dataset(
+ init_successful = init_duckdb_from_parquet(
dataset_name=dataset_key, db_target_path=final_db_path
)
-
- if not initialization_successful:
+ if not init_successful:
typer.secho(
(
f"Dataset '{dataset_name}' initialization FAILED. "
@@ -166,82 +253,118 @@ def dataset_init_cmd(
"Verifying database integrity..."
)
- # Basic verification by querying a known table
verification_table_name = dataset_config.get("primary_verification_table")
if not verification_table_name:
logger.warning(
- f"No 'primary_verification_table' configured for '{dataset_name}'. "
- "Skipping DB query test."
+ f"No 'primary_verification_table' configured for '{dataset_name}'. Skipping DB query test."
)
typer.secho(
(
f"Dataset '{dataset_name}' initialized to {final_db_path}. "
- f"Raw files at {raw_files_storage_path.resolve()}."
+ f"Parquet at {pq_root}."
),
fg=typer.colors.GREEN,
)
+ else:
+ try:
+ record_count = verify_table_rowcount(final_db_path, verification_table_name)
+ typer.secho(
+ f"Database verification successful: Found {record_count} records in table '{verification_table_name}'.",
+ fg=typer.colors.GREEN,
+ )
+ typer.secho(
+ f"Dataset '{dataset_name}' ready at {final_db_path}. Parquet at {pq_root}.",
+ fg=typer.colors.BRIGHT_GREEN,
+ )
+ except Exception as e:
+ logger.error(
+ f"Unexpected error during database verification: {e}", exc_info=True
+ )
+ typer.secho(
+ f"An unexpected error occurred during database verification: {e}",
+ fg=typer.colors.RED,
+ err=True,
+ )
+
+ # Set active dataset to match init target
+ if dataset_key == "mimic-iv-demo":
+ set_active_dataset("demo")
+ elif dataset_key == "mimic-iv-full":
+ set_active_dataset("full")
+
+
+@app.command("use")
+def use_cmd(
+ target: Annotated[
+ str,
+ typer.Argument(
+ help="Select active dataset: demo | full | bigquery", metavar="TARGET"
+ ),
+ ],
+):
+ """Set the active dataset selection for the project."""
+ target = target.lower()
+ if target not in ("demo", "full", "bigquery"):
typer.secho(
- "Skipped database query test as no verification table is set in config.",
- fg=typer.colors.YELLOW,
+ "Target must be one of: demo, full, bigquery", fg=typer.colors.RED, err=True
)
- return
+ raise typer.Exit(code=1)
- try:
- conn = sqlite3.connect(final_db_path)
- cursor = conn.cursor()
- # A simple count query is usually safe and informative.
- query = f"SELECT COUNT(*) FROM {verification_table_name};"
- logger.debug(f"Executing verification query: '{query}' on {final_db_path}")
- cursor.execute(query)
- count_result = cursor.fetchone()
- conn.close()
-
- if count_result is None:
- raise sqlite3.Error(
- f"Query on table '{verification_table_name}' returned no result (None)."
+ if target in ("demo", "full"):
+ availability = detect_available_local_datasets()[target]
+ if not availability["parquet_present"]:
+ typer.secho(
+ f"Parquet directory missing at {availability['parquet_root']}. Cannot activate '{target}'.",
+ fg=typer.colors.RED,
+ err=True,
)
+ raise typer.Exit(code=1)
- record_count = count_result[0]
- typer.secho(
- (
- f"Database verification successful: Found {record_count} records in "
- f"table '{verification_table_name}'."
- ),
- fg=typer.colors.GREEN,
- )
- typer.secho(
- (
- f"Dataset '{dataset_name}' ready at {final_db_path}. "
- f"Raw files at {raw_files_storage_path.resolve()}."
- ),
- fg=typer.colors.BRIGHT_GREEN,
- )
- except sqlite3.Error as e:
- logger.error(
- (
- f"SQLite error during verification query on table "
- f"'{verification_table_name}': {e}"
- ),
- exc_info=True,
- )
- typer.secho(
- (
- f"Error verifying table '{verification_table_name}': {e}. "
- f"The database was created at {final_db_path}, but the test query "
- "failed. The data might be incomplete or corrupted."
- ),
- fg=typer.colors.RED,
- err=True,
- )
- except Exception as e: # Catch any other unexpected errors
- logger.error(
- f"Unexpected error during database verification: {e}", exc_info=True
- )
- typer.secho(
- f"An unexpected error occurred during database verification: {e}",
- fg=typer.colors.RED,
- err=True,
- )
+ set_active_dataset(target)
+ typer.secho(f"Active dataset set to '{target}'.", fg=typer.colors.GREEN)
+
+
+@app.command("status")
+def status_cmd():
+ """Show active dataset, local DB path, Parquet presence, quick counts and sizes."""
+ active = get_active_dataset() or "(unset)"
+ typer.secho(
+ f"Active dataset: {active}",
+ fg=typer.colors.BRIGHT_GREEN if active != "(unset)" else typer.colors.YELLOW,
+ )
+
+ availability = detect_available_local_datasets()
+
+ for label in ("demo", "full"):
+ info = availability[label]
+ typer.secho(f"\n=== {label.upper()} ===", fg=typer.colors.BRIGHT_BLUE)
+
+ parquet_icon = "ā
" if info["parquet_present"] else "ā"
+ db_icon = "ā
" if info["db_present"] else "ā"
+
+ typer.echo(f" parquet_present: {parquet_icon} db_present: {db_icon}")
+ typer.echo(f" parquet_root: {info['parquet_root']}")
+ typer.echo(f" db_path: {info['db_path']}")
+
+ if info["parquet_present"]:
+ try:
+ size_bytes = compute_parquet_dir_size(Path(info["parquet_root"]))
+ size_gb = float(size_bytes) / (1024**3)
+ typer.echo(f" parquet_size_gb: {size_gb:.4f} GB")
+ except Exception:
+ typer.echo(" parquet_size_gb: (skipped)")
+
+ # Try a quick rowcount on the verification table if db present
+ ds_name = "mimic-iv-demo" if label == "demo" else "mimic-iv-full"
+ cfg = get_dataset_config(ds_name)
+ if info["db_present"] and cfg:
+ try:
+ count = verify_table_rowcount(
+ Path(info["db_path"]), cfg["primary_verification_table"]
+ )
+ typer.echo(f" {cfg['primary_verification_table']}_rowcount: {count:,}")
+ except Exception:
+ typer.echo(" rowcount: (skipped)")
@app.command("config")
@@ -258,15 +381,15 @@ def config_cmd(
typer.Option(
"--backend",
"-b",
- help="Backend to use (sqlite or bigquery). Default: sqlite",
+ help="Backend to use (duckdb or bigquery). Default: duckdb",
),
- ] = "sqlite",
+ ] = "duckdb",
db_path: Annotated[
str | None,
typer.Option(
"--db-path",
"-p",
- help="Path to SQLite database (for sqlite backend)",
+ help="Path to DuckDB database (for duckdb backend)",
),
] = None,
project_id: Annotated[
@@ -340,7 +463,8 @@ def config_cmd(
raise typer.Exit(code=1)
# Validate backend-specific arguments
- if backend == "sqlite" and project_id:
+ # duckdb: db_path allowed, project_id not allowed
+ if backend == "duckdb" and project_id:
typer.secho(
"ā Error: --project-id can only be used with --backend bigquery",
fg=typer.colors.RED,
@@ -348,15 +472,14 @@ def config_cmd(
)
raise typer.Exit(code=1)
+ # bigquery: requires project_id, db_path not allowed
if backend == "bigquery" and db_path:
typer.secho(
- "ā Error: --db-path can only be used with --backend sqlite",
+ "ā Error: --db-path can only be used with --backend duckdb",
fg=typer.colors.RED,
err=True,
)
raise typer.Exit(code=1)
-
- # Require project_id for BigQuery backend
if backend == "bigquery" and not project_id:
typer.secho(
"ā Error: --project-id is required when using --backend bigquery",
@@ -377,14 +500,26 @@ def config_cmd(
)
raise typer.Exit(code=1)
- # Build command arguments
+ # Build command arguments with smart defaults inferred from runtime config
cmd = [sys.executable, str(script_path)]
- if backend != "sqlite":
+ # Always pass backend if not duckdb; duckdb is the script default
+ if backend != "duckdb":
cmd.extend(["--backend", backend])
- if backend == "sqlite" and db_path:
- cmd.extend(["--db-path", db_path])
+ # For duckdb, infer db_path from active dataset if not provided
+ if backend == "duckdb":
+ if db_path:
+ inferred_db_path = Path(db_path).resolve()
+ else:
+ active_dataset = get_active_dataset()
+ if not active_dataset:
+ # default to demo if nothing is set
+ inferred_db_path = get_default_database_path("mimic-iv-demo")
+ else:
+ inferred_db_path = get_default_database_path(active_dataset)
+ cmd.extend(["--db-path", str(inferred_db_path)])
+
elif backend == "bigquery" and project_id:
cmd.extend(["--project-id", project_id])
@@ -427,7 +562,7 @@ def config_cmd(
if quick:
cmd.append("--quick")
- if backend != "sqlite":
+ if backend != "duckdb":
cmd.extend(["--backend", backend])
if server_name != "m3":
@@ -439,7 +574,7 @@ def config_cmd(
if working_directory:
cmd.extend(["--working-directory", working_directory])
- if backend == "sqlite" and db_path:
+ if backend == "duckdb" and db_path:
cmd.extend(["--db-path", db_path])
elif backend == "bigquery" and project_id:
cmd.extend(["--project-id", project_id])
diff --git a/src/m3/config.py b/src/m3/config.py
index eaa7e51..fd094e7 100644
--- a/src/m3/config.py
+++ b/src/m3/config.py
@@ -1,3 +1,4 @@
+import json
import logging
from pathlib import Path
@@ -34,9 +35,9 @@ def _get_project_root() -> Path:
_PROJECT_ROOT = _get_project_root()
_PROJECT_DATA_DIR = _PROJECT_ROOT / "m3_data"
-DEFAULT_DATABASES_DIR = _PROJECT_DATA_DIR / "databases"
-DEFAULT_RAW_FILES_DIR = _PROJECT_DATA_DIR / "raw_files"
-
+_DEFAULT_DATABASES_DIR = _PROJECT_DATA_DIR / "databases"
+_DEFAULT_PARQUET_DIR = _PROJECT_DATA_DIR / "parquet"
+_RUNTIME_CONFIG_PATH = _PROJECT_DATA_DIR / "config.json"
# --------------------------------------------------
# Dataset configurations (add more entries as needed)
@@ -45,10 +46,21 @@ def _get_project_root() -> Path:
"mimic-iv-demo": {
"file_listing_url": "https://physionet.org/files/mimic-iv-demo/2.2/",
"subdirectories_to_scan": ["hosp", "icu"],
- "default_db_filename": "mimic_iv_demo.db",
- "primary_verification_table": "hosp_admissions", # Table name in SQLite DB
+ "default_duckdb_filename": "mimic_iv_demo.duckdb",
+ "primary_verification_table": "hosp_admissions",
+ },
+ "mimic-iv-full": {
+ "file_listing_url": None,
+ "subdirectories_to_scan": ["hosp", "icu"],
+ "default_duckdb_filename": "mimic_iv_full.duckdb",
+ "primary_verification_table": "hosp_admissions",
},
- # add other datasets here...
+}
+
+# Dataset name aliases used on the CLI
+CLI_DATASET_ALIASES = {
+ "demo": "mimic-iv-demo",
+ "full": "mimic-iv-full",
}
@@ -62,28 +74,155 @@ 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,
+ Return the default local DuckDB path for a given dataset,
under /m3_data/databases/.
"""
+
cfg = get_dataset_config(dataset_name)
- if cfg and "default_db_filename" in cfg:
- DEFAULT_DATABASES_DIR.mkdir(parents=True, exist_ok=True)
- return DEFAULT_DATABASES_DIR / cfg["default_db_filename"]
+ if not cfg:
+ logger.warning(
+ f"Unknown dataset, cannot determine default DB path: {dataset_name}"
+ )
+ return None
- logger.warning(f"Missing default_db_filename for dataset: {dataset_name}")
- return None
+ _DEFAULT_DATABASES_DIR.mkdir(parents=True, exist_ok=True)
+ db_fname = cfg.get("default_duckdb_filename")
+ if not db_fname:
+ logger.warning(f"Missing default DuckDB filename for dataset: {dataset_name}")
+ return None
+ return _DEFAULT_DATABASES_DIR / db_fname
-def get_dataset_raw_files_path(dataset_name: str) -> Path | None:
+def get_dataset_parquet_root(dataset_name: str) -> Path | None:
"""
- Return the raw-file storage path for a dataset,
- under /m3_data/raw_files//.
+ Return the Parquet root for a dataset under
+ /m3_data/parquet//.
"""
cfg = get_dataset_config(dataset_name)
- if cfg:
- path = DEFAULT_RAW_FILES_DIR / dataset_name.lower()
- path.mkdir(parents=True, exist_ok=True)
- return path
-
- logger.warning(f"Unknown dataset, cannot determine raw path: {dataset_name}")
+ if not cfg:
+ logger.warning(
+ f"Unknown dataset, cannot determine Parquet root: {dataset_name}"
+ )
+ return None
+ path = _DEFAULT_PARQUET_DIR / dataset_name.lower()
+ path.mkdir(parents=True, exist_ok=True)
+ return path
+
+
+# -----------------------------
+# Runtime config (active dataset)
+# -----------------------------
+def _ensure_data_dirs():
+ _DEFAULT_DATABASES_DIR.mkdir(parents=True, exist_ok=True)
+ _DEFAULT_PARQUET_DIR.mkdir(parents=True, exist_ok=True)
+ _PROJECT_DATA_DIR.mkdir(parents=True, exist_ok=True)
+
+
+def _get_default_runtime_config() -> dict:
+ return {
+ "active_dataset": None,
+ "duckdb_paths": {
+ "demo": str(get_default_database_path("mimic-iv-demo") or ""),
+ "full": str(get_default_database_path("mimic-iv-full") or ""),
+ },
+ "parquet_roots": {
+ "demo": str(get_dataset_parquet_root("mimic-iv-demo") or ""),
+ "full": str(get_dataset_parquet_root("mimic-iv-full") or ""),
+ },
+ }
+
+
+def load_runtime_config() -> dict:
+ """Load runtime configuration from /m3_data/config.json or use default"""
+ _ensure_data_dirs()
+ if _RUNTIME_CONFIG_PATH.exists():
+ try:
+ return json.loads(_RUNTIME_CONFIG_PATH.read_text())
+ except Exception:
+ logger.warning("Could not parse runtime config; using defaults")
+ # defaults
+ return _get_default_runtime_config()
+
+
+def save_runtime_config(cfg: dict) -> None:
+ _ensure_data_dirs()
+ _RUNTIME_CONFIG_PATH.write_text(json.dumps(cfg, indent=2))
+
+
+def _has_parquet_files(path: Path | None) -> bool:
+ return bool(path and path.exists() and any(path.rglob("*.parquet")))
+
+
+def detect_available_local_datasets() -> dict:
+ """Return presence flags for demo/full based on Parquet roots and DuckDB files."""
+ cfg = load_runtime_config()
+ demo_parquet_path = (
+ Path(cfg["parquet_roots"]["demo"])
+ if cfg["parquet_roots"]["demo"]
+ else get_dataset_parquet_root("mimic-iv-demo")
+ )
+ full_parquet_path = (
+ Path(cfg["parquet_roots"]["full"])
+ if cfg["parquet_roots"]["full"]
+ else get_dataset_parquet_root("mimic-iv-full")
+ )
+ demo_db_path = (
+ Path(cfg["duckdb_paths"]["demo"])
+ if cfg["duckdb_paths"]["demo"]
+ else get_default_database_path("mimic-iv-demo")
+ )
+ full_db_path = (
+ Path(cfg["duckdb_paths"]["full"])
+ if cfg["duckdb_paths"]["full"]
+ else get_default_database_path("mimic-iv-full")
+ )
+ return {
+ "demo": {
+ "parquet_present": _has_parquet_files(demo_parquet_path),
+ "db_present": bool(demo_db_path and demo_db_path.exists()),
+ "parquet_root": str(demo_parquet_path) if demo_parquet_path else "",
+ "db_path": str(demo_db_path) if demo_db_path else "",
+ },
+ "full": {
+ "parquet_present": _has_parquet_files(full_parquet_path),
+ "db_present": bool(full_db_path and full_db_path.exists()),
+ "parquet_root": str(full_parquet_path) if full_parquet_path else "",
+ "db_path": str(full_db_path) if full_db_path else "",
+ },
+ }
+
+
+def get_active_dataset() -> str | None:
+ cfg = load_runtime_config()
+ active = cfg.get("active_dataset")
+ if active in CLI_DATASET_ALIASES:
+ return CLI_DATASET_ALIASES[active]
+ if active == "bigquery":
+ return "bigquery"
+ # Auto-detect default: prefer demo, then full
+ availability = detect_available_local_datasets()
+ if availability["demo"]["parquet_present"]:
+ return CLI_DATASET_ALIASES["demo"]
+ if availability["full"]["parquet_present"]:
+ return CLI_DATASET_ALIASES["full"]
+
+ logger.warning("Unknown active_dataset value in config: %s", active)
return None
+
+
+def set_active_dataset(choice: str) -> None:
+ if choice not in ("demo", "full", "bigquery"):
+ raise ValueError("active_dataset must be one of: demo, full, bigquery")
+ cfg = load_runtime_config()
+ cfg["active_dataset"] = choice
+ save_runtime_config(cfg)
+
+
+def get_duckdb_path_for(choice: str) -> Path | None:
+ key = "mimic-iv-demo" if choice == "demo" else "mimic-iv-full"
+ return get_default_database_path(key) if choice in ("demo", "full") else None
+
+
+def get_parquet_root_for(choice: str) -> Path | None:
+ key = "mimic-iv-demo" if choice == "demo" else "mimic-iv-full"
+ return get_dataset_parquet_root(key) if choice in ("demo", "full") else None
diff --git a/src/m3/data_io.py b/src/m3/data_io.py
index dffb973..f5d7d92 100644
--- a/src/m3/data_io.py
+++ b/src/m3/data_io.py
@@ -1,12 +1,25 @@
+import os
+import time
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from datetime import timedelta
from pathlib import Path
from urllib.parse import urljoin, urlparse
-import polars as pl
+import duckdb
import requests
import typer
from bs4 import BeautifulSoup
-from m3.config import get_dataset_config, get_dataset_raw_files_path, logger
+from m3.config import (
+ get_dataset_config,
+ get_dataset_parquet_root,
+ get_default_database_path,
+ logger,
+)
+
+########################################################
+# Download functionality
+########################################################
COMMON_USER_AGENT = (
"Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 "
@@ -176,159 +189,296 @@ def _download_dataset_files(
return downloaded_count == len(unique_files_to_process)
-def _load_csv_with_robust_parsing(csv_file_path: Path, table_name: str) -> pl.DataFrame:
+def download_dataset(dataset_name: str, output_root: Path) -> bool:
"""
- Load a CSV file with proper type inference by scanning the entire file.
+ Public wrapper to download a supported dataset's CSV files.
+ - Currently intended for 'mimic-iv-demo' (public demo); extendable for others.
+ - Downloads into output_root preserving subdirectory structure (e.g., hosp/, icu/).
"""
- df = pl.read_csv(
- source=csv_file_path,
- infer_schema_length=None, # Scan entire file for proper type inference
- try_parse_dates=True,
- ignore_errors=False,
- null_values=["", "NULL", "null", "\\N", "NA"],
- )
+ cfg = get_dataset_config(dataset_name)
+ if not cfg:
+ logger.error(f"Unsupported dataset: {dataset_name}")
+ return False
+ if not cfg.get("file_listing_url"):
+ logger.error(
+ f"Dataset '{dataset_name}' does not have a configured listing URL. "
+ "This version only supports public demo download."
+ )
+ return False
+
+ output_root.mkdir(parents=True, exist_ok=True)
+ return _download_dataset_files(dataset_name, cfg, output_root)
+
+
+########################################################
+# CSV to Parquet conversion
+########################################################
+
- # Log empty columns (this is normal, not an error)
- if df.height > 0:
- empty_columns = [col for col in df.columns if df[col].is_null().all()]
- if empty_columns:
- logger.info(
- f" Table '{table_name}': Found {len(empty_columns)} empty column(s): "
- f"{', '.join(empty_columns[:5])}"
- + (
- f" (and {len(empty_columns) - 5} more)"
- if len(empty_columns) > 5
- else ""
+def _csv_to_parquet_all(src_root: Path, parquet_root: Path) -> bool:
+ """
+ Convert all CSV files in the source directory to Parquet files.
+ - Streams via DuckDB COPY to keep memory low
+ - Low concurrency to avoid parallel memory spikes
+ - Tunable via env:
+ M3_CONVERT_MAX_WORKERS (default: 4)
+ M3_DUCKDB_MEM (default: 3GB)
+ M3_DUCKDB_THREADS (default: 2)
+ """
+ parquet_paths: list[Path] = []
+ csv_files = list(src_root.rglob("*.csv.gz"))
+ if not csv_files:
+ logger.error(f"No CSV files found in {src_root}")
+ return False
+
+ # Optional: process small files first so progress moves smoothly
+ try:
+ csv_files.sort(key=lambda p: p.stat().st_size)
+ except Exception:
+ pass
+
+ def _convert_one(csv_gz: Path) -> tuple[Path | None, float]:
+ """Convert one CSV file and return the output path and time taken."""
+ start = time.time()
+ rel = csv_gz.relative_to(src_root)
+ out = parquet_root / rel.with_suffix("").with_suffix(".parquet")
+ out.parent.mkdir(parents=True, exist_ok=True)
+
+ con = duckdb.connect()
+ try:
+ mem_limit = os.environ.get("M3_DUCKDB_MEM", "3GB")
+ threads = int(os.environ.get("M3_DUCKDB_THREADS", "2"))
+ con.execute(f"SET memory_limit='{mem_limit}'")
+ con.execute(f"PRAGMA threads={threads}")
+
+ # Streamed CSV -> Parquet conversion with robust parsing
+ sql = f"""
+ COPY (
+ SELECT * FROM read_csv_auto(
+ '{csv_gz.as_posix()}',
+ sample_size=-1,
+ auto_detect=true,
+ nullstr=['', 'NULL', 'NA', 'N/A', '___'],
+ ignore_errors=false
+ )
)
- )
+ TO '{out.as_posix()}' (FORMAT PARQUET, COMPRESSION ZSTD);
+ """
+ con.execute(sql)
+ elapsed = time.time() - start
+ return out, elapsed
+ finally:
+ con.close()
+
+ start_time = time.time()
+ max_workers = max(1, int(os.environ.get("M3_CONVERT_MAX_WORKERS", "4")))
- return df
+ total_files = len(csv_files)
+ completed = 0
+ with ThreadPoolExecutor(max_workers=max_workers) as ex:
+ futures = {ex.submit(_convert_one, f): f for f in csv_files}
-def _etl_csv_collection_to_sqlite(csv_source_dir: Path, db_target_path: Path) -> bool:
- """Loads all .csv.gz files from a directory structure into an SQLite database."""
- db_target_path.parent.mkdir(parents=True, exist_ok=True)
- # Polars uses this format for SQLite connections
- db_connection_uri = f"sqlite:///{db_target_path.resolve()}"
+ logger.info(
+ f"Converting {total_files} CSV files to Parquet using {max_workers} workers..."
+ )
+
+ for fut in as_completed(futures):
+ try:
+ result_path, _ = fut.result()
+ if result_path is not None:
+ parquet_paths.append(result_path)
+ completed += 1
+
+ elapsed = time.time() - start_time
+ logger.info(
+ f"Progress: {completed}/{total_files} files "
+ f"({100 * completed / total_files:.1f}%) - "
+ f"Elapsed: {timedelta(seconds=int(elapsed))!s}"
+ )
+ except Exception as e:
+ csv_file = futures[fut]
+ logger.error(f"Parquet conversion failed for {csv_file}: {e}")
+ ex.shutdown(cancel_futures=True)
+ return False
+
+ elapsed_time = time.time() - start_time
logger.info(
- f"Starting ETL: loading CSVs from '{csv_source_dir}' to SQLite DB "
- f"at '{db_target_path}'"
+ f"\u2713 Converted {len(parquet_paths)} files to Parquet under {parquet_root} "
+ f"in {timedelta(seconds=int(elapsed_time))!s}"
)
+ return True
+
+
+def convert_csv_to_parquet(
+ dataset_name: str, csv_root: Path, parquet_root: Path
+) -> bool:
+ """
+ Public wrapper to convert CSV.gz files to Parquet for a dataset.
+ - csv_root: root folder containing hosp/ and icu/ CSV.gz files
+ - parquet_root: destination root for Parquet files mirroring structure
+ """
+ if not csv_root.exists():
+ logger.error(f"CSV root not found: {csv_root}")
+ return False
+ parquet_root.mkdir(parents=True, exist_ok=True)
+ return _csv_to_parquet_all(csv_root, parquet_root)
+
+
+########################################################
+# DuckDB functions
+########################################################
+
+
+def init_duckdb_from_parquet(dataset_name: str, db_target_path: Path) -> bool:
+ """
+ Initialize or refresh a DuckDB for the dataset by creating views over Parquet.
+
+ Parquet root must exist under:
+ /m3_data/parquet//
+ """
+ dataset_config = get_dataset_config(dataset_name)
+ if not dataset_config:
+ logger.error(f"Configuration for dataset '{dataset_name}' not found.")
+ return False
- csv_file_paths = list(csv_source_dir.rglob("*.csv.gz"))
- if not csv_file_paths:
+ parquet_root = get_dataset_parquet_root(dataset_name)
+ if not parquet_root or not parquet_root.exists():
logger.error(
- "ETL Error: No .csv.gz files found (recursively) in source directory: "
- f"{csv_source_dir}"
+ f"Missing Parquet directory for '{dataset_name}' at {parquet_root}. "
+ "Place Parquet files under the expected path or run the future download command."
)
return False
- successfully_loaded_count = 0
- files_with_errors = []
- logger.info(f"Found {len(csv_file_paths)} .csv.gz files for ETL process.")
-
- for i, csv_file_path in enumerate(csv_file_paths):
- # Generate table name from file path relative to the source directory
- # e.g., source_dir/hosp/admissions.csv.gz -> hosp_admissions
- relative_path = csv_file_path.relative_to(csv_source_dir)
- table_name_parts = [part.lower() for part in relative_path.parts]
- table_name = (
- "_".join(table_name_parts)
- .replace(".csv.gz", "")
- .replace("-", "_")
- .replace(".", "_")
- )
+ logger.info(
+ f"Creating or refreshing views in {db_target_path} for Parquet under {parquet_root}"
+ )
+ return _create_duckdb_with_views(db_target_path, parquet_root)
- logger.info(
- f"[{i + 1}/{len(csv_file_paths)}] ETL: Processing '{relative_path}' "
- f"into SQLite table '{table_name}'..."
- )
- try:
- # Use the robust parsing function
- df = _load_csv_with_robust_parsing(csv_file_path, table_name)
-
- df.write_database(
- table_name=table_name,
- connection=db_connection_uri,
- if_table_exists="replace", # Overwrite table if it exists
- engine="sqlalchemy", # Recommended engine for Polars with SQLite
- )
- logger.info(
- f" Successfully loaded '{relative_path}' into table '{table_name}' "
- f"({df.height} rows, {df.width} columns)."
- )
- successfully_loaded_count += 1
+def _create_duckdb_with_views(db_path: Path, parquet_root: Path) -> bool:
+ """
+ Create a DuckDB database and define one view per Parquet file,
+ using the proper table naming structure that matches MIMIC-IV expectations.
- except Exception as e:
- err_msg = (
- f"Unexpected error during ETL for '{relative_path}' "
- f"(target table '{table_name}'): {e}"
+ For example:
+ - hosp/admissions.parquet ā view: hosp_admissions
+ - icu/chartevents.parquet ā view: icu_chartevents
+ """
+ con = duckdb.connect(str(db_path))
+ try:
+ # Find all parquet files
+ parquet_files = list(parquet_root.rglob("*.parquet"))
+ if not parquet_files:
+ logger.error(f"No Parquet files found in {parquet_root}")
+ return False
+
+ # Optimize DuckDB settings
+ cpu_count = os.cpu_count() or 4
+ con.execute(f"PRAGMA threads={cpu_count}")
+ con.execute("SET memory_limit='8GB'") # adjust to your machine
+
+ logger.info(f"Creating {len(parquet_files)} views in DuckDB...")
+ start_time = time.time()
+ created = 0
+
+ for idx, pq in enumerate(parquet_files, 1):
+ # Get relative path from parquet_root
+ rel = pq.relative_to(parquet_root)
+
+ # Build view name from directory structure + filename
+ # e.g., hosp/admissions.parquet -> hosp_admissions
+ parts = [*list(rel.parent.parts), rel.stem] # stem removes .parquet
+
+ # Clean and join parts
+ view_name = "_".join(
+ p.lower().replace("-", "_").replace(".", "_") for p in parts if p != "."
)
- logger.error(err_msg, exc_info=True)
- files_with_errors.append(f"{relative_path}: {e!s}")
- # Continue to process other files even if one fails
-
- if files_with_errors:
- logger.warning(
- "ETL completed with errors during processing for "
- f"{len(files_with_errors)} file(s):"
+
+ # Create view pointing to the specific parquet file
+ sql = f"""
+ CREATE OR REPLACE VIEW {view_name} AS
+ SELECT * FROM read_parquet('{pq.as_posix()}');
+ """
+
+ try:
+ con.execute(sql)
+ created += 1
+
+ # Progress logging
+ if idx % 5 == 0 or idx == len(parquet_files):
+ elapsed = time.time() - start_time
+ avg_time = elapsed / idx
+ eta_seconds = avg_time * (len(parquet_files) - idx)
+ logger.info(
+ f"Progress: {idx}/{len(parquet_files)} views "
+ f"({100 * idx / len(parquet_files):.1f}%) - "
+ f"Last: {view_name} - "
+ f"ETA: {timedelta(seconds=int(eta_seconds))!s}"
+ )
+ except Exception as e:
+ logger.error(f"Failed to create view {view_name} from {pq}: {e}")
+ raise
+
+ con.commit()
+ elapsed_time = time.time() - start_time
+ logger.info(
+ f"ā Created {created} views in {db_path} in "
+ f"{timedelta(seconds=int(elapsed_time))!s}"
)
- for detail in files_with_errors:
- logger.warning(f" - {detail}")
- # Strict success: all found files must be loaded without Polars/DB errors.
- if successfully_loaded_count == len(csv_file_paths):
+ # List all created views for verification
+ views_result = con.execute(
+ "SELECT table_name FROM information_schema.tables WHERE table_type='VIEW' ORDER BY table_name"
+ ).fetchall()
logger.info(
- f"All {len(csv_file_paths)} CSV files successfully processed & loaded into "
- f"{db_target_path}."
+ f"Created views: {', '.join(v[0] for v in views_result[:10])}{'...' if len(views_result) > 10 else ''}"
)
+
return True
- elif successfully_loaded_count > 0:
- logger.warning(
- f"Partially completed ETL: Loaded {successfully_loaded_count} out of "
- f"{len(csv_file_paths)} files. Some files encountered errors during "
- "their individual processing and were not loaded."
- )
- return False
- else: # No files were successfully loaded
- logger.error(
- "ETL process failed: No CSV files were successfully loaded into the "
- f"database from {csv_source_dir}."
- )
- return False
+ finally:
+ con.close()
-def initialize_dataset(dataset_name: str, db_target_path: Path) -> bool:
- """Initializes a dataset: downloads files and loads them into a database."""
- dataset_config = get_dataset_config(dataset_name)
- if not dataset_config:
- logger.error(f"Configuration for dataset '{dataset_name}' not found.")
- return False
+########################################################
+# Verification and utilities
+########################################################
- raw_files_root_dir = get_dataset_raw_files_path(dataset_name)
- raw_files_root_dir.mkdir(parents=True, exist_ok=True)
- logger.info(f"Starting initialization for dataset: {dataset_name}")
- download_ok = _download_dataset_files(
- dataset_name, dataset_config, raw_files_root_dir
- )
+def verify_table_rowcount(db_path: Path, table_name: str) -> int:
+ con = duckdb.connect(str(db_path))
+ try:
+ row = con.execute(f"SELECT COUNT(*) FROM {table_name}").fetchone()
+ if row is None:
+ raise RuntimeError("No result")
+ return int(row[0])
+ finally:
+ con.close()
- if not download_ok:
+
+def ensure_duckdb_for_dataset(
+ dataset_key: str,
+) -> tuple[bool, Path | None, Path | None]:
+ """
+ Ensure DuckDB exists and views are created for the dataset ('mimic-iv-demo'|'mimic-iv-full').
+ Returns (ok, db_path, parquet_root).
+ """
+ db_path = get_default_database_path(dataset_key)
+ parquet_root = get_dataset_parquet_root(dataset_key)
+ if not parquet_root or not parquet_root.exists():
logger.error(
- f"Download phase failed for dataset '{dataset_name}'. ETL skipped."
+ f"Parquet directory missing: {parquet_root}. Expected at /m3_data/parquet/{dataset_key}/"
)
- return False
-
- logger.info(f"Download phase complete for '{dataset_name}'. Starting ETL phase.")
- etl_ok = _etl_csv_collection_to_sqlite(raw_files_root_dir, db_target_path)
+ return False, db_path, parquet_root
+ ok = _create_duckdb_with_views(db_path, parquet_root)
+ return ok, db_path, parquet_root
- if not etl_ok:
- logger.error(f"ETL phase failed for dataset '{dataset_name}'.")
- return False
- logger.info(
- f"Dataset '{dataset_name}' successfully initialized. "
- f"Database at: {db_target_path}"
- )
- return True
+def compute_parquet_dir_size(parquet_root: Path) -> int:
+ total = 0
+ for p in parquet_root.rglob("*.parquet"):
+ try:
+ total += p.stat().st_size
+ except OSError:
+ pass
+ return total
diff --git a/src/m3/mcp_client_configs/dynamic_mcp_config.py b/src/m3/mcp_client_configs/dynamic_mcp_config.py
index d49d776..a879761 100644
--- a/src/m3/mcp_client_configs/dynamic_mcp_config.py
+++ b/src/m3/mcp_client_configs/dynamic_mcp_config.py
@@ -10,6 +10,8 @@
from pathlib import Path
from typing import Any
+from m3.config import get_active_dataset, get_default_database_path
+
# Error messages
_DATABASE_PATH_ERROR_MSG = (
"Could not determine default database path for mimic-iv-demo.\n"
@@ -21,7 +23,10 @@ class MCPConfigGenerator:
"""Generator for MCP server configurations."""
def __init__(self):
- self.current_dir = Path(__file__).parent.parent.absolute()
+ p = Path(__file__).resolve()
+ while p != p.parent and not (p / "pyproject.toml").exists():
+ p = p.parent
+ self.current_dir = p
self.default_python = self._get_default_python()
def _get_default_python(self) -> str:
@@ -49,7 +54,7 @@ def generate_config(
server_name: str = "m3",
python_path: str | None = None,
working_directory: str | None = None,
- backend: str = "sqlite",
+ backend: str = "duckdb",
db_path: str | None = None,
project_id: str | None = None,
additional_env: dict[str, str] | None = None,
@@ -78,8 +83,21 @@ def generate_config(
}
# Add backend-specific environment variables
- if backend == "sqlite" and db_path:
- env["M3_DB_PATH"] = db_path
+ if backend == "duckdb":
+ if db_path:
+ env["M3_DB_PATH"] = db_path
+ else:
+ active = get_active_dataset()
+ if not active:
+ raise ValueError(
+ "Could not determine default DuckDB path; run `m3 init ...` first "
+ "or pass --db-path explicitly."
+ )
+ default_path = get_default_database_path(active)
+ if not default_path:
+ raise ValueError(_DATABASE_PATH_ERROR_MSG)
+ env["M3_DB_PATH"] = str(default_path)
+
elif backend == "bigquery" and project_id:
env["M3_PROJECT_ID"] = project_id
env["GOOGLE_CLOUD_PROJECT"] = project_id
@@ -154,7 +172,7 @@ def interactive_config(self) -> dict[str, Any]:
# Backend selection - simplified
print("\nChoose backend:")
- print("1. SQLite (local database)")
+ print("1. DuckDB (local database)")
print("2. BigQuery (Google Cloud)")
while True:
@@ -163,16 +181,14 @@ def interactive_config(self) -> dict[str, Any]:
break
print("Please enter 1 or 2")
- backend = "sqlite" if backend_choice == "1" else "bigquery"
+ backend = "duckdb" if backend_choice == "1" else "bigquery"
# Backend-specific configuration
db_path = None
project_id = None
- if backend == "sqlite":
- print("\nš SQLite Configuration:")
- from m3.config import get_default_database_path
-
+ if backend == "duckdb":
+ print("\nš DuckDB Configuration:")
default_db_path = get_default_database_path("mimic-iv-demo")
if default_db_path is None:
raise ValueError(_DATABASE_PATH_ERROR_MSG)
@@ -180,7 +196,7 @@ def interactive_config(self) -> dict[str, Any]:
db_path = (
input(
- "SQLite database path (optional, press Enter to use default): "
+ "DuckDB database path (optional, press Enter to use default): "
).strip()
or None
)
@@ -278,10 +294,8 @@ def print_config_info(config: dict[str, Any]):
if "M3_DB_PATH" in server_config["env"]:
print(f"š¾ 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
-
+ elif server_config["env"].get("M3_BACKEND") in ("duckdb",):
+ # Show the default path when using DuckDB backend
default_path = get_default_database_path("mimic-iv-demo")
if default_path is None:
raise ValueError(_DATABASE_PATH_ERROR_MSG)
@@ -344,12 +358,12 @@ def main():
parser.add_argument("--working-directory", help="Working directory for the server")
parser.add_argument(
"--backend",
- choices=["sqlite", "bigquery"],
- default="sqlite",
- help="Backend to use (default: sqlite)",
+ choices=["duckdb", "bigquery"],
+ default="duckdb",
+ help="Backend to use (default: duckdb)",
)
parser.add_argument(
- "--db-path", help="Path to SQLite database (for sqlite backend)"
+ "--db-path", help="Path to DuckDB database (for duckdb backend)"
)
parser.add_argument(
"--project-id", help="Google Cloud project ID (for bigquery backend)"
@@ -372,7 +386,7 @@ def main():
args = parser.parse_args()
# Validate backend-specific arguments
- if args.backend == "sqlite" and args.project_id:
+ if args.backend in ("duckdb",) and args.project_id:
print(
"ā Error: --project-id can only be used with --backend bigquery",
file=sys.stderr,
@@ -381,7 +395,7 @@ def main():
if args.backend == "bigquery" and args.db_path:
print(
- "ā Error: --db-path can only be used with --backend sqlite",
+ "ā Error: --db-path can only be used with --backend duckdb",
file=sys.stderr,
)
sys.exit(1)
diff --git a/src/m3/mcp_client_configs/setup_claude_desktop.py b/src/m3/mcp_client_configs/setup_claude_desktop.py
index e3d0ab9..e2ae2b2 100644
--- a/src/m3/mcp_client_configs/setup_claude_desktop.py
+++ b/src/m3/mcp_client_configs/setup_claude_desktop.py
@@ -41,7 +41,10 @@ def get_claude_config_path():
def get_current_directory():
"""Get the current M3 project directory."""
- return Path(__file__).parent.parent.absolute()
+ p = Path(__file__).resolve()
+ while p != p.parent and not (p / "pyproject.toml").exists():
+ p = p.parent
+ return p
def get_python_path():
@@ -57,7 +60,7 @@ def get_python_path():
def create_mcp_config(
- backend="sqlite",
+ backend="duckdb",
db_path=None,
project_id=None,
oauth2_enabled=False,
@@ -79,7 +82,7 @@ def create_mcp_config(
}
# Add backend-specific environment variables
- if backend == "sqlite" and db_path:
+ if backend == "duckdb" and db_path:
config["mcpServers"]["m3"]["env"]["M3_DB_PATH"] = db_path
elif backend == "bigquery" and project_id:
config["mcpServers"]["m3"]["env"]["M3_PROJECT_ID"] = project_id
@@ -113,7 +116,7 @@ def create_mcp_config(
def setup_claude_desktop(
- backend="sqlite",
+ backend="duckdb",
db_path=None,
project_id=None,
oauth2_enabled=False,
@@ -159,8 +162,10 @@ def setup_claude_desktop(
print(f"š Config file: {claude_config_path}")
print(f"š§ Backend: {backend}")
- if backend == "sqlite":
- db_path_display = db_path or "default (m3_data/databases/mimic_iv_demo.db)"
+ if backend == "duckdb":
+ db_path_display = (
+ db_path or "default (m3_data/databases/mimic_iv_demo.duckdb)"
+ )
print(f"š¾ Database: {db_path_display}")
elif backend == "bigquery":
project_display = project_id or "physionet-data"
@@ -201,12 +206,12 @@ def main():
)
parser.add_argument(
"--backend",
- choices=["sqlite", "bigquery"],
- default="sqlite",
- help="Backend to use (default: sqlite)",
+ choices=["duckdb", "bigquery"],
+ default="duckdb",
+ help="Backend to use (default: duckdb)",
)
parser.add_argument(
- "--db-path", help="Path to SQLite database (for sqlite backend)"
+ "--db-path", help="Path to DuckDB database (for duckdb backend)"
)
parser.add_argument(
"--project-id", help="Google Cloud project ID (for bigquery backend)"
@@ -227,12 +232,12 @@ def main():
args = parser.parse_args()
# Validate backend-specific arguments
- if args.backend == "sqlite" and args.project_id:
+ if args.backend in ("duckdb",) and args.project_id:
print("ā Error: --project-id can only be used with --backend bigquery")
exit(1)
if args.backend == "bigquery" and args.db_path:
- print("ā Error: --db-path can only be used with --backend sqlite")
+ print("ā Error: --db-path can only be used with --backend duckdb")
exit(1)
# Require project_id for BigQuery backend
diff --git a/src/m3/mcp_server.py b/src/m3/mcp_server.py
index cc8bd91..1a7ad6f 100644
--- a/src/m3/mcp_server.py
+++ b/src/m3/mcp_server.py
@@ -1,13 +1,12 @@
"""
M3 MCP Server - MIMIC-IV + MCP + Models
-Provides MCP tools for querying MIMIC-IV data via SQLite or BigQuery.
+Provides MCP tools for querying MIMIC-IV data via DuckDB (local) or BigQuery.
"""
import os
-import sqlite3
from pathlib import Path
-import pandas as pd
+import duckdb
import sqlparse
from fastmcp import FastMCP
@@ -137,17 +136,15 @@ def _init_backend():
# Initialize OAuth2 authentication
init_oauth2()
- _backend = os.getenv("M3_BACKEND", "sqlite")
+ _backend = os.getenv("M3_BACKEND", "duckdb")
- if _backend == "sqlite":
+ if _backend == "duckdb":
_db_path = os.getenv("M3_DB_PATH")
if not _db_path:
- # Use default database path
- _db_path = get_default_database_path("mimic-iv-demo")
-
- # Ensure the database exists
- if not Path(_db_path).exists():
- raise FileNotFoundError(f"SQLite database not found: {_db_path}")
+ path = get_default_database_path("mimic-iv-demo")
+ _db_path = str(path) if path else None
+ if not _db_path or not Path(_db_path).exists():
+ raise FileNotFoundError(f"DuckDB database not found: {_db_path}")
elif _backend == "bigquery":
try:
@@ -175,8 +172,8 @@ def _init_backend():
def _get_backend_info() -> str:
"""Get current backend information for display in responses."""
- if _backend == "sqlite":
- return f"š§ **Current Backend:** SQLite (local database)\nš **Database Path:** {_db_path}\n"
+ if _backend == "duckdb":
+ return f"š§ **Current Backend:** DuckDB (local database)\nš **Database Path:** {_db_path}\n"
else:
return f"š§ **Current Backend:** BigQuery (cloud database)\nāļø **Project ID:** {_project_id}\n"
@@ -189,24 +186,22 @@ def _get_backend_info() -> str:
# from calling other MCP tools, which violates the MCP protocol.
-def _execute_sqlite_query(sql_query: str) -> str:
- """Execute SQLite query - internal function."""
+def _execute_duckdb_query(sql_query: str) -> str:
+ """Execute DuckDB query - internal function."""
try:
- conn = sqlite3.connect(_db_path)
+ conn = duckdb.connect(_db_path)
try:
- df = pd.read_sql_query(sql_query, conn)
-
+ df = conn.execute(sql_query).df()
if df.empty:
return "No results found"
-
- # Limit output size
if len(df) > 50:
- result = df.head(50).to_string(index=False)
- result += f"\n... ({len(df)} total rows, showing first 50)"
+ out = (
+ df.head(50).to_string(index=False)
+ + f"\n... ({len(df)} total rows, showing first 50)"
+ )
else:
- result = df.to_string(index=False)
-
- return result
+ out = df.to_string(index=False)
+ return out
finally:
conn.close()
except Exception as e:
@@ -259,8 +254,8 @@ def _execute_query_internal(sql_query: str) -> str:
return f"ā **Security Error:** {message}\n\nš” **Tip:** Only SELECT statements are allowed for data analysis."
try:
- if _backend == "sqlite":
- return _execute_sqlite_query(sql_query)
+ if _backend == "duckdb":
+ return _execute_duckdb_query(sql_query)
else: # bigquery
return _execute_bigquery_query(sql_query)
except Exception as e:
@@ -356,11 +351,17 @@ def get_database_schema() -> str:
Returns:
List of all available tables in the database with current backend info
"""
- if _backend == "sqlite":
- query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+ if _backend == "duckdb":
+ query = """
+ SELECT table_name
+ FROM information_schema.tables
+ WHERE table_schema = 'main'
+ ORDER BY table_name
+ """
result = _execute_query_internal(query)
return f"{_get_backend_info()}\nš **Available Tables:**\n{result}"
- else: # bigquery
+
+ elif _backend == "bigquery":
# Show fully qualified table names that are ready to copy-paste into queries
query = """
SELECT CONCAT('`physionet-data.mimiciv_3_1_hosp.', table_name, '`') as query_ready_table_name
@@ -397,19 +398,19 @@ def get_table_info(table_name: str, show_sample: bool = True) -> str:
"""
backend_info = _get_backend_info()
- if _backend == "sqlite":
+ if _backend == "duckdb":
# Get column information
- pragma_query = f"PRAGMA table_info({table_name})"
+ pragma_query = f"PRAGMA table_info('{table_name}')"
try:
- result = _execute_sqlite_query(pragma_query)
+ result = _execute_duckdb_query(pragma_query)
if "error" in result.lower():
return f"{backend_info}ā Table '{table_name}' not found. Use get_database_schema() to see available tables."
info_result = f"{backend_info}š **Table:** {table_name}\n\n**Column Information:**\n{result}"
if show_sample:
- sample_query = f"SELECT * FROM {table_name} LIMIT 3"
- sample_result = _execute_sqlite_query(sample_query)
+ sample_query = f"SELECT * FROM '{table_name}' LIMIT 3"
+ sample_result = _execute_duckdb_query(sample_query)
info_result += (
f"\n\nš **Sample Data (first 3 rows):**\n{sample_result}"
)
@@ -430,7 +431,7 @@ def get_table_info(table_name: str, show_sample: bool = True) -> str:
# Validate BigQuery qualified name format: project.dataset.table
if len(parts) != 3:
error_msg = (
- f"{_get_backend_info()}ā **Invalid qualified table name:** `{table_name}`\n\n"
+ f"{backend_info}ā **Invalid qualified table name:** `{table_name}`\n\n"
"**Expected format:** `project.dataset.table`\n"
"**Example:** `physionet-data.mimiciv_3_1_hosp.diagnoses_icd`\n\n"
"**Available MIMIC-IV datasets:**\n"
@@ -553,7 +554,7 @@ def get_icu_stays(patient_id: int | None = None, limit: int = 10) -> str:
return "Error: Invalid limit. Must be a positive integer between 1 and 10000."
# Try common ICU table names based on backend
- if _backend == "sqlite":
+ if _backend == "duckdb":
icustays_table = "icu_icustays"
else: # bigquery
icustays_table = "`physionet-data.mimiciv_3_1_icu.icustays`"
@@ -603,7 +604,7 @@ def get_lab_results(
return "Error: Invalid limit. Must be a positive integer between 1 and 10000."
# Try common lab table names based on backend
- if _backend == "sqlite":
+ if _backend == "duckdb":
labevents_table = "hosp_labevents"
else: # bigquery
labevents_table = "`physionet-data.mimiciv_3_1_hosp.labevents`"
@@ -658,7 +659,7 @@ def get_race_distribution(limit: int = 10) -> str:
return "Error: Invalid limit. Must be a positive integer between 1 and 10000."
# Try common admissions table names based on backend
- if _backend == "sqlite":
+ if _backend == "duckdb":
admissions_table = "hosp_admissions"
else: # bigquery
admissions_table = "`physionet-data.mimiciv_3_1_hosp.admissions`"
diff --git a/tests/test_cli.py b/tests/test_cli.py
index e6181cd..8e55966 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -19,7 +19,9 @@ def inject_version(monkeypatch):
def test_help_shows_app_name():
result = runner.invoke(app, ["--help"])
+ # exit code 0 for successful help display
assert result.exit_code == 0
+ # help output contains the app name
assert "M3 CLI" in result.stdout
@@ -31,6 +33,7 @@ def test_version_option_exits_zero_and_shows_version():
def test_unknown_command_reports_error():
result = runner.invoke(app, ["not-a-cmd"])
+ # unknown command should fail
assert result.exit_code != 0
# Check both stdout and stderr since error messages might go to either depending on environment
error_message = "No such command 'not-a-cmd'"
@@ -41,56 +44,38 @@ def test_unknown_command_reports_error():
)
-@patch("m3.cli.initialize_dataset")
-@patch("sqlite3.connect")
-def test_init_command_respects_custom_db_path(
- mock_sqlite_connect, mock_initialize_dataset
-):
- """Test that m3 init --db-path correctly uses custom database path override."""
- # Setup mocks
- mock_initialize_dataset.return_value = True
-
- # Mock sqlite connection and cursor for verification query
- mock_cursor = mock_sqlite_connect.return_value.cursor.return_value
- mock_cursor.fetchone.return_value = (100,) # Mock row count result
+@patch("m3.cli.init_duckdb_from_parquet")
+@patch("m3.cli.verify_table_rowcount")
+def test_init_command_duckdb_custom_path(mock_rowcount, mock_init):
+ """Test that m3 init --db-path uses custom database path override and DuckDB flow."""
+ mock_init.return_value = True
+ mock_rowcount.return_value = 100
with tempfile.TemporaryDirectory() as temp_dir:
- custom_db_path = Path(temp_dir) / "custom_mimic.db"
- # Resolve the path to handle symlinks (like /var -> /private/var on macOS)
+ custom_db_path = Path(temp_dir) / "custom_mimic.duckdb"
resolved_custom_db_path = custom_db_path.resolve()
+ # Also ensure a deterministic parquet path exists for the dataset discovery.
+ with patch("m3.cli.get_dataset_parquet_root") as mock_parquet_root:
+ repo_root = Path(__file__).resolve().parents[1]
+ mock_parquet_root.return_value = repo_root / "m3_data/parquet/mimic-iv-demo"
+ with patch.object(Path, "exists", return_value=True):
+ result = runner.invoke(
+ app, ["init", "mimic-iv-demo", "--db-path", str(custom_db_path)]
+ )
- # Run the init command with custom db path
- result = runner.invoke(
- app, ["init", "mimic-iv-demo", "--db-path", str(custom_db_path)]
- )
-
- # Assert command succeeded
assert result.exit_code == 0
-
- # Verify the output mentions the custom path (either original or resolved form)
assert (
str(custom_db_path) in result.stdout
or str(resolved_custom_db_path) in result.stdout
)
- assert "Target database path:" in result.stdout
+ assert "DuckDB path:" in result.stdout
- # Verify initialize_dataset was called with the resolved custom path
- mock_initialize_dataset.assert_called_once_with(
+ # initializer should be called with the resolved path
+ mock_init.assert_called_once_with(
dataset_name="mimic-iv-demo", db_target_path=resolved_custom_db_path
)
-
- # Verify sqlite connection was attempted with the resolved custom path
- mock_sqlite_connect.assert_called_with(resolved_custom_db_path)
-
-
-def test_config_validation_sqlite_with_project_id():
- """Test that sqlite backend rejects project-id parameter."""
- result = runner.invoke(
- app, ["config", "claude", "--backend", "sqlite", "--project-id", "test"]
- )
- assert result.exit_code == 1
- # Check output - error messages from typer usually go to stdout
- assert "project-id can only be used with --backend bigquery" in result.output
+ # verification query should be attempted
+ mock_rowcount.assert_called()
def test_config_validation_bigquery_with_db_path():
@@ -98,19 +83,30 @@ def test_config_validation_bigquery_with_db_path():
result = runner.invoke(
app, ["config", "claude", "--backend", "bigquery", "--db-path", "/test/path"]
)
+ # should fail when db-path is provided with bigquery
assert result.exit_code == 1
- # Check output - error messages from typer usually go to stdout
- assert "db-path can only be used with --backend sqlite" in result.output
+ assert "db-path can only be used with --backend duckdb" in result.output
def test_config_validation_bigquery_requires_project_id():
"""Test that bigquery backend requires project-id parameter."""
result = runner.invoke(app, ["config", "claude", "--backend", "bigquery"])
+ # missing project-id should fail for bigquery backend
assert result.exit_code == 1
- # Check output - error messages from typer usually go to stdout
assert "project-id is required when using --backend bigquery" in result.output
+def test_config_validation_duckdb_with_project_id():
+ """Test that duckdb backend rejects project-id parameter."""
+ result = runner.invoke(
+ app, ["config", "claude", "--backend", "duckdb", "--project-id", "test"]
+ )
+ # should fail when project-id is provided with duckdb
+ assert result.exit_code == 1
+ # Check output - error messages from typer usually go to stdout
+ assert "project-id can only be used with --backend bigquery" in result.output
+
+
@patch("subprocess.run")
def test_config_claude_success(mock_subprocess):
"""Test successful Claude Desktop configuration."""
@@ -120,10 +116,10 @@ def test_config_claude_success(mock_subprocess):
assert result.exit_code == 0
assert "Claude Desktop configuration completed" in result.stdout
- # Verify subprocess was called with correct script
mock_subprocess.assert_called_once()
call_args = mock_subprocess.call_args[0][0]
- assert "setup_claude_desktop.py" in call_args[1] # Script path is second argument
+ # correct script should be invoked
+ assert "setup_claude_desktop.py" in call_args[1]
@patch("subprocess.run")
@@ -135,10 +131,9 @@ def test_config_universal_quick_mode(mock_subprocess):
assert result.exit_code == 0
assert "Generating M3 MCP configuration" in result.stdout
- # Verify subprocess was called with dynamic config script
mock_subprocess.assert_called_once()
call_args = mock_subprocess.call_args[0][0]
- assert "dynamic_mcp_config.py" in call_args[1] # Script path is second argument
+ assert "dynamic_mcp_config.py" in call_args[1]
assert "--quick" in call_args
@@ -148,6 +143,97 @@ def test_config_script_failure(mock_subprocess):
mock_subprocess.side_effect = subprocess.CalledProcessError(1, "cmd")
result = runner.invoke(app, ["config", "claude"])
+ # command should return failure exit code when subprocess fails
assert result.exit_code == 1
# Just verify that the command failed with the right exit code
# The specific error message may vary
+
+
+@patch("subprocess.run")
+@patch("m3.cli.get_default_database_path")
+@patch("m3.cli.get_active_dataset")
+def test_config_claude_infers_db_path_demo(
+ mock_active, mock_get_default, mock_subprocess
+):
+ mock_active.return_value = None # unset -> default to demo
+ mock_get_default.return_value = Path("/tmp/inferred-demo.duckdb")
+ mock_subprocess.return_value = MagicMock(returncode=0)
+
+ result = runner.invoke(app, ["config", "claude"])
+ assert result.exit_code == 0
+
+ # subprocess run should be called with inferred --db-path
+ call_args = mock_subprocess.call_args[0][0]
+ assert "--db-path" in call_args
+ assert "/tmp/inferred-demo.duckdb" in call_args
+
+ # Should have asked for demo duckdb path
+ mock_get_default.assert_called()
+
+
+@patch("subprocess.run")
+@patch("m3.cli.get_default_database_path")
+@patch("m3.cli.get_active_dataset")
+def test_config_claude_infers_db_path_full(
+ mock_active, mock_get_default, mock_subprocess
+):
+ mock_active.return_value = "full"
+ mock_get_default.return_value = Path("/tmp/inferred-full.duckdb")
+ mock_subprocess.return_value = MagicMock(returncode=0)
+
+ result = runner.invoke(app, ["config", "claude"])
+ assert result.exit_code == 0
+
+ call_args = mock_subprocess.call_args[0][0]
+ assert "--db-path" in call_args
+ assert "/tmp/inferred-full.duckdb" in call_args
+
+
+@patch("m3.cli.set_active_dataset")
+@patch("m3.cli.detect_available_local_datasets")
+def test_use_full_happy_path(mock_detect, mock_set_active):
+ mock_detect.return_value = {
+ "demo": {
+ "parquet_present": False,
+ "db_present": False,
+ "parquet_root": "/tmp/demo",
+ "db_path": "/tmp/demo.duckdb",
+ },
+ "full": {
+ "parquet_present": True,
+ "db_present": False,
+ "parquet_root": "/tmp/full",
+ "db_path": "/tmp/full.duckdb",
+ },
+ }
+
+ result = runner.invoke(app, ["use", "full"])
+ assert result.exit_code == 0
+ assert "Active dataset set to 'full'." in result.stdout
+ mock_set_active.assert_called_once_with("full")
+
+
+@patch("m3.cli.compute_parquet_dir_size", return_value=123)
+@patch("m3.cli.get_active_dataset", return_value="full")
+@patch("m3.cli.detect_available_local_datasets")
+def test_status_happy_path(mock_detect, mock_active, mock_size):
+ mock_detect.return_value = {
+ "demo": {
+ "parquet_present": True,
+ "db_present": False,
+ "parquet_root": "/tmp/demo",
+ "db_path": "/tmp/demo.duckdb",
+ },
+ "full": {
+ "parquet_present": True,
+ "db_present": False,
+ "parquet_root": "/tmp/full",
+ "db_path": "/tmp/full.duckdb",
+ },
+ }
+
+ result = runner.invoke(app, ["status"])
+ assert result.exit_code == 0
+ assert "Active dataset: full" in result.stdout
+ size_gb = 123 / (1024**3)
+ assert f"parquet_size_gb: {size_gb:.4f} GB" in result.stdout
diff --git a/tests/test_config.py b/tests/test_config.py
index 6b159f3..c317c04 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -2,7 +2,7 @@
from m3.config import (
get_dataset_config,
- get_dataset_raw_files_path,
+ get_dataset_parquet_root,
get_default_database_path,
)
@@ -10,7 +10,7 @@
def test_get_dataset_config_known():
cfg = get_dataset_config("mimic-iv-demo")
assert isinstance(cfg, dict)
- assert cfg.get("default_db_filename") == "mimic_iv_demo.db"
+ assert cfg.get("default_duckdb_filename") == "mimic_iv_demo.duckdb"
def test_get_dataset_config_unknown():
@@ -21,10 +21,10 @@ def test_default_paths(tmp_path, monkeypatch):
# Redirect default dirs to a temp location
import m3.config as cfg_mod
- monkeypatch.setattr(cfg_mod, "DEFAULT_DATABASES_DIR", tmp_path / "dbs")
- monkeypatch.setattr(cfg_mod, "DEFAULT_RAW_FILES_DIR", tmp_path / "raw")
+ monkeypatch.setattr(cfg_mod, "_DEFAULT_DATABASES_DIR", tmp_path / "dbs")
+ monkeypatch.setattr(cfg_mod, "_DEFAULT_PARQUET_DIR", tmp_path / "parquet")
db_path = get_default_database_path("mimic-iv-demo")
- raw_path = get_dataset_raw_files_path("mimic-iv-demo")
+ raw_path = get_dataset_parquet_root("mimic-iv-demo")
# They should be Path objects and exist
assert isinstance(db_path, Path)
assert db_path.parent.exists()
@@ -35,6 +35,6 @@ def test_default_paths(tmp_path, monkeypatch):
def test_raw_path_includes_dataset_name(tmp_path, monkeypatch):
import m3.config as cfg_mod
- monkeypatch.setattr(cfg_mod, "DEFAULT_RAW_FILES_DIR", tmp_path / "raw")
- raw_path = get_dataset_raw_files_path("mimic-iv-demo")
+ monkeypatch.setattr(cfg_mod, "_DEFAULT_PARQUET_DIR", tmp_path / "parquet")
+ raw_path = get_dataset_parquet_root("mimic-iv-demo")
assert "mimic-iv-demo" in str(raw_path)
diff --git a/tests/test_config_scripts.py b/tests/test_config_scripts.py
index 2430c77..57b8e89 100644
--- a/tests/test_config_scripts.py
+++ b/tests/test_config_scripts.py
@@ -14,8 +14,8 @@
class TestMCPConfigGenerator:
"""Test the MCPConfigGenerator class."""
- def test_generate_config_sqlite_default(self):
- """Test generating SQLite config with defaults."""
+ def test_generate_config_duckdb_default(self):
+ """Test generating DuckDB config with defaults."""
generator = MCPConfigGenerator()
with (
@@ -24,7 +24,7 @@ def test_generate_config_sqlite_default(self):
):
config = generator.generate_config()
- assert config["mcpServers"]["m3"]["env"]["M3_BACKEND"] == "sqlite"
+ assert config["mcpServers"]["m3"]["env"]["M3_BACKEND"] == "duckdb"
assert "M3_PROJECT_ID" not in config["mcpServers"]["m3"]["env"]
assert config["mcpServers"]["m3"]["args"] == ["-m", "m3.mcp_server"]
@@ -47,8 +47,8 @@ def test_generate_config_bigquery_with_project(self):
== "test-project"
)
- def test_generate_config_sqlite_with_db_path(self):
- """Test generating SQLite config with custom database path."""
+ def test_generate_config_duckdb_with_db_path(self):
+ """Test generating DuckDB config with custom database path."""
generator = MCPConfigGenerator()
with (
@@ -56,13 +56,13 @@ def test_generate_config_sqlite_with_db_path(self):
patch.object(generator, "_validate_directory", return_value=True),
):
config = generator.generate_config(
- backend="sqlite", db_path="/custom/path/database.db"
+ backend="duckdb", db_path="/custom/path/database.duckdb"
)
- assert config["mcpServers"]["m3"]["env"]["M3_BACKEND"] == "sqlite"
+ assert config["mcpServers"]["m3"]["env"]["M3_BACKEND"] == "duckdb"
assert (
config["mcpServers"]["m3"]["env"]["M3_DB_PATH"]
- == "/custom/path/database.db"
+ == "/custom/path/database.duckdb"
)
def test_generate_config_custom_server_name(self):
@@ -93,7 +93,7 @@ def test_generate_config_additional_env_vars(self):
env = config["mcpServers"]["m3"]["env"]
assert env["DEBUG"] == "true"
assert env["LOG_LEVEL"] == "info"
- assert env["M3_BACKEND"] == "sqlite" # Default should still be there
+ assert env["M3_BACKEND"] == "duckdb" # Default should still be there
def test_validation_invalid_python_path(self):
"""Test that invalid Python path raises error."""
diff --git a/tests/test_data_io.py b/tests/test_data_io.py
index cc7e44f..6e9352f 100644
--- a/tests/test_data_io.py
+++ b/tests/test_data_io.py
@@ -1,6 +1,40 @@
+import gzip
+from unittest import mock
+
+import duckdb
import requests
-from m3.data_io import COMMON_USER_AGENT, _scrape_urls_from_html_page
+from m3.data_io import (
+ COMMON_USER_AGENT,
+ _scrape_urls_from_html_page,
+ compute_parquet_dir_size,
+ convert_csv_to_parquet,
+ init_duckdb_from_parquet,
+ verify_table_rowcount,
+)
+
+
+def test_compute_parquet_dir_size_empty(tmp_path):
+ size = compute_parquet_dir_size(tmp_path)
+ assert size == 0
+
+
+def test_verify_table_rowcount_with_temp_duckdb(tmp_path):
+ db_path = tmp_path / "test.duckdb"
+ con = duckdb.connect(str(db_path))
+ try:
+ con.execute("CREATE VIEW temp_numbers AS SELECT 1 AS x UNION ALL SELECT 2 AS x")
+ con.commit()
+ finally:
+ con.close()
+
+ count = verify_table_rowcount(db_path, "temp_numbers")
+ assert count == 2
+
+
+# ------------------------------------------------------------
+# Scraping tests
+# ------------------------------------------------------------
class DummyResponse:
@@ -48,3 +82,60 @@ def test_common_user_agent_header():
# Ensure the constant is set and looks like a UA string
assert isinstance(COMMON_USER_AGENT, str)
assert "Mozilla/" in COMMON_USER_AGENT
+
+
+# ------------------------------------------------------------
+# CSV -> Parquet conversion and DuckDB init tests
+# ------------------------------------------------------------
+
+
+def _write_gz_csv(path, text):
+ with gzip.open(path, "wt", encoding="utf-8") as f:
+ f.write(text)
+
+
+def test_convert_csv_to_parquet_and_init_duckdb(tmp_path, monkeypatch):
+ # Prepare a minimal CSV.gz under hosp/
+ src_root = tmp_path / "src"
+ hosp_dir = src_root / "hosp"
+ hosp_dir.mkdir(parents=True, exist_ok=True)
+ csv_gz = hosp_dir / "sample.csv.gz"
+
+ _write_gz_csv(
+ csv_gz,
+ "col1,col2\n" # header
+ "1,foo\n"
+ "2,bar\n",
+ )
+
+ # Convert to Parquet under dst root
+ dst_root = tmp_path / "parquet"
+ ok = convert_csv_to_parquet("mimic-iv-demo", src_root, dst_root)
+ assert ok # conversion succeeded
+
+ out_parquet = dst_root / "hosp" / "sample.parquet"
+ assert out_parquet.exists() # parquet file created
+
+ # Quick verify via DuckDB
+ con = duckdb.connect()
+ try:
+ cnt = con.execute(
+ f"SELECT COUNT(*) FROM read_parquet('{out_parquet.as_posix()}')"
+ ).fetchone()[0]
+ finally:
+ con.close()
+ assert cnt == 2 # two data rows
+
+ # Initialize DuckDB views, patching the parquet root resolver
+ db_path = tmp_path / "test.duckdb"
+ with mock.patch("m3.data_io.get_dataset_parquet_root", return_value=dst_root):
+ init_ok = init_duckdb_from_parquet("mimic-iv-demo", db_path)
+ assert init_ok # views created
+
+ # Query the created view name hosp_sample
+ con = duckdb.connect(str(db_path))
+ try:
+ cnt = con.execute("SELECT COUNT(*) FROM hosp_sample").fetchone()[0]
+ finally:
+ con.close()
+ assert cnt == 2
diff --git a/tests/test_mcp_server.py b/tests/test_mcp_server.py
index 334ad5f..643a158 100644
--- a/tests/test_mcp_server.py
+++ b/tests/test_mcp_server.py
@@ -3,7 +3,6 @@
"""
import os
-import sqlite3
from pathlib import Path
from unittest.mock import Mock, patch
@@ -13,7 +12,8 @@
# Mock the database path check during import to handle CI environments
with patch("pathlib.Path.exists", return_value=True):
with patch(
- "m3.mcp_server.get_default_database_path", return_value=Path("/fake/test.db")
+ "m3.mcp_server.get_default_database_path",
+ return_value=Path("/fake/test.duckdb"),
):
from m3.mcp_server import _init_backend, mcp
@@ -36,31 +36,31 @@ def test_server_instance_exists(self):
assert mcp is not None
assert mcp.name == "m3"
- def test_backend_init_sqlite_default(self):
- """Test SQLite backend initialization with defaults."""
- with patch.dict(os.environ, {"M3_BACKEND": "sqlite"}, clear=True):
+ def test_backend_init_duckdb_default(self):
+ """Test DuckDB backend initialization with defaults."""
+ with patch.dict(os.environ, {"M3_BACKEND": "duckdb"}, clear=True):
with patch("m3.mcp_server.get_default_database_path") as mock_path:
- mock_path.return_value = Path("/fake/path.db")
+ mock_path.return_value = Path("/fake/path.duckdb")
with patch("pathlib.Path.exists", return_value=True):
_init_backend()
# If no exception raised, initialization succeeded
- def test_backend_init_sqlite_custom_path(self):
- """Test SQLite backend initialization with custom path."""
+ def test_backend_init_duckdb_custom_path(self):
+ """Test DuckDB backend initialization with custom path."""
with patch.dict(
os.environ,
- {"M3_BACKEND": "sqlite", "M3_DB_PATH": "/custom/path.db"},
+ {"M3_BACKEND": "duckdb", "M3_DB_PATH": "/custom/path.duckdb"},
clear=True,
):
with patch("pathlib.Path.exists", return_value=True):
_init_backend()
# If no exception raised, initialization succeeded
- def test_backend_init_sqlite_missing_db(self):
- """Test SQLite backend initialization with missing database."""
- with patch.dict(os.environ, {"M3_BACKEND": "sqlite"}, clear=True):
+ def test_backend_init_duckdb_missing_db(self):
+ """Test DuckDB backend initialization with missing database."""
+ with patch.dict(os.environ, {"M3_BACKEND": "duckdb"}, clear=True):
with patch("m3.mcp_server.get_default_database_path") as mock_path:
- mock_path.return_value = Path("/fake/path.db")
+ mock_path.return_value = Path("/fake/path.duckdb")
with patch("pathlib.Path.exists", return_value=False):
with pytest.raises(FileNotFoundError):
_init_backend()
@@ -93,60 +93,62 @@ class TestMCPTools:
@pytest.fixture
def test_db(self, tmp_path):
- """Create a test SQLite database."""
- db_path = tmp_path / "test.db"
-
- # Create test database with MIMIC-IV-like structure
- conn = sqlite3.connect(db_path)
- cursor = conn.cursor()
-
- # Create icu_icustays table
- cursor.execute("""
- CREATE TABLE icu_icustays (
- subject_id INTEGER,
- hadm_id INTEGER,
- stay_id INTEGER,
- intime TEXT,
- outtime TEXT
+ """Create a test DuckDB database."""
+ import duckdb
+
+ db_path = tmp_path / "test.duckdb"
+ con = duckdb.connect(str(db_path))
+ try:
+ con.execute(
+ """
+ CREATE TABLE icu_icustays (
+ subject_id INTEGER,
+ hadm_id INTEGER,
+ stay_id INTEGER,
+ intime TIMESTAMP,
+ outtime TIMESTAMP
+ )
+ """
)
- """)
- cursor.execute("""
- INSERT INTO icu_icustays (subject_id, hadm_id, stay_id, intime, outtime)
- VALUES
- (10000032, 20000001, 30000001, '2180-07-23 15:00:00', '2180-07-24 12:00:00'),
- (10000033, 20000002, 30000002, '2180-08-15 10:30:00', '2180-08-16 14:15:00')
- """)
-
- # Create hosp_labevents table
- cursor.execute("""
- CREATE TABLE hosp_labevents (
- subject_id INTEGER,
- hadm_id INTEGER,
- itemid INTEGER,
- charttime TEXT,
- value TEXT
+ con.execute(
+ """
+ INSERT INTO icu_icustays (subject_id, hadm_id, stay_id, intime, outtime) VALUES
+ (10000032, 20000001, 30000001, '2180-07-23 15:00:00', '2180-07-24 12:00:00'),
+ (10000033, 20000002, 30000002, '2180-08-15 10:30:00', '2180-08-16 14:15:00')
+ """
)
- """)
- cursor.execute("""
- INSERT INTO hosp_labevents (subject_id, hadm_id, itemid, charttime, value)
- VALUES
- (10000032, 20000001, 50912, '2180-07-23 16:00:00', '120'),
- (10000033, 20000002, 50912, '2180-08-15 11:00:00', '95')
- """)
-
- conn.commit()
- conn.close()
+ con.execute(
+ """
+ CREATE TABLE hosp_labevents (
+ subject_id INTEGER,
+ hadm_id INTEGER,
+ itemid INTEGER,
+ charttime TIMESTAMP,
+ value TEXT
+ )
+ """
+ )
+ con.execute(
+ """
+ INSERT INTO hosp_labevents (subject_id, hadm_id, itemid, charttime, value) VALUES
+ (10000032, 20000001, 50912, '2180-07-23 16:00:00', '120'),
+ (10000033, 20000002, 50912, '2180-08-15 11:00:00', '95')
+ """
+ )
+ con.commit()
+ finally:
+ con.close()
return str(db_path)
@pytest.mark.asyncio
async def test_tools_via_client(self, test_db):
"""Test MCP tools through the FastMCP client."""
- # Set up environment for SQLite backend with OAuth2 disabled
+ # Set up environment for DuckDB backend with OAuth2 disabled
with patch.dict(
os.environ,
{
- "M3_BACKEND": "sqlite",
+ "M3_BACKEND": "duckdb",
"M3_DB_PATH": test_db,
"M3_OAUTH2_ENABLED": "false",
},
@@ -191,7 +193,7 @@ async def test_security_checks(self, test_db):
with patch.dict(
os.environ,
{
- "M3_BACKEND": "sqlite",
+ "M3_BACKEND": "duckdb",
"M3_DB_PATH": test_db,
"M3_OAUTH2_ENABLED": "false",
},
@@ -226,7 +228,7 @@ async def test_invalid_sql(self, test_db):
with patch.dict(
os.environ,
{
- "M3_BACKEND": "sqlite",
+ "M3_BACKEND": "duckdb",
"M3_DB_PATH": test_db,
"M3_OAUTH2_ENABLED": "false",
},
@@ -247,7 +249,7 @@ async def test_empty_results(self, test_db):
with patch.dict(
os.environ,
{
- "M3_BACKEND": "sqlite",
+ "M3_BACKEND": "duckdb",
"M3_DB_PATH": test_db,
"M3_OAUTH2_ENABLED": "false",
},
@@ -268,11 +270,11 @@ async def test_empty_results(self, test_db):
@pytest.mark.asyncio
async def test_oauth2_authentication_required(self, test_db):
"""Test that OAuth2 authentication is required when enabled."""
- # Set up environment for SQLite backend with OAuth2 enabled
+ # Set up environment for DuckDB backend with OAuth2 enabled
with patch.dict(
os.environ,
{
- "M3_BACKEND": "sqlite",
+ "M3_BACKEND": "duckdb",
"M3_DB_PATH": test_db,
"M3_OAUTH2_ENABLED": "true",
"M3_OAUTH2_ISSUER_URL": "https://auth.example.com",
diff --git a/uv.lock b/uv.lock
index e2af58c..60bc079 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
version = 1
-revision = 2
+revision = 3
requires-python = ">=3.10"
resolution-markers = [
"python_full_version >= '3.13'",
@@ -8,6 +8,148 @@ resolution-markers = [
"python_full_version < '3.11'",
]
+[[package]]
+name = "aiohappyeyeballs"
+version = "2.6.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558", size = 22760, upload-time = "2025-03-12T01:42:48.764Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/0f/15/5bf3b99495fb160b63f95972b81750f18f7f4e02ad051373b669d17d44f2/aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8", size = 15265, upload-time = "2025-03-12T01:42:47.083Z" },
+]
+
+[[package]]
+name = "aiohttp"
+version = "3.13.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "aiohappyeyeballs" },
+ { name = "aiosignal" },
+ { name = "async-timeout", marker = "python_full_version < '3.11'" },
+ { name = "attrs" },
+ { name = "frozenlist" },
+ { name = "multidict" },
+ { name = "propcache" },
+ { name = "yarl" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/1c/ce/3b83ebba6b3207a7135e5fcaba49706f8a4b6008153b4e30540c982fae26/aiohttp-3.13.2.tar.gz", hash = "sha256:40176a52c186aefef6eb3cad2cdd30cd06e3afbe88fe8ab2af9c0b90f228daca", size = 7837994, upload-time = "2025-10-28T20:59:39.937Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/6d/34/939730e66b716b76046dedfe0842995842fa906ccc4964bba414ff69e429/aiohttp-3.13.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2372b15a5f62ed37789a6b383ff7344fc5b9f243999b0cd9b629d8bc5f5b4155", size = 736471, upload-time = "2025-10-28T20:55:27.924Z" },
+ { url = "https://files.pythonhosted.org/packages/fd/cf/dcbdf2df7f6ca72b0bb4c0b4509701f2d8942cf54e29ca197389c214c07f/aiohttp-3.13.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e7f8659a48995edee7229522984bd1009c1213929c769c2daa80b40fe49a180c", size = 493985, upload-time = "2025-10-28T20:55:29.456Z" },
+ { url = "https://files.pythonhosted.org/packages/9d/87/71c8867e0a1d0882dcbc94af767784c3cb381c1c4db0943ab4aae4fed65e/aiohttp-3.13.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:939ced4a7add92296b0ad38892ce62b98c619288a081170695c6babe4f50e636", size = 489274, upload-time = "2025-10-28T20:55:31.134Z" },
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