csrlite 0.1.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

csrlite/ie/ie.py

@@ -0,0 +1,405 @@
+# pyre-strict
+"""
+Inclusion/Exclusion (IE) Table Analysis Functions
+
+This module provides a pipeline for IE summary analysis:
+- ie_ard: Generate Analysis Results Data (ARD)
+- ie_df: Transform ARD to display format
+- ie_rtf: Generate formatted RTF output
+- study_plan_to_ie_summary: Batch generation from StudyPlan
+"""
+
+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_listing, create_rtf_table_n_pct
+from ..common.utils import apply_common_filters
+
+
+def study_plan_to_ie_summary(
+    study_plan: StudyPlan,
+) -> list[str]:
+    """
+    Generate IE Summary Table outputs for all analyses defined in StudyPlan.
+    """
+    # Meta data
+    analysis_type = "ie_summary"
+    output_dir = study_plan.output_dir
+    title = "Summary of Protocol Deviations (Inclusion/Exclusion)"
+    # footnote = ["Percentages are based on the number of enrolled participants."]
+
+    # Defaults
+    criteria_df_name = "adie"
+
+    # Ensure output directory exists
+    Path(output_dir).mkdir(parents=True, exist_ok=True)
+
+    # Initialize parser
+    parser = StudyPlanParser(study_plan)
+
+    # Get expanded plan (Manually expansion to avoid AttributeError)
+    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:
+        ie_plans = plan_df.filter(pl.col("analysis") == analysis_type)
+    else:
+        ie_plans = pl.DataFrame()
+
+    generated_files = []
+
+    # Iterate over analyses
+    for analysis in ie_plans.iter_rows(named=True):
+        # Load data
+        # Note: IE analysis needs both ADSL (for population/group) and ADIE (for criteria)
+        pop_name = analysis.get("population", "enrolled")
+        group_kw = analysis.get("group")  # Can be None
+
+        try:
+            if group_kw:
+                # Load Filtered Population (ADSL) with Group
+                adsl, group_col = parser.get_population_data(pop_name, group_kw)
+                group_col = group_col.upper()
+                grp_suffix = group_col
+            else:
+                # Load Filtered Population (ADSL) without Group
+                # Manual load + filter since get_population_data requires group
+                (adsl_raw,) = parser.get_datasets("adsl")
+                pop_filter = parser.get_population_filter(pop_name)
+
+                adsl, _ = apply_common_filters(
+                    population=adsl_raw,
+                    observation=None,
+                    population_filter=pop_filter,
+                    observation_filter=None,
+                )
+
+                group_col = None
+                grp_suffix = "total"
+
+        except ValueError as e:
+            print(f"Error loading population: {e}")
+            continue
+
+        # Load ADIE
+        try:
+            (adie,) = parser.get_datasets(criteria_df_name)
+        except ValueError as e:
+            print(f"Error loading datasets: {e}")
+            continue
+
+        # Output filename
+        filename = f"{analysis_type}_{pop_name}_{grp_suffix}.rtf".lower()
+        output_path = f"{output_dir}/{filename}"
+
+        # Generate ARD
+        ard = ie_ard(adsl=adsl, adie=adie, group_col=group_col)
+
+        # Generate DF
+        df = ie_df(ard)
+
+        # Generate RTF
+        ie_rtf(df, output_path, title=title)
+
+        generated_files.append(output_path)
+
+    return generated_files
+
+
+def ie_ard(adsl: pl.DataFrame, adie: pl.DataFrame, group_col: str | None = None) -> pl.DataFrame:
+    """
+    Generate Analysis Results Data (ARD) for IE Table.
+
+    Structure:
+    - Total Screening Failures
+    - Exclusion Criteria Met
+      - [Detail]
+    - Inclusion Criteria Not Met
+      - [Detail]
+    """
+    # If group_col is None, create a dummy group column
+    actual_group_col: str = group_col if group_col else "Total"
+
+    # 1. Prepare Data
+    # Join ADIE to ADSL to get treatment group info
+    df_joined: pl.DataFrame = adie.join(
+        adsl.select(["USUBJID"] + ([group_col] if group_col else [])), on="USUBJID", how="inner"
+    )
+
+    if not group_col:
+        # Add dummy Total column
+        df_joined = df_joined.with_columns(pl.lit("Total").alias("Total"))
+
+    # Define hierarchy
+    results: list[dict[str, Any]] = []
+
+    # Get distinct groups
+    groups: list[str]
+    if group_col:
+        groups_raw: list[str | None] = sorted(adsl.select(group_col).unique().to_series().to_list())
+        groups = [g for g in groups_raw if g is not None]
+    else:
+        groups = ["Total"]
+
+    # Helper to calculate n and pct (pct of what? usually pct of failures? or pct of screened?)
+    # Usually IE table % is based on Total Screening Failures.
+    # Let's count Total Screening Failures per Group first.
+
+    # Total Screening Failures (Subjects present in ADIE)
+    # Note: A subject can match multiple criteria.
+    total_failures_by_group = df_joined.group_by(actual_group_col).agg(
+        pl.col("USUBJID").n_unique().alias("count")
+    )
+
+    total_failures_map: dict[str, int] = {
+        row[actual_group_col]: row["count"] for row in total_failures_by_group.iter_rows(named=True)
+    }
+
+    # Helper for row generation
+    def add_row(
+        label: str, filter_expr: pl.Expr | None = None, is_header: bool = False, indent: int = 0
+    ) -> None:
+        row_data: dict[str, Any] = {"label": label, "indent": indent, "is_header": is_header}
+
+        for g in groups:
+            # Filter data for this group
+            g_df = df_joined.filter(pl.col(actual_group_col) == g)
+
+            if filter_expr is not None:
+                # Filter specific criteria
+                g_df = g_df.filter(filter_expr)
+
+            n = g_df.select("USUBJID").n_unique()
+
+            # Pct based on total failures in that group?
+            denom = total_failures_map.get(g, 0)
+            pct = (n / denom * 100) if denom > 0 else 0.0
+
+            row_data[f"count_{g}"] = n
+            row_data[f"pct_{g}"] = pct
+
+        results.append(row_data)
+
+    # 1. Total Screening Failures
+    add_row("Total Screening Failures")
+
+    # 2. Exclusion Criteria Met
+    excl_expr = pl.col("PARAMCAT") == "EXCLUSION CRITERIA MET"
+    add_row("Exclusion Criteria Met", excl_expr, is_header=True, indent=1)
+
+    # Details for Exclusion
+    excl_params = (
+        df_joined.filter(excl_expr).select("PARAM").unique().sort("PARAM").to_series().to_list()
+    )
+    for param in excl_params:
+        add_row(param, excl_expr & (pl.col("PARAM") == param), indent=2)
+
+    # 3. Inclusion Criteria Not Met
+    incl_expr = pl.col("PARAMCAT") == "INCLUSION CRITERIA NOT MET"
+    add_row("Inclusion Criteria Not Met", incl_expr, is_header=True, indent=1)
+
+    # Details for Inclusion
+    incl_params = (
+        df_joined.filter(incl_expr).select("PARAM").unique().sort("PARAM").to_series().to_list()
+    )
+    for param in incl_params:
+        add_row(param, incl_expr & (pl.col("PARAM") == param), indent=2)
+
+    return pl.DataFrame(results)
+
+
+def ie_df(ard: pl.DataFrame) -> pl.DataFrame:
+    """Transform ARD to display DataFrame."""
+    # Find 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]
+
+    # Create valid Polars expressions for selecting columns
+    # Apply indentation: 3 spaces per indent level
+    # Note: Using \u00A0 (NBSP) might be safer for RTF if spaces get collapsed,
+    # but regular spaces usually work in table cells. Let's start with regular spaces.
+
+    select_exprs = [
+        (pl.lit("   ").repeat_by(pl.col("indent")).list.join("") + pl.col("label")).alias(
+            "Criteria"
+        )
+    ]
+
+    for g in groups:
+        # Format n (%)
+        # We need to construct the string.
+        # Polars string formatting
+        # format: "{n} ({pct:.1f})"
+
+        # Note: Polars doesn't have f-string strictly in expressions like python
+        # We use strict casting and concatenation
+
+        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 ie_rtf(df: pl.DataFrame, output_path: str, title: str = "") -> None:
+    """Generate RTF."""
+
+    # Rename Criteria column to empty string for display if needed or keep as is?
+    # Usually "Criteria".
+
+    # Calculate number of columns
+    n_cols = len(df.columns)
+
+    # Build first-level column headers (use actual column names)
+    col_header_1 = list(df.columns)
+
+    # Build second-level column headers (empty for first, "n (%)" for groups)
+    col_header_2 = [""] + ["n (%)"] * (n_cols - 1)
+
+    # Calculate column widths - auto-calculate
+    # [n_cols-1, 1, 1, 1, ...]
+    col_widths = [float(n_cols - 1)] + [1.0] * (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=None,
+        source=None,
+    )
+
+    rtf_doc.write_rtf(output_path)
+
+
+def study_plan_to_ie_listing(
+    study_plan: StudyPlan,
+) -> list[str]:
+    """
+    Generate IE Listing outputs.
+    """
+    # Meta data
+    analysis_type = "ie_listing"
+    output_dir = study_plan.output_dir
+    title = "Listing of Protocol Deviations"
+
+    # Ensure output directory exists
+    Path(output_dir).mkdir(parents=True, exist_ok=True)
+
+    # Initialize parser
+    parser = StudyPlanParser(study_plan)
+
+    # Get expanded plan (Manually expansion to avoid AttributeError)
+    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)
+
+    # Filter for ie_listing if user specified it, otherwise we might trigger it manually
+    # But for now let's assume if this function is called, we want to run for "ie_listing"
+    # If the user only asked for "ie_listing", we might need to add it to the plan
+    # or just run it blindly for all?
+    # Usually we filter by analysis_type.
+    if "analysis" in plan_df.columns:
+        listing_plans = plan_df.filter(pl.col("analysis") == analysis_type)
+    else:
+        listing_plans = pl.DataFrame()
+
+    # If no specific listing plans are found, maybe we should just generate one
+    # default one for the whole study?
+    # But sticking to the pattern:
+    generated_files = []
+
+    # If listing_plans is empty, let's create a default one to ensure we generate
+    # something for the user
+    # since they explicitly asked for it.
+    if listing_plans.height == 0:
+        # Create a dummy row to force generation
+        listing_plans = pl.DataFrame([{"population": "enrolled", "analysis": analysis_type}])
+
+    for analysis in listing_plans.iter_rows(named=True):
+        # Load ADSL
+        pop_name = analysis.get("population", "enrolled")
+
+        try:
+            # Load Filtered Population (ADSL) without Group
+            # (Listings usually don't group by columns like tables)
+            # But if they did, we'd handle it. For now, just load raw ADSL.
+            (adsl_raw,) = parser.get_datasets("adsl")
+            # We could filter, but user just said "show USUBJID and DCSREAS from adsl".
+            # Applying population filter if possible.
+            pop_filter = parser.get_population_filter(pop_name)
+
+            adsl, _ = apply_common_filters(
+                population=adsl_raw,
+                observation=None,
+                population_filter=pop_filter,
+                observation_filter=None,
+            )
+
+        except ValueError as e:
+            print(f"Error loading population: {e}")
+            continue
+
+        # Output filename
+        filename = f"{analysis_type}_{pop_name}.rtf".lower()
+        output_path = f"{output_dir}/{filename}"
+
+        # Generate DF
+        df = ie_listing_df(adsl)
+
+        # Generate RTF
+        ie_listing_rtf(df, output_path, title=title)
+
+        generated_files.append(output_path)
+
+    return generated_files
+
+
+def ie_listing_df(adsl: pl.DataFrame) -> pl.DataFrame:
+    """Select columns for Listing."""
+    # Check if DCSREAS exists
+    cols = ["USUBJID", "DCSREAS"]
+    available = [c for c in cols if c in adsl.columns]
+    return adsl.select(available)
+
+
+def ie_listing_rtf(df: pl.DataFrame, output_path: str, title: str = "") -> None:
+    """Generate RTF Listing."""
+
+    col_widths = [1.5, 3.5]  # Approximate ratio
+
+    rtf_doc = create_rtf_listing(
+        df=df,
+        col_header=list(df.columns),
+        col_widths=col_widths,
+        title=[title],
+        footnote=None,
+        source=None,
+    )
+
+    rtf_doc.write_rtf(output_path)

{csrlite-0.1.0.dist-info → csrlite-0.2.1.dist-info}/METADATA

@@ -1,68 +1,68 @@
-Metadata-Version: 2.4
-Name: csrlite
-Version: 0.1.0
-Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
-Author-email: Clinical Biostatistics Team <biostat@example.com>
-License: MIT
-Project-URL: Homepage, https://github.com/elong0527/csrlite
-Project-URL: Documentation, https://elong0527.github.io/csrlite
-Project-URL: Repository, https://github.com/elong0527/csrlite.git
-Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
-Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: pydantic>=2.0.0
-Requires-Dist: pyyaml>=6.0
-Requires-Dist: polars>=0.20.0
-Requires-Dist: rtflite>=2.1.1
-Provides-Extra: rtf
-Requires-Dist: rtflite; extra == "rtf"
-Provides-Extra: plotting
-Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
-Requires-Dist: plotly>=5.0.0; extra == "plotting"
-Provides-Extra: dev
-Requires-Dist: pytest>=7.0.0; extra == "dev"
-Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
-Requires-Dist: black>=22.0.0; extra == "dev"
-Requires-Dist: isort>=5.0.0; extra == "dev"
-Requires-Dist: mypy>=1.0.0; extra == "dev"
-Requires-Dist: pytest>=9.0.1; extra == "dev"
-Requires-Dist: jupyter>=1.1.1; extra == "dev"
-Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
-Requires-Dist: nbformat>=5.10.4; extra == "dev"
-Requires-Dist: ruff>=0.1.0; extra == "dev"
-Requires-Dist: pyre-check>=0.9.18; extra == "dev"
-Provides-Extra: all
-Requires-Dist: rtflite; extra == "all"
-Requires-Dist: matplotlib>=3.5.0; extra == "all"
-Requires-Dist: plotly>=5.0.0; extra == "all"
-
-# csrlite
-
-[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
-[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
-[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-
-A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
-
-## Installation
-
-```bash
-pip install csrlite
-```
-
-## Documentation
-
-Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
-
-## License
-
-MIT License - see [LICENSE](LICENSE) file for details.
+Metadata-Version: 2.4
+Name: csrlite
+Version: 0.2.1
+Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
+Author-email: Clinical Biostatistics Team <biostat@example.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
+Project-URL: Repository, https://github.com/elong0527/csrlite.git
+Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
+Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: polars>=0.20.0
+Requires-Dist: rtflite>=2.1.1
+Provides-Extra: rtf
+Requires-Dist: rtflite; extra == "rtf"
+Provides-Extra: plotting
+Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
+Requires-Dist: plotly>=5.0.0; extra == "plotting"
+Provides-Extra: dev
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pytest>=9.0.1; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: isort>=7.0.0; extra == "dev"
+Requires-Dist: ruff>=0.14.8; extra == "dev"
+Requires-Dist: mypy>=1.19.0; extra == "dev"
+Requires-Dist: quarto>=0.1.0; extra == "dev"
+Requires-Dist: pyre-check>=0.9.18; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
+Requires-Dist: nbformat>=5.10.4; extra == "dev"
+Provides-Extra: all
+Requires-Dist: rtflite; extra == "all"
+Requires-Dist: matplotlib>=3.5.0; extra == "all"
+Requires-Dist: plotly>=5.0.0; extra == "all"
+
+# csrlite
+
+[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
+[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
+
+## Installation
+
+```bash
+pip install csrlite
+```
+
+## Documentation
+
+Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) file for details.

csrlite-0.2.1.dist-info/RECORD

@@ -0,0 +1,20 @@
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+csrlite/ae/__init__.py,sha256=Pp661SGbsoYoXLmd24dUQB_lx1jYKWEsCEPjgVg5UUU,15
+csrlite/ae/ae_listing.py,sha256=fZWhYmi_Vzp974z-3o7EQ9joizEjF0mio2eB5_I8ghU,18883
+csrlite/ae/ae_specific.py,sha256=P1glCd5K_ur_KexxbVaC79BmowgQSMI9K8xdzL6OmIM,17505
+csrlite/ae/ae_summary.py,sha256=Vk4bUonnjAji2zeJkiPHW7nwgpwUG1UfbuzH4M0w1MM,14093
+csrlite/ae/ae_utils.py,sha256=tOVOdsj-TRTw1w5T4JqFTYUwTfOppZWGlRHi6nkNWRA,2073
+csrlite/common/config.py,sha256=qWFTNSaeWnqAagXM6FwACdQafXLG_nFWxFHEk5dAo-I,912
+csrlite/common/count.py,sha256=T9nB9hYdc2jIIuV9HISK2ZS0wXNV_FUBDCKW_VVM1fQ,9078
+csrlite/common/parse.py,sha256=J4UkmNlG10mrJ-O68-po1LlfLchK_kSvfdU1GOaAYgQ,9627
+csrlite/common/plan.py,sha256=tYnK-5TVCoGWobxkqmasYYYkc9DJlHmOiTIcrP3MFRo,13293
+csrlite/common/rtf.py,sha256=g1n765i2HPpwkh6aQOzlw4UmCC21-JMZEezFtUaO6U8,4440
+csrlite/common/utils.py,sha256=XLUQqYtEm4SLNImvNDxAuj9OOu6Eogm3_uIp0vyfpfQ,1143
+csrlite/common/yaml_loader.py,sha256=ZPgXw5X9eitMHCPEJBHzeYtcjesEQ8sP0hOFSYnzrgk,3142
+csrlite/disposition/__init__.py,sha256=AiLW7Os7SBFrvvkaUMrxYEntK15_XXT0HYpZQxBx7ro,87
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