csrlite 0.2.1__py3-none-any.whl → 0.3.0__py3-none-any.whl

csrlite/mh/mh_listing.py

@@ -0,0 +1,209 @@
+# pyre-strict
+"""
+Medical History (MH) Listing Analysis Functions
+"""
+
+from pathlib import Path
+
+import polars as pl
+
+from ..common.parse import StudyPlanParser
+from ..common.plan import StudyPlan
+from ..common.rtf import create_rtf_listing
+from ..common.utils import apply_common_filters
+
+
+def mh_listing(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None = "SAFFL = 'Y'",
+    observation_filter: str | None = "MHOCCUR = 'Y'",
+    id: tuple[str, str] = ("USUBJID", "Subject ID"),
+    title: list[str] | None = None,
+    footnote: list[str] | None = None,
+    source: list[str] | None = None,
+    output_file: str = "mh_listing.rtf",
+    population_columns: list[tuple[str, str]] | None = None,
+    observation_columns: list[tuple[str, str]] | None = None,
+    sort_columns: list[str] | None = None,
+) -> str:
+    """
+    Generate Medical History Listing.
+    """
+    if title is None:
+        title = ["Listing of Medical History"]
+
+    # Generate DF
+    df = mh_listing_df(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+        id_col=id[0],
+        pop_cols=population_columns,
+        obs_cols=observation_columns,
+        sort_cols=sort_columns,
+    )
+
+    # Generate RTF
+    mh_listing_rtf(df=df, output_path=output_file, title=title, footnote=footnote, source=source)
+
+    return output_file
+
+
+def mh_listing_df(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    id_col: str,
+    pop_cols: list[tuple[str, str]] | None,
+    obs_cols: list[tuple[str, str]] | None,
+    sort_cols: list[str] | None,
+) -> pl.DataFrame:
+    # Defaults
+    if pop_cols is None:
+        # Default interesting cols from ADSL
+        pop_cols = [("TRT01A", "Treatment"), ("AGE", "Age"), ("SEX", "Sex")]
+
+    if obs_cols is None:
+        # Default from ADMH
+        obs_cols = [
+            ("MHSEQ", "Seq"),
+            ("MHBODSYS", "System Organ Class"),
+            ("MHDECOD", "Preferred Term"),
+            ("MHSTDTC", "Start Date"),
+            ("MHENRTPT", "Status"),
+        ]
+
+    # Apply filters
+    adsl, adq = apply_common_filters(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+    )
+
+    if adq is None:
+        raise ValueError("Observation data is missing")
+
+    # Join
+    # Select specific columns from ADSL
+    pop_col_names = [c[0] for c in pop_cols]
+    # Ensure ID is there
+    if id_col not in pop_col_names:
+        pop_col_names = [id_col] + pop_col_names
+
+    adsl_sub = adsl.select(pop_col_names)
+
+    joined = adq.join(adsl_sub, on=id_col, how="inner")
+
+    # Sort
+    if sort_cols:
+        # Check if cols exist
+        valid_sorts = [c for c in sort_cols if c in joined.columns]
+        if valid_sorts:
+            joined = joined.sort(valid_sorts)
+
+    # Select display columns (id + pop + obs)
+    display_cols = [id_col] + [c[0] for c in pop_cols if c[0] != id_col] + [c[0] for c in obs_cols]
+    final_df = joined.select([c for c in display_cols if c in joined.columns])
+
+    # Rename for display?
+    # Usually listing keeps raw names or we Map them.
+    # The create_rtf_listing function takes col_header list.
+
+    return final_df
+
+
+def mh_listing_rtf(
+    df: pl.DataFrame,
+    output_path: str,
+    title: list[str] | str,
+    footnote: list[str] | None,
+    source: list[str] | None,
+) -> None:
+    if df.is_empty():
+        return
+
+    # Generate headers from predefined mapping or current logic?
+    # Here we just use column names for simplicity or we could pass headers.
+    # We didn't output headers from mh_listing_df.
+    # Let's assume the order is maintained.
+
+    headers = list(df.columns)
+
+    # Approximate widths
+    # ID: 1, TRT: 1.5, AGE: 0.5, SEX: 0.5, SEQ: 0.5, SOC: 2, PT: 2, DATE: 1, STATUS: 1
+    # Total ~ 10 units?
+    # Simple uniform distribution or weighted?
+    n_cols = len(headers)
+    col_widths = [1.0] * n_cols
+
+    rtf_doc = create_rtf_listing(
+        df=df,
+        col_header=headers,
+        col_widths=col_widths,
+        title=title,
+        footnote=footnote,
+        source=source,
+    )
+
+    rtf_doc.write_rtf(output_path)
+
+
+def study_plan_to_mh_listing(study_plan: StudyPlan) -> list[str]:
+    """
+    Batch generate MH listings.
+    """
+    analysis_type = "mh_listing"
+    output_dir = study_plan.output_dir
+
+    parser = StudyPlanParser(study_plan)
+
+    plans = study_plan.study_data.get("plans", [])
+    all_specs = []
+    for plan_data in plans:
+        expanded = study_plan.expander.expand_plan(plan_data)
+        for p in expanded:
+            all_specs.append(study_plan.expander.create_analysis_spec(p))
+
+    plan_df = pl.DataFrame(all_specs)
+
+    if "analysis" in plan_df.columns:
+        mh_plans = plan_df.filter(pl.col("analysis") == analysis_type)
+    else:
+        mh_plans = pl.DataFrame()
+
+    generated_files = []
+
+    for analysis in mh_plans.iter_rows(named=True):
+        pop_name = analysis.get("population", "enrolled")
+
+        try:
+            # Load Population
+            adsl, _ = parser.get_population_data(pop_name, "trt01a")  # dummy group
+
+            (admh,) = parser.get_datasets("admh")
+
+            filename = f"{analysis_type}_{pop_name}.rtf".lower()
+            output_path = f"{output_dir}/{filename}"
+            Path(output_path).parent.mkdir(parents=True, exist_ok=True)
+
+            mh_listing(
+                population=adsl,
+                observation=admh,
+                population_filter=None,
+                observation_filter=None,  # Show all?
+                output_file=output_path,
+                title=["Listing of Medical History", f"({pop_name} Population)"],
+                source=["Source: ADSL, ADMH"],
+            )
+
+            generated_files.append(output_path)
+
+        except Exception as e:
+            print(f"Error generating MH listing: {e}")
+            continue
+
+    return generated_files

csrlite/mh/mh_summary.py

@@ -0,0 +1,333 @@
+# pyre-strict
+"""
+Medical History (MH) Summary Analysis Functions
+"""
+
+from pathlib import Path
+from typing import Any
+
+import polars as pl
+
+from ..common.parse import StudyPlanParser
+from ..common.plan import StudyPlan
+from ..common.rtf import create_rtf_table_n_pct
+from ..common.utils import apply_common_filters
+
+
+def mh_summary(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None = "SAFFL = 'Y'",
+    observation_filter: str | None = "MHOCCUR = 'Y'",
+    id: tuple[str, str] = ("USUBJID", "Subject ID"),
+    group: tuple[str, str] = ("TRT01A", "Treatment"),
+    variables: list[tuple[str, str]] | None = None,
+    title: list[str] | None = None,
+    footnote: list[str] | None = None,
+    source: list[str] | None = None,
+    output_file: str = "mh_summary.rtf",
+) -> str:
+    """
+    Generate Medical History Summary Table.
+    """
+    if title is None:
+        title = ["Summary of Medical History by Body System and Preferred Term"]
+
+    if variables is None:
+        # Default hierarchy: Body System -> Preferred Term
+        variables = [("MHBODSYS", "System Organ Class"), ("MHDECOD", "Preferred Term")]
+
+    # Generate ARD
+    ard = mh_summary_ard(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+        group_col=group[0],
+        id_col=id[0],
+        variables=variables,
+    )
+
+    # Transform to Display DF
+    df = mh_summary_df(ard)
+
+    # Generate RTF
+    mh_summary_rtf(df=df, output_path=output_file, title=title, footnote=footnote, source=source)
+
+    return output_file
+
+
+def mh_summary_ard(
+    population: pl.DataFrame,
+    observation: pl.DataFrame,
+    population_filter: str | None,
+    observation_filter: str | None,
+    group_col: str,
+    id_col: str,
+    variables: list[tuple[str, str]],
+) -> pl.DataFrame:
+    """
+    Generate ARD for MH Summary.
+    Hierarchy is often Body System -> Preferred Term.
+    """
+
+    # Apply filters
+    adsl, adq = apply_common_filters(
+        population=population,
+        observation=observation,
+        population_filter=population_filter,
+        observation_filter=observation_filter,
+    )
+
+    if adq is None:
+        # Should not happen as we passed observation df
+        raise ValueError("Observation data is missing")
+
+    # This summary usually nests MHDECOD under MHBODSYS
+    # Structure:
+    # Any Medical History (1=1)
+    #   Body System 1
+    #     Term A
+    #     Term B
+
+    # We can reuse count_subject_with_observation but it handles list of flexible conditions.
+    # For nested structure, we might need manual construction or nested calls.
+
+    # Let's assume standard 2-level nesting: MHBODSYS -> MHDECOD
+    # Check if variables match this pattern
+
+    # Identify the hierarchy columns
+    # If standard usage: variables=[("MHBODSYS", "SOC"), ("MHDECOD", "PT")]
+
+    # We will build a list of (filter_expr, label, indent_level, is_header)
+
+    specs: list[dict[str, Any]] = []
+
+    # 1. Overall "Any Medical History"
+    specs.append(
+        {"filter": pl.lit(True), "label": "Any Medical History", "indent": 0, "is_header": False}
+    )
+
+    # Get distinct Body Systems
+    bodsys_list: list[str | None] = (
+        adq.select("MHBODSYS").unique().sort("MHBODSYS").to_series().to_list()
+    )
+
+    for sys in bodsys_list:
+        if sys is None:
+            continue
+
+        # Add Body System Row
+        specs.append(
+            {
+                "filter": pl.col("MHBODSYS") == sys,
+                "label": sys,
+                "indent": 1,
+                "is_header": False,  # It has counts
+            }
+        )
+
+        # Get distinct Terms within this System
+        terms: list[str | None] = (
+            adq.filter(pl.col("MHBODSYS") == sys)
+            .select("MHDECOD")
+            .unique()
+            .sort("MHDECOD")
+            .to_series()
+            .to_list()
+        )
+
+        for term in terms:
+            if term is None:
+                continue
+            specs.append(
+                {
+                    "filter": (pl.col("MHBODSYS") == sys) & (pl.col("MHDECOD") == term),
+                    "label": term,
+                    "indent": 2,
+                    "is_header": False,
+                }
+            )
+
+    # Now calculate counts for each spec
+    results: list[dict[str, Any]] = []
+
+    # Get total population counts by group
+    pop_counts = adsl.group_by(group_col).count().sort(group_col)
+    groups: list[Any] = pop_counts.select(group_col).to_series().to_list()
+    # Pre-calculate totals map
+    pop_totals: dict[Any, int] = {
+        row[group_col]: row["count"] for row in pop_counts.iter_rows(named=True)
+    }
+
+    # Helper to calculate row
+    def calc_row(
+        spec: dict[str, Any], obs_data: pl.DataFrame, pop_data: pl.DataFrame
+    ) -> dict[str, Any]:
+        row_res = {"label": spec["label"], "indent": spec["indent"], "is_header": spec["is_header"]}
+
+        # Filter observation data based on spec string/expr
+        # Note: count_subject_with_observation logic handles join.
+        # We can simulate logic here.
+
+        # 1. Filter ADQ based on criteria
+        filtered_obs = obs_data.filter(spec["filter"])
+
+        # 2. Join with ADSL to get groups (inner join to count only subjects in population)
+        # But we already filtered ADSL (population).
+
+        subset = filtered_obs.join(pop_data.select([id_col, group_col]), on=id_col, how="inner")
+
+        # 3. Group by Group Col
+        counts = subset.select(id_col, group_col).unique().group_by(group_col).count()
+        counts_map = {row[group_col]: row["count"] for row in counts.iter_rows(named=True)}
+
+        for g in groups:
+            n = counts_map.get(g, 0)
+            denom = pop_totals.get(g, 0)
+            pct = (n / denom * 100.0) if denom > 0 else 0.0
+            row_res[f"count_{g}"] = n
+            row_res[f"pct_{g}"] = pct
+
+        return row_res
+
+    for spec in specs:
+        results.append(calc_row(spec, adq, adsl))
+
+    return pl.DataFrame(results)
+
+
+def mh_summary_df(ard: pl.DataFrame) -> pl.DataFrame:
+    """
+    Transform ARD to Display DataFrame.
+    """
+    if ard.is_empty():
+        return pl.DataFrame()
+
+    # Identify group columns
+    cols = ard.columns
+    group_cols = [c for c in cols if c.startswith("count_")]
+    groups = [c.replace("count_", "") for c in group_cols]
+
+    select_exprs = [
+        (pl.lit("   ").repeat_by(pl.col("indent")).list.join("") + pl.col("label")).alias(
+            "Medical History"
+        )
+    ]
+
+    for g in groups:
+        col_n = pl.col(f"count_{g}")
+        col_pct = pl.col(f"pct_{g}")
+
+        fmt = (
+            col_n.cast(pl.Utf8)
+            + " ("
+            + col_pct.map_elements(lambda x: f"{x:.1f}", return_dtype=pl.Utf8)
+            + ")"
+        ).alias(g)
+
+        select_exprs.append(fmt)
+
+    return ard.select(select_exprs)
+
+
+def mh_summary_rtf(
+    df: pl.DataFrame,
+    output_path: str,
+    title: list[str] | str,
+    footnote: list[str] | None,
+    source: list[str] | None,
+) -> None:
+    """
+    Generate RTF document.
+    """
+    if df.is_empty():
+        # Handle empty case?
+        return
+
+    n_cols = len(df.columns)
+    col_width_first = 2.5
+    remaining_width = 7.0  # Approx page width
+    col_width_others = remaining_width / (n_cols - 1)
+    col_widths = [col_width_first] + [col_width_others] * (n_cols - 1)
+
+    col_header_1 = list(df.columns)
+    col_header_2 = [""] + ["n (%)"] * (n_cols - 1)
+
+    rtf_doc = create_rtf_table_n_pct(
+        df=df,
+        col_header_1=col_header_1,
+        col_header_2=col_header_2,
+        col_widths=col_widths,
+        title=title,
+        footnote=footnote,
+        source=source,
+    )
+
+    rtf_doc.write_rtf(output_path)
+
+
+def study_plan_to_mh_summary(study_plan: StudyPlan) -> list[str]:
+    """
+    Batch generate MH summaries from study plan.
+    """
+    analysis_type = "mh_summary"
+    output_dir = study_plan.output_dir
+
+    # Initialize parser
+    parser = StudyPlanParser(study_plan)
+
+    # Get plans
+    plans = study_plan.study_data.get("plans", [])
+    all_specs = []
+    for plan_data in plans:
+        expanded = study_plan.expander.expand_plan(plan_data)
+        for p in expanded:
+            all_specs.append(study_plan.expander.create_analysis_spec(p))
+
+    plan_df = pl.DataFrame(all_specs)
+
+    if "analysis" in plan_df.columns:
+        mh_plans = plan_df.filter(pl.col("analysis") == analysis_type)
+    else:
+        mh_plans = pl.DataFrame()
+
+    generated_files = []
+
+    for analysis in mh_plans.iter_rows(named=True):
+        pop_name = analysis.get("population", "enrolled")
+        group_kw = analysis.get("group", "trt01a")  # specific key?
+
+        try:
+            # Load Population
+            adsl, group_col = parser.get_population_data(pop_name, group_kw)
+
+            # Load MH Data
+            # Note: Assuming 'admh' is the dataset name
+            (admh,) = parser.get_datasets("admh")
+
+            filename = f"{analysis_type}_{pop_name}_{group_kw}.rtf".lower()
+            output_path = f"{output_dir}/{filename}"
+            Path(output_path).parent.mkdir(parents=True, exist_ok=True)
+
+            mh_summary(
+                population=adsl,
+                observation=admh,
+                population_filter=None,  # Already filtered by parser
+                observation_filter="MHOCCUR = 'Y'",
+                group=(group_col, group_col),  # Use actual col name
+                output_file=output_path,
+                title=[
+                    "Summary of Medical History by System Organ Class and Preferred Term",
+                    f"({pop_name} Population)",
+                ],
+                source=["Source: ADSL, ADMH"],
+            )
+
+            generated_files.append(output_path)
+
+        except Exception as e:
+            print(f"Error generating MH summary: {e}")
+            continue
+
+    return generated_files