csrlite 0.2.0__tar.gz → 0.3.0__tar.gz

{csrlite-0.2.0/src/csrlite.egg-info → csrlite-0.3.0}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: csrlite
-Version: 0.2.0
+Version: 0.3.0
 Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
-Author-email: Clinical Biostatistics Team <biostat@example.com>
+Author-email: Yilong Zhang <elong0527@gmail.com>, Ming-Chun Chen <hellomingchun@gmail.com>
 License: MIT
 Project-URL: Homepage, https://github.com/elong0527/csrlite
 Project-URL: Documentation, https://elong0527.github.io/csrlite

{csrlite-0.2.0 → csrlite-0.3.0}/pyproject.toml

@@ -4,9 +4,12 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "csrlite"
-version = "0.2.0"
+version = "0.3.0"
 description = "A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials"
-authors = [{name = "Clinical Biostatistics Team", email = "biostat@example.com"}]
+authors = [
+    {name = "Yilong Zhang", email = "elong0527@gmail.com"},
+    {name = "Ming-Chun Chen", email = "hellomingchun@gmail.com"}
+]
 license = {text = "MIT"}
 readme = "README.md"
 requires-python = ">=3.10"
@@ -150,6 +153,11 @@ ignore = []
 dev = [
     "jupyter>=1.1.1",
     "jupyter-cache>=1.0.1",
+    "mypy>=1.19.0",
     "nbclient>=0.10.2",
     "notebook>=7.5.0",
+    "pyre-check>=0.9.25",
+    "pytest>=9.0.2",
+    "pytest-cov>=7.0.0",
+    "ruff>=0.14.8",
 ]

{csrlite-0.2.0 → csrlite-0.3.0}/src/csrlite/__init__.py

@@ -13,6 +13,14 @@ from .ae.ae_summary import (  # AE summary functions
     ae_summary,
     study_plan_to_ae_summary,
 )
+from .cm.cm_listing import (  # CM listing functions
+    cm_listing,
+    study_plan_to_cm_listing,
+)
+from .cm.cm_summary import (
+    cm_summary,
+    study_plan_to_cm_summary,
+)
 from .common.config import config
 from .common.count import (
     count_subject,
@@ -26,6 +34,29 @@ from .common.plan import (  # Core classes
     load_plan,
 )
 from .disposition.disposition import study_plan_to_disposition_summary
+from .ie.ie_listing import (
+    ie_listing_df,
+    ie_listing_rtf,
+    study_plan_to_ie_listing,
+)
+from .ie.ie_summary import (
+    ie_ard,
+    ie_df,
+    ie_rtf,
+    study_plan_to_ie_summary,
+)
+from .mh.mh_listing import (
+    mh_listing,
+    study_plan_to_mh_listing,
+)
+from .mh.mh_summary import (
+    mh_summary,
+    study_plan_to_mh_summary,
+)
+from .pd.pd_listing import (
+    pd_listing,
+    study_plan_to_pd_listing,
+)
 
 # Configure logging
 logging.basicConfig(
@@ -47,6 +78,11 @@ __all__ = [
     "study_plan_to_ae_summary",
     "study_plan_to_ae_specific",
     "study_plan_to_ae_listing",
+    # CM analysis
+    "cm_listing",
+    "study_plan_to_cm_listing",
+    "cm_summary",
+    "study_plan_to_cm_summary",
     # Disposition analysis
     "study_plan_to_disposition_summary",
     # Count functions
@@ -55,4 +91,20 @@ __all__ = [
     # Parse utilities
     "StudyPlanParser",
     "parse_filter_to_sql",
+    # IE analysis
+    "ie_ard",
+    "ie_df",
+    "ie_rtf",
+    "study_plan_to_ie_summary",
+    "ie_listing_df",
+    "ie_listing_rtf",
+    "study_plan_to_ie_listing",
+    # PD analysis
+    "pd_listing",
+    "study_plan_to_pd_listing",
+    # MH analysis
+    "mh_listing",
+    "study_plan_to_mh_listing",
+    "mh_summary",
+    "study_plan_to_mh_summary",
 ]

csrlite-0.3.0/src/csrlite/cm/cm_listing.py

@@ -0,0 +1,497 @@
+# pyre-strict
+"""
+Concomitant Medications (CM) Listing Functions
+
+This module provides functions for generating detailed CM listings showing individual
+medication records with key details like medication name, dose, route, etc.
+
+The two-step pipeline:
+- cm_listing_ard: Filter, select, sort, and rename columns (returns display-ready data)
+- cm_listing_rtf: Generate formatted RTF output
+- cm_listing: Complete pipeline wrapper
+- study_plan_to_cm_listing: Batch generation from StudyPlan
+
+Uses Polars native SQL capabilities for data manipulation and parse.py utilities
+for StudyPlan parsing.
+"""
+
+from pathlib import Path
+from typing import Any
+
+import polars as pl
+from rtflite import RTFBody, RTFColumnHeader, RTFDocument, RTFFootnote, RTFPage, RTFSource, RTFTitle
+
+from ..common.parse import StudyPlanParser
+from ..common.plan import StudyPlan
+from ..common.utils import apply_common_filters
+
+
+def cm_listing_ard(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    parameter_filter: str | None,
+    id: tuple[str, str],
+    population_columns: list[tuple[str, str]] | None = None,
+    observation_columns: list[tuple[str, str]] | None = None,
+    sort_columns: list[str] | None = None,
+    page_by: list[str] | None = None,
+) -> pl.DataFrame:
+    """
+    Generate Analysis Results Data (ARD) for CM listing.
+
+    Filters and joins population and observation data, then selects relevant columns.
+
+    Args:
+        population: Population DataFrame (subject-level data, e.g., ADSL)
+        observation: Observation DataFrame (event data, e.g., ADCM)
+        population_filter: SQL WHERE clause for population (can be None)
+        observation_filter: SQL WHERE clause for observation (can be None)
+        parameter_filter: SQL WHERE clause for parameter filtering (can be None)
+        id: Tuple (variable_name, label) for ID column
+        population_columns: List of tuples (variable_name, label) from population
+        observation_columns: List of tuples (variable_name, label) from observation
+        sort_columns: List of column names to sort by. If None, sorts by id column.
+
+    Returns:
+        pl.DataFrame: Filtered and joined records with selected columns
+    """
+    id_var_name, id_var_label = id
+
+    # Apply common filters
+    population_filtered, observation_to_filter = apply_common_filters(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+        parameter_filter=parameter_filter,
+    )
+
+    assert observation_to_filter is not None
+
+    # Filter observation to include only subjects in filtered population
+    observation_filtered = observation_to_filter.filter(
+        pl.col(id_var_name).is_in(population_filtered[id_var_name].to_list())
+    )
+
+    # Determine which observation columns to select
+    if observation_columns is None:
+        # Default: select id column only
+        obs_cols = [id_var_name]
+    else:
+        # Extract variable names from tuples
+        obs_col_names = [var_name for var_name, _ in observation_columns]
+        # Ensure id is included
+        obs_cols = [id_var_name] + [col for col in obs_col_names if col != id_var_name]
+
+    # Select available observation columns
+    obs_cols_available = [col for col in obs_cols if col in observation_filtered.columns]
+    result = observation_filtered.select(obs_cols_available)
+
+    # Join with population to add population columns
+    if population_columns is not None:
+        # Extract variable names from tuples
+        pop_col_names = [var_name for var_name, _ in population_columns]
+        # Select id + requested population columns
+        pop_cols = [id_var_name] + [col for col in pop_col_names if col != id_var_name]
+        pop_cols_available = [col for col in pop_cols if col in population_filtered.columns]
+        population_subset = population_filtered.select(pop_cols_available)
+
+        # Left join to preserve all observation records
+        result = result.join(population_subset, on=id_var_name, how="left")
+
+    # Create __index__ column for pagination
+    # Default to using the id column as the index
+    if id_var_name in result.columns:
+        result = result.with_columns(
+            (pl.lit(f"{id_var_label} = ") + pl.col(id_var_name).cast(pl.Utf8)).alias("__index__")
+        )
+
+    # Use page_by columns if provided and they exist
+    existing_page_by_cols = [col for col in page_by if col in result.columns] if page_by else []
+
+    if existing_page_by_cols:
+        # Create a mapping from column name to label
+        column_labels = {id_var_name: id_var_label}
+        if population_columns:
+            for var_name, var_label in population_columns:
+                column_labels[var_name] = var_label
+
+        # Ensure the order of labels matches the order of columns in page_by
+        index_expressions = []
+        for col_name in existing_page_by_cols:
+            label = column_labels.get(col_name, col_name)
+            index_expressions.append(pl.lit(f"{label} = ") + pl.col(col_name).cast(pl.Utf8))
+
+        result = result.with_columns(
+            pl.concat_str(index_expressions, separator=", ").alias("__index__")
+        )
+
+        page_by_remove = [col for col in (page_by or []) if col != id_var_name]
+        result = result.drop(page_by_remove)
+
+    if "__index__" in result.columns:
+        # Get all columns except __index__
+        other_columns = [col for col in result.columns if col != "__index__"]
+        # Reorder to have __index__ first
+        result = result.select(["__index__"] + other_columns)
+
+    # Sort by specified columns or default to id column
+    if sort_columns is None:
+        # Default: sort by id column if it exists in result
+        if id_var_name in result.columns:
+            result = result.sort(id_var_name)
+    else:
+        # Sort by specified columns that exist in result
+        cols_to_sort = [col for col in sort_columns if col in result.columns]
+        if cols_to_sort:
+            result = result.sort(cols_to_sort)
+
+    return result
+
+
+def cm_listing_rtf(
+    df: pl.DataFrame,
+    column_labels: dict[str, str],
+    title: list[str],
+    footnote: list[str] | None,
+    source: list[str] | None,
+    col_rel_width: list[float] | None = None,
+    group_by: list[str] | None = None,
+    page_by: list[str] | None = None,
+    orientation: str = "landscape",
+) -> RTFDocument:
+    """
+    Generate RTF table from CM listing display DataFrame.
+
+    Creates a formatted RTF table with column headers and optional section grouping/pagination.
+
+    Args:
+        df: Display DataFrame from cm_listing_ard
+        column_labels: Dictionary mapping column names to display labels
+        title: Title(s) for the table as list of strings
+        footnote: Optional footnote(s) as list of strings
+        source: Optional source note(s) as list of strings
+        col_rel_width: Optional list of relative column widths. If None, auto-calculated
+                       as equal widths for all columns
+        group_by: Optional list of column names to group by for section headers within pages.
+                  Should only contain population columns (e.g., ["TRT01A", "USUBJID"])
+        page_by: Optional list of column names to trigger new pages when values change.
+                 Should only contain population columns (e.g., ["TRT01A"])
+        orientation: Page orientation ("portrait" or "landscape"), default is "landscape"
+
+    Returns:
+        RTFDocument: RTF document object that can be written to file
+    """
+    # Calculate number of columns
+    n_cols = len(df.columns)
+
+    # Build column headers using labels
+    col_header = [column_labels.get(col, col) for col in df.columns]
+
+    # Calculate column widths
+    if col_rel_width is None:
+        col_widths = [1.0] * n_cols
+    else:
+        col_widths = col_rel_width
+
+    # Normalize title, footnote, source to lists
+    title_list = title
+    footnote_list: list[str] = footnote or []
+    source_list: list[str] = source or []
+
+    # Build RTF document
+    rtf_components: dict[str, Any] = {
+        "df": df,
+        "rtf_page": RTFPage(orientation=orientation),
+        "rtf_title": RTFTitle(text=title_list),
+        "rtf_column_header": [
+            RTFColumnHeader(
+                text=col_header[1:],
+                col_rel_width=col_widths[1:],
+                text_justification=["l"] + ["c"] * (n_cols - 1),
+            ),
+        ],
+        "rtf_body": RTFBody(
+            col_rel_width=col_widths,
+            text_justification=["l"] * n_cols,
+            border_left=["single"],
+            border_top=["single"] + [""] * (n_cols - 1),
+            border_bottom=["single"] + [""] * (n_cols - 1),
+            group_by=group_by,
+            page_by=page_by,
+        ),
+    }
+
+    # Add optional footnote
+    if footnote_list:
+        rtf_components["rtf_footnote"] = RTFFootnote(text=footnote_list)
+
+    # Add optional source
+    if source_list:
+        rtf_components["rtf_source"] = RTFSource(text=source_list)
+
+    # Create RTF document
+    doc = RTFDocument(**rtf_components)
+
+    return doc
+
+
+def cm_listing(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    parameter_filter: str | None,
+    id: tuple[str, str],
+    title: list[str],
+    footnote: list[str] | None,
+    source: list[str] | None,
+    output_file: str,
+    population_columns: list[tuple[str, str]] | None = None,
+    observation_columns: list[tuple[str, str]] | None = None,
+    sort_columns: list[str] | None = None,
+    group_by: list[str] | None = None,
+    page_by: list[str] | None = None,
+    col_rel_width: list[float] | None = None,
+    orientation: str = "landscape",
+) -> str:
+    """
+    Complete CM listing pipeline wrapper.
+
+    This function orchestrates the two-step pipeline:
+    1. cm_listing_ard: Filter, join, select, and sort columns
+    2. cm_listing_rtf: Generate RTF output with optional grouping/pagination
+
+    Args:
+        population: Population DataFrame (subject-level data, e.g., ADSL)
+        observation: Observation DataFrame (event data, e.g., ADCM)
+        population_filter: SQL WHERE clause for population (can be None)
+        observation_filter: SQL WHERE clause for observation (can be None)
+        parameter_filter: SQL WHERE clause for parameter filtering (can be None)
+        id: Tuple (variable_name, label) for ID column
+        title: Title for RTF output as list of strings
+        footnote: Optional footnote for RTF output as list of strings
+        source: Optional source for RTF output as list of strings
+        output_file: File path to write RTF output
+        population_columns: Optional list of tuples (variable_name, label) from population
+        observation_columns: Optional list of tuples (variable_name, label) from observation
+        sort_columns: Optional list of column names to sort by. If None, sorts by id column.
+        group_by: Optional list of column names to group by for section headers
+                  (population columns only)
+        page_by: Optional list of column names to trigger new pages (population columns only)
+        col_rel_width: Optional column widths for RTF output
+        orientation: Page orientation ("portrait" or "landscape"), default is "landscape"
+
+    Returns:
+        str: Path to the generated RTF file
+    """
+    # Step 1: Generate ARD (includes filtering, joining, and selecting)
+    df = cm_listing_ard(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+        parameter_filter=parameter_filter,
+        id=id,
+        population_columns=population_columns,
+        observation_columns=observation_columns,
+        sort_columns=sort_columns,
+        page_by=page_by,
+    )
+
+    # Build column labels from tuples
+    id_var_name, id_var_label = id
+    column_labels = {id_var_name: id_var_label}
+
+    # Add observation column labels
+    if observation_columns is not None:
+        for var_name, var_label in observation_columns:
+            column_labels[var_name] = var_label
+
+    # Add population column labels
+    if population_columns is not None:
+        for var_name, var_label in population_columns:
+            column_labels[var_name] = var_label
+
+    # Set __index__ header to empty string
+    column_labels["__index__"] = ""
+
+    # Step 2: Generate RTF and write to file
+    rtf_doc = cm_listing_rtf(
+        df=df,
+        column_labels=column_labels,
+        title=title,
+        footnote=footnote,
+        source=source,
+        col_rel_width=col_rel_width,
+        group_by=group_by,
+        page_by=["__index__"],
+        orientation=orientation,
+    )
+    rtf_doc.write_rtf(output_file)
+
+    return output_file
+
+
+def study_plan_to_cm_listing(
+    study_plan: StudyPlan,
+) -> list[str]:
+    """
+    Generate CM listing RTF outputs for all analyses defined in StudyPlan.
+
+    This function reads the expanded plan from StudyPlan and generates
+    an RTF listing for each cm_listing analysis specification automatically.
+
+    Args:
+        study_plan: StudyPlan object with loaded datasets and analysis specifications
+
+    Returns:
+        list[str]: List of paths to generated RTF files
+    """
+
+    # Meta data
+    analysis = "cm_listing"
+    output_dir = study_plan.output_dir
+    # Auto-adjust column widths based on typical content
+    col_rel_width = [1.0] * 12  # Estimate based on number of columns
+    footnote = None
+    source = None
+
+    population_df_name = "adsl"
+    observation_df_name = "adcm"
+
+    id = ("USUBJID", "Subject ID")
+    # Column configuration with labels - easy to customize
+    # Population columns (demographics) - group variable will be added dynamically
+    population_columns_base = [
+        ("AGE", "Age"),
+        ("SEX", "Sex"),
+        ("RACE", "Race"),
+    ]
+
+    # Observation columns (event details)
+    # Adjusted based on available columns in adcm.parquet
+    observation_columns_base = [
+        ("CMSEQ", "Sequence"),
+        ("CMCAT", "Category"),
+        ("ASTDT", "Start Date"),
+        ("AENDT", "End Date"),
+        ("CMINDC", "Indication"),
+        ("CMTRT", "Medication"),
+        ("CMDECOD", "Standardized Name"),
+        ("CMDOSE", "Dose"),
+        ("CMDOSU", "Unit"),
+        ("CMROUTE", "Route"),
+        ("CMFREQ", "Frequency"),
+        ("CMENDPT", "End Point"),
+    ]
+
+    # Sorting configuration
+    sort_columns = ["TRT01A", "USUBJID", "ASTDT", "CMSEQ"]
+    page_by = ["USUBJID", "SEX", "RACE", "AGE", "TRT01A"]
+    group_by = ["USUBJID"]
+
+    # Create output directory if it doesn't exist
+    Path(output_dir).mkdir(parents=True, exist_ok=True)
+
+    # Initialize parser
+    parser = StudyPlanParser(study_plan)
+
+    # Get expanded plan DataFrame
+    plan_df = study_plan.get_plan_df()
+
+    # Filter for CM listing analyses
+    cm_plans = plan_df.filter(pl.col("analysis") == analysis)
+
+    rtf_files = []
+
+    # Generate RTF for each analysis
+    for row in cm_plans.iter_rows(named=True):
+        population = row["population"]
+        observation = row.get("observation")
+        parameter = row.get("parameter")
+        group = row.get("group")
+
+        # Validate group is specified
+        if group is None:
+            raise ValueError(
+                f"Group not specified in YAML for analysis: population={population}, "
+                f"observation={observation}, parameter={parameter}. "
+                "Please add group to your YAML plan."
+            )
+
+        # Get datasets using parser
+        population_df, observation_df = parser.get_datasets(population_df_name, observation_df_name)
+
+        # Get filters using parser
+        population_filter = parser.get_population_filter(population)
+        obs_filter = parser.get_observation_filter(observation)
+
+        # Get group variable name from YAML
+        group_var_name, group_labels = parser.get_group_info(group)
+
+        # Determine group variable label
+        group_var_label = group_labels[0] if group_labels else "Treatment"
+
+        # Build columns dynamically from base configuration with labels
+        population_columns = population_columns_base + [(group_var_name, group_var_label)]
+        observation_columns = observation_columns_base
+
+        # Dynamic sort and page configuration
+        sort_columns = [group_var_name, "USUBJID", "ASTDT", "CMSEQ"]
+        page_by = ["USUBJID", "SEX", "RACE", "AGE", group_var_name]
+
+        # Get parameter filter if parameter is specified
+        parameter_filter = None
+        if parameter:
+            # Assuming similar parameter structure, though CM might just use subsets
+            param_names, param_filters, param_labels, _ = parser.get_parameter_info(parameter)
+            # For cm_listing, use the first filter
+            parameter_filter = param_filters[0] if param_filters else None
+
+        # Build title
+        title_parts = ["Listing of Concomitant Medications"]
+
+        if observation:
+            obs_kw = study_plan.keywords.observations.get(observation)
+            if obs_kw and obs_kw.label:
+                title_parts.append(obs_kw.label)
+
+        pop_kw = study_plan.keywords.populations.get(population)
+        if pop_kw and pop_kw.label:
+            title_parts.append(pop_kw.label)
+
+        # Build output filename
+        filename = f"{analysis}_{population}"
+        if observation:
+            filename += f"_{observation}"
+        if parameter:
+            filename += f"_{parameter.replace(';', '_')}"
+        filename += ".rtf"
+        output_file = str(Path(output_dir) / filename)
+
+        # Generate RTF
+        rtf_path = cm_listing(
+            population=population_df,
+            observation=observation_df,
+            population_filter=population_filter,
+            observation_filter=obs_filter,
+            parameter_filter=parameter_filter,
+            id=id,
+            title=title_parts,
+            footnote=footnote,
+            source=source,
+            output_file=output_file,
+            population_columns=population_columns,
+            observation_columns=observation_columns,
+            sort_columns=sort_columns,
+            col_rel_width=col_rel_width,
+            group_by=group_by,
+            page_by=page_by,
+        )
+
+        rtf_files.append(rtf_path)
+
+    return rtf_files