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

csrlite/ae/ae_utils.py

@@ -1,132 +1,62 @@
-# pyre-strict
-from typing import Any
-
-import polars as pl
-from rtflite import RTFBody, RTFColumnHeader, RTFDocument, RTFFootnote, RTFPage, RTFSource, RTFTitle
-
-
-def get_ae_parameter_title(param: Any, prefix: str = "Participants With") -> str:
-    """
-    Extract title from parameter for ae_* title generation.
-
-    Args:
-        param: Parameter object with terms attribute
-        prefix: Prefix for the title (e.g. "Participants With", "Listing of Participants With")
-
-    Returns:
-        Title string for the analysis
-    """
-    default_suffix = "Adverse Events"
-
-    if not param:
-        return f"{prefix} {default_suffix}"
-
-    # Check for terms attribute
-    if hasattr(param, "terms") and param.terms and isinstance(param.terms, dict):
-        terms = param.terms
-
-        # Preprocess to empty strings (avoiding None)
-        before = terms.get("before", "").title()
-        after = terms.get("after", "").title()
-
-        # Build title and clean up extra spaces
-        title = f"{prefix} {before} {default_suffix} {after}"
-        return " ".join(title.split())  # Remove extra spaces
-
-    # Fallback to default
-    return f"{prefix} {default_suffix}"
-
-
-def get_ae_parameter_row_labels(param: Any) -> tuple[str, str]:
-    """
-    Generate n_with and n_without row labels based on parameter terms.
-
-    Returns:
-        Tuple of (n_with_label, n_without_label)
-    """
-    # Default labels
-    default_with = "    with one or more adverse events"
-    default_without = "    with no adverse events"
-
-    if not param or not hasattr(param, "terms") or not param.terms:
-        return (default_with, default_without)
-
-    terms = param.terms
-    before = terms.get("before", "").lower()
-    after = terms.get("after", "").lower()
-
-    # Build dynamic labels with leading indentation
-    with_label = f"with one or more {before} adverse events {after}"
-    without_label = f"with no {before} adverse events {after}"
-
-    # Clean up extra spaces and add back the 4-space indentation
-    with_label = "    " + " ".join(with_label.split())
-    without_label = "    " + " ".join(without_label.split())
-
-    return (with_label, without_label)
-
-
-def create_ae_rtf_table(
-    df: pl.DataFrame,
-    col_header_1: list[str],
-    col_header_2: list[str] | None,
-    col_widths: list[float] | None,
-    title: list[str] | str,
-    footnote: list[str] | str | None,
-    source: list[str] | str | None,
-    borders_2: bool = True,
-    orientation: str = "landscape",
-) -> RTFDocument:
-    """
-    Create a standardized RTF table document with 1 or 2 header rows.
-    """
-    n_cols = len(df.columns)
-
-    # Calculate column widths if None - simple default
-    if col_widths is None:
-        col_widths = [1] * n_cols
-
-    # Normalize metadata
-    title_list = [title] if isinstance(title, str) else title
-    footnote_list = [footnote] if isinstance(footnote, str) else (footnote or [])
-    source_list = [source] if isinstance(source, str) else (source or [])
-
-    headers = [
-        RTFColumnHeader(
-            text=col_header_1,
-            col_rel_width=col_widths,
-            text_justification=["l"] + ["c"] * (n_cols - 1),
-        )
-    ]
-
-    if col_header_2:
-        h2_kwargs = {
-            "text": col_header_2,
-            "col_rel_width": col_widths,
-            "text_justification": ["l"] + ["c"] * (n_cols - 1),
-        }
-        if borders_2:
-            h2_kwargs["border_left"] = ["single"]
-            h2_kwargs["border_top"] = [""]
-
-        headers.append(RTFColumnHeader(**h2_kwargs))
-
-    rtf_components: dict[str, Any] = {
-        "df": df,
-        "rtf_page": RTFPage(orientation=orientation),
-        "rtf_title": RTFTitle(text=title_list),
-        "rtf_column_header": headers,
-        "rtf_body": RTFBody(
-            col_rel_width=col_widths,
-            text_justification=["l"] + ["c"] * (n_cols - 1),
-            border_left=["single"] * n_cols,
-        ),
-    }
-
-    if footnote_list:
-        rtf_components["rtf_footnote"] = RTFFootnote(text=footnote_list)
-
-    if source_list:
-        rtf_components["rtf_source"] = RTFSource(text=source_list)
-
-    return RTFDocument(**rtf_components)
+from typing import Any
+
+
+def get_ae_parameter_title(param: Any, prefix: str = "Participants With") -> str:
+    """
+    Extract title from parameter for ae_* title generation.
+
+    Args:
+        param: Parameter object with terms attribute
+        prefix: Prefix for the title (e.g. "Participants With", "Listing of Participants With")
+
+    Returns:
+        Title string for the analysis
+    """
+    default_suffix = "Adverse Events"
+
+    if not param:
+        return f"{prefix} {default_suffix}"
+
+    # Check for terms attribute
+    if hasattr(param, "terms") and param.terms and isinstance(param.terms, dict):
+        terms = param.terms
+
+        # Preprocess to empty strings (avoiding None)
+        before = terms.get("before", "").title()
+        after = terms.get("after", "").title()
+
+        # Build title and clean up extra spaces
+        title = f"{prefix} {before} {default_suffix} {after}"
+        return " ".join(title.split())  # Remove extra spaces
+
+    # Fallback to default
+    return f"{prefix} {default_suffix}"
+
+
+def get_ae_parameter_row_labels(param: Any) -> tuple[str, str]:
+    """
+    Generate n_with and n_without row labels based on parameter terms.
+
+    Returns:
+        Tuple of (n_with_label, n_without_label)
+    """
+    # Default labels
+    default_with = "    with one or more adverse events"
+    default_without = "    with no adverse events"
+
+    if not param or not hasattr(param, "terms") or not param.terms:
+        return (default_with, default_without)
+
+    terms = param.terms
+    before = terms.get("before", "").lower()
+    after = terms.get("after", "").lower()
+
+    # Build dynamic labels with leading indentation
+    with_label = f"with one or more {before} adverse events {after}"
+    without_label = f"with no {before} adverse events {after}"
+
+    # Clean up extra spaces and add back the 4-space indentation
+    with_label = "    " + " ".join(with_label.split())
+    without_label = "    " + " ".join(without_label.split())
+
+    return (with_label, without_label)

csrlite/common/config.py

@@ -0,0 +1,34 @@
+# pyre-strict
+"""
+Central configuration for csrlite.
+"""
+
+from typing import Literal, Optional
+
+from pydantic import BaseModel, ConfigDict, Field
+
+
+class CsrLiteConfig(BaseModel):
+    """
+    Global configuration for csrlite library.
+    """
+
+    # Column Name Defaults
+    id_col: str = Field(default="USUBJID", description="Subject Identifier Column")
+    group_col: Optional[str] = Field(default=None, description="Treatment Group Column")
+
+    # Missing Value Handling
+    missing_str: str = Field(
+        default="__missing__", description="String to represent missing string values"
+    )
+
+    # Logging
+    logging_level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = Field(
+        default="INFO", description="Default logging level"
+    )
+
+    model_config = ConfigDict(validate_assignment=True)
+
+
+# Global configuration instance
+config = CsrLiteConfig()