cdxml-toolkit 0.5.0__py3-none-any.whl

cdxml_toolkit/analysis/parse_analysis_file.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+"""
+parse_analysis_file.py — Unified LCMS / NMR PDF parser.
+
+Detects whether a PDF is an LCMS report (Waters MassLynx standard or manual
+integration) or an NMR report, then delegates to the appropriate parser and
+returns a normalised dict.
+
+Python API:
+    from cdxml_toolkit.analysis.parse_analysis_file import parse_analysis_file
+    result = parse_analysis_file("KL-7001-011-purified.pdf")
+    # result["file_type"]  -> "lcms" or "nmr"
+    # result["data"]       -> parsed data dict
+"""
+
+from __future__ import annotations
+
+import dataclasses
+import traceback
+from typing import Any, Dict
+
+
+def _dataclass_to_dict(obj: Any) -> Any:
+    """Recursively convert dataclasses (and lists/dicts thereof) to plain dicts."""
+    if dataclasses.is_dataclass(obj) and not isinstance(obj, type):
+        return {k: _dataclass_to_dict(v) for k, v in dataclasses.asdict(obj).items()}
+    if isinstance(obj, list):
+        return [_dataclass_to_dict(i) for i in obj]
+    if isinstance(obj, dict):
+        return {k: _dataclass_to_dict(v) for k, v in obj.items()}
+    return obj
+
+
+def parse_analysis_file(pdf_path: str) -> Dict[str, Any]:
+    """Detect and parse an LCMS or NMR PDF report.
+
+    Detection order:
+      1. Waters MassLynx standard report  → ``parse_report()``
+      2. Waters MassLynx manual integration → ``parse_manual_report()``
+      3. NMR PDF (MestReNova)             → ``extract_nmr_data()``
+      4. None of the above               → error dict
+
+    Args:
+        pdf_path: Absolute or relative path to the PDF file.
+
+    Returns:
+        Dict with keys:
+            ok (bool)
+            file_type ("lcms" | "nmr") — only present when ok=True
+            file_path (str)
+            data (dict) — parsed content; structure depends on file_type:
+                lcms (standard):  LCMSReport as dict
+                lcms (manual):    ManualLCMSReport as dict, plus
+                                  "variant": "manual_integration"
+                nmr:              {"nmr_strings": ["1H NMR ..."]}
+            error (str) — only present when ok=False
+    """
+    from cdxml_toolkit.analysis.lcms_analyzer import (
+        is_waters_report,
+        parse_report,
+        is_manual_integration,
+        parse_manual_report,
+    )
+    from cdxml_toolkit.analysis.deterministic.procedure_writer import extract_nmr_data
+
+    base_result: Dict[str, Any] = {"file_path": pdf_path}
+
+    # --- Attempt 1: standard Waters report ---
+    try:
+        if is_waters_report(pdf_path):
+            report = parse_report(pdf_path)
+            return {
+                **base_result,
+                "ok": True,
+                "file_type": "lcms",
+                "data": _dataclass_to_dict(report),
+            }
+    except Exception as exc:
+        return {
+            **base_result,
+            "ok": False,
+            "file_type": "lcms",
+            "error": f"Waters report detected but parsing failed: {exc}",
+            "traceback": traceback.format_exc(),
+        }
+
+    # --- Attempt 2: manual integration report ---
+    try:
+        if is_manual_integration(pdf_path):
+            report = parse_manual_report(pdf_path)
+            data = _dataclass_to_dict(report)
+            data["variant"] = "manual_integration"
+            return {
+                **base_result,
+                "ok": True,
+                "file_type": "lcms",
+                "data": data,
+            }
+    except Exception as exc:
+        return {
+            **base_result,
+            "ok": False,
+            "file_type": "lcms",
+            "error": f"Manual integration report detected but parsing failed: {exc}",
+            "traceback": traceback.format_exc(),
+        }
+
+    # --- Attempt 3: NMR PDF ---
+    try:
+        nmr_strings = extract_nmr_data(pdf_path)
+        if nmr_strings:
+            return {
+                **base_result,
+                "ok": True,
+                "file_type": "nmr",
+                "data": {"nmr_strings": nmr_strings},
+            }
+    except Exception as exc:
+        return {
+            **base_result,
+            "ok": False,
+            "error": f"NMR extraction failed: {exc}",
+            "traceback": traceback.format_exc(),
+        }
+
+    # --- Nothing matched ---
+    return {
+        **base_result,
+        "ok": False,
+        "error": (
+            "Could not detect file type: not a Waters standard report, "
+            "not a manual integration export, and no NMR data strings found."
+        ),
+    }