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DQA (Validation) API Reference

CLIFpy's Data Quality Assessment (DQA) module provides comprehensive validation organized around three pillars: Conformance, Completeness, and Plausibility. All checks support dual backends (Polars and DuckDB) and return structured result objects.

For a user-guide introduction, see Data Quality Assessment (DQA).

Result Classes

clifpy.utils.validator.DQAConformanceResult 

DQAConformanceResult(check_type, table_name)

Container for DQA conformance check results.

Source code in clifpy/utils/validator.py 
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def __init__(self, check_type: str, table_name: str):
    self.check_type = check_type
    self.table_name = table_name
    self.passed = True
    self.errors: List[Dict[str, Any]] = []
    self.warnings: List[Dict[str, Any]] = []
    self.info: List[Dict[str, Any]] = []
    self.metrics: Dict[str, Any] = {}

clifpy.utils.validator.DQACompletenessResult 

DQACompletenessResult(check_type, table_name)

Container for DQA completeness check results.

Source code in clifpy/utils/validator.py 
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def __init__(self, check_type: str, table_name: str):
    self.check_type = check_type
    self.table_name = table_name
    self.passed = True
    self.errors: List[Dict[str, Any]] = []
    self.warnings: List[Dict[str, Any]] = []
    self.info: List[Dict[str, Any]] = []
    self.metrics: Dict[str, Any] = {}

clifpy.utils.validator.DQAPlausibilityResult 

DQAPlausibilityResult(check_type, table_name)

Container for DQA plausibility check results.

Source code in clifpy/utils/validator.py 
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def __init__(self, check_type: str, table_name: str):
    self.check_type = check_type
    self.table_name = table_name
    self.passed = True
    self.errors: List[Dict[str, Any]] = []
    self.warnings: List[Dict[str, Any]] = []
    self.info: List[Dict[str, Any]] = []
    self.metrics: Dict[str, Any] = {}

Conformance Checks

Conformance checks verify that data matches expected structure, schema, types, and allowed values.

A.1 — Table Presence

clifpy.utils.validator.check_table_exists 

check_table_exists(table_path, table_name, filetype='parquet')

Check if a table file exists at the specified path.

Parameters:

Name Type Description Default
table_path str or Path

Directory containing the table files

 required
table_name str

Name of the table to check

 required
filetype str

File extension (parquet, csv, etc.)

 'parquet'

Returns:

Type Description
DQAConformanceResult

Result object with check status
Source code in clifpy/utils/validator.py 
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def check_table_exists(
    table_path: Union[str, Path],
    table_name: str,
    filetype: str = 'parquet'
) -> DQAConformanceResult:
    """
    Check if a table file exists at the specified path.

    Parameters
    ----------
    table_path : str or Path
        Directory containing the table files
    table_name : str
        Name of the table to check
    filetype : str
        File extension (parquet, csv, etc.)

    Returns
    -------
    DQAConformanceResult
        Result object with check status
    """
    result = DQAConformanceResult("table_exists", table_name)

    table_path = Path(table_path)
    expected_file = table_path / f"{table_name}.{filetype}"

    if expected_file.exists():
        result.add_info(f"Table file found: {expected_file}")
        result.metrics["file_path"] = str(expected_file)
        result.metrics["file_size_mb"] = expected_file.stat().st_size / (1024 * 1024)
    else:
        result.add_error(
            f"Table file not found: {expected_file}",
            {"expected_path": str(expected_file)}
        )

    return result

clifpy.utils.validator.check_table_presence 

check_table_presence(df, table_name)

Check that a loaded DataFrame has rows and columns.

Parameters:

Name Type Description Default
df pd.DataFrame, pl.DataFrame, or pl.LazyFrame

Data to validate (already loaded)

 required
table_name str

Name of the table

 required
Source code in clifpy/utils/validator.py 
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def check_table_presence(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str
) -> DQAConformanceResult:
    """
    Check that a loaded DataFrame has rows and columns.

    Parameters
    ----------
    df : pd.DataFrame, pl.DataFrame, or pl.LazyFrame
        Data to validate (already loaded)
    table_name : str
        Name of the table
    """
    _logger.debug("check_table_presence: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_table_presence_polars(df, table_name)
    else:
        result = check_table_presence_duckdb(df, table_name)
    _logger.debug("check_table_presence: table '%s' — rows=%s, cols=%s",
                  table_name, result.metrics.get("row_count"), result.metrics.get("column_count"))
    return result

A.2 — Required Columns

clifpy.utils.validator.check_required_columns 

check_required_columns(df, schema, table_name)

Check if all required columns are present.

Parameters:

Name Type Description Default
df pd.DataFrame, pl.DataFrame, or pl.LazyFrame

Data to validate (already loaded)

 required
schema dict

Table schema containing required_columns

 required
table_name str

Name of the table

 required
Source code in clifpy/utils/validator.py 
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def check_required_columns(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> DQAConformanceResult:
    """
    Check if all required columns are present.

    Parameters
    ----------
    df : pd.DataFrame, pl.DataFrame, or pl.LazyFrame
        Data to validate (already loaded)
    schema : dict
        Table schema containing required_columns
    table_name : str
        Name of the table
    """
    _logger.debug("check_required_columns: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_required_columns_polars(df, schema, table_name)
    else:
        result = check_required_columns_duckdb(df, schema, table_name)
    if result.metrics.get("total_missing", 0) > 0:
        _logger.info("check_required_columns: table '%s' missing %d of %d required columns",
                     table_name, result.metrics["total_missing"], result.metrics.get("total_required", 0))
    _logger.debug("check_required_columns: table '%s' — required=%s, present=%s, missing=%s",
                  table_name, result.metrics.get("total_required"),
                  result.metrics.get("total_present"), result.metrics.get("total_missing"))
    return result

B.1 — Data Types

clifpy.utils.validator.check_column_dtypes 

check_column_dtypes(df, schema, table_name)

Check if columns have correct data types.

Parameters:

Name Type Description Default
df pd.DataFrame, pl.DataFrame, or pl.LazyFrame

Data to validate (already loaded)

 required
schema dict

Table schema

 required
table_name str

Name of the table

 required
Source code in clifpy/utils/validator.py 
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def check_column_dtypes(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> DQAConformanceResult:
    """
    Check if columns have correct data types.

    Parameters
    ----------
    df : pd.DataFrame, pl.DataFrame, or pl.LazyFrame
        Data to validate (already loaded)
    schema : dict
        Table schema
    table_name : str
        Name of the table
    """
    _logger.debug("check_column_dtypes: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_column_dtypes_polars(df, schema, table_name)
    else:
        result = check_column_dtypes_duckdb(df, schema, table_name)
    _logger.debug("check_column_dtypes: table '%s' — checked=%s, errors=%s, warnings=%s",
                  table_name, result.metrics.get("columns_checked"),
                  result.metrics.get("dtype_errors"), result.metrics.get("dtype_warnings"))
    return result

B.2 — Datetime Format

clifpy.utils.validator.check_datetime_format 

check_datetime_format(df, schema, table_name, expected_tz='UTC')

Validate datetime columns are in correct format.

Source code in clifpy/utils/validator.py 
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def check_datetime_format(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str,
    expected_tz: str = 'UTC'
) -> DQAConformanceResult:
    """Validate datetime columns are in correct format."""
    _logger.debug("check_datetime_format: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_datetime_format_polars(df, schema, table_name, expected_tz)
    else:
        result = check_datetime_format_duckdb(df, schema, table_name, expected_tz)
    _logger.debug("check_datetime_format: table '%s' — columns_checked=%s",
                  table_name, result.metrics.get("datetime_columns_checked"))
    return result

B.3 — Lab Reference Units

clifpy.utils.validator.check_lab_reference_units 

check_lab_reference_units(df, schema, table_name='labs')

Check if lab reference units match schema definitions.

Source code in clifpy/utils/validator.py 
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def check_lab_reference_units(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str = 'labs'
) -> DQAConformanceResult:
    """Check if lab reference units match schema definitions."""
    _logger.debug("check_lab_reference_units: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_lab_reference_units_polars(df, schema, table_name)
    else:
        result = check_lab_reference_units_duckdb(df, schema, table_name)
    _logger.debug("check_lab_reference_units: table '%s' — valid=%s, invalid_categories=%s",
                  table_name, result.metrics.get("valid_units"),
                  result.metrics.get("invalid_unit_categories"))
    return result

B.4 — Categorical Values

clifpy.utils.validator.check_categorical_values 

check_categorical_values(df, schema, table_name)

Check if categorical values match mCIDE permissible values.

Source code in clifpy/utils/validator.py 
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def check_categorical_values(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> DQAConformanceResult:
    """Check if categorical values match mCIDE permissible values."""
    _logger.debug("check_categorical_values: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_categorical_values_polars(df, schema, table_name)
    else:
        result = check_categorical_values_duckdb(df, schema, table_name)
    _logger.debug("check_categorical_values: table '%s' — columns_checked=%s, columns_with_invalid=%s",
                  table_name, result.metrics.get("category_columns_checked"),
                  result.metrics.get("columns_with_invalid_values"))
    return result

B.5 — Category-to-Group Mapping

clifpy.utils.validator.check_category_group_mapping 

check_category_group_mapping(df, schema, table_name)

Check if category-to-group mappings match schema definitions.

Source code in clifpy/utils/validator.py 
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def check_category_group_mapping(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> DQAConformanceResult:
    """Check if category-to-group mappings match schema definitions."""
    _logger.debug("check_category_group_mapping: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_category_group_mapping_polars(df, schema, table_name)
    else:
        result = check_category_group_mapping_duckdb(df, schema, table_name)
    _logger.debug("check_category_group_mapping: table '%s' — completed", table_name)
    return result

Completeness Checks

Completeness checks evaluate missing data, conditional requirements, and referential coverage.

A.1 — Missingness

clifpy.utils.validator.check_missingness 

check_missingness(df, schema, table_name, error_threshold=50.0, warning_threshold=10.0)

Check missingness in required columns.

Parameters:

Name Type Description Default
df pd.DataFrame, pl.DataFrame, or pl.LazyFrame

Data to validate (already loaded)

 required
schema dict

Table schema containing required_columns

 required
table_name str

Name of the table

 required
error_threshold float

Percent missing above which an error is raised

 50.0
warning_threshold float

Percent missing above which a warning is raised

 10.0

Returns:

Type Description
DQACompletenessResult

Result containing missingness statistics
Source code in clifpy/utils/validator.py 
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def check_missingness(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str,
    error_threshold: float = 50.0,
    warning_threshold: float = 10.0
) -> DQACompletenessResult:
    """
    Check missingness in required columns.

    Parameters
    ----------
    df : pd.DataFrame, pl.DataFrame, or pl.LazyFrame
        Data to validate (already loaded)
    schema : dict
        Table schema containing required_columns
    table_name : str
        Name of the table
    error_threshold : float
        Percent missing above which an error is raised
    warning_threshold : float
        Percent missing above which a warning is raised

    Returns
    -------
    DQACompletenessResult
        Result containing missingness statistics
    """
    _logger.debug("check_missingness: starting for table '%s' (error_threshold=%.1f%%, warning_threshold=%.1f%%)",
                  table_name, error_threshold, warning_threshold)
    if _ACTIVE_BACKEND == 'polars':
        result = check_missingness_polars(df, schema, table_name, error_threshold, warning_threshold)
    else:
        result = check_missingness_duckdb(df, schema, table_name, error_threshold, warning_threshold)
    if result.errors:
        for err in result.errors:
            _logger.info("check_missingness: table '%s' — %s", table_name, err["message"])
    _logger.debug("check_missingness: table '%s' — columns_checked=%s",
                  table_name, result.metrics.get("required_columns_checked"))
    return result

A.2 — Conditional Requirements

clifpy.utils.validator.check_conditional_requirements 

check_conditional_requirements(df, table_name, conditions=None)

Check conditional required fields.

Source code in clifpy/utils/validator.py 
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def check_conditional_requirements(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    conditions: Optional[List[Dict[str, Any]]] = None
) -> DQACompletenessResult:
    """Check conditional required fields."""
    n_conditions = len(conditions) if conditions else 0
    _logger.debug("check_conditional_requirements: starting for table '%s' (%d explicit conditions)",
                  table_name, n_conditions)
    if _ACTIVE_BACKEND == 'polars':
        result = check_conditional_requirements_polars(df, table_name, conditions)
    else:
        result = check_conditional_requirements_duckdb(df, table_name, conditions)
    if result.warnings:
        _logger.info("check_conditional_requirements: table '%s' — %d violations found",
                     table_name, len(result.warnings))
    _logger.debug("check_conditional_requirements: table '%s' complete", table_name)
    return result

B — mCIDE Value Coverage

clifpy.utils.validator.check_mcide_value_coverage 

check_mcide_value_coverage(df, schema, table_name)

Check if all mCIDE standardized values are present in the data.

Source code in clifpy/utils/validator.py 
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def check_mcide_value_coverage(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> DQACompletenessResult:
    """Check if all mCIDE standardized values are present in the data."""
    _logger.debug("check_mcide_value_coverage: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_mcide_value_coverage_polars(df, schema, table_name)
    else:
        result = check_mcide_value_coverage_duckdb(df, schema, table_name)
    _logger.debug("check_mcide_value_coverage: table '%s' — columns_checked=%s",
                  table_name, result.metrics.get("category_columns_checked"))
    return result

C.1 — Relational Integrity

clifpy.utils.validator.check_relational_integrity 

check_relational_integrity(target_df, reference_df, target_table, reference_table, key_column)

Check bidirectional relational integrity between tables.

Runs the backend-specific check in both directions: - Forward (reference → target): What percentage of reference IDs appear in the target table? (e.g., "what % of hospitalizations have labs?") - Reverse (target → reference): What percentage of target IDs exist in the reference table? (e.g., "what % of lab hosp_ids are valid?")

Parameters:

Name Type Description Default
target_df DataFrame

The target table (e.g., labs).

 required
reference_df DataFrame

The reference table (e.g., hospitalization).

 required
target_table str

Name of the target table.

 required
reference_table str

Name of the reference table.

 required
key_column str

The shared key column (e.g., hospitalization_id).

 required

Returns:

Type Description
DQACompletenessResult

Consolidated result with forward/reverse coverage metrics.
Source code in clifpy/utils/validator.py 
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def check_relational_integrity(
    target_df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    reference_df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    target_table: str,
    reference_table: str,
    key_column: str
) -> DQACompletenessResult:
    """Check bidirectional relational integrity between tables.

    Runs the backend-specific check in both directions:
    - **Forward** (reference → target): What percentage of reference IDs
      appear in the target table?  (e.g., "what % of hospitalizations
      have labs?")
    - **Reverse** (target → reference): What percentage of target IDs
      exist in the reference table?  (e.g., "what % of lab hosp_ids are
      valid?")

    Parameters
    ----------
    target_df : DataFrame
        The target table (e.g., labs).
    reference_df : DataFrame
        The reference table (e.g., hospitalization).
    target_table : str
        Name of the target table.
    reference_table : str
        Name of the reference table.
    key_column : str
        The shared key column (e.g., ``hospitalization_id``).

    Returns
    -------
    DQACompletenessResult
        Consolidated result with forward/reverse coverage metrics.
    """
    _logger.debug(
        "check_relational_integrity: '%s' <-> '%s' on key '%s'",
        target_table, reference_table, key_column,
    )
    result = DQACompletenessResult(
        "relational_integrity",
        f"{target_table}<->{reference_table}",
    )

    # Pick the right backend dispatcher
    _backend_fn = (check_relational_integrity_polars
                   if _ACTIVE_BACKEND == 'polars'
                   else check_relational_integrity_duckdb)

    try:
        # Forward: reference → target  (source=reference, ref=target)
        fwd = _backend_fn(
            reference_df, target_df, reference_table, target_table, key_column
        )
        # Reverse: target → reference  (source=target, ref=reference)
        rev = _backend_fn(
            target_df, reference_df, target_table, reference_table, key_column
        )

        result.metrics["forward_coverage_percent"] = fwd.metrics.get("coverage_percent", 0)
        result.metrics["forward_orphan_ids"] = fwd.metrics.get("orphan_ids", 0)
        result.metrics["forward_reference_unique_ids"] = fwd.metrics.get("source_unique_ids", 0)
        result.metrics["reverse_coverage_percent"] = rev.metrics.get("coverage_percent", 0)
        result.metrics["reverse_orphan_ids"] = rev.metrics.get("orphan_ids", 0)
        result.metrics["reverse_target_unique_ids"] = rev.metrics.get("source_unique_ids", 0)

        # Propagate warnings/errors from both directions
        for w in fwd.warnings:
            result.add_warning(w['message'], w.get("details", {}))
        for w in rev.warnings:
            result.add_warning(w['message'], w.get("details", {}))
        for e in fwd.errors:
            result.add_error(e['message'], e.get("details", {}))
        for e in rev.errors:
            result.add_error(e['message'], e.get("details", {}))

        # Info when both directions are clean (no errors AND no warnings)
        if fwd.passed and rev.passed and not fwd.warnings and not rev.warnings:
            result.add_info(
                f"Full bidirectional coverage for {key_column} between "
                f"{target_table} and {reference_table}"
            )

        _logger.info(
            "check_relational_integrity: '%s' <-> '%s' — "
            "fwd_coverage=%.1f%%, rev_coverage=%.1f%%",
            target_table, reference_table,
            result.metrics["forward_coverage_percent"],
            result.metrics["reverse_coverage_percent"],
        )

    except Exception as e:
        _logger.error(
            "Check 'relational_integrity' failed for '%s' <-> '%s': %s",
            target_table, reference_table, e,
        )
        result.add_error(f"Error checking relational integrity: {str(e)}")

    return result

Plausibility Checks

Plausibility checks validate logical consistency, temporal ordering, and clinical reasonableness.

A.1 — Temporal Ordering

clifpy.utils.validator.check_temporal_ordering 

check_temporal_ordering(df, table_name, temporal_rules=None, warning_threshold=0.0, error_threshold=10.0)

Check that datetime pairs follow expected temporal ordering.

Source code in clifpy/utils/validator.py 
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def check_temporal_ordering(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    temporal_rules: Optional[List[Dict[str, str]]] = None,
    warning_threshold: float = 0.0,
    error_threshold: float = 10.0,
) -> DQAPlausibilityResult:
    """Check that datetime pairs follow expected temporal ordering."""
    _logger.debug("check_temporal_ordering: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_temporal_ordering_polars(df, table_name, temporal_rules,
                                                warning_threshold=warning_threshold,
                                                error_threshold=error_threshold)
    else:
        result = check_temporal_ordering_duckdb(df, table_name, temporal_rules,
                                                warning_threshold=warning_threshold,
                                                error_threshold=error_threshold)
    _logger.debug("check_temporal_ordering: table '%s' — pairs_checked=%s",
                  table_name, result.metrics.get("pairs_checked"))
    return result

A.2 — Numeric Range Plausibility

clifpy.utils.validator.check_numeric_range_plausibility 

check_numeric_range_plausibility(df, table_name, outlier_config=None, warning_threshold=0.0, error_threshold=10.0)

Check numeric values are within plausible ranges.

Source code in clifpy/utils/validator.py 
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def check_numeric_range_plausibility(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    outlier_config: Optional[Dict[str, Any]] = None,
    warning_threshold: float = 0.0,
    error_threshold: float = 10.0,
) -> DQAPlausibilityResult:
    """Check numeric values are within plausible ranges."""
    _logger.debug("check_numeric_range_plausibility: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_numeric_range_plausibility_polars(df, table_name, outlier_config,
                                                         warning_threshold=warning_threshold,
                                                         error_threshold=error_threshold)
    else:
        result = check_numeric_range_plausibility_duckdb(df, table_name, outlier_config,
                                                         warning_threshold=warning_threshold,
                                                         error_threshold=error_threshold)
    _logger.debug("check_numeric_range_plausibility: table '%s' — columns_checked=%s",
                  table_name, result.metrics.get("columns_checked"))
    return result

A.3 — Field-Level Plausibility

clifpy.utils.validator.check_field_plausibility 

check_field_plausibility(df, table_name, rules=None)

Check field-level plausibility constraints.

Source code in clifpy/utils/validator.py 
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def check_field_plausibility(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    rules: Optional[List[Dict[str, Any]]] = None,
) -> DQAPlausibilityResult:
    """Check field-level plausibility constraints."""
    _logger.debug("check_field_plausibility: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_field_plausibility_polars(df, table_name, rules)
    else:
        result = check_field_plausibility_duckdb(df, table_name, rules)
    _logger.debug("check_field_plausibility: table '%s' — rules_checked=%s",
                  table_name, result.metrics.get("rules_checked"))
    return result

A.4 — Medication Dose Unit Consistency

clifpy.utils.validator.check_medication_dose_unit_consistency 

check_medication_dose_unit_consistency(df, table_name, warning_threshold=0.0, error_threshold=10.0)

Check medication dose unit consistency.

Source code in clifpy/utils/validator.py 
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def check_medication_dose_unit_consistency(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    warning_threshold: float = 0.0,
    error_threshold: float = 10.0,
) -> DQAPlausibilityResult:
    """Check medication dose unit consistency."""
    _logger.debug("check_medication_dose_unit_consistency: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_medication_dose_unit_consistency_polars(df, table_name,
                                                               warning_threshold=warning_threshold,
                                                               error_threshold=error_threshold)
    else:
        result = check_medication_dose_unit_consistency_duckdb(df, table_name,
                                                               warning_threshold=warning_threshold,
                                                               error_threshold=error_threshold)
    _logger.debug("check_medication_dose_unit_consistency: table '%s' — violations=%s",
                  table_name, result.metrics.get("unit_pattern_violations"))
    return result

B.1 — Cross-Table Temporal Plausibility

clifpy.utils.validator.check_cross_table_temporal_plausibility 

check_cross_table_temporal_plausibility(target_df, hospitalization_df, target_table, time_columns, warning_threshold=0.0, error_threshold=10.0)

Check that datetime values fall within hospitalization bounds.

Source code in clifpy/utils/validator.py 
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def check_cross_table_temporal_plausibility(
    target_df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    hospitalization_df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    target_table: str,
    time_columns: List[str],
    warning_threshold: float = 0.0,
    error_threshold: float = 10.0,
) -> DQAPlausibilityResult:
    """Check that datetime values fall within hospitalization bounds."""
    _logger.debug("check_cross_table_temporal_plausibility: starting for table '%s'", target_table)
    if _ACTIVE_BACKEND == 'polars':
        result = check_cross_table_temporal_plausibility_polars(
            target_df, hospitalization_df, target_table, time_columns,
            warning_threshold=warning_threshold, error_threshold=error_threshold)
    else:
        result = check_cross_table_temporal_plausibility_duckdb(
            target_df, hospitalization_df, target_table, time_columns,
            warning_threshold=warning_threshold, error_threshold=error_threshold)
    _logger.debug("check_cross_table_temporal_plausibility: table '%s' complete", target_table)
    return result

C.1 — Overlapping Periods

clifpy.utils.validator.check_overlapping_periods 

check_overlapping_periods(df, table_name, entity_col='hospitalization_id', start_col='in_dttm', end_col='out_dttm')

Check for overlapping time periods within entities.

Source code in clifpy/utils/validator.py 
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def check_overlapping_periods(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    entity_col: str = 'hospitalization_id',
    start_col: str = 'in_dttm',
    end_col: str = 'out_dttm',
) -> DQAPlausibilityResult:
    """Check for overlapping time periods within entities."""
    _logger.debug("check_overlapping_periods: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_overlapping_periods_polars(df, table_name, entity_col, start_col, end_col)
    else:
        result = check_overlapping_periods_duckdb(df, table_name, entity_col, start_col, end_col)
    _logger.debug("check_overlapping_periods: table '%s' — overlaps=%s",
                  table_name, result.metrics.get("overlapping_records"))
    return result

C.2 — Category Temporal Consistency

clifpy.utils.validator.check_category_temporal_consistency 

check_category_temporal_consistency(df, schema, table_name, time_column=None, hosp_years=None)

Check category distribution consistency over time.

Source code in clifpy/utils/validator.py 
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def check_category_temporal_consistency(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str,
    time_column: Optional[str] = None,
    hosp_years: Optional[set] = None,
) -> DQAPlausibilityResult:
    """Check category distribution consistency over time."""
    _logger.debug("check_category_temporal_consistency: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_category_temporal_consistency_polars(df, schema, table_name, time_column, hosp_years)
    else:
        result = check_category_temporal_consistency_duckdb(df, schema, table_name, time_column, hosp_years)
    _logger.debug("check_category_temporal_consistency: table '%s' — columns_checked=%s",
                  table_name, result.metrics.get("category_columns_checked"))
    return result

D.1 — Duplicate Composite Keys

clifpy.utils.validator.check_duplicate_composite_keys 

check_duplicate_composite_keys(df, table_name, composite_keys=None, schema=None, warning_threshold=0.0, error_threshold=10.0)

Check for duplicate composite keys.

Source code in clifpy/utils/validator.py 
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def check_duplicate_composite_keys(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    table_name: str,
    composite_keys: Optional[List[str]] = None,
    schema: Optional[Dict[str, Any]] = None,
    warning_threshold: float = 0.0,
    error_threshold: float = 10.0,
) -> DQAPlausibilityResult:
    """Check for duplicate composite keys."""
    _logger.debug("check_duplicate_composite_keys: starting for table '%s'", table_name)
    if _ACTIVE_BACKEND == 'polars':
        result = check_duplicate_composite_keys_polars(df, table_name, composite_keys, schema,
                                                       warning_threshold=warning_threshold,
                                                       error_threshold=error_threshold)
    else:
        result = check_duplicate_composite_keys_duckdb(df, table_name, composite_keys, schema,
                                                       warning_threshold=warning_threshold,
                                                       error_threshold=error_threshold)
    _logger.debug("check_duplicate_composite_keys: table '%s' — duplicates=%s",
                  table_name, result.metrics.get("duplicate_records"))
    return result

Cross-Table Checks

These checks operate across multiple loaded tables to validate relational and temporal consistency.

clifpy.utils.validator.run_relational_integrity_checks 

run_relational_integrity_checks(tables)

Auto-detect and run relational integrity checks for loaded tables.

Reads FK rules from validation_rules.yaml and runs :func:check_relational_integrity for every applicable (table, fk_column) pair.

Parameters:

Name Type Description Default
tables list

Objects with .table_name (str) and .df (DataFrame) attributes — typically :class:BaseTable instances.

 required

Returns:

Type Description
Dict[str, Dict[str, DQACompletenessResult]]

{table_name: {fk_column: DQACompletenessResult}}.
Source code in clifpy/utils/validator.py 
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def run_relational_integrity_checks(
    tables: list,
) -> Dict[str, Dict[str, DQACompletenessResult]]:
    """Auto-detect and run relational integrity checks for loaded tables.

    Reads FK rules from ``validation_rules.yaml`` and runs
    :func:`check_relational_integrity` for every applicable
    (table, fk_column) pair.

    Parameters
    ----------
    tables : list
        Objects with ``.table_name`` (str) and ``.df`` (DataFrame)
        attributes — typically :class:`BaseTable` instances.

    Returns
    -------
    Dict[str, Dict[str, DQACompletenessResult]]
        ``{table_name: {fk_column: DQACompletenessResult}}``.
    """
    _logger.info("run_relational_integrity_checks: starting with %d tables", len(tables))

    # Build lookup: table_name -> (DataFrame, schema_col_names)
    # Convert pandas DataFrames to Polars when the Polars backend is active,
    # matching the pattern used by run_conformance_checks / run_completeness_checks.
    lookup = {}
    for obj in tables:
        df = obj.df
        if _ACTIVE_BACKEND == 'polars' and isinstance(df, pd.DataFrame):
            _logger.debug("Converting pandas DataFrame to Polars for table '%s'", obj.table_name)
            df = pl.from_pandas(df)
        # Extract schema-defined column names (only check FK columns that belong
        # to the table's schema, not extra columns that happen to be in the data).
        schema = getattr(obj, 'schema', None) or {}
        schema_cols = {c['name'] for c in schema.get('columns', [])} if schema.get('columns') else None
        lookup[obj.table_name] = (df, schema_cols)

    # Load FK rules
    fk_rules = _load_validation_rules().get('relational_integrity', {})
    _logger.debug("run_relational_integrity_checks: loaded %d FK rules", len(fk_rules))

    results: Dict[str, Dict[str, DQACompletenessResult]] = {}

    for table_name, (df, schema_cols) in lookup.items():
        # Use schema columns when available; fall back to DataFrame columns
        if schema_cols is not None:
            col_names = schema_cols
        elif HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
            lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
            col_names = set(lf.collect_schema().names())
        else:
            col_names = set(df.columns.tolist())

        for fk_column, rule in fk_rules.items():
            if fk_column not in col_names:
                continue

            ref_table_name = rule['references_table']

            # Skip self-references
            if ref_table_name == table_name:
                _logger.debug(
                    "run_relational_integrity_checks: skipping self-ref "
                    "%s.%s -> %s", table_name, fk_column, ref_table_name,
                )
                continue

            # Skip if the reference table isn't loaded
            if ref_table_name not in lookup:
                _logger.debug(
                    "run_relational_integrity_checks: skipping %s.%s — "
                    "reference table '%s' not loaded",
                    table_name, fk_column, ref_table_name,
                )
                continue

            _logger.info(
                "run_relational_integrity_checks: checking %s.%s -> %s",
                table_name, fk_column, ref_table_name,
            )
            result = check_relational_integrity(
                target_df=df,
                reference_df=lookup[ref_table_name][0],
                target_table=table_name,
                reference_table=ref_table_name,
                key_column=fk_column,
            )
            results.setdefault(table_name, {})[fk_column] = result

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_relational_integrity_checks: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

clifpy.utils.validator.run_cross_table_completeness_checks 

run_cross_table_completeness_checks(tables)

Run cross-table conditional completeness checks (K.5) on full DataFrames.

Parameters:

Name Type Description Default
tables list

Objects with .table_name and .df attributes.

 required

Returns:

Type Description
Dict[str, Dict[str, DQACompletenessResult]]

Results keyed by target table name.
Source code in clifpy/utils/validator.py 
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def run_cross_table_completeness_checks(
    tables: list,
) -> Dict[str, Dict[str, DQACompletenessResult]]:
    """Run cross-table conditional completeness checks (K.5) on full DataFrames.

    Parameters
    ----------
    tables : list
        Objects with ``.table_name`` and ``.df`` attributes.

    Returns
    -------
    Dict[str, Dict[str, DQACompletenessResult]]
        Results keyed by **target** table name.
    """
    _logger.info("run_cross_table_completeness_checks: starting with %d tables", len(tables))

    ct_cond_rules = _load_validation_rules().get('cross_table_conditional_requirements', [])
    if not ct_cond_rules:
        return {}

    lookup = {}
    for obj in tables:
        tname = getattr(obj, 'table_name', '').replace('clif_', '')
        tdf = obj.df
        if _ACTIVE_BACKEND == 'polars' and isinstance(tdf, pd.DataFrame):
            tdf = pl.from_pandas(tdf)
        lookup[tname] = tdf

    results: Dict[str, Dict[str, DQACompletenessResult]] = {}

    for rule in ct_cond_rules:
        rule_key = f"{rule['source_column']}_{rule['target_column']}"
        source_table = rule['source_table']
        target_table = rule['target_table']
        join_col = rule['join_column']

        if source_table not in lookup or target_table not in lookup:
            continue

        src_df = lookup[source_table]
        tgt_df = lookup[target_table]
        match_values = [str(v).strip().lower() for v in rule['source_value']]

        # Get source IDs matching condition
        if HAS_POLARS and isinstance(src_df, (pl.DataFrame, pl.LazyFrame)):
            lf = src_df if isinstance(src_df, pl.LazyFrame) else src_df.lazy()
            if rule['source_column'] not in lf.collect_schema().names() or join_col not in lf.collect_schema().names():
                continue
            matched = (
                lf.filter(
                    pl.col(rule['source_column']).cast(pl.Utf8).str.strip_chars().str.to_lowercase().is_in(match_values)
                )
                .select(pl.col(join_col).drop_nulls().unique())
                .collect(streaming=True)
            )
            source_ids = set(matched[join_col].to_list())
        else:
            if rule['source_column'] not in src_df.columns or join_col not in src_df.columns:
                continue
            mask = src_df[rule['source_column']].astype(str).str.strip().str.lower().isin(match_values)
            source_ids = set(src_df.loc[mask, join_col].dropna().unique().tolist())

        # Get target IDs with non-null target column (also exclude empty strings)
        if HAS_POLARS and isinstance(tgt_df, (pl.DataFrame, pl.LazyFrame)):
            lf = tgt_df if isinstance(tgt_df, pl.LazyFrame) else tgt_df.lazy()
            schema_names = lf.collect_schema().names()
            if rule['target_column'] not in schema_names or join_col not in schema_names:
                continue
            tcol = pl.col(rule['target_column'])
            not_null_filter = tcol.is_not_null()
            dtype = lf.collect_schema()[rule['target_column']]
            if dtype == pl.Utf8 or dtype == pl.String:
                not_null_filter = not_null_filter & (tcol.str.strip_chars().str.len_chars() > 0)
            matched = (
                lf.filter(not_null_filter)
                .select(pl.col(join_col).drop_nulls().unique())
                .collect(streaming=True)
            )
            target_ids = set(matched[join_col].to_list())
        else:
            if rule['target_column'] not in tgt_df.columns or join_col not in tgt_df.columns:
                continue
            target_col = tgt_df[rule['target_column']]
            mask = target_col.notna()
            if hasattr(target_col, 'str') and target_col.dtype == 'object':
                mask = mask & (target_col.astype(str).str.strip() != '')
            target_ids = set(tgt_df.loc[mask, join_col].dropna().unique().tolist())

        result = DQACompletenessResult(
            "cross_table_conditional_completeness",
            f"{source_table}->{target_table}",
        )

        if not source_ids:
            result.add_info(
                f"No {rule['source_column']} = {rule['source_value']} found in "
                f"{source_table}; cross-table conditional check not triggered"
            )
            results.setdefault(target_table, {})[rule_key] = result
            continue

        missing_ids = source_ids - target_ids
        total = len(source_ids)
        missing_count = len(missing_ids)
        pct = round(missing_count / total * 100, 1) if total > 0 else 0

        result.metrics["total_matching_source"] = total
        result.metrics["missing_in_target"] = missing_count
        result.metrics["coverage_percent"] = round(100 - pct, 2)

        if missing_ids:
            sample = sorted(list(missing_ids))[:10]
            result.add_warning(
                f"{missing_count}/{total} patients discharged as {rule['source_value']} "
                f"in {source_table} are missing {rule['target_column']} in {target_table} "
                f"({pct}% missing)",
                {
                    "column": rule['target_column'],
                    "missing_count": missing_count,
                    "total_matching": total,
                    "percent_missing": pct,
                    "sample_ids": sample,
                    "source_condition": f"{rule['source_column']} in {rule['source_value']}",
                },
            )
        else:
            result.add_info(
                f"All {total} patients discharged as {rule['source_value']} in "
                f"{source_table} have {rule['target_column']} in {target_table}"
            )

        results.setdefault(target_table, {})[rule_key] = result

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_cross_table_completeness_checks: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

clifpy.utils.validator.run_cross_table_plausibility_checks 

run_cross_table_plausibility_checks(tables, plausibility_thresholds=None)

Run cross-table plausibility checks (B.1).

Parameters:

Name Type Description Default
tables list

Objects with .table_name and .df attributes.

 required
plausibility_thresholds dict

Override default plausibility thresholds per check.

 None

Returns:

Type Description
Dict[str, Dict[str, DQAPlausibilityResult]]

{table_name: {"cross_table_temporal": DQAPlausibilityResult}}.
Source code in clifpy/utils/validator.py 
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def run_cross_table_plausibility_checks(
    tables: list,
    plausibility_thresholds: Optional[Dict[str, Dict[str, float]]] = None,
) -> Dict[str, Dict[str, DQAPlausibilityResult]]:
    """Run cross-table plausibility checks (B.1).

    Parameters
    ----------
    tables : list
        Objects with ``.table_name`` and ``.df`` attributes.
    plausibility_thresholds : dict, optional
        Override default plausibility thresholds per check.

    Returns
    -------
    Dict[str, Dict[str, DQAPlausibilityResult]]
        ``{table_name: {"cross_table_temporal": DQAPlausibilityResult}}``.
    """
    _logger.info("run_cross_table_plausibility_checks: starting with %d tables", len(tables))

    # Merge caller overrides with defaults
    thresholds = {k: dict(v) for k, v in _DEFAULT_PLAUSIBILITY_THRESHOLDS.items()}
    if plausibility_thresholds:
        for check_name, overrides in plausibility_thresholds.items():
            if check_name in thresholds:
                thresholds[check_name].update(overrides)
            else:
                thresholds[check_name] = overrides

    lookup = {}
    for obj in tables:
        tdf = obj.df
        if _ACTIVE_BACKEND == 'polars' and isinstance(tdf, pd.DataFrame):
            tdf = pl.from_pandas(tdf)
        lookup[obj.table_name] = tdf

    if 'hospitalization' not in lookup:
        _logger.info("Hospitalization table not loaded; skipping cross-table plausibility")
        return {}

    hosp_df = lookup['hospitalization']
    results: Dict[str, Dict[str, DQAPlausibilityResult]] = {}

    for tbl_name, tdf in lookup.items():
        if tbl_name == 'hospitalization':
            continue
        time_cols = _CROSS_TABLE_TIME_COLUMNS.get(tbl_name, [])
        if not time_cols:
            continue

        if HAS_POLARS and isinstance(tdf, (pl.DataFrame, pl.LazyFrame)):
            lf = tdf if isinstance(tdf, pl.LazyFrame) else tdf.lazy()
            actual_cols = lf.collect_schema().names()
        else:
            actual_cols = tdf.columns.tolist()

        available_time_cols = [c for c in time_cols if c in actual_cols]
        if not available_time_cols or 'hospitalization_id' not in actual_cols:
            continue

        result = check_cross_table_temporal_plausibility(
            tdf, hosp_df, tbl_name, available_time_cols,
            **thresholds['cross_table_temporal']
        )
        results.setdefault(tbl_name, {})["cross_table_temporal"] = result

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_cross_table_plausibility_checks: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

Orchestration

High-level functions that run groups of checks or the full DQA suite.

Single-Table Orchestration

clifpy.utils.validator.run_conformance_checks 

run_conformance_checks(df, schema, table_name)

Run all conformance checks on a table.

Parameters:

Name Type Description Default
df DataFrame

The data to validate

 required
schema dict

Schema for the table

 required
table_name str

Name of the table

 required

Returns:

Type Description
Dict[str, DQAConformanceResult]

Dictionary of check results keyed by check type
Source code in clifpy/utils/validator.py 
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def run_conformance_checks(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str
) -> Dict[str, DQAConformanceResult]:
    """
    Run all conformance checks on a table.

    Parameters
    ----------
    df : DataFrame
        The data to validate
    schema : dict
        Schema for the table
    table_name : str
        Name of the table

    Returns
    -------
    Dict[str, DQAConformanceResult]
        Dictionary of check results keyed by check type
    """
    _logger.info("Running conformance checks for table '%s' using %s backend", table_name, _ACTIVE_BACKEND)

    # Convert pandas DataFrame to Polars if the active backend is Polars
    if _ACTIVE_BACKEND == 'polars' and isinstance(df, pd.DataFrame):
        _logger.debug("Converting pandas DataFrame to Polars for table '%s'", table_name)
        df = pl.from_pandas(df)

    results = {}

    results['table_presence'] = check_table_presence(df, table_name)
    gc.collect()

    results['required_columns'] = check_required_columns(df, schema, table_name)
    gc.collect()

    results['column_dtypes'] = check_column_dtypes(df, schema, table_name)
    gc.collect()

    results['datetime_format'] = check_datetime_format(df, schema, table_name)
    gc.collect()

    if table_name == 'labs':
        results['lab_reference_units'] = check_lab_reference_units(df, schema, table_name)
        gc.collect()

    results['categorical_values'] = check_categorical_values(df, schema, table_name)
    gc.collect()

    results['category_group_mapping'] = check_category_group_mapping(df, schema, table_name)
    gc.collect()

    passed = sum(1 for r in results.values() if r.passed)
    failed = len(results) - passed
    _logger.info("Conformance checks complete for '%s': %d passed, %d failed", table_name, passed, failed)

    return results

clifpy.utils.validator.run_completeness_checks 

run_completeness_checks(df, schema, table_name, error_threshold=50.0, warning_threshold=10.0)

Run all completeness checks on a table.

Parameters:

Name Type Description Default
df DataFrame

The data to validate

 required
schema dict

Schema for the table

 required
table_name str

Name of the table

 required
error_threshold float

Percent missing above which an error is raised

 50.0
warning_threshold float

Percent missing above which a warning is raised

 10.0

Returns:

Type Description
Dict[str, DQACompletenessResult]

Dictionary of check results keyed by check type
Source code in clifpy/utils/validator.py 
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def run_completeness_checks(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str,
    error_threshold: float = 50.0,
    warning_threshold: float = 10.0
) -> Dict[str, DQACompletenessResult]:
    """
    Run all completeness checks on a table.

    Parameters
    ----------
    df : DataFrame
        The data to validate
    schema : dict
        Schema for the table
    table_name : str
        Name of the table
    error_threshold : float
        Percent missing above which an error is raised
    warning_threshold : float
        Percent missing above which a warning is raised

    Returns
    -------
    Dict[str, DQACompletenessResult]
        Dictionary of check results keyed by check type
    """
    _logger.info("Running completeness checks for table '%s' using %s backend", table_name, _ACTIVE_BACKEND)

    # Convert pandas DataFrame to Polars if the active backend is Polars
    if _ACTIVE_BACKEND == 'polars' and isinstance(df, pd.DataFrame):
        _logger.debug("Converting pandas DataFrame to Polars for table '%s'", table_name)
        df = pl.from_pandas(df)

    results = {}

    results['missingness'] = check_missingness(
        df, schema, table_name, error_threshold, warning_threshold
    )
    gc.collect()

    results['conditional_requirements'] = check_conditional_requirements(df, table_name)
    gc.collect()

    results['mcide_value_coverage'] = check_mcide_value_coverage(df, schema, table_name)
    gc.collect()

    passed = sum(1 for r in results.values() if r.passed)
    failed = len(results) - passed
    _logger.info("Completeness checks complete for '%s': %d passed, %d failed", table_name, passed, failed)

    return results

clifpy.utils.validator.run_plausibility_checks 

run_plausibility_checks(df, schema, table_name, hosp_years=None, plausibility_thresholds=None)

Run all single-table plausibility checks on a table.

Parameters:

Name Type Description Default
df DataFrame

The data to validate

 required
schema dict

Schema for the table

 required
table_name str

Name of the table

 required
plausibility_thresholds dict

Override default plausibility thresholds per check.

 None

Returns:

Type Description
Dict[str, DQAPlausibilityResult]

Dictionary of check results keyed by check type
Source code in clifpy/utils/validator.py 
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def run_plausibility_checks(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: str,
    hosp_years: Optional[set] = None,
    plausibility_thresholds: Optional[Dict[str, Dict[str, float]]] = None,
) -> Dict[str, DQAPlausibilityResult]:
    """
    Run all single-table plausibility checks on a table.

    Parameters
    ----------
    df : DataFrame
        The data to validate
    schema : dict
        Schema for the table
    table_name : str
        Name of the table
    plausibility_thresholds : dict, optional
        Override default plausibility thresholds per check.

    Returns
    -------
    Dict[str, DQAPlausibilityResult]
        Dictionary of check results keyed by check type
    """
    _logger.info("Running plausibility checks for table '%s' using %s backend", table_name, _ACTIVE_BACKEND)

    # Merge caller overrides with defaults
    thresholds = {k: dict(v) for k, v in _DEFAULT_PLAUSIBILITY_THRESHOLDS.items()}
    if plausibility_thresholds:
        for check_name, overrides in plausibility_thresholds.items():
            if check_name in thresholds:
                thresholds[check_name].update(overrides)
            else:
                thresholds[check_name] = overrides

    if _ACTIVE_BACKEND == 'polars' and isinstance(df, pd.DataFrame):
        _logger.debug("Converting pandas DataFrame to Polars for table '%s'", table_name)
        df = pl.from_pandas(df)

    results = {}

    # A.1 Temporal ordering
    results['temporal_ordering'] = check_temporal_ordering(
        df, table_name, **thresholds['temporal_ordering'])
    gc.collect()

    # A.2 Numeric range plausibility
    results['numeric_range_plausibility'] = check_numeric_range_plausibility(
        df, table_name, **thresholds['numeric_range_plausibility'])
    gc.collect()

    # A.3 Field-level plausibility
    results['field_plausibility'] = check_field_plausibility(df, table_name)
    gc.collect()

    # A.4 Medication dose unit consistency (only for med tables)
    if table_name in ('medication_admin_continuous', 'medication_admin_intermittent'):
        results['medication_dose_unit_consistency'] = check_medication_dose_unit_consistency(
            df, table_name, **thresholds['medication_dose_unit_consistency'])
        gc.collect()

    # C.1 Overlapping periods
    overlap_rules = _load_validation_rules().get('overlapping_periods', {}).get(table_name)
    if overlap_rules:
        results['overlapping_periods'] = check_overlapping_periods(
            df, table_name,
            entity_col=overlap_rules.get('entity_column', 'hospitalization_id'),
            start_col=overlap_rules.get('start_column', 'in_dttm'),
            end_col=overlap_rules.get('end_column', 'out_dttm'),
        )
        gc.collect()

    # C.2 Category temporal consistency
    results['category_temporal_consistency'] = check_category_temporal_consistency(df, schema, table_name, hosp_years=hosp_years)
    gc.collect()

    # D.1 Duplicate composite keys
    results['duplicate_composite_keys'] = check_duplicate_composite_keys(
        df, table_name, schema=schema, **thresholds['duplicate_composite_keys'])
    gc.collect()

    passed = sum(1 for r in results.values() if r.passed)
    failed = len(results) - passed
    _logger.info("Plausibility checks complete for '%s': %d passed, %d failed", table_name, passed, failed)
    return results

clifpy.utils.validator.run_full_dqa 

run_full_dqa(df, schema=None, table_name='', tables=None, error_threshold=50.0, warning_threshold=10.0, hosp_years=None, plausibility_thresholds=None)

Run the complete DQA suite on a single table.

Orchestrates conformance checks, completeness checks, plausibility checks, and — when tables is provided — auto-detected relational integrity and cross-table plausibility checks.

Parameters:

Name Type Description Default
df DataFrame

The data to validate.

 required
schema dict

Schema for the table. When None (the default), the schema is loaded automatically from the built-in schemas using table_name.

 None
table_name str

Name of the table.

 ''
tables list

Objects with .table_name and .df attributes (e.g. :class:BaseTable instances). When provided, relational integrity and cross-table plausibility checks are run.

 None
error_threshold float

Percent missing above which an error is raised (default 50).

 50.0
warning_threshold float

Percent missing above which a warning is raised (default 10).

 10.0
hosp_years set

Pre-extracted hospitalization years for P.6 temporal consistency. When provided, skips scanning the hospitalization table to extract years.

 None
plausibility_thresholds dict

Override default plausibility thresholds per check.

 None

Returns:

Type Description
Dict[str, Any]

Keys: table_name, backend, conformance, completeness, relational, plausibility.
Source code in clifpy/utils/validator.py 
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def run_full_dqa(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Optional[Dict[str, Any]] = None,
    table_name: str = "",
    tables: Optional[list] = None,
    error_threshold: float = 50.0,
    warning_threshold: float = 10.0,
    hosp_years: Optional[set] = None,
    plausibility_thresholds: Optional[Dict[str, Dict[str, float]]] = None,
) -> Dict[str, Any]:
    """Run the complete DQA suite on a single table.

    Orchestrates conformance checks, completeness checks, plausibility
    checks, and — when *tables* is provided — auto-detected relational
    integrity and cross-table plausibility checks.

    Parameters
    ----------
    df : DataFrame
        The data to validate.
    schema : dict, optional
        Schema for the table.  When *None* (the default), the schema is
        loaded automatically from the built-in schemas using *table_name*.
    table_name : str
        Name of the table.
    tables : list, optional
        Objects with ``.table_name`` and ``.df`` attributes (e.g.
        :class:`BaseTable` instances).  When provided, relational
        integrity and cross-table plausibility checks are run.
    error_threshold : float
        Percent missing above which an error is raised (default 50).
    warning_threshold : float
        Percent missing above which a warning is raised (default 10).
    hosp_years : set, optional
        Pre-extracted hospitalization years for P.6 temporal consistency.
        When provided, skips scanning the hospitalization table to
        extract years.
    plausibility_thresholds : dict, optional
        Override default plausibility thresholds per check.

    Returns
    -------
    Dict[str, Any]
        Keys: ``table_name``, ``backend``, ``conformance``,
        ``completeness``, ``relational``, ``plausibility``.
    """
    if not table_name:
        raise ValueError("table_name is required")
    if schema is None:
        schema = _load_schema(table_name)
        if schema is None:
            raise FileNotFoundError(
                f"No built-in schema found for table '{table_name}'. "
                "Pass a schema dict explicitly."
            )
    _logger.info("Starting full DQA for table: %s", table_name)

    results: Dict[str, Any] = {
        'table_name': table_name,
        'backend': _ACTIVE_BACKEND,
        'conformance': {},
        'completeness': {},
        'relational': {},
        'plausibility': {},
    }

    results['conformance'] = {
        k: v.to_dict()
        for k, v in run_conformance_checks(df, schema, table_name).items()
    }

    results['completeness'] = {
        k: v.to_dict()
        for k, v in run_completeness_checks(
            df, schema, table_name, error_threshold, warning_threshold
        ).items()
    }

    if tables is not None:
        rel_results = run_relational_integrity_checks(tables)
        if table_name in rel_results:
            results['relational'] = {
                k: v.to_dict()
                for k, v in rel_results[table_name].items()
            }

    # Extract hospitalization years for P.6 temporal consistency context
    # (skip scan if hosp_years was provided by caller)
    if hosp_years is None and tables is not None:
        for obj in tables:
            tname = getattr(obj, 'table_name', '').replace('clif_', '')
            if tname == 'hospitalization':
                hdf = obj.df
                if HAS_POLARS and isinstance(hdf, (pl.DataFrame, pl.LazyFrame)):
                    hlf = hdf if isinstance(hdf, pl.LazyFrame) else hdf.lazy()
                    hcols = hlf.collect_schema().names()
                    if 'admission_dttm' in hcols:
                        hosp_years = set(
                            hlf.select(pl.col('admission_dttm').dt.year().alias('yr'))
                            .filter(pl.col('yr').is_not_null())
                            .unique()
                            .collect()
                            .get_column('yr')
                            .to_list()
                        )
                elif isinstance(hdf, pd.DataFrame) and 'admission_dttm' in hdf.columns:
                    hosp_years = set(
                        int(y) for y in hdf['admission_dttm'].dropna().dt.year.unique()
                    )
                break

    # Plausibility checks (single-table)
    results['plausibility'] = {
        k: v.to_dict()
        for k, v in run_plausibility_checks(
            df, schema, table_name, hosp_years=hosp_years,
            plausibility_thresholds=plausibility_thresholds,
        ).items()
    }

    # Cross-table plausibility checks (when tables provided)
    if tables is not None:
        cross_plaus = run_cross_table_plausibility_checks(
            tables, plausibility_thresholds=plausibility_thresholds)
        if table_name in cross_plaus:
            for k, v in cross_plaus[table_name].items():
                results['plausibility'][k] = v.to_dict()

    gc.collect()
    _logger.info("Completed full DQA for table: %s", table_name)
    return results

Cache-Based Cross-Table Pipeline

For memory-optimized cross-table validation, extract lightweight caches and run checks without keeping full DataFrames in memory.

clifpy.utils.validator.extract_cross_table_cache 

extract_cross_table_cache(table_obj)

Extract a lightweight cache from a single table object.

Used by the optimised pipeline in CLIF-TableOne's runner to avoid keeping full DataFrames in memory for cross-table checks.

Parameters:

Name Type Description Default
table_obj BaseTable

Object with .table_name, .df, and .schema attributes.

 required

Returns:

Type Description
dict

Keys: table_name, fk_ids, schema_cols, temporal_df, hosp_bounds_df, hosp_years.
Source code in clifpy/utils/validator.py 
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def extract_cross_table_cache(table_obj) -> Dict[str, Any]:
    """Extract a lightweight cache from a single table object.

    Used by the optimised pipeline in CLIF-TableOne's runner to avoid
    keeping full DataFrames in memory for cross-table checks.

    Parameters
    ----------
    table_obj : BaseTable
        Object with ``.table_name``, ``.df``, and ``.schema`` attributes.

    Returns
    -------
    dict
        Keys: ``table_name``, ``fk_ids``, ``schema_cols``,
        ``temporal_df``, ``hosp_bounds_df``, ``hosp_years``.
    """
    tname = getattr(table_obj, 'table_name', '').replace('clif_', '')
    df = table_obj.df
    schema = getattr(table_obj, 'schema', None) or {}

    # Schema-defined column names
    schema_cols = (
        {c['name'] for c in schema.get('columns', [])}
        if schema.get('columns') else None
    )

    # Determine actual columns in the DataFrame
    if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
        lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
        actual_cols = set(lf.collect_schema().names())
    else:
        actual_cols = set(df.columns.tolist())

    # Use schema cols when available; fall back to actual cols
    col_names = schema_cols if schema_cols is not None else actual_cols

    # --- FK ID sets ---
    fk_rules = _load_validation_rules().get('relational_integrity', {})
    fk_ids: Dict[str, set] = {}
    for fk_column in fk_rules:
        if fk_column not in col_names or fk_column not in actual_cols:
            continue
        if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
            lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
            id_series = (
                lf.select(pl.col(fk_column).drop_nulls().unique())
                .collect(streaming=True)
            )
            fk_ids[fk_column] = set(id_series[fk_column].to_list())
        else:
            fk_ids[fk_column] = set(df[fk_column].dropna().unique().tolist())

    # --- Temporal subset for cross-table plausibility ---
    time_cols = _CROSS_TABLE_TIME_COLUMNS.get(tname, [])
    temporal_df = None
    if time_cols and 'hospitalization_id' in actual_cols:
        needed = ['hospitalization_id'] + [c for c in time_cols if c in actual_cols]
        if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
            lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
            temporal_df = lf.select(needed).collect()
        else:
            temporal_df = df[needed].copy()

    # --- Hospitalization-specific caches ---
    hosp_bounds_df = None
    hosp_years = None
    if tname == 'hospitalization':
        if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
            lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
            hosp_cols_available = set(lf.collect_schema().names())
            bound_cols = [c for c in ['hospitalization_id', 'admission_dttm', 'discharge_dttm']
                          if c in hosp_cols_available]
            if 'hospitalization_id' in bound_cols:
                hosp_bounds_df = lf.select(bound_cols).collect()
            if 'admission_dttm' in hosp_cols_available:
                hosp_years = set(
                    lf.select(pl.col('admission_dttm').dt.year().alias('yr'))
                    .filter(pl.col('yr').is_not_null())
                    .unique()
                    .collect()
                    .get_column('yr')
                    .to_list()
                )
        elif isinstance(df, pd.DataFrame):
            bound_cols = [c for c in ['hospitalization_id', 'admission_dttm', 'discharge_dttm']
                          if c in df.columns]
            if 'hospitalization_id' in bound_cols:
                hosp_bounds_df = df[bound_cols].copy()
            if 'admission_dttm' in df.columns:
                hosp_years = set(
                    int(y) for y in df['admission_dttm'].dropna().dt.year.unique()
                )

    # --- Cross-table conditional requirements cache ---
    ct_cond_rules = _load_validation_rules().get('cross_table_conditional_requirements', [])
    conditional_source_ids: Dict[str, set] = {}
    conditional_target_ids: Dict[str, set] = {}

    for rule in ct_cond_rules:
        rule_key = f"{rule['source_column']}_{rule['target_column']}"
        join_col = rule['join_column']

        if tname == rule['source_table'] and join_col in actual_cols and rule['source_column'] in actual_cols:
            # Extract join_column IDs where source_column matches source_value (case-insensitive)
            match_values = [str(v).strip().lower() for v in rule['source_value']]
            if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
                lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
                matched = (
                    lf.filter(
                        pl.col(rule['source_column']).cast(pl.Utf8).str.strip_chars().str.to_lowercase().is_in(match_values)
                    )
                    .select(pl.col(join_col).drop_nulls().unique())
                    .collect(streaming=True)
                )
                conditional_source_ids[rule_key] = set(matched[join_col].to_list())
            else:
                mask = df[rule['source_column']].astype(str).str.strip().str.lower().isin(match_values)
                conditional_source_ids[rule_key] = set(df.loc[mask, join_col].dropna().unique().tolist())

        if tname == rule['target_table'] and join_col in actual_cols and rule['target_column'] in actual_cols:
            # Extract join_column IDs where target_column is not null (and not empty string)
            if HAS_POLARS and isinstance(df, (pl.DataFrame, pl.LazyFrame)):
                lf = df if isinstance(df, pl.LazyFrame) else df.lazy()
                tcol = pl.col(rule['target_column'])
                # Handle both datetime and string columns: not null AND not empty string
                not_null_filter = tcol.is_not_null()
                dtype = lf.collect_schema()[rule['target_column']]
                if dtype == pl.Utf8 or dtype == pl.String:
                    not_null_filter = not_null_filter & (tcol.str.strip_chars().str.len_chars() > 0)
                matched = (
                    lf.filter(not_null_filter)
                    .select(pl.col(join_col).drop_nulls().unique())
                    .collect(streaming=True)
                )
                conditional_target_ids[rule_key] = set(matched[join_col].to_list())
            else:
                target_col = df[rule['target_column']]
                mask = target_col.notna()
                # If string dtype, also exclude empty/whitespace-only strings
                if hasattr(target_col, 'str') and target_col.dtype == 'object':
                    mask = mask & (target_col.astype(str).str.strip() != '')
                conditional_target_ids[rule_key] = set(df.loc[mask, join_col].dropna().unique().tolist())

    cache = {
        'table_name': tname,
        'fk_ids': fk_ids,
        'schema_cols': schema_cols,
        'temporal_df': temporal_df,
        'hosp_bounds_df': hosp_bounds_df,
        'hosp_years': hosp_years,
        'conditional_source_ids': conditional_source_ids,
        'conditional_target_ids': conditional_target_ids,
    }
    _logger.info(
        "extract_cross_table_cache: table='%s', fk_keys=%s, temporal=%s, hosp_bounds=%s, "
        "cond_source_keys=%s, cond_target_keys=%s",
        tname, list(fk_ids.keys()), temporal_df is not None, hosp_bounds_df is not None,
        list(conditional_source_ids.keys()), list(conditional_target_ids.keys()),
    )
    return cache

clifpy.utils.validator.run_relational_integrity_checks_from_cache 

run_relational_integrity_checks_from_cache(caches)

Run relational integrity checks using pre-extracted caches.

Equivalent to :func:run_relational_integrity_checks but operates on Python set objects (FK ID sets) instead of scanning full DataFrames.

Parameters:

Name Type Description Default
caches dict

{table_name: cache_dict} as returned by :func:extract_cross_table_cache.

 required

Returns:

Type Description
Dict[str, Dict[str, DQACompletenessResult]]

Same structure as :func:run_relational_integrity_checks.
Source code in clifpy/utils/validator.py 
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def run_relational_integrity_checks_from_cache(
    caches: Dict[str, Dict[str, Any]],
) -> Dict[str, Dict[str, DQACompletenessResult]]:
    """Run relational integrity checks using pre-extracted caches.

    Equivalent to :func:`run_relational_integrity_checks` but operates on
    Python ``set`` objects (FK ID sets) instead of scanning full DataFrames.

    Parameters
    ----------
    caches : dict
        ``{table_name: cache_dict}`` as returned by
        :func:`extract_cross_table_cache`.

    Returns
    -------
    Dict[str, Dict[str, DQACompletenessResult]]
        Same structure as :func:`run_relational_integrity_checks`.
    """
    _logger.info(
        "run_relational_integrity_checks_from_cache: starting with %d cached tables",
        len(caches),
    )

    fk_rules = _load_validation_rules().get('relational_integrity', {})
    results: Dict[str, Dict[str, DQACompletenessResult]] = {}

    for table_name, cache in caches.items():
        col_names = cache['schema_cols'] if cache['schema_cols'] is not None else set(cache['fk_ids'].keys())

        for fk_column, rule in fk_rules.items():
            if fk_column not in col_names:
                continue

            ref_table_name = rule['references_table']

            if ref_table_name == table_name:
                continue

            if ref_table_name not in caches:
                _logger.debug(
                    "run_relational_integrity_checks_from_cache: skipping %s.%s — "
                    "reference table '%s' not cached",
                    table_name, fk_column, ref_table_name,
                )
                continue

            # Get the FK ID sets
            source_ids = cache['fk_ids'].get(fk_column)
            if source_ids is None:
                continue

            ref_cache = caches[ref_table_name]
            ref_ids = ref_cache['fk_ids'].get(fk_column)
            if ref_ids is None:
                # Reference table doesn't have this FK column cached — skip
                continue

            _logger.info(
                "run_relational_integrity_checks_from_cache: checking %s.%s -> %s",
                table_name, fk_column, ref_table_name,
            )

            # Build the bidirectional result (same structure as check_relational_integrity)
            result = DQACompletenessResult(
                "relational_integrity",
                f"{table_name}<->{ref_table_name}",
            )

            try:
                # Forward: reference -> target (source=ref, ref=target)
                fwd_orphans = ref_ids - source_ids
                fwd_total = len(ref_ids)
                fwd_orphan_count = len(fwd_orphans)
                fwd_coverage = ((fwd_total - fwd_orphan_count) / fwd_total * 100) if fwd_total > 0 else 100

                # Reverse: target -> reference (source=target, ref=reference)
                rev_orphans = source_ids - ref_ids
                rev_total = len(source_ids)
                rev_orphan_count = len(rev_orphans)
                rev_coverage = ((rev_total - rev_orphan_count) / rev_total * 100) if rev_total > 0 else 100

                result.metrics["forward_coverage_percent"] = round(fwd_coverage, 2)
                result.metrics["forward_orphan_ids"] = fwd_orphan_count
                result.metrics["forward_reference_unique_ids"] = fwd_total
                result.metrics["reverse_coverage_percent"] = round(rev_coverage, 2)
                result.metrics["reverse_orphan_ids"] = rev_orphan_count
                result.metrics["reverse_target_unique_ids"] = rev_total

                # Forward warnings/errors
                if fwd_orphans:
                    result.add_warning(
                        f"{fwd_orphan_count}/{fwd_total} {fk_column} values in {ref_table_name} "
                        f"not found in {table_name} ({round(fwd_coverage, 1)}% coverage)",
                        {"orphan_count": fwd_orphan_count,
                         "sample_orphan_ids": list(fwd_orphans)[:10],
                         "coverage_percent": round(fwd_coverage, 2)}
                    )

                # Reverse warnings/errors
                if rev_orphans:
                    result.add_warning(
                        f"{rev_orphan_count}/{rev_total} {fk_column} values in {table_name} "
                        f"not found in {ref_table_name} ({round(rev_coverage, 1)}% coverage)",
                        {"orphan_count": rev_orphan_count,
                         "sample_orphan_ids": list(rev_orphans)[:10],
                         "coverage_percent": round(rev_coverage, 2)}
                    )

                if not fwd_orphans and not rev_orphans:
                    result.add_info(
                        f"Full bidirectional coverage for {fk_column} between "
                        f"{table_name} and {ref_table_name}"
                    )

                _logger.info(
                    "run_relational_integrity_checks_from_cache: '%s' <-> '%s' — "
                    "fwd_coverage=%.1f%%, rev_coverage=%.1f%%",
                    table_name, ref_table_name, fwd_coverage, rev_coverage,
                )

            except Exception as e:
                _logger.error(
                    "Cached relational check failed for '%s' <-> '%s': %s",
                    table_name, ref_table_name, e,
                )
                result.add_error(f"Error checking relational integrity: {str(e)}")

            results.setdefault(table_name, {})[fk_column] = result

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_relational_integrity_checks_from_cache: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

clifpy.utils.validator.run_cross_table_completeness_checks_from_cache 

run_cross_table_completeness_checks_from_cache(caches)

Run cross-table conditional completeness checks (K.5) from caches.

For each YAML rule in cross_table_conditional_requirements, computes the set of join-column IDs that satisfy the source condition but are missing the required target column value.

Parameters:

Name Type Description Default
caches dict

{table_name: cache_dict} as returned by :func:extract_cross_table_cache.

 required

Returns:

Type Description
Dict[str, Dict[str, DQACompletenessResult]]

Results keyed by target table name, then by a descriptive check key.
Source code in clifpy/utils/validator.py 
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def run_cross_table_completeness_checks_from_cache(
    caches: Dict[str, Dict[str, Any]],
) -> Dict[str, Dict[str, DQACompletenessResult]]:
    """Run cross-table conditional completeness checks (K.5) from caches.

    For each YAML rule in ``cross_table_conditional_requirements``, computes
    the set of join-column IDs that satisfy the source condition but are
    missing the required target column value.

    Parameters
    ----------
    caches : dict
        ``{table_name: cache_dict}`` as returned by
        :func:`extract_cross_table_cache`.

    Returns
    -------
    Dict[str, Dict[str, DQACompletenessResult]]
        Results keyed by **target** table name, then by a descriptive
        check key.
    """
    _logger.info(
        "run_cross_table_completeness_checks_from_cache: starting with %d cached tables",
        len(caches),
    )

    ct_cond_rules = _load_validation_rules().get('cross_table_conditional_requirements', [])
    if not ct_cond_rules:
        return {}

    results: Dict[str, Dict[str, DQACompletenessResult]] = {}

    for rule in ct_cond_rules:
        rule_key = f"{rule['source_column']}_{rule['target_column']}"
        source_table = rule['source_table']
        target_table = rule['target_table']

        # Both tables must be cached
        if source_table not in caches or target_table not in caches:
            _logger.debug(
                "K.5: skipping rule '%s' — source '%s' or target '%s' not cached",
                rule_key, source_table, target_table,
            )
            continue

        source_cache = caches[source_table]
        target_cache = caches[target_table]

        source_ids = source_cache.get('conditional_source_ids', {}).get(rule_key)
        target_ids = target_cache.get('conditional_target_ids', {}).get(rule_key)

        result = DQACompletenessResult(
            "cross_table_conditional_completeness",
            f"{source_table}->{target_table}",
        )

        if source_ids is None or target_ids is None:
            result.add_info(
                "No cross-table conditional requirements applicable"
            )
            results.setdefault(target_table, {})[rule_key] = result
            continue

        if not source_ids:
            result.add_info(
                f"No {rule['source_column']} = {rule['source_value']} found in "
                f"{source_table}; cross-table conditional check not triggered"
            )
            results.setdefault(target_table, {})[rule_key] = result
            continue

        missing_ids = source_ids - target_ids
        total = len(source_ids)
        missing_count = len(missing_ids)
        pct = round(missing_count / total * 100, 1) if total > 0 else 0

        result.metrics["total_matching_source"] = total
        result.metrics["missing_in_target"] = missing_count
        result.metrics["coverage_percent"] = round(100 - pct, 2)

        if missing_ids:
            sample = sorted(list(missing_ids))[:10]
            result.add_warning(
                f"{missing_count}/{total} patients discharged as {rule['source_value']} "
                f"in {source_table} are missing {rule['target_column']} in {target_table} "
                f"({pct}% missing)",
                {
                    "column": rule['target_column'],
                    "missing_count": missing_count,
                    "total_matching": total,
                    "percent_missing": pct,
                    "sample_ids": sample,
                    "source_condition": f"{rule['source_column']} in {rule['source_value']}",
                },
            )
        else:
            result.add_info(
                f"All {total} patients discharged as {rule['source_value']} in "
                f"{source_table} have {rule['target_column']} in {target_table}"
            )

        results.setdefault(target_table, {})[rule_key] = result
        _logger.info(
            "K.5: %s->%s rule '%s': %d/%d missing (%.1f%%)",
            source_table, target_table, rule_key, missing_count, total, pct,
        )

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_cross_table_completeness_checks_from_cache: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

clifpy.utils.validator.run_cross_table_plausibility_checks_from_cache 

run_cross_table_plausibility_checks_from_cache(caches, plausibility_thresholds=None)

Run cross-table plausibility checks using pre-extracted caches.

Equivalent to :func:run_cross_table_plausibility_checks but uses cached temporal subset DataFrames and hospitalization bounds instead of full DataFrames.

Parameters:

Name Type Description Default
caches dict

{table_name: cache_dict} as returned by :func:extract_cross_table_cache.

 required
plausibility_thresholds dict

Override default plausibility thresholds per check.

 None

Returns:

Type Description
Dict[str, Dict[str, DQAPlausibilityResult]]

Same structure as :func:run_cross_table_plausibility_checks.
Source code in clifpy/utils/validator.py 
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def run_cross_table_plausibility_checks_from_cache(
    caches: Dict[str, Dict[str, Any]],
    plausibility_thresholds: Optional[Dict[str, Dict[str, float]]] = None,
) -> Dict[str, Dict[str, DQAPlausibilityResult]]:
    """Run cross-table plausibility checks using pre-extracted caches.

    Equivalent to :func:`run_cross_table_plausibility_checks` but uses
    cached temporal subset DataFrames and hospitalization bounds instead
    of full DataFrames.

    Parameters
    ----------
    caches : dict
        ``{table_name: cache_dict}`` as returned by
        :func:`extract_cross_table_cache`.
    plausibility_thresholds : dict, optional
        Override default plausibility thresholds per check.

    Returns
    -------
    Dict[str, Dict[str, DQAPlausibilityResult]]
        Same structure as :func:`run_cross_table_plausibility_checks`.
    """
    _logger.info(
        "run_cross_table_plausibility_checks_from_cache: starting with %d cached tables",
        len(caches),
    )

    # Merge caller overrides with defaults
    thresholds = {k: dict(v) for k, v in _DEFAULT_PLAUSIBILITY_THRESHOLDS.items()}
    if plausibility_thresholds:
        for check_name, overrides in plausibility_thresholds.items():
            if check_name in thresholds:
                thresholds[check_name].update(overrides)
            else:
                thresholds[check_name] = overrides

    # Need hospitalization bounds
    hosp_cache = caches.get('hospitalization')
    if hosp_cache is None or hosp_cache.get('hosp_bounds_df') is None:
        _logger.info("Hospitalization cache not available; skipping cross-table plausibility")
        return {}

    hosp_bounds_df = hosp_cache['hosp_bounds_df']
    # Ensure hosp_bounds_df matches active backend
    if _ACTIVE_BACKEND == 'polars' and isinstance(hosp_bounds_df, pd.DataFrame):
        hosp_bounds_df = pl.from_pandas(hosp_bounds_df)

    results: Dict[str, Dict[str, DQAPlausibilityResult]] = {}

    for tbl_name, cache in caches.items():
        if tbl_name == 'hospitalization':
            continue

        temporal_df = cache.get('temporal_df')
        if temporal_df is None:
            continue

        # Ensure temporal_df matches active backend
        if _ACTIVE_BACKEND == 'polars' and isinstance(temporal_df, pd.DataFrame):
            temporal_df = pl.from_pandas(temporal_df)

        time_cols = _CROSS_TABLE_TIME_COLUMNS.get(tbl_name, [])
        if not time_cols:
            continue

        # Determine available time columns in the cached temporal subset
        if HAS_POLARS and isinstance(temporal_df, (pl.DataFrame, pl.LazyFrame)):
            actual_cols = (temporal_df.collect_schema().names()
                          if isinstance(temporal_df, pl.LazyFrame)
                          else temporal_df.columns)
        else:
            actual_cols = temporal_df.columns.tolist()

        available_time_cols = [c for c in time_cols if c in actual_cols]
        if not available_time_cols or 'hospitalization_id' not in actual_cols:
            continue

        result = check_cross_table_temporal_plausibility(
            temporal_df, hosp_bounds_df, tbl_name, available_time_cols,
            **thresholds['cross_table_temporal']
        )
        results.setdefault(tbl_name, {})["cross_table_temporal"] = result

    checked = sum(len(v) for v in results.values())
    _logger.info(
        "run_cross_table_plausibility_checks_from_cache: completed %d checks across %d tables",
        checked, len(results),
    )
    return results

Report Generation

clifpy.utils.report_generator.collect_dqa_issues 

collect_dqa_issues(validation_data)

Collect errors, warnings, and info messages from run_full_dqa output.

Returns (category_scores, all_issues) where each issue is a dict with category, check_type, severity ('error'/'warning'/'info'), message, details, plus enriched fields: rule_code, rule_description, column_field.

Source code in clifpy/utils/report_generator.py 
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def collect_dqa_issues(validation_data: Dict[str, Any]):
    """Collect errors, warnings, and info messages from run_full_dqa output.

    Returns (category_scores, all_issues) where each issue is a dict with
    category, check_type, severity ('error'/'warning'/'info'), message, details,
    plus enriched fields: rule_code, rule_description, column_field.
    """
    category_scores = {}
    all_issues: List[Dict[str, Any]] = []

    for category in DQA_CATEGORIES:
        checks = validation_data.get(category, {})
        if not checks:
            continue
        for check_name, d in checks.items():
            for err in d['errors']:
                issue = {
                    'category': category,
                    'check_type': d['check_type'],
                    'severity': 'error',
                    'message': err.get('message', ''),
                    'details': err.get('details', {}),
                }
                enriched = enrich_issue(issue, check_key=check_name)
                if enriched is not None:
                    all_issues.append(enriched)
            for warn in d['warnings']:
                issue = {
                    'category': category,
                    'check_type': d['check_type'],
                    'severity': 'warning',
                    'message': warn.get('message', ''),
                    'details': warn.get('details', {}),
                }
                enriched = enrich_issue(issue, check_key=check_name)
                if enriched is not None:
                    all_issues.append(enriched)
            for info_msg in d.get('info', []):
                issue = {
                    'category': category,
                    'check_type': d['check_type'],
                    'severity': 'info',
                    'message': info_msg.get('message', ''),
                    'details': info_msg.get('details', {}),
                }
                enriched = enrich_issue(issue, check_key=check_name)
                if enriched is not None:
                    all_issues.append(enriched)

    # Compute scores from enriched findings so summary matches detail counts
    for category in DQA_CATEGORIES:
        cat_issues = [i for i in all_issues if i['category'] == category]
        if cat_issues:
            cat_passed = sum(1 for i in cat_issues if i['severity'] in ('info', 'warning'))
            category_scores[category] = (cat_passed, len(cat_issues))

    return category_scores, all_issues

clifpy.utils.report_generator.generate_validation_pdf 

generate_validation_pdf(validation_data, table_name, output_path, site_name=None, feedback=None)

Generate a PDF report from DQA validation results.

Parameters:

Name Type Description Default
validation_data dict

Output from run_full_dqa (keys: conformance, completeness, relational, plausibility).

 required
table_name str

Name of the table.

 required
output_path str

Path where PDF should be saved.

 required
site_name str

Name of the site/hospital.

 None
feedback dict

User feedback with 'user_decisions' keyed by error_id.

 None

Returns:

Type Description
str

Path to generated PDF file.
Source code in clifpy/utils/report_generator.py 
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def generate_validation_pdf(validation_data: Dict[str, Any],
                            table_name: str, output_path: str,
                            site_name: Optional[str] = None,
                            feedback: Optional[Dict[str, Any]] = None) -> str:
    """
    Generate a PDF report from DQA validation results.

    Parameters
    ----------
    validation_data : dict
        Output from run_full_dqa (keys: conformance, completeness,
        relational, plausibility).
    table_name : str
        Name of the table.
    output_path : str
        Path where PDF should be saved.
    site_name : str, optional
        Name of the site/hospital.
    feedback : dict, optional
        User feedback with 'user_decisions' keyed by error_id.

    Returns
    -------
    str
        Path to generated PDF file.
    """
    category_scores, all_issues = collect_dqa_issues(validation_data)

    # Build feedback lookup: error_id -> decision dict
    feedback_lookup: Dict[str, Dict[str, Any]] = {}
    if feedback and feedback.get('user_decisions'):
        feedback_lookup = feedback['user_decisions']

    # Build set of rejected error IDs so we can adjust summary counts
    rejected_ids: set = {
        eid for eid, d in feedback_lookup.items()
        if d.get('decision') == 'rejected'
    }

    total_passed = sum(p for p, _ in category_scores.values())
    total_checks = sum(t for _, t in category_scores.values())
    error_count = sum(1 for i in all_issues if i['severity'] == 'error')
    warning_count = sum(1 for i in all_issues if i['severity'] == 'warning')

    # Adjust counts: rejected errors no longer count as errors
    if rejected_ids:
        rejected_error_count = sum(
            1 for i in all_issues
            if i['severity'] == 'error' and _make_error_id(i) in rejected_ids
        )
        error_count -= rejected_error_count
        total_passed += rejected_error_count

    # --- Build PDF ---
    doc = SimpleDocTemplate(output_path, pagesize=letter)
    story = []
    styles = getSampleStyleSheet()

    primary_color = colors.HexColor('#1F4E79')
    text_dark = colors.HexColor('#2C3E50')
    text_medium = colors.HexColor('#5D6D7E')
    header_bg = colors.HexColor('#F5F6FA')
    pass_bg = colors.HexColor('#E8F5E8')
    fail_bg = colors.HexColor('#FFEAEA')
    warn_bg = colors.HexColor('#FFF3E0')

    title_style = ParagraphStyle(
        'CustomTitle', parent=styles['Heading1'],
        fontSize=22, textColor=primary_color, spaceAfter=24,
        alignment=TA_CENTER, fontName='Helvetica-Bold',
    )
    heading_style = ParagraphStyle(
        'CustomHeading', parent=styles['Heading2'],
        fontSize=14, textColor=text_dark, spaceAfter=10,
        spaceBefore=16, fontName='Helvetica-Bold',
    )
    timestamp_style = ParagraphStyle(
        'TimestampStyle', parent=styles['Normal'],
        fontSize=8, textColor=text_medium, alignment=1,
        fontName='Helvetica',
    )

    # Cell styles for issue detail tables
    cell_style = ParagraphStyle(
        'CellStyle', parent=styles['Normal'],
        fontSize=7, leading=9, fontName='Helvetica',
        textColor=text_dark,
    )
    cell_bold_style = ParagraphStyle(
        'CellBoldStyle', parent=cell_style,
        fontName='Helvetica-Bold',
    )

    # Timestamp
    ts = Table(
        [[Paragraph(f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}", timestamp_style)]],
        colWidths=[7.5 * inch],
    )
    ts.setStyle(TableStyle([
        ('ALIGN', (0, 0), (0, 0), 'RIGHT'),
        ('TOPPADDING', (0, 0), (0, 0), -24),
        ('BOTTOMPADDING', (0, 0), (0, 0), 2),
    ]))
    story.append(ts)

    # Title
    title_text = f"{site_name + ' ' if site_name else ''}CLIF DQA Report Card"
    story.append(Paragraph(title_text, title_style))
    story.append(Paragraph(f"{table_name.title()} Table", heading_style))
    story.append(Spacer(1, 0.2 * inch))

    # --- Feedback banner (only when feedback with decisions exists) ---
    has_feedback = bool(feedback_lookup)
    if has_feedback:
        n_accepted = sum(1 for d in feedback_lookup.values() if d.get('decision') == 'accepted')
        n_rejected = sum(1 for d in feedback_lookup.values() if d.get('decision') == 'rejected')
        if n_accepted > 0 or n_rejected > 0:
            from datetime import datetime as _dt
            _raw_ts = feedback.get('timestamp', '')
            try:
                fb_ts = _dt.fromisoformat(_raw_ts).strftime('%Y-%m-%d %H:%M')
            except (ValueError, TypeError):
                fb_ts = _raw_ts
            banner_style = ParagraphStyle(
                'FeedbackBanner', parent=styles['Normal'],
                fontSize=8, textColor=colors.HexColor('#1F4E79'),
                fontName='Helvetica',
            )
            banner_text = (
                f"<i>This report was updated based on feedback provided on {fb_ts}. "
                f"Accepted: {n_accepted} | Rejected: {n_rejected}</i>"
            )
            banner_tbl = Table(
                [[Paragraph(banner_text, banner_style)]],
                colWidths=[7.5 * inch],
            )
            banner_tbl.setStyle(TableStyle([
                ('BACKGROUND', (0, 0), (0, 0), colors.HexColor('#E8F0FE')),
                ('TOPPADDING', (0, 0), (0, 0), 6),
                ('BOTTOMPADDING', (0, 0), (0, 0), 6),
                ('LEFTPADDING', (0, 0), (0, 0), 10),
                ('RIGHTPADDING', (0, 0), (0, 0), 10),
            ]))
            story.append(banner_tbl)
            story.append(Spacer(1, 0.15 * inch))

    # --- DQA Summary Table ---
    story.append(Paragraph("DQA Summary", heading_style))
    summary_header = ['Category', 'Non-Error', 'Total', 'Errors', 'Warnings']
    summary_rows = [summary_header]
    for category in DQA_CATEGORIES:
        if category not in category_scores:
            continue
        passed, total = category_scores[category]
        cat_issues = [i for i in all_issues if i['category'] == category]
        cat_errors = sum(1 for i in cat_issues if i['severity'] == 'error')
        cat_warnings = sum(1 for i in cat_issues if i['severity'] == 'warning')
        # Adjust for rejected errors in this category
        if rejected_ids:
            cat_rejected = sum(
                1 for i in cat_issues
                if i['severity'] == 'error' and _make_error_id(i) in rejected_ids
            )
            cat_errors -= cat_rejected
            passed += cat_rejected
        summary_rows.append([category.title(), str(passed), str(total),
                             str(cat_errors), str(cat_warnings)])
    summary_rows.append(['Overall', str(total_passed), str(total_checks),
                         str(error_count), str(warning_count)])

    summary_tbl = Table(summary_rows, colWidths=[2 * inch, 0.8 * inch, 0.8 * inch,
                                                  0.8 * inch, 0.8 * inch])
    tbl_style = [
        ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
        ('FONTSIZE', (0, 0), (-1, -1), 9),
        ('BACKGROUND', (0, 0), (-1, 0), header_bg),
        ('TEXTCOLOR', (0, 0), (-1, -1), text_dark),
        ('GRID', (0, 0), (-1, -1), 0.5, colors.HexColor('#DADADA')),
        ('TOPPADDING', (0, 0), (-1, -1), 6),
        ('BOTTOMPADDING', (0, 0), (-1, -1), 6),
        ('LEFTPADDING', (0, 0), (-1, -1), 10),
        ('RIGHTPADDING', (0, 0), (-1, -1), 10),
    ]
    # Color-code error/warning cells
    for row_idx in range(1, len(summary_rows)):
        errors_val = int(summary_rows[row_idx][3])
        warnings_val = int(summary_rows[row_idx][4])
        if errors_val > 0:
            tbl_style.append(('BACKGROUND', (3, row_idx), (3, row_idx), fail_bg))
        else:
            tbl_style.append(('BACKGROUND', (3, row_idx), (3, row_idx), pass_bg))
        if warnings_val > 0:
            tbl_style.append(('BACKGROUND', (4, row_idx), (4, row_idx), warn_bg))
        else:
            tbl_style.append(('BACKGROUND', (4, row_idx), (4, row_idx), pass_bg))
    summary_tbl.setStyle(TableStyle(tbl_style))
    story.append(summary_tbl)
    story.append(Spacer(1, 0.3 * inch))

    # --- Data Profile Table ---
    table_stats = validation_data.get('table_stats', [])
    if table_stats:
        story.append(Paragraph("Data Profile", heading_style))
        total_rows = validation_data.get('total_rows', 0)
        profile_subtitle = ParagraphStyle(
            'ProfileSubtitle', parent=styles['Normal'],
            fontSize=9, textColor=text_medium, fontName='Helvetica',
        )
        story.append(Paragraph(f"Total Rows: {total_rows:,}", profile_subtitle))
        story.append(Spacer(1, 0.1 * inch))

        profile_header = ['Column', 'Dtype', 'Null', 'Null%', 'Unique', 'Min', 'Max']
        profile_rows = [profile_header]
        for s in table_stats:
            profile_rows.append([
                s['column'], s['dtype'],
                f"{s['null_count']:,}",
                f"{s['null_pct']:.1f}%", f"{s['unique']:,}",
                s.get('min') or '', s.get('max') or '',
            ])

        profile_col_widths = [1.6 * inch, 0.9 * inch,
                              0.6 * inch, 0.6 * inch, 0.6 * inch,
                              1.3 * inch, 1.3 * inch]
        profile_tbl = Table(profile_rows, colWidths=profile_col_widths)

        profile_style = [
            ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
            ('FONTSIZE', (0, 0), (-1, -1), 7),
            ('BACKGROUND', (0, 0), (-1, 0), header_bg),
            ('TEXTCOLOR', (0, 0), (-1, -1), text_dark),
            ('GRID', (0, 0), (-1, -1), 0.5, colors.HexColor('#DADADA')),
            ('TOPPADDING', (0, 0), (-1, -1), 3),
            ('BOTTOMPADDING', (0, 0), (-1, -1), 3),
            ('LEFTPADDING', (0, 0), (-1, -1), 4),
            ('RIGHTPADDING', (0, 0), (-1, -1), 4),
            # Right-align numeric columns (Non-Null, Null, Null%, Unique)
            ('ALIGN', (2, 0), (-1, -1), 'RIGHT'),
        ]
        # Color-code Null% cells
        amber_bg = colors.HexColor('#FFF3E0')
        red_light_bg = colors.HexColor('#FFEAEA')
        for row_idx, s in enumerate(table_stats, 1):
            if s['null_pct'] > 50:
                profile_style.append(('BACKGROUND', (3, row_idx), (3, row_idx), red_light_bg))
            elif s['null_pct'] > 10:
                profile_style.append(('BACKGROUND', (3, row_idx), (3, row_idx), amber_bg))

        profile_tbl.setStyle(TableStyle(profile_style))
        story.append(profile_tbl)
        story.append(Spacer(1, 0.3 * inch))

    # --- Per-category issue details as structured tables ---
    rejected_bg = colors.HexColor('#E0E0E0')
    rejected_text = colors.HexColor('#999999')

    if all_issues:
        story.append(PageBreak())
        story.append(Paragraph(f"Issue Details ({len(all_issues)})", heading_style))

        # Column widths — add status column only when feedback exists
        if has_feedback:
            detail_col_widths = [1.0 * inch, 0.5 * inch, 1.7 * inch,
                                 1.1 * inch, 0.5 * inch, 2.2 * inch, 0.5 * inch]
        else:
            detail_col_widths = [1.0 * inch, 0.5 * inch, 1.7 * inch,
                                 1.1 * inch, 0.5 * inch, 2.7 * inch]

        for category in DQA_CATEGORIES:
            cat_issues = [i for i in all_issues if i['category'] == category]
            if not cat_issues:
                continue

            story.append(Paragraph(f"{category.title()} ({len(cat_issues)})", heading_style))

            # Header row
            header_row = [
                Paragraph('<b>metric</b>', cell_bold_style),
                Paragraph('<b>rule</b>', cell_bold_style),
                Paragraph('<b>rule_description</b>', cell_bold_style),
                Paragraph('<b>column_field</b>', cell_bold_style),
                Paragraph('<b>severity</b>', cell_bold_style),
                Paragraph('<b>finding</b>', cell_bold_style),
            ]
            if has_feedback:
                header_row.append(Paragraph('<b>status</b>', cell_bold_style))
            table_data = [header_row]

            for issue in cat_issues:
                severity_upper = issue['severity'].upper()
                finding_text = truncate_comment(issue.get('finding', issue['message']))
                # Build finding cell: text + optional sparkline for temporal checks
                spark_width = 2.0 * inch if has_feedback else 2.5 * inch
                yearly_counts = issue.get('details', {}).get('yearly_counts')
                if yearly_counts:
                    finding_cell = [
                        Paragraph(escape(finding_text), cell_style),
                        Spacer(1, 2),
                        YearlySparkBar(yearly_counts, width=spark_width, height=16),
                    ]
                else:
                    finding_cell = Paragraph(escape(finding_text), cell_style)
                row = [
                    Paragraph(escape(category), cell_style),
                    Paragraph(escape(issue.get('rule_code', '')), cell_style),
                    Paragraph(escape(issue.get('rule_description', '')), cell_style),
                    Paragraph(escape(issue.get('column_field', 'NA')), cell_style),
                    Paragraph(escape(severity_upper), cell_style),
                    finding_cell,
                ]
                if has_feedback:
                    if issue['severity'] == 'error':
                        error_id = _make_error_id(issue)
                        decision_info = feedback_lookup.get(error_id, {})
                        status_text = decision_info.get('decision', '').upper()
                        row.append(Paragraph(escape(status_text), cell_style))
                    else:
                        row.append(Paragraph('', cell_style))
                table_data.append(row)

            detail_tbl = Table(table_data, colWidths=detail_col_widths,
                               repeatRows=1)

            # Base table style
            detail_style = [
                ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
                ('FONTSIZE', (0, 0), (-1, -1), 7),
                ('BACKGROUND', (0, 0), (-1, 0), header_bg),
                ('TEXTCOLOR', (0, 0), (-1, -1), text_dark),
                ('GRID', (0, 0), (-1, -1), 0.5, colors.HexColor('#DADADA')),
                ('TOPPADDING', (0, 0), (-1, -1), 3),
                ('BOTTOMPADDING', (0, 0), (-1, -1), 3),
                ('LEFTPADDING', (0, 0), (-1, -1), 4),
                ('RIGHTPADDING', (0, 0), (-1, -1), 4),
                ('VALIGN', (0, 0), (-1, -1), 'TOP'),
            ]

            # Color-code rows by severity, override with grey for rejected
            for row_idx, issue in enumerate(cat_issues, 1):
                error_id = _make_error_id(issue)
                decision = feedback_lookup.get(error_id, {}).get('decision', '')
                if decision == 'rejected':
                    detail_style.append(('BACKGROUND', (0, row_idx), (-1, row_idx), rejected_bg))
                    detail_style.append(('TEXTCOLOR', (0, row_idx), (-1, row_idx), rejected_text))
                elif issue['severity'] == 'error':
                    detail_style.append(('BACKGROUND', (0, row_idx), (-1, row_idx), fail_bg))
                elif issue['severity'] == 'warning':
                    detail_style.append(('BACKGROUND', (0, row_idx), (-1, row_idx), warn_bg))

            detail_tbl.setStyle(TableStyle(detail_style))
            story.append(detail_tbl)

            # Add note about monthly trend CSVs for temporal consistency checks
            temporal_cols = sorted({
                i['column_field'] for i in cat_issues
                if i.get('check_type') == 'category_temporal_consistency'
                and i.get('column_field')
            })
            if temporal_cols:
                file_list = ", ".join(
                    f"{table_name}_{col}_monthly.csv" for col in temporal_cols
                )
                note_text = (
                    f"<i>P.6 Category temporal consistency — monthly breakdown available at: "
                    f"clifpy/monthly_trends/ ({file_list})</i>"
                )
                note_style = ParagraphStyle(
                    'NoteStyle', parent=styles['Normal'],
                    fontSize=7, textColor=colors.HexColor('#555555'),
                )
                story.append(Paragraph(note_text, note_style))

            story.append(Spacer(1, 0.2 * inch))
    else:
        story.append(Paragraph("No validation issues found!", styles['Normal']))

    doc.build(story)
    return output_path

clifpy.utils.report_generator.generate_text_report 

generate_text_report(validation_data, table_name, output_path, site_name=None)

Generate a plain-text DQA report.

Parameters match generate_validation_pdf.

Source code in clifpy/utils/report_generator.py 
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def generate_text_report(validation_data: Dict[str, Any],
                         table_name: str, output_path: str,
                         site_name: Optional[str] = None) -> str:
    """
    Generate a plain-text DQA report.

    Parameters match generate_validation_pdf.
    """
    category_scores, all_issues = collect_dqa_issues(validation_data)
    total_passed = sum(p for p, _ in category_scores.values())
    total_checks = sum(t for _, t in category_scores.values())
    error_count = sum(1 for i in all_issues if i['severity'] == 'error')
    warning_count = sum(1 for i in all_issues if i['severity'] == 'warning')

    lines = []
    lines.append("=" * 120)
    lines.append("CLIF 2.1 DQA VALIDATION REPORT")
    lines.append(f"{table_name.upper()} TABLE")
    lines.append("=" * 120)
    lines.append("")
    if site_name:
        lines.append(f"Site: {site_name}")
    lines.append(f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}")
    lines.append("")

    # DQA Summary
    lines.append("-" * 120)
    lines.append("DQA SUMMARY")
    lines.append("-" * 120)
    lines.append(f"  {'Category':20s}  {'Passed':>6s}  {'Total':>5s}  {'Errors':>6s}  {'Warnings':>8s}")
    lines.append(f"  {'-'*20}  {'-'*6}  {'-'*5}  {'-'*6}  {'-'*8}")
    for category in DQA_CATEGORIES:
        if category not in category_scores:
            continue
        passed, total = category_scores[category]
        cat_issues = [i for i in all_issues if i['category'] == category]
        cat_errors = sum(1 for i in cat_issues if i['severity'] == 'error')
        cat_warnings = sum(1 for i in cat_issues if i['severity'] == 'warning')
        lines.append(f"  {category.title():20s}  {passed:>6d}  {total:>5d}  {cat_errors:>6d}  {cat_warnings:>8d}")
    lines.append(f"  {'Overall':20s}  {total_passed:>6d}  {total_checks:>5d}  {error_count:>6d}  {warning_count:>8d}")
    lines.append("")

    # Data Profile
    table_stats = validation_data.get('table_stats', [])
    if table_stats:
        lines.append("-" * 120)
        lines.append("DATA PROFILE")
        lines.append("-" * 120)
        total_rows = validation_data.get('total_rows', 0)
        lines.append(f"  Total Rows: {total_rows:,}")
        lines.append("")
        w_col, w_dtype, w_null, w_pct, w_uniq, w_min, w_max = 25, 12, 8, 8, 10, 20, 20
        hdr = (f"  {'Column':<{w_col}}"
               f"{'Dtype':<{w_dtype}}"
               f"{'Null':>{w_null}}"
               f"{'Null%':>{w_pct}}"
               f"{'Unique':>{w_uniq}}"
               f"  {'Min':<{w_min}}"
               f"{'Max':<{w_max}}")
        lines.append(hdr)
        lines.append("  " + "-" * (w_col + w_dtype + w_null + w_pct + w_uniq + 2 + w_min + w_max))
        for s in table_stats:
            col_name = s['column']
            if len(col_name) > w_col - 2:
                col_name = col_name[:w_col - 4] + '..'
            col_min = s.get('min') or ''
            col_max = s.get('max') or ''
            lines.append(
                f"  {col_name:<{w_col}}"
                f"{s['dtype']:<{w_dtype}}"
                f"{s['null_count']:>{w_null},}"
                f"{s['null_pct']:>{w_pct}.1f}%"
                f"{s['unique']:>{w_uniq},}"
                f"  {col_min:<{w_min}}"
                f"{col_max:<{w_max}}"
            )
        lines.append("")

    # Issue details as tabular text
    if all_issues:
        lines.append("=" * 120)
        lines.append(f"ISSUE DETAILS ({len(all_issues)})")
        lines.append("=" * 120)

        # Column widths for text alignment
        w_metric, w_rule, w_desc, w_col, w_sev = 14, 6, 30, 18, 10

        for category in DQA_CATEGORIES:
            cat_issues = [i for i in all_issues if i['category'] == category]
            if not cat_issues:
                continue

            lines.append("")
            lines.append(f"-- {category.title()} ({len(cat_issues)}) --")
            lines.append("")

            # Header
            hdr = (f"  {'metric':<{w_metric}}"
                   f"{'rule':<{w_rule}}"
                   f"{'rule_description':<{w_desc}}"
                   f"{'column_field':<{w_col}}"
                   f"{'severity':<{w_sev}}"
                   f"finding")
            lines.append(hdr)
            lines.append("  " + "-" * 116)

            for issue in cat_issues:
                severity_upper = issue['severity'].upper()
                rule_code = issue.get('rule_code', '')
                rule_desc = issue.get('rule_description', '')
                col_field = issue.get('column_field', 'NA')
                finding = issue.get('finding', issue['message'])

                # Truncate long fields for text display
                if len(rule_desc) > w_desc - 2:
                    rule_desc = rule_desc[:w_desc - 4] + '..'
                if len(col_field) > w_col - 2:
                    col_field = col_field[:w_col - 4] + '..'

                line = (f"  {category:<{w_metric}}"
                        f"{rule_code:<{w_rule}}"
                        f"{rule_desc:<{w_desc}}"
                        f"{col_field:<{w_col}}"
                        f"{severity_upper:<{w_sev}}"
                        f"{finding}")
                lines.append(line)
    else:
        lines.append("No validation issues found!")

    lines.append("")
    lines.append("=" * 120)
    lines.append("END OF REPORT")
    lines.append("=" * 120)

    with open(output_path, 'w') as f:
        f.write('\n'.join(lines))

    return output_path

Backward Compatibility

clifpy.utils.validator.validate_dataframe 

validate_dataframe(df, schema, table_name=None, plausibility_thresholds=None)

Validate a dataframe against schema and return list of errors.

This function provides compatibility with CLIF-TableOne's expected validation interface.

Parameters:

Name Type Description Default
df pd.DataFrame, pl.DataFrame, or pl.LazyFrame

Data to validate

 required
schema dict

Table schema containing columns, required_columns, etc.

 required
table_name str

Name of the table (inferred from schema if not provided)

 None
plausibility_thresholds dict

Override default plausibility thresholds per check.

 None

Returns:

Type Description
List[Dict[str, Any]]

List of error dictionaries with keys: - type: str - Error type/check name - description: str - Human-readable error description - details: dict - Additional error details - category: str - 'schema' or 'data_quality'
Source code in clifpy/utils/validator.py 
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def validate_dataframe(
    df: Union[pd.DataFrame, 'pl.DataFrame', 'pl.LazyFrame'],
    schema: Dict[str, Any],
    table_name: Optional[str] = None,
    plausibility_thresholds: Optional[Dict[str, Dict[str, float]]] = None,
) -> List[Dict[str, Any]]:
    """
    Validate a dataframe against schema and return list of errors.

    This function provides compatibility with CLIF-TableOne's expected
    validation interface.

    Parameters
    ----------
    df : pd.DataFrame, pl.DataFrame, or pl.LazyFrame
        Data to validate
    schema : dict
        Table schema containing columns, required_columns, etc.
    table_name : str, optional
        Name of the table (inferred from schema if not provided)
    plausibility_thresholds : dict, optional
        Override default plausibility thresholds per check.

    Returns
    -------
    List[Dict[str, Any]]
        List of error dictionaries with keys:
        - type: str - Error type/check name
        - description: str - Human-readable error description
        - details: dict - Additional error details
        - category: str - 'schema' or 'data_quality'
    """
    table_name = table_name or schema.get('table_name', 'unknown')
    _logger.info("validate_dataframe: starting validation for table '%s'", table_name)
    errors = []

    # Schema-level checks (affect 'incomplete' status)
    schema_checks = ['required_columns', 'column_dtypes']

    # Run conformance checks
    conformance_results = run_conformance_checks(df, schema, table_name)
    for check_name, result in conformance_results.items():
        category = 'schema' if check_name in schema_checks else 'data_quality'

        for err in result.errors:
            errors.append({
                'type': _format_check_type(check_name),
                'description': err['message'],
                'details': err.get('details', {}),
                'category': category
            })

        # Include warnings as data quality issues
        for warn in result.warnings:
            errors.append({
                'type': _format_check_type(check_name),
                'description': warn['message'],
                'details': warn.get('details', {}),
                'category': 'data_quality',
                'severity': 'warning'
            })

    # Run completeness checks
    completeness_results = run_completeness_checks(df, schema, table_name)
    for check_name, result in completeness_results.items():
        for err in result.errors:
            errors.append({
                'type': _format_check_type(check_name),
                'description': err['message'],
                'details': err.get('details', {}),
                'category': 'data_quality'
            })

        for warn in result.warnings:
            errors.append({
                'type': _format_check_type(check_name),
                'description': warn['message'],
                'details': warn.get('details', {}),
                'category': 'data_quality',
                'severity': 'warning'
            })

    # Run plausibility checks
    plausibility_results = run_plausibility_checks(
        df, schema, table_name,
        plausibility_thresholds=plausibility_thresholds,
    )
    for check_name, result in plausibility_results.items():
        for err in result.errors:
            errors.append({
                'type': _format_check_type(check_name),
                'description': err['message'],
                'details': err.get('details', {}),
                'category': 'data_quality'
            })

        for warn in result.warnings:
            errors.append({
                'type': _format_check_type(check_name),
                'description': warn['message'],
                'details': warn.get('details', {}),
                'category': 'data_quality',
                'severity': 'warning'
            })

    gc.collect()
    error_count = sum(1 for e in errors if e.get('severity', 'error') == 'error')
    warning_count = sum(1 for e in errors if e.get('severity') == 'warning')
    _logger.info("validate_dataframe: table '%s' complete — %d errors, %d warnings",
                 table_name, error_count, warning_count)
    return errors

clifpy.utils.validator.format_clifpy_error 

format_clifpy_error(error, row_count, table_name)

Format a validation error for display.

Parameters:

Name Type Description Default
error dict

Error dictionary from validate_dataframe()

 required
row_count int

Total row count of the table

 required
table_name str

Name of the table

 required

Returns:

Type Description
dict

Formatted error with type, description, category, and details
Source code in clifpy/utils/validator.py 
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def format_clifpy_error(
    error: Dict[str, Any],
    row_count: int,
    table_name: str
) -> Dict[str, Any]:
    """
    Format a validation error for display.

    Parameters
    ----------
    error : dict
        Error dictionary from validate_dataframe()
    row_count : int
        Total row count of the table
    table_name : str
        Name of the table

    Returns
    -------
    dict
        Formatted error with type, description, category, and details
    """
    formatted = {
        'type': error.get('type', 'Unknown Error'),
        'description': error.get('description', str(error)),
        'category': error.get('category', 'other'),
        'details': error.get('details', {}),
        'table_name': table_name,
        'row_count': row_count
    }

    # Add severity if present
    if 'severity' in error:
        formatted['severity'] = error['severity']

    return formatted

clifpy.utils.validator.determine_validation_status 

determine_validation_status(errors, required_columns=None, table_name=None)

Determine validation status based on errors.

Status Logic: - INCOMPLETE (red): Missing required columns OR non-castable datatype errors OR 100% null in required columns - PARTIAL (yellow): Required columns present but has data quality issues (missing categorical values, high missingness, etc.) - COMPLETE (green): All required columns present, no critical issues

Parameters:

Name Type Description Default
errors list

List of formatted error dictionaries

 required
required_columns list

List of required column names

 None
table_name str

Name of the table (for table-specific logic)

 None

Returns:

Type Description
str

'complete', 'partial', or 'incomplete'
Source code in clifpy/utils/validator.py 
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def determine_validation_status(
    errors: List[Dict[str, Any]],
    required_columns: Optional[List[str]] = None,
    table_name: Optional[str] = None
) -> str:
    """
    Determine validation status based on errors.

    Status Logic:
    - INCOMPLETE (red): Missing required columns OR non-castable datatype errors
      OR 100% null in required columns
    - PARTIAL (yellow): Required columns present but has data quality issues
      (missing categorical values, high missingness, etc.)
    - COMPLETE (green): All required columns present, no critical issues

    Parameters
    ----------
    errors : list
        List of formatted error dictionaries
    required_columns : list, optional
        List of required column names
    table_name : str, optional
        Name of the table (for table-specific logic)

    Returns
    -------
    str
        'complete', 'partial', or 'incomplete'
    """
    if not errors:
        _logger.debug("determine_validation_status: no errors — status='complete'")
        return 'complete'

    # Check for schema-level errors that make data incomplete
    for error in errors:
        error_type = error.get('type', '').lower()
        category = error.get('category', '')
        details = error.get('details', {})
        severity = error.get('severity', 'error')

        # Missing required columns -> incomplete
        if 'missing required columns' in error_type or 'missing_columns' in details:
            _logger.debug("determine_validation_status: missing required columns — status='incomplete'")
            return 'incomplete'

        # Non-castable data type errors -> incomplete
        if 'data type' in error_type and category == 'schema':
            if details.get('castable') is False:
                _logger.debug("determine_validation_status: non-castable dtype — status='incomplete'")
                return 'incomplete'

        # 100% missingness in required columns -> incomplete
        if 'missingness' in error_type and severity != 'warning':
            pct_missing = details.get('percent_missing', 0)
            column = details.get('column', '')
            if pct_missing >= 100 and required_columns and column in required_columns:
                _logger.debug("determine_validation_status: 100%% null in '%s' — status='incomplete'", column)
                return 'incomplete'

    # Has errors but not critical -> partial
    has_errors = any(
        e.get('severity', 'error') == 'error'
        for e in errors
    )

    if has_errors:
        _logger.debug("determine_validation_status: has non-critical errors — status='partial'")
        return 'partial'

    # Only warnings -> complete
    _logger.debug("determine_validation_status: warnings only — status='complete'")
    return 'complete'

clifpy.utils.validator.classify_errors_by_status_impact 

classify_errors_by_status_impact(errors, required_columns, table_name, config_timezone=None)

Classify errors into status-affecting and informational categories.

Used by PDF/report generators to separate critical errors from informational messages.

Parameters:

Name Type Description Default
errors dict

Dictionary with keys 'schema_errors', 'data_quality_issues', 'other_errors'

 required
required_columns list

List of required column names

 required
table_name str

Name of the table

 required
config_timezone str

Configured timezone (to filter timezone-related errors)

 None

Returns:

Type Description
dict

Dictionary with 'status_affecting' and 'informational', each containing 'schema_errors', 'data_quality_issues', and 'other_errors' lists
Source code in clifpy/utils/validator.py 
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def classify_errors_by_status_impact(
    errors: Dict[str, List[Dict[str, Any]]],
    required_columns: List[str],
    table_name: str,
    config_timezone: Optional[str] = None
) -> Dict[str, Dict[str, List[Dict[str, Any]]]]:
    """
    Classify errors into status-affecting and informational categories.

    Used by PDF/report generators to separate critical errors from
    informational messages.

    Parameters
    ----------
    errors : dict
        Dictionary with keys 'schema_errors', 'data_quality_issues', 'other_errors'
    required_columns : list
        List of required column names
    table_name : str
        Name of the table
    config_timezone : str, optional
        Configured timezone (to filter timezone-related errors)

    Returns
    -------
    dict
        Dictionary with 'status_affecting' and 'informational', each containing
        'schema_errors', 'data_quality_issues', and 'other_errors' lists
    """
    status_affecting = {
        'schema_errors': [],
        'data_quality_issues': [],
        'other_errors': []
    }
    informational = {
        'schema_errors': [],
        'data_quality_issues': [],
        'other_errors': []
    }

    # Columns that are optional and shouldn't affect status
    optional_columns = {
        'patient': ['race', 'ethnicity', 'language'],
        'hospitalization': ['discharge_category'],
    }
    table_optional = optional_columns.get(table_name, [])

    # Process each error category
    for category_key in ['schema_errors', 'data_quality_issues', 'other_errors']:
        for error in errors.get(category_key, []):
            error_type = error.get('type', '').lower()
            details = error.get('details', {})
            description = error.get('description', '').lower()

            is_informational = False

            # Filter out timezone errors for configured timezone
            if config_timezone and 'timezone' in error_type:
                if config_timezone.lower() in description:
                    is_informational = True

            # Filter out optional column issues
            column = details.get('column', '')
            if column in table_optional:
                is_informational = True

            # mCIDE coverage gaps are informational
            if 'mcide' in error_type or 'coverage' in error_type:
                is_informational = True

            # Plausibility warnings are informational; plausibility errors affect status
            plausibility_keywords = ['temporal ordering', 'numeric range', 'field plausibility',
                                     'dose unit', 'overlapping', 'distribution shift',
                                     'duplicate composite', 'cross-table temporal']
            is_plausibility = any(p in error_type for p in plausibility_keywords)
            if is_plausibility and error.get('severity') == 'warning':
                is_informational = True

            # Warnings are generally informational
            if error.get('severity') == 'warning':
                is_informational = True

            # Classify into appropriate bucket
            if is_informational:
                informational[category_key].append(error)
            else:
                status_affecting[category_key].append(error)

    return {
        'status_affecting': status_affecting,
        'informational': informational
    }

clifpy.utils.validator.get_validation_summary 

get_validation_summary(validation_results)

Generate a text summary of validation results.

Parameters:

Name Type Description Default
validation_results dict

Validation results from validate() method

 required

Returns:

Type Description
str

Human-readable summary string
Source code in clifpy/utils/validator.py 
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def get_validation_summary(validation_results: Dict[str, Any]) -> str:
    """
    Generate a text summary of validation results.

    Parameters
    ----------
    validation_results : dict
        Validation results from validate() method

    Returns
    -------
    str
        Human-readable summary string
    """
    status = validation_results.get('status', 'unknown')
    errors = validation_results.get('errors', {})

    schema_count = len(errors.get('schema_errors', []))
    dq_count = len(errors.get('data_quality_issues', []))
    other_count = len(errors.get('other_errors', []))
    total = schema_count + dq_count + other_count

    status_emoji = {
        'complete': '✓',
        'partial': '⚠',
        'incomplete': '✗'
    }

    summary_parts = [
        f"Status: {status_emoji.get(status, '?')} {status.upper()}"
    ]

    if total > 0:
        summary_parts.append(f"Issues: {total} total")
        if schema_count:
            summary_parts.append(f"  - Schema: {schema_count}")
        if dq_count:
            summary_parts.append(f"  - Data Quality: {dq_count}")
        if other_count:
            summary_parts.append(f"  - Other: {other_count}")
    else:
        summary_parts.append("No issues found")

    return '\n'.join(summary_parts)