cdxml-toolkit 0.5.0__py3-none-any.whl

cdxml_toolkit/perception/eln_csv_parser.py

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+"""
+ELN CSV Parser — Findmolecule ELN export file parser.
+
+Parses semicolon-delimited CSV exports from Findmolecule ELN into structured
+dataclasses.  The CSV format uses @TYPE rows to delimit sections (REACTANT,
+SOLVENT, PRODUCT, ANALYSIS).
+
+This module is pure stdlib — no external dependencies.
+
+Originally part of procedure_writer.py; extracted into the package so that
+eln_enrichment.py and reaction_parser.py can import it without depending on
+private root-level scripts.
+"""
+
+import csv
+import html as html_mod
+import re
+from dataclasses import dataclass, field
+from typing import Dict, List, Optional
+
+
+# ---------------------------------------------------------------------------
+# Data structures
+# ---------------------------------------------------------------------------
+
+@dataclass
+class ReagentInfo:
+    name: str
+    mass: str
+    mmol: str
+    equiv: str
+    mw: float
+    is_substrate: bool
+    supplier: str
+    volume: str
+
+
+@dataclass
+class SolventInfo:
+    name: str
+    volume: str
+    concentration: str
+
+
+@dataclass
+class ProductInfo:
+    name: str
+    mw: float
+    theoretical_mass: str
+    obtained_mass: str
+    yield_pct: str
+
+
+@dataclass
+class LCMSFileInfo:
+    path: str
+    filename: str
+    category: str       # "tracking", "workup", "purification", "final"
+    sort_key: float     # numeric key for chronological sorting
+    report: Optional[object] = None
+    group_prefix: Optional[str] = None     # tracking group prefix
+    method_variant: Optional[str] = None   # filename-derived method hint
+
+
+@dataclass
+class ExperimentData:
+    experiment_name: str
+    labbook_name: str
+    procedure_html: str
+    procedure_text: str
+    reaction_type: str
+    start_date: str
+    reactants: List[ReagentInfo] = field(default_factory=list)
+    solvents: List[SolventInfo] = field(default_factory=list)
+    product: Optional[ProductInfo] = None
+    lcms_files: List[LCMSFileInfo] = field(default_factory=list)
+    nmr_pdfs: List[str] = field(default_factory=list)
+    nmr_data: List[str] = field(default_factory=list)
+    sm_mass: Optional[float] = None       # CSV-derived MW (fallback)
+    product_mass: Optional[float] = None  # CSV-derived MW (fallback)
+    cdx_path: Optional[str] = None
+    rxn_path: Optional[str] = None
+
+
+# ---------------------------------------------------------------------------
+# HTML / text utilities
+# ---------------------------------------------------------------------------
+
+def strip_html(html_str: str) -> str:
+    """Strip HTML tags and convert to plain text."""
+    text = re.sub(r'<br\s*/?>', '\n', html_str)
+    text = re.sub(r'</p>\s*<p[^>]*>', '\n\n', text)
+    text = re.sub(r'<p[^>]*>', '', text)
+    text = re.sub(r'</p>', '\n', text)
+    text = re.sub(r'<img[^>]*>', '', text)
+    # Remove all remaining tags
+    text = re.sub(r'<[^>]+>', '', text)
+    # Decode HTML entities (covers &nbsp; &lt; &gt; &amp; &deg; &#nnn; etc.)
+    text = html_mod.unescape(text)
+    # Clean up whitespace
+    text = re.sub(r'[ \t]+', ' ', text)
+    text = re.sub(r'\n[ \t]+', '\n', text)
+    text = re.sub(r'\n{3,}', '\n\n', text)
+    return text.strip()
+
+
+def extract_procedure_body(full_text: str) -> str:
+    """Extract the procedure portion, cutting off literature references."""
+    # "Reference:" marks start of literature references
+    idx = full_text.find('Reference:')
+    if idx > 0:
+        body = full_text[:idx].strip()
+    else:
+        body = full_text.strip()
+    # Also cut Chinese text blocks (common in patent references)
+    m = re.search(r'[\u4e00-\u9fff]', body)
+    if m and m.start() > 50:
+        body = body[:m.start()].strip()
+    return body
+
+
+# ---------------------------------------------------------------------------
+# CSV parser
+# ---------------------------------------------------------------------------
+
+def parse_eln_csv(csv_path: str) -> Optional[ExperimentData]:
+    """Parse a Findmolecule ELN CSV export.
+
+    Parameters
+    ----------
+    csv_path : str
+        Path to the semicolon-delimited CSV file.
+
+    Returns
+    -------
+    ExperimentData or None if the file has fewer than 2 rows.
+    """
+    with open(csv_path, 'r', encoding='utf-8-sig') as f:
+        reader = csv.reader(f, delimiter=';', quotechar='"')
+        rows = list(reader)
+
+    if len(rows) < 2:
+        return None
+
+    # Row 0: metadata headers, Row 1: metadata values
+    meta_headers = rows[0]
+    meta_values = rows[1]
+    metadata: Dict[str, str] = {}
+    for h, v in zip(meta_headers, meta_values):
+        metadata[h] = v
+
+    # Parse @TYPE sections
+    sections: Dict[str, list] = {
+        'REACTANT': [], 'SOLVENT': [], 'PRODUCT': [], 'ANALYSIS': []
+    }
+    current_headers: List[str] = []
+
+    for row in rows[2:]:
+        if not row:
+            continue
+        if row[0] == '@TYPE':
+            current_headers = row[1:]
+            continue
+        type_name = row[0]
+        if type_name in sections:
+            data: Dict[str, str] = {}
+            for i, h in enumerate(current_headers):
+                if i + 1 < len(row):
+                    data[h] = row[i + 1]
+                else:
+                    data[h] = ''
+            sections[type_name].append(data)
+
+    # Build ExperimentData
+    procedure_html = metadata.get('PROCEDURE', '')
+    procedure_text = extract_procedure_body(strip_html(procedure_html))
+
+    exp = ExperimentData(
+        experiment_name=metadata.get('EXPERIENCE_NAME', ''),
+        labbook_name=metadata.get('LABBOOK_NAME', ''),
+        procedure_html=procedure_html,
+        procedure_text=procedure_text,
+        reaction_type=metadata.get('EXPERIENCE_TYPE_NAME', ''),
+        start_date=metadata.get('STARTED_ON', ''),
+    )
+
+    # Reactants
+    for r in sections['REACTANT']:
+        mw_str = r.get('MOL_WEIGHT', '0')
+        try:
+            mw = float(mw_str) if mw_str else 0.0
+        except ValueError:
+            mw = 0.0
+        reagent = ReagentInfo(
+            name=r.get('REACTANT', '').strip(),
+            mass=r.get('MASS', ''),
+            mmol=r.get('MMOL', ''),
+            equiv=r.get('EQUIV', ''),
+            mw=mw,
+            is_substrate=r.get('SUBSTRATE', '').lower() == 'true',
+            supplier=r.get('SOURCE_SUPPLIER', ''),
+            volume=r.get('VOLUME', ''),
+        )
+        exp.reactants.append(reagent)
+
+    # Solvents
+    for s in sections['SOLVENT']:
+        solvent = SolventInfo(
+            name=s.get('SOLVENT', ''),
+            volume=s.get('VOLUME', ''),
+            concentration=s.get('CONCENTRATION', ''),
+        )
+        exp.solvents.append(solvent)
+
+    # Product
+    for p in sections['PRODUCT']:
+        mw_str = p.get('MOL_WEIGHT', '0')
+        try:
+            mw = float(mw_str) if mw_str else 0.0
+        except ValueError:
+            mw = 0.0
+        exp.product = ProductInfo(
+            name=p.get('PRODUCT_NAME', ''),
+            mw=mw,
+            theoretical_mass=p.get('MASS', ''),
+            obtained_mass=p.get('MASS OBTAINED', ''),
+            yield_pct=p.get('YIELD', ''),
+        )
+
+    # SM mass from substrate row (pick the largest-MW substrate,
+    # since small-MW reagents like HCl can also be marked as substrate)
+    substrate_mws = [r.mw for r in exp.reactants if r.is_substrate and r.mw > 50]
+    if substrate_mws:
+        exp.sm_mass = max(substrate_mws)
+
+    # Product mass — use CSV MW directly
+    if exp.product and exp.product.mw > 0:
+        exp.product_mass = exp.product.mw
+
+    return exp