| """ | |
| Get All Results | Cannabis Results | |
| Copyright (c) 2024 Cannlytics | |
| Authors: | |
| Keegan Skeate <https://github.com/keeganskeate> | |
| Created: 7/10/2024 | |
| Updated: 8/14/2024 | |
| License: <https://github.com/cannlytics/cannlytics/blob/main/LICENSE> | |
| Description: | |
| Aggregate cannabis test data from states with permitted cannabis use: | |
| - Alaska | |
| ✓ California | |
| - Colorado | |
| ✓ Connecticut | |
| ✓ Florida | |
| ✓ Hawaii | |
| ✓ Maryland | |
| ✓ Massachusetts | |
| ✓ Michigan | |
| ✓ Nevada | |
| ✓ New York | |
| ✓ Oregon | |
| ✓ Rhode Island | |
| ✓ Utah | |
| ✓ Washington | |
| """ | |
| # Standard imports: | |
| import json | |
| import os | |
| # External imports: | |
| from cannlytics.data.coas import standardize_results | |
| from cannlytics.data.coas.parsing import find_unique_analytes | |
| import pandas as pd | |
| def get_all_results( | |
| data_dir, | |
| subsets=None, | |
| ext='csv', | |
| version='latest', | |
| verbose=True, | |
| ): | |
| """Save all of the lab results to a single CSV file.""" | |
| # Read all of the latest datafiles. | |
| all_data = [] | |
| for root, _, files in os.walk(data_dir): | |
| for file in files: | |
| if 'all' in file: | |
| continue | |
| if file.endswith(f'{version}.{ext}'): | |
| file_path = os.path.join(root, file) | |
| if verbose: | |
| print(f"Reading {file_path}") | |
| if ext == 'jsonl': | |
| subset_data = pd.read_json(file_path, lines=True) | |
| elif ext == 'csv': | |
| try: | |
| subset_data = pd.read_csv(file_path, low_memory=False) | |
| except: | |
| subset_data = pd.read_excel(file_path.replace('.csv', '.xlsx')) | |
| else: | |
| subset_data = pd.read_excel(file_path) | |
| all_data.append(subset_data) | |
| if verbose: | |
| print(f"Read {len(subset_data):,} results from {file_path}") | |
| # Merge historic MI results. | |
| # TODO: Separate this logic into `get_results_mi.py` | |
| # import ast | |
| # from cannlytics.data.coas import CoADoc | |
| # from cannlytics.utils import snake_case, convert_to_numeric | |
| # datafile = r"D:\data\cannabis_results\data\mi\mi-results-psi-labs-2022-07-12.xlsx" | |
| # psi_results = pd.read_excel(datafile) | |
| # psi_results['lab_state'] = 'MI' | |
| # psi_results['producer_state'] = 'MI' | |
| # psi_results['date'] = pd.to_datetime(psi_results['date_tested'], format='mixed', errors='coerce') | |
| # psi_results['week'] = psi_results['date'].dt.to_period('W').astype(str) | |
| # psi_results['month'] = psi_results['date'].dt.to_period('M').astype(str) | |
| # psi_results = psi_results.sort_values('date') | |
| # Add a `key` to the PSI Labs results. | |
| # parser = CoADoc() | |
| # fixed_results = [] | |
| # for i, row in psi_results.iterrows(): | |
| # fixed_result = [] | |
| # sample_results = ast.literal_eval(row['results']) | |
| # for result in sample_results: | |
| # name = result['name'] | |
| # key = parser.analytes.get(snake_case(name), snake_case(name)) | |
| # value = convert_to_numeric(result['value'].replace('%', '').strip()) | |
| # fixed_result.append({ | |
| # 'key': key, | |
| # 'name': name, | |
| # 'value': value, | |
| # 'margin_of_error': result.get('margin_of_error'), | |
| # 'limit': result.get('limit'), | |
| # 'status': result.get('status'), | |
| # }) | |
| # fixed_results.append(json.dumps(fixed_result)) | |
| # psi_results['results'] = fixed_results | |
| # analytes = find_unique_analytes(psi_results) | |
| # nuisance_analytes = [ | |
| # '', | |
| # '1_2_dimethoxy_ethane', | |
| # '2_2_dimethyl_butane', | |
| # '2_3_dimethyl_butane', | |
| # '3_methyl_pentane', | |
| # 'metrc_mi_cannabinoids_status', | |
| # 'metrc_mi_cannabinoids_value', | |
| # 'n_n_dimethylformamide', | |
| # 'percent_active_cbd', | |
| # # TODO: Standardize these analytes. | |
| # # 'xylene' | |
| # # 'hexane', | |
| # # 'hexanes', | |
| # # 'transnerolidol_1', | |
| # # 'transnerolidol_2', | |
| # ] | |
| # analytes = set(analytes) - set(nuisance_analytes) | |
| # analytes = sorted(list(analytes)) | |
| # psi_results = standardize_results(psi_results, analytes) | |
| # outfile_csv = r'D:\data\cannabis_results\data\mi\mi-results-psi-labs-2022-07-12.csv' | |
| # psi_results.to_csv(outfile_csv, index=False) | |
| # print('Saved CSV:', outfile_csv) | |
| # DEV: Merge historic PSI Labs results. | |
| datafile = r"D:\data\cannabis_results\data\mi\mi-results-psi-labs-2022-07-12.xlsx" | |
| psi_results = pd.read_excel(datafile) | |
| all_data.append(psi_results) | |
| if verbose: | |
| print('Added %i historic lab results for PSI Labs.' % len(psi_results)) | |
| # Save all of the licenses. | |
| aggregate = pd.concat(all_data) | |
| outfile = os.path.join(data_dir, 'all/all-results-latest.csv') | |
| aggregate.to_csv(outfile, index=False) | |
| if verbose: | |
| print('Aggregated %i results.' % len(aggregate)) | |
| print('Saved CSV:', outfile) | |
| features = {x: 'string' for x in aggregate.columns} | |
| print('Number of features:', len(features)) | |
| print('Features:', features) | |
| return aggregate | |
| # === Test === | |
| # [✓] Tested: 2024-08-14 by Keegan Skeate <keegan@cannlytics> | |
| if __name__ == '__main__': | |
| # Get all of the results. | |
| get_all_results(data_dir='D://data/cannabis_results/data') | |