debase 0.6.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

debase/substrate_scope_extractor.py

@@ -296,12 +296,14 @@ def limited_caption_concat(*pdf_paths: str | Path, max_chars: int = MAX_CHARS) -
     
     return "\n".join(chunks)
 
-def extract_figure_image(pdf_paths: List[Path], figure_ref: str) -> Optional[str]:
+def extract_figure_image(pdf_paths: List[Path], figure_ref: str, caption_hint: Optional[str] = None, document_hint: Optional[str] = None) -> Optional[str]:
     """Extract figure as a page region when embedded images aren't available.
     
     Args:
         pdf_paths: List of PDF paths to search
         figure_ref: Figure reference to search for (e.g., "Figure 3" or "Figure 3(a)")
+        caption_hint: Optional caption text to help identify the exact figure
+        document_hint: Optional hint about which document to search ("manuscript" or "supplementary")
         
     Returns:
         Base64-encoded PNG string or None if not found
@@ -318,43 +320,120 @@ def extract_figure_image(pdf_paths: List[Path], figure_ref: str) -> Optional[str
         log.info("Extracting entire figure '%s' from reference '%s'", base_figure_ref, figure_ref)
     else:
         base_figure_ref = figure_ref
+    
+    # Determine which PDFs to search based on document hint
+    if document_hint and len(pdf_paths) > 1:
+        if document_hint.lower() == "manuscript":
+            # ONLY search in manuscript (first PDF)
+            search_paths = [pdf_paths[0]]
+            log.info("Searching ONLY in manuscript document for '%s' (hint: %s)", figure_ref, document_hint)
+        elif document_hint.lower() == "supplementary":
+            # ONLY search in SI (second PDF if available)
+            search_paths = [pdf_paths[1]] if len(pdf_paths) > 1 else pdf_paths
+            log.info("Searching ONLY in supplementary document for '%s' (hint: %s)", figure_ref, document_hint)
+        else:
+            # No specific hint, search all PDFs
+            search_paths = list(pdf_paths)
+    else:
+        # No hint or single PDF, search all available
+        search_paths = list(pdf_paths)
         
-    for pdf_path in pdf_paths:
+    # Extract figure number BEFORE the loop (e.g., "Figure 3" -> "3", "Figure S3" -> "S3", "Fig. 3" -> "3")
+    figure_num = base_figure_ref.replace('Figure ', '').replace('figure ', '').replace('Fig. ', '').replace('fig. ', '').replace('Fig ', '').replace('fig ', '')
+    
+    for pdf_idx, pdf_path in enumerate(search_paths):
         doc = _open_doc(pdf_path)
         try:
+            log.debug("Searching %s (document %d/%d) with %d pages for figure '%s'", 
+                     pdf_path.name, pdf_idx + 1, len(search_paths), doc.page_count, figure_num)
+                     
             for page_num in range(doc.page_count):
                 page = doc.load_page(page_num)
                 page_text = page.get_text()
                 
+                # Debug: Check if page contains any mention of the figure
+                if figure_num.lower() in page_text.lower():
+                    log.debug("Page %d contains mention of figure number '%s'", page_num + 1, figure_num)
+                
                 # Check if this page contains the figure caption
                 found = False
                 caption_rect = None
                 
-                # Extract figure number (e.g., "Figure 3" -> "3", "Figure S3" -> "S3")
-                figure_num = base_figure_ref.replace('Figure ', '').replace('figure ', '')
+                # First try to find using caption hint if provided
+                if caption_hint and len(caption_hint) > 10:
+                    # Try to find a unique portion of the caption
+                    # Start with longer snippets and work down to shorter ones
+                    caption_lengths = [100, 50, 30, 20]
+                    
+                    for length in caption_lengths:
+                        if len(caption_hint) >= length:
+                            snippet = caption_hint[:length]
+                            # Clean up the snippet to avoid partial words
+                            if length < len(caption_hint):
+                                # Try to end at a word boundary
+                                last_space = snippet.rfind(' ')
+                                if last_space > length * 0.6:  # Don't trim too much
+                                    snippet = snippet[:last_space]
+                            
+                            if snippet in page_text:
+                                caption_instances = page.search_for(snippet, quads=False)
+                                if caption_instances:
+                                    caption_rect = caption_instances[0]
+                                    found = True
+                                    log.info("Found figure using caption snippet (%d chars) on page %d", len(snippet), page_num + 1)
+                                    break
                 
-                # Look for actual figure captions using regex patterns
-                caption_patterns = [
-                    rf"^Figure\s+{re.escape(figure_num)}\.",  # "Figure 3." at start of line
-                    rf"^Figure\s+{re.escape(figure_num)}:",   # "Figure 3:" at start of line
-                    rf"^Figure\s+{re.escape(figure_num)}\s+[A-Z]",  # "Figure 3 Substrate scope"
-                    rf"Figure\s+{re.escape(figure_num)}\s*\.",  # "Figure 3." anywhere
-                    rf"Figure\s+{re.escape(figure_num)}\s*:",  # "Figure 3:" anywhere
-                ]
+                # If not found with hint, look for actual figure captions using regex patterns
+                if not found:
+                    caption_patterns = [
+                        # More flexible patterns to match various formats
+                        rf"^Figure\s+{re.escape(figure_num)}[\s\.\:]",  # "Figure 3." or "Figure 3:" or "Figure 3 " at start
+                        rf"^Fig\.?\s*{re.escape(figure_num)}[\s\.\:]",  # "Fig. 3." or "Fig 3:" at start
+                        rf"Figure\s+{re.escape(figure_num)}[\s\.\:]",  # "Figure 3." anywhere
+                        rf"Fig\.?\s*{re.escape(figure_num)}[\s\.\:]",  # "Fig. 3." anywhere
+                        rf"^Figure\s+{re.escape(figure_num)}\s+[A-Z]",  # "Figure 3 Substrate scope"
+                        rf"^Fig\.?\s*{re.escape(figure_num)}\s+[A-Z]",  # "Fig. 3 Substrate"
+                        # Special patterns for edge cases
+                        rf"Fig\.\s*{re.escape(figure_num)}\s*\|",  # "Fig. 3 |"
+                        rf"^\s*{re.escape(figure_num)}\.",  # Just "3." at line start (some formats)
+                    ]
+                    
+                    for pattern in caption_patterns:
+                        matches = re.search(pattern, page_text, re.MULTILINE | re.IGNORECASE)
+                        if matches:
+                            # Found actual figure caption, get its position
+                            caption_text = matches.group(0)
+                            caption_instances = page.search_for(caption_text, quads=False)
+                            if caption_instances:
+                                caption_rect = caption_instances[0]
+                                found = True
+                                log.info("Found actual figure caption '%s' on page %d", caption_text, page_num + 1)
+                                break
                 
-                for pattern in caption_patterns:
-                    matches = re.search(pattern, page_text, re.MULTILINE | re.IGNORECASE)
-                    if matches:
-                        # Found actual figure caption, get its position
-                        caption_text = matches.group(0)
-                        caption_instances = page.search_for(caption_text, quads=False)
-                        if caption_instances:
-                            caption_rect = caption_instances[0]
-                            found = True
-                            log.info("Found actual figure caption '%s' on page %d", caption_text, page_num + 1)
-                            break
+                if not found:
+                    # Try a fuzzy search for lines that look like figure captions
+                    lines = page_text.split('\n')
+                    for i, line in enumerate(lines):
+                        line_stripped = line.strip()
+                        line_lower = line_stripped.lower()
+                        
+                        # Check if this looks like a figure caption (starts with fig/figure)
+                        # and NOT an inline reference (which would have text before it)
+                        if (line_lower.startswith(('fig.', 'fig ', 'figure')) and 
+                            figure_num.lower() in line_lower and 
+                            len(line_stripped) < 200 and
+                            not line_lower.endswith(')')):  # Exclude inline refs like "(Fig. 2)"
+                            
+                            # Found a potential caption line
+                            caption_instances = page.search_for(line_stripped[:50], quads=False)
+                            if caption_instances:
+                                caption_rect = caption_instances[0]
+                                found = True
+                                log.info("Found figure via fuzzy search: '%s' on page %d", line_stripped[:50], page_num + 1)
+                                break
                 
                 if not found:
+                    # Skip this page if we didn't find the actual figure caption
                     continue
                 
                 log.info("Found figure caption on page %d at y=%.0f", page_num + 1, caption_rect.y0)
@@ -536,15 +615,29 @@ def _build_caption_index(pdf_paths: List[Path]) -> Dict[str, Dict[str, Any]]:
     
     return caption_index
 
-def _extract_text_around_reference(pdf_paths: List[Path], ref: str, context_chars: int = 2000) -> str:
+def _extract_text_around_reference(pdf_paths: List[Path], ref: str, context_chars: int = 2000, document_hint: Optional[str] = None) -> str:
     """Extract text around a specific reference using caption index."""
     import re
     
-    # Build caption index if not already built
-    if not hasattr(_extract_text_around_reference, '_caption_index'):
-        _extract_text_around_reference._caption_index = _build_caption_index(pdf_paths)
-    
-    caption_index = _extract_text_around_reference._caption_index
+    # Filter PDFs based on document hint BEFORE building caption index
+    search_paths = pdf_paths
+    if document_hint and len(pdf_paths) > 1:
+        if document_hint.lower() == "manuscript":
+            # ONLY search in manuscript (first PDF)
+            search_paths = [pdf_paths[0]]
+            log.info("Text extraction: Searching ONLY in manuscript document for '%s'", ref)
+        elif document_hint.lower() == "supplementary":
+            # ONLY search in SI (second PDF if available)
+            search_paths = [pdf_paths[1]] if len(pdf_paths) > 1 else pdf_paths
+            log.info("Text extraction: Searching ONLY in supplementary document for '%s'", ref)
+    
+    # Build caption index from filtered paths
+    # Use a cache key that includes the document hint
+    cache_key = f"_caption_index_{document_hint or 'all'}"
+    if not hasattr(_extract_text_around_reference, cache_key):
+        setattr(_extract_text_around_reference, cache_key, _build_caption_index(search_paths))
+    
+    caption_index = getattr(_extract_text_around_reference, cache_key)
     ref_lower = ref.lower().strip()
     
     # Try multiple matching strategies
@@ -581,6 +674,8 @@ def _extract_text_around_reference(pdf_paths: List[Path], ref: str, context_char
                 if info not in matches:
                     matches.append(info)
     
+    # No need to filter by document hint here since we already filtered the PDFs
+    
     # Extract text from matches
     extracted_sections = []
     for match in matches:
@@ -1135,17 +1230,24 @@ Your task is to:
 4. Note that not all campaigns have substrate scope data - it's okay to return empty results if no substrate scope data exists for this campaign
 5. Determine which enzyme variants from this campaign were tested in substrate scope studies
 
+IMPORTANT FIGURE REFERENCE RULES:
+- For figures, ALWAYS return the main figure number only (e.g., "Figure 2", NOT "Figure 2a" or "Figure 2(a)")
+- Include the figure caption if available to help with identification
+- The extraction system will handle retrieving the entire figure including all sub-panels
+
 Return your analysis as JSON array (max {max_results} locations, or empty array if no substrate scope data for this campaign):
 [
   {{
-    "location": "Description of where the data is found",
+    "location": "Main figure/table reference (e.g., 'Figure 2', 'Table S1', NOT 'Figure 2a')",
     "type": "table|figure|text",
     "confidence": 0.0-1.0,
     "enzyme_variants": ["list of enzyme IDs found"],
     "substrates_tested": ["list of substrates if identifiable"],
     "campaign_match": true/false,
     "is_substrate_scope": true/false,
-    "model_reaction_excluded": "reason why this is not a model reaction"
+    "model_reaction_excluded": "reason why this is not a model reaction",
+    "caption": "Include the figure/table caption if available",
+    "document": "manuscript|supplementary - specify whether this location is in the main manuscript or supplementary information"
   }}
 ]
 
@@ -1173,16 +1275,34 @@ def identify_iupac_sections(
     debug_dir: str | Path | None = None,
 ) -> List[dict]:
     """Identify sections containing IUPAC names from SI table of contents."""
-    # Extract only SI TOC pages (first 5 pages of SI)
+    # Extract SI TOC pages and scan for compound synthesis sections
     si_toc_text = ""
     if pdf_paths and len(pdf_paths) > 1:
         si_pdf = pdf_paths[1]  # Second PDF is SI
         doc = _open_doc(si_pdf)
         try:
-            for page_num in range(min(5, doc.page_count)):
+            # First get TOC from first 10 pages
+            for page_num in range(min(10, doc.page_count)):
                 page = doc.load_page(page_num)
                 page_text = page.get_text()
                 si_toc_text += f"\n[SI Page {page_num + 1}]\n{page_text}"
+            
+            # Also scan for pages containing "synthesis of" or "characterization" patterns
+            compound_section_pages = []
+            for page_num in range(doc.page_count):
+                page = doc.load_page(page_num)
+                page_text = page.get_text().lower()
+                if any(pattern in page_text for pattern in [
+                    "synthesis of 1", "synthesis of 3", "compound 1", "compound 3",
+                    "characterization data", "nmr data", "1h nmr", "13c nmr"
+                ]):
+                    compound_section_pages.append(page_num + 1)
+            
+            if compound_section_pages:
+                log.info("Found potential compound characterization on SI pages: %s", compound_section_pages[:10])
+                # Add a hint about these pages
+                si_toc_text += f"\n\n[Additional compound characterization detected on pages: {compound_section_pages[:10]}]"
+                
         finally:
             doc.close()
     
@@ -1652,17 +1772,17 @@ def _extract_text_for_compound_mapping(
                 if page_text:
                     extraction_text += f"\n\n=== Section: '{section_title}' starting from page {page_range} ===\n{page_text}"
             else:
-                # Try title-based extraction as fallback
-                section_text = _extract_sections_by_title(pdf_paths, [section_title], max_chars_per_section=10000)
+                # Try title-based extraction as fallback with more content
+                section_text = _extract_sections_by_title(pdf_paths, [section_title], max_chars_per_section=30000)
                 if section_text:
                     extraction_text += section_text
         
         if not extraction_text:
-            log.warning("No text extracted from IUPAC sections, falling back to limited text")
-            extraction_text = text_fallback[:30_000]
+            log.warning("No text extracted from IUPAC sections, using full text")
+            extraction_text = text_fallback
     else:
-        # Fallback to limited text
-        extraction_text = text_fallback[:30_000]
+        # Fallback to full text - no limit
+        extraction_text = text_fallback
     
     return extraction_text
 
@@ -1706,24 +1826,19 @@ def extract_compound_mappings(
                  len(missing_compounds), sorted(missing_compounds))
         log.info("Expanding search to additional sections...")
         
-        # Define additional sections that might contain compound definitions
-        additional_sections = [
-            "Engineering strategy",
-            "Screening for benzyl acrylate cyclopropanation",
-            "Evolution campaign", 
-            "General procedure",
-            "Experimental procedures",
-            "Materials and methods",
-            "Substrate synthesis"
-        ]
+        # For expanded search, use full manuscript and SI text
+        log.info("Using full manuscript and SI text for comprehensive compound search")
         
-        # Extract text from additional sections
-        additional_text = _extract_sections_by_title(
-            pdf_paths, additional_sections, max_chars_per_section=5000
-        )
+        # Extract complete text from both PDFs
+        additional_text = ""
+        for i, pdf_path in enumerate(pdf_paths):
+            doc_type = "manuscript" if i == 0 else "supplementary"
+            doc_text = extract_text(pdf_path)
+            additional_text += f"\n\n=== FULL {doc_type.upper()} TEXT ===\n{doc_text}"
+            log.info("Added %d chars from %s", len(doc_text), doc_type)
         
         if additional_text:
-            log.info("Extracted %d chars from additional sections", len(additional_text))
+            log.info("Total expanded text: %d chars", len(additional_text))
             
             # Second extraction attempt with expanded text
             expanded_mappings = _extract_compound_mappings_from_text(
@@ -1865,31 +1980,59 @@ def extract_substrate_scope_entries_for_campaign(
     all_refs = []
     
     if locations:
-        # Include ALL locations, not just primary
-        location_strs = []
-        for loc in locations[:3]:  # Up to 3 locations
-            loc_str = loc.get('location', '')
-            location_strs.append(loc_str)
-            all_refs.append(loc_str)
+        # Sort locations by confidence and use only the PRIMARY (most confident) location
+        sorted_locations = sorted(locations, key=lambda x: x.get('confidence', 0), reverse=True)
+        primary_location = sorted_locations[0] if sorted_locations else None
         
-        extraction_hints = f"\nSubstrate scope locations for campaign {campaign_id}: {', '.join(location_strs)}"
+        if primary_location:
+            primary_ref = primary_location.get('location', '')
+            all_refs = [primary_ref]  # Only extract from primary location
+            
+            extraction_hints = f"\nPRIMARY substrate scope location for campaign {campaign_id}: {primary_ref}"
+            extraction_hints += f"\nLocation confidence: {primary_location.get('confidence', 0)}%"
+            extraction_hints += f"\nLocation type: {primary_location.get('type', 'unknown')}"
         
         # Focus on campaign-specific enzyme variants
         extraction_hints += f"\nTarget enzymes for this campaign: {', '.join(enzyme_ids)}"
     
-    # Extract text from ALL identified locations (like the original function did)
+    # Extract text from ONLY the primary location
     extraction_texts = []
     figure_images = {}
     
+    # Create a mapping of location strings to their full location data
+    location_map = {loc.get('location', ''): loc for loc in locations}
+    
     for ref in all_refs:
         if ref and pdf_paths:
-            ref_text = _extract_text_around_reference(pdf_paths, ref, context_chars=5000)
+            # Get document hint for this reference
+            document_hint = location_map.get(ref, {}).get('document', '')
+            ref_text = _extract_text_around_reference(pdf_paths, ref, context_chars=5000, document_hint=document_hint)
             if ref_text:
                 extraction_texts.append(f"\n=== Data from {ref} ===\n{ref_text}")
                 
                 # Extract figure images for this reference (crop page around figure)
                 try:
-                    fig_base64 = extract_figure_image(pdf_paths, ref)
+                    # Get caption hint if available
+                    caption_hint = location_map.get(ref, {}).get('caption', '')
+                    
+                    # If we have a good caption, try to extract based on caption pattern
+                    if caption_hint and len(caption_hint) > 20:
+                        # Extract the figure reference from the caption itself
+                        import re
+                        caption_fig_match = re.match(r'((?:Figure|Fig\.?)\s*\d+[a-zA-Z]?)', caption_hint, re.IGNORECASE)
+                        if caption_fig_match:
+                            # Use the figure reference from the caption for more accurate matching
+                            fig_ref_from_caption = caption_fig_match.group(1)
+                            log.info("Campaign %s - using figure reference from caption: '%s' (original: '%s')", 
+                                    campaign_id, fig_ref_from_caption, ref)
+                            fig_base64 = extract_figure_image(pdf_paths, fig_ref_from_caption, caption_hint=caption_hint, document_hint=document_hint)
+                        else:
+                            # Fallback to original reference
+                            fig_base64 = extract_figure_image(pdf_paths, ref, caption_hint=caption_hint, document_hint=document_hint)
+                    else:
+                        # No caption hint, use original reference
+                        fig_base64 = extract_figure_image(pdf_paths, ref, caption_hint=caption_hint, document_hint=document_hint)
+                    
                     if fig_base64:
                         figure_images[ref] = fig_base64
                         log.info("Campaign %s - extracted cropped figure image for %s", campaign_id, ref)
@@ -1942,6 +2085,14 @@ IMPORTANT INSTRUCTIONS:
 4. Not all campaigns have substrate scope data - if no substrate scope data exists for this campaign, return an empty array
 5. Include all relevant reaction performance data (yield, ee, ttn, etc.)
 
+CRITICAL DATA ACCURACY REQUIREMENTS:
+- BE EXTREMELY CAREFUL about which substrate ID maps to which yield, TTN, and selectivity values
+- Each substrate entry should have its OWN yield, ee, and TTN values - do not mix up values between substrates
+- If looking at a table or figure, carefully match each substrate with its corresponding row/bar/data point
+- Double-check that substrate 1a's data is not confused with substrate 1b's data, etc.
+- If values are unclear or ambiguous for a specific substrate, return null rather than guessing
+- Pay special attention when extracting from figures - ensure you're reading the correct bar/point for each substrate
+
 {extraction_hints}
 
 Return your analysis as JSON in this format:
@@ -2287,13 +2438,15 @@ def get_substrate_scope(
         if should_extract:
             figure_ref = location_str
             confidence = loc.get('confidence', 0)
+            caption_hint = loc.get('caption', '')
             log.info("Extracting image for %s (confidence: %d%%, type: %s)", figure_ref, confidence, location_type)
             
             # Use appropriate extraction function based on type
             if 'scheme' in location_str.lower() or location_type == 'scheme':
                 figure_image = extract_scheme_image(pdf_paths, figure_ref)
             else:
-                figure_image = extract_figure_image(pdf_paths, figure_ref)
+                document_hint = loc.get('document', '')
+                figure_image = extract_figure_image(pdf_paths, figure_ref, caption_hint=caption_hint, document_hint=document_hint)
                 
             if figure_image:
                 log.info("Successfully extracted %s image for %s (%d bytes)", 

{debase-0.6.1.dist-info → debase-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: debase
-Version: 0.6.1
+Version: 0.7.0
 Summary: Enzyme lineage analysis and sequence extraction package
 Home-page: https://github.com/YuemingLong/DEBase
 Author: DEBase Team

debase-0.7.0.dist-info/RECORD

@@ -0,0 +1,18 @@
+debase/__init__.py,sha256=YeKveGj_8fwuu5ozoK2mUU86so_FjiCwsvg1d_lYVZU,586
+debase/__main__.py,sha256=LbxYt2x9TG5Ced7LpzzX_8gkWyXeZSlVHzqHfqAiPwQ,160
+debase/_version.py,sha256=eraKmkwzA-nS1rqm0gvetysX_jPj7RUdCTZBi3t9g6g,49
+debase/build_db.py,sha256=bW574GxsL1BJtDwM19urLbciPcejLzfraXZPpzm09FQ,7167
+debase/campaign_utils.py,sha256=6Mo6ps8gIOxBrfNNshvny-9GTKBt8UARc8t59o1obAk,4756
+debase/caption_pattern.py,sha256=F1cxQxyQDmzw3ogi3zXJp7iEvOdFdIN2kDzLrUg_amE,2043
+debase/cleanup_sequence.py,sha256=XbA0pZFFIJRJf4XCEN-j4s7dnkdXN9mYdbcuz-ZSjg4,75520
+debase/enzyme_lineage_extractor.py,sha256=7BGkjp7Pl31etWrkjBw2f2KO3fd_1IJLjUnxvUswXuw,194404
+debase/lineage_format.py,sha256=NhpkeBFE94t50uLAuE47ZP3Ti12XvzPHYt-k-_d7OLA,59730
+debase/reaction_info_extractor.py,sha256=tmL-VBMtRKVy36QMTTLSCy9PU4RLpwaJyPRfc8jIalU,198299
+debase/substrate_scope_extractor.py,sha256=AQFJ-6wvKFVZJ5vTwvYMez_v02W2ic95HQF5shidGFY,129282
+debase/wrapper.py,sha256=Vcad6c_f3jZHpefZMP9XJPI3fo7w-pCgcSqEEQyDgS0,24559
+debase-0.7.0.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
+debase-0.7.0.dist-info/METADATA,sha256=Wsz_cofQy3NaS_icwm6p0unDOlBknaggce2JQc-4k2c,4047
+debase-0.7.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+debase-0.7.0.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
+debase-0.7.0.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
+debase-0.7.0.dist-info/RECORD,,

debase-0.6.1.dist-info/RECORD

@@ -1,18 +0,0 @@
-debase/__init__.py,sha256=YeKveGj_8fwuu5ozoK2mUU86so_FjiCwsvg1d_lYVZU,586
-debase/__main__.py,sha256=LbxYt2x9TG5Ced7LpzzX_8gkWyXeZSlVHzqHfqAiPwQ,160
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