masster 0.5.19__tar.gz → 0.5.21__tar.gz

{masster-0.5.19 → masster-0.5.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.19
+Version: 0.5.21
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.5.19 → masster-0.5.21}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.19"
+version = "0.5.21"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.5.19 → masster-0.5.21}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.19"
+__version__ = "0.5.21"
 
 
 def get_version():

{masster-0.5.19 → masster-0.5.21}/src/masster/lib/lib.py

@@ -46,6 +46,7 @@ annotations = lib.annotate_features(sample.features_df)
 """
 
 import os
+import json
 from typing import Optional, Union, List, Dict, Any, TYPE_CHECKING
 import warnings
 
@@ -685,6 +686,142 @@ class Lib:
             if skipped_compounds > 0:
                 print(f"All {total_compounds} compounds were skipped due to invalid formulas")
     
+    def import_json(self, 
+                   jsonfile: str, 
+                   polarity: Optional[str] = None,
+                   adducts: Optional[List[str]] = None,
+                   min_probability: float = 0.03) -> None:
+        """
+        Import compound library from a JSON file created by csv_to_json.py.
+        
+        This method reads a JSON file with the structure created by csv_to_json.py
+        and generates adduct variants for each compound.
+        
+        Args:
+            jsonfile: Path to the JSON file
+            polarity: Ionization polarity ("positive", "negative", or None for positive)
+            adducts: Specific adducts to generate. If None, generates defaults for the polarity
+            min_probability: Minimum probability threshold for adduct filtering
+            
+        Expected JSON structure:
+            {
+                "version": "1.0",
+                "creation_date": "2025-10-07T09:17:06.142290",
+                "description": "Converted from CSV file...",
+                "source_file": "filename.csv",
+                "record_count": 123,
+                "data": [
+                    {
+                        "name": "compound name",
+                        "smiles": "SMILES string",
+                        "inchikey": "InChI key",
+                        "formula": "molecular formula",
+                        "db_id": "database ID",
+                        "db": "database name"
+                    },
+                    ...
+                ]
+            }
+            
+        Raises:
+            FileNotFoundError: If JSON file doesn't exist
+            ValueError: If JSON structure is invalid or required data is missing
+        """
+        if not os.path.exists(jsonfile):
+            raise FileNotFoundError(f"JSON file not found: {jsonfile}")
+        
+        # Read and parse JSON file
+        try:
+            with open(jsonfile, 'r', encoding='utf-8') as f:
+                json_data = json.load(f)
+        except json.JSONDecodeError as e:
+            raise ValueError(f"Invalid JSON file: {e}") from e
+        except Exception as e:
+            raise ValueError(f"Error reading JSON file: {e}") from e
+        
+        # Validate JSON structure
+        if not isinstance(json_data, dict):
+            raise ValueError("JSON file must contain a dictionary at root level")
+        
+        if "data" not in json_data:
+            raise ValueError("JSON file must contain a 'data' field with compound records")
+        
+        data = json_data["data"]
+        if not isinstance(data, list):
+            raise ValueError("'data' field must be a list of compound records")
+        
+        # Extract metadata for reporting
+        version = json_data.get("version", "unknown")
+        source_file = json_data.get("source_file", "unknown")
+        record_count = json_data.get("record_count", len(data))
+        
+        print(f"Loading JSON library: version {version}, source: {source_file}, records: {record_count}")
+        
+        # Process each compound
+        all_variants = []
+        cmpd_id_counter = 1
+        lib_id_counter = 1
+        total_compounds = 0
+        skipped_compounds = 0
+        
+        for compound_record in data:
+            total_compounds += 1
+            
+            # Validate required fields
+            if not isinstance(compound_record, dict):
+                skipped_compounds += 1
+                continue
+            
+            formula = compound_record.get("formula", "")
+            if not formula or not isinstance(formula, str):
+                skipped_compounds += 1
+                continue
+            
+            # Extract compound data, handling both CSV column names and JSON field names
+            compound_level_uid = cmpd_id_counter
+            cmpd_id_counter += 1
+            
+            compound_data = {
+                "name": compound_record.get("name", compound_record.get("Name", "")),
+                "shortname": compound_record.get("shortname", ""),
+                "class": compound_record.get("class", ""),
+                "smiles": compound_record.get("smiles", compound_record.get("SMILES", "")),
+                "inchi": compound_record.get("inchi", compound_record.get("InChI", "")),
+                "inchikey": compound_record.get("inchikey", compound_record.get("InChIKey", "")),
+                "formula": formula,
+                "rt": self._safe_float_conversion(compound_record.get("rt", compound_record.get("RT", None))),
+                "db_id": compound_record.get("db_id", compound_record.get("database_id", None)),
+                "db": compound_record.get("db", compound_record.get("database", None)),
+                "cmpd_uid": compound_level_uid,
+            }
+            
+            # Generate adduct variants
+            variants, lib_id_counter = self._generate_adduct_variants(
+                compound_data, adducts=adducts, polarity=polarity, 
+                lib_id_counter=lib_id_counter, min_probability=min_probability
+            )
+            all_variants.extend(variants)
+            
+            # Track if compound was skipped due to invalid formula
+            if len(variants) == 0:
+                skipped_compounds += 1
+        
+        # Convert to DataFrame and store
+        if all_variants:
+            new_lib_df = pl.DataFrame(all_variants)
+            
+            # Combine with existing data if any
+            if self.lib_df is not None and len(self.lib_df) > 0:
+                self.lib_df = pl.concat([self.lib_df, new_lib_df])
+            else:
+                self.lib_df = new_lib_df
+                
+            print(f"Imported {len(all_variants)} library entries from {jsonfile}")
+        else:
+            print(f"No valid compounds found in {jsonfile}")
+            if skipped_compounds > 0:
+                print(f"All {total_compounds} compounds were skipped due to invalid formulas")
+    
     def _map_csv_columns(self, columns: List[str]) -> Dict[str, str]:
         """
         Map CSV column names to standardized internal names (case-insensitive).

{masster-0.5.19 → masster-0.5.21}/src/masster/study/id.py

@@ -21,10 +21,10 @@ def lib_load(
 
     Args:
         study: Study instance
-        lib_source: either a CSV file path (str) or a Lib instance
-        polarity: ionization polarity ("positive" or "negative") - used when lib_source is a CSV path.
+        lib_source: either a CSV/JSON file path (str) or a Lib instance
+        polarity: ionization polarity ("positive" or "negative") - used when lib_source is a CSV/JSON path.
                  If None, uses study.polarity automatically.
-        adducts: specific adducts to generate - used when lib_source is a CSV path
+        adducts: specific adducts to generate - used when lib_source is a CSV/JSON path
         iso: isotope generation mode ("13C" to generate 13C isotopes, None for no isotopes)
 
     Side effects:
@@ -38,7 +38,7 @@ def lib_load(
         Lib = None
 
     if lib_source is None:
-        raise ValueError("lib_source must be a CSV file path (str) or a Lib instance")
+        raise ValueError("lib_source must be a CSV/JSON file path (str) or a Lib instance")
 
     # Use study polarity if not explicitly provided
     if polarity is None:
@@ -52,15 +52,23 @@ def lib_load(
             polarity = "positive"  # Default fallback
         study.logger.debug(f"Using study polarity: {polarity}")
 
-    # Handle string input (CSV file path)
+    # Handle string input (CSV or JSON file path)
     if isinstance(lib_source, str):
         if Lib is None:
             raise ImportError(
-                "Could not import masster.lib.lib.Lib - required for CSV loading",
+                "Could not import masster.lib.lib.Lib - required for CSV/JSON loading",
             )
 
         lib_obj = Lib()
-        lib_obj.import_csv(lib_source, polarity=polarity, adducts=adducts)
+        
+        # Determine file type by extension
+        if lib_source.lower().endswith('.json'):
+            lib_obj.import_json(lib_source, polarity=polarity, adducts=adducts)
+        elif lib_source.lower().endswith('.csv'):
+            lib_obj.import_csv(lib_source, polarity=polarity, adducts=adducts)
+        else:
+            # Default to CSV behavior for backward compatibility
+            lib_obj.import_csv(lib_source, polarity=polarity, adducts=adducts)
 
     # Handle Lib instance
     elif Lib is not None and isinstance(lib_source, Lib):
@@ -72,7 +80,7 @@ def lib_load(
 
     else:
         raise TypeError(
-            "lib_source must be a CSV file path (str), a masster.lib.Lib instance, or have a 'lib_df' attribute",
+            "lib_source must be a CSV/JSON file path (str), a masster.lib.Lib instance, or have a 'lib_df' attribute",
         )
 
     # Ensure lib_df is populated
@@ -101,7 +109,7 @@ def lib_load(
     # Store pointer and DataFrame on study
     study._lib = lib_obj
 
-    # Add source_id column with filename (without path) if loading from CSV
+    # Add source_id column with filename (without path) if loading from CSV/JSON
     if isinstance(lib_source, str):
         import os
         filename_only = os.path.basename(lib_source)

{masster-0.5.19 → masster-0.5.21}/src/masster/wizard/wizard.py

@@ -838,7 +838,7 @@ class Wizard:
             f"Polarity detected: {source_info.get('polarity', 'unknown')}",
             "Files created:"]
         for file_path in files_created:
-            instructions.append(f"  ✅ {str(Path(file_path).resolve())}")
+            instructions.append(f"  [OK] {str(Path(file_path).resolve())}")
         
         # Find the workflow script name from created files
         workflow_script_name = "1_masster_workflow.py"
@@ -877,7 +877,7 @@ class Wizard:
             # Add test mode print after the masster version line
             if 'print("masster' in line and 'Automated MS Data Analysis")' in line:
                 lines.insert(i + 1, '        if TEST_MODE:')
-                lines.insert(i + 2, '            print("🧪 TEST MODE: Processing single file only")')
+                lines.insert(i + 2, '            print("[TEST] TEST MODE: Processing single file only")')
                 break
         
         # Add mode info after num_cores print
@@ -894,7 +894,7 @@ class Wizard:
                 lines.insert(i + 2, '        # Limit to first file in test mode')
                 lines.insert(i + 3, '        if TEST_MODE:')
                 lines.insert(i + 4, '            raw_files = raw_files[:1]')
-                lines.insert(i + 5, '            print(f"\\n🧪 TEST MODE: Processing only first file: {raw_files[0].name}")')
+                lines.insert(i + 5, '            print(f"\\n[TEST] TEST MODE: Processing only first file: {raw_files[0].name}")')
                 break
         
         # Modify num_cores for test mode
@@ -909,7 +909,7 @@ class Wizard:
                 lines.insert(i + 1, '        ')
                 lines.insert(i + 2, '        # Stop here if test-only mode')
                 lines.insert(i + 3, '        if TEST_ONLY:')
-                lines.insert(i + 4, '            print("\\n🧪 TEST ONLY mode: Stopping after successful single file processing")')
+                lines.insert(i + 4, '            print("\\n[TEST] TEST ONLY mode: Stopping after successful single file processing")')
                 lines.insert(i + 5, '            print(f"Test file created: {sample5_files[0]}")')
                 lines.insert(i + 6, '            print("\\nTo run full batch, use: wizard.run()")')
                 lines.insert(i + 7, '            total_time = time.time() - start_time')
@@ -985,7 +985,7 @@ class Wizard:
                     "status": "error",
                     "message": "Workflow script not found. Please run create_scripts() first.",
                     "instructions": [
-                        "❌ Missing 1_masster_workflow.py",
+                        "[ERROR] Missing 1_masster_workflow.py",
                         "Run: wizard.create_scripts()",
                         "Then: wizard.run()"
                     ]
@@ -1008,8 +1008,8 @@ class Wizard:
                     env['MASSTER_TEST_ONLY'] = '1'
                 
             # Execute the workflow script
-            print(f"🚀 Executing {mode_label} processing workflow...")
-            print(f"📄 Running: {workflow_script_path.name}")
+            print(f">> Executing {mode_label} processing workflow...")
+            print(f"[SCRIPT] Running: {workflow_script_path.name}")
             print("=" * 60)
             
             import subprocess
@@ -1022,16 +1022,16 @@ class Wizard:
             if success:
                 print("=" * 60)
                 if test_only:
-                    print("✅ Test-only processing completed successfully!")
-                    print("📋 Single file validated - ready for full batch")
+                    print("[OK] Test-only processing completed successfully!")
+                    print("[INFO] Single file validated - ready for full batch")
                     print("   wizard.run()")
                 elif test_mode:
-                    print("✅ Test processing completed successfully!")
-                    print("📋 Next step: Run full batch")
+                    print("[OK] Test processing completed successfully!")
+                    print("[INFO] Next step: Run full batch")
                     print("   wizard.run()")
                 else:
-                    print("✅ Sample processing completed successfully!")
-                    print("📋 Next step: Run interactive analysis")
+                    print("[OK] Sample processing completed successfully!")
+                    print("[INFO] Next step: Run interactive analysis")
                     print("   uv run marimo edit 2_interactive_analysis.py")
                 print("=" * 60)
                 
@@ -1042,7 +1042,7 @@ class Wizard:
                     "status": "success",
                     "message": f"{mode_label.capitalize()} processing completed successfully",
                     "instructions": [
-                        f"✅ {mode_label.capitalize()} processing completed",
+                        f"[OK] {mode_label.capitalize()} processing completed",
                         next_step
                     ]
                 }
@@ -1051,7 +1051,7 @@ class Wizard:
                     "status": "error",
                     "message": f"Workflow execution failed with return code {result.returncode}",
                     "instructions": [
-                        "❌ Check the error messages above",
+                        "[ERROR] Check the error messages above",
                         "Review parameters in 1_masster_workflow.py",
                         f"Try running manually: python {workflow_script_path.name}"
                     ]
@@ -1062,7 +1062,7 @@ class Wizard:
                 "status": "error",
                 "message": f"Failed to execute workflow: {e}",
                 "instructions": [
-                    "❌ Execution failed",
+                    "[ERROR] Execution failed",
                     "Check that source files exist and are accessible",
                     "Verify folder permissions"
                 ]