tools-only M4 Python API
The M4 Python API provides programmatic access to clinical datasets for code execution environments. It mirrors the MCP tools but returns native Python types (DataFrames, dicts) instead of formatted strings.
When to Use the API vs MCP Tools
Use the Python API when:
- Complex clinical analysis - Multi-step analyses that require intermediate results, joins across queries, or statistical computations
- Large result sets - Query results with thousands of rows can be stored in DataFrames without dumping into context
- Mathematical operations - Aggregations, percentile calculations, statistical tests, and counting that benefit from pandas/numpy
- Iterative exploration - Building up analysis through multiple queries where each step informs the next
Use MCP tools when:
- Simple one-off queries where the result fits comfortably in context
- Interactive exploration where you want to see results immediately
Required Workflow
You must follow this sequence:
set_dataset()- Select which dataset to query (REQUIRED FIRST)get_schema()/get_table_info()- Explore available tablesexecute_query()- Run SQL queries
from m4 import set_dataset, get_schema, get_table_info, execute_query
# Step 1: Always set dataset first
set_dataset("mimic-iv") # or "mimic-iv-demo", "eicu", "mimic-iv-note"
# Step 2: Explore schema
schema = get_schema()
print(schema['tables']) # List of table names
# Step 3: Inspect specific tables before querying
info = get_table_info("mimiciv_hosp.patients")
print(info['schema']) # DataFrame with column names, types
print(info['sample']) # DataFrame with sample rows
# Step 4: Execute queries
df = execute_query("SELECT gender, COUNT(*) as n FROM mimiciv_hosp.patients GROUP BY gender")
# Returns pd.DataFrame - use pandas operations freely
API Reference
Dataset Management
| Function | Returns | Description |
|---|---|---|
list_datasets() |
list[str] |
Available dataset names |
set_dataset(name) |
str |
Set active dataset (confirmation message) |
get_active_dataset() |
str |
Get current dataset name |
Tabular Data (requires TABULAR modality)
| Function | Returns | Description |
|---|---|---|
get_schema() |
dict |
{'backend_info': str, 'tables': list[str]} |
get_table_info(table, show_sample=True) |
dict |
{'schema': DataFrame, 'sample': DataFrame} |
execute_query(sql) |
DataFrame |
Query results as pandas DataFrame |
Clinical Notes (requires NOTES modality)
| Function | Returns | Description |
|---|---|---|
search_notes(query, note_type, limit, snippet_length) |
dict |
{'results': dict[str, DataFrame]} |
get_note(note_id, max_length) |
dict |
{'text': str, 'subject_id': int, ...} |
list_patient_notes(subject_id, note_type, limit) |
dict |
{'notes': dict[str, DataFrame]} |
Error Handling
M4 uses a hierarchy of exceptions. Catch specific types to handle errors appropriately:
M4Error (base)
├── DatasetError # Dataset doesn't exist or not configured
├── QueryError # SQL syntax error, table not found, query failed
└── ModalityError # Tool incompatible with dataset (e.g., notes on tabular-only)
Recovery patterns:
from m4 import execute_query, set_dataset, DatasetError, QueryError, ModalityError
try:
df = execute_query("SELECT * FROM mimiciv_hosp.patients")
except DatasetError as e:
# No dataset selected, or dataset not found
# Recovery: call set_dataset() first, or check list_datasets()
set_dataset("mimic-iv")
df = execute_query("SELECT * FROM mimiciv_hosp.patients")
except QueryError as e:
# SQL error or table not found
# Recovery: check table name with get_schema(), fix SQL syntax
print(f"Query failed: {e}")
except ModalityError as e:
# Tried notes function on tabular-only dataset
# Recovery: switch to dataset with NOTES modality
set_dataset("mimic-iv-note")
Displaying Results
Use show() from the vitrine module to present query results to the researcher in the browser:
from m4 import execute_query
from vitrine import show
df = execute_query("SELECT gender, COUNT(*) as n FROM mimiciv_hosp.patients GROUP BY gender")
df.to_csv("output/demographics.csv", index=False) # Save for reproducibility
show(df, title="Demographics", study="my-study") # Show for review
For blocking review (agent waits for researcher approval), use show(df, wait=True, prompt="Proceed?"). For the full display API, invoke the /vitrine-api skill.
Dataset State
Important: Dataset selection is module-level state that persists across function calls.
set_dataset("mimic-iv")
df1 = execute_query("SELECT COUNT(*) FROM mimiciv_hosp.patients") # Uses mimic-iv
set_dataset("eicu")
df2 = execute_query("SELECT COUNT(*) FROM patient") # Uses eicu
MCP Tool Equivalence
The Python API mirrors MCP tools but with better return types:
| MCP Tool | Python Function | MCP Returns | Python Returns |
|---|---|---|---|
execute_query |
execute_query() |
Formatted string | pd.DataFrame |
get_database_schema |
get_schema() |
Formatted string | dict with tables list |
get_table_info |
get_table_info() |
Formatted string | dict with schema/sample DataFrames |
Use the Python API when you need to:
- Chain queries in analysis pipelines
- Perform pandas operations on results
- Avoid parsing formatted output
NOTE: All queries use canonical schema.table names (e.g., mimiciv_hosp.patients, mimiciv_icu.icustays). These names work on both the local DuckDB backend and the BigQuery backend — no need to adjust table names per backend.