import re import secrets import base64 import time import pandas as pd from faker import Faker from gradio import Progress from typing import List, Dict, Any from presidio_analyzer import AnalyzerEngine, BatchAnalyzerEngine, DictAnalyzerResult, RecognizerResult from presidio_anonymizer import AnonymizerEngine, BatchAnonymizerEngine from presidio_anonymizer.entities import OperatorConfig, ConflictResolutionStrategy from tools.helper_functions import output_folder, get_file_path_end, read_file, detect_file_type from tools.load_spacy_model_custom_recognisers import nlp_analyser, score_threshold # Use custom version of analyze_dict to be able to track progress from tools.presidio_analyzer_custom import analyze_dict fake = Faker("en_UK") def fake_first_name(x): return fake.first_name() def initial_clean(text): #### Some of my cleaning functions html_pattern_regex = r'<.*?>|&([a-z0-9]+|#[0-9]{1,6}|#x[0-9a-f]{1,6});|\xa0| ' html_start_pattern_end_dots_regex = r'<(.*?)\.\.' non_ascii_pattern = r'[^\x00-\x7F]+' multiple_spaces_regex = r'\s{2,}' # Define a list of patterns and their replacements patterns = [ (html_pattern_regex, ' '), (html_start_pattern_end_dots_regex, ' '), (non_ascii_pattern, ' '), (multiple_spaces_regex, ' ') ] # Apply each regex replacement for pattern, replacement in patterns: text = re.sub(pattern, replacement, text) return text def process_recognizer_result(result, recognizer_result, data_row, dictionary_key, df_dict, keys_to_keep): output = [] if hasattr(result, 'value'): text = result.value[data_row] else: text = "" if isinstance(recognizer_result, list): for sub_result in recognizer_result: if isinstance(text, str): found_text = text[sub_result.start:sub_result.end] else: found_text = '' analysis_explanation = {key: sub_result.__dict__[key] for key in keys_to_keep} analysis_explanation.update({ 'data_row': str(data_row), 'column': list(df_dict.keys())[dictionary_key], 'entity': found_text }) output.append(str(analysis_explanation)) return output # Writing decision making process to file def generate_decision_process_output(analyzer_results: List[DictAnalyzerResult], df_dict: Dict[str, List[Any]]) -> str: """ Generate a detailed output of the decision process for entity recognition. This function takes the results from the analyzer and the original data dictionary, and produces a string output detailing the decision process for each recognized entity. It includes information such as entity type, position, confidence score, and the context in which the entity was found. Args: analyzer_results (List[DictAnalyzerResult]): The results from the entity analyzer. df_dict (Dict[str, List[Any]]): The original data in dictionary format. Returns: str: A string containing the detailed decision process output. """ decision_process_output = [] keys_to_keep = ['entity_type', 'start', 'end'] # Run through each column to analyse for PII for i, result in enumerate(analyzer_results): # If a single result if isinstance(result, RecognizerResult): decision_process_output.extend(process_recognizer_result(result, result, 0, i, df_dict, keys_to_keep)) # If a list of results elif isinstance(result, list) or isinstance(result, DictAnalyzerResult): for x, recognizer_result in enumerate(result.recognizer_results): decision_process_output.extend(process_recognizer_result(result, recognizer_result, x, i, df_dict, keys_to_keep)) else: try: decision_process_output.extend(process_recognizer_result(result, result, 0, i, df_dict, keys_to_keep)) except Exception as e: print(e) decision_process_output_str = '\n'.join(decision_process_output) print("decision_process_output_str:\n\n", decision_process_output_str) return decision_process_output_str def anon_consistent_names(df): # ## Pick out common names and replace them with the same person value df_dict = df.to_dict(orient="list") analyzer = AnalyzerEngine() batch_analyzer = BatchAnalyzerEngine(analyzer_engine=analyzer) analyzer_results = batch_analyzer.analyze_dict(df_dict, language="en") analyzer_results = list(analyzer_results) # + tags=[] text = analyzer_results[3].value # + tags=[] recognizer_result = str(analyzer_results[3].recognizer_results) # + tags=[] recognizer_result # + tags=[] data_str = recognizer_result # abbreviated for brevity # Adjusting the parse_dict function to handle trailing ']' # Splitting the main data string into individual list strings list_strs = data_str[1:-1].split('], [') def parse_dict(s): s = s.strip('[]') # Removing any surrounding brackets items = s.split(', ') d = {} for item in items: key, value = item.split(': ') if key == 'score': d[key] = float(value) elif key in ['start', 'end']: d[key] = int(value) else: d[key] = value return d # Re-running the improved processing code result = [] for lst_str in list_strs: # Splitting each list string into individual dictionary strings dict_strs = lst_str.split(', type: ') dict_strs = [dict_strs[0]] + ['type: ' + s for s in dict_strs[1:]] # Prepending "type: " back to the split strings # Parsing each dictionary string dicts = [parse_dict(d) for d in dict_strs] result.append(dicts) #result # + tags=[] names = [] for idx, paragraph in enumerate(text): paragraph_texts = [] for dictionary in result[idx]: if dictionary['type'] == 'PERSON': paragraph_texts.append(paragraph[dictionary['start']:dictionary['end']]) names.append(paragraph_texts) # + tags=[] # Flatten the list of lists and extract unique names unique_names = list(set(name for sublist in names for name in sublist)) # + tags=[] fake_names = pd.Series(unique_names).apply(fake_first_name) # + tags=[] mapping_df = pd.DataFrame(data={"Unique names":unique_names, "Fake names": fake_names}) # + tags=[] # Convert mapping dataframe to dictionary # Convert mapping dataframe to dictionary, adding word boundaries for full-word match name_map = {r'\b' + k + r'\b': v for k, v in zip(mapping_df['Unique names'], mapping_df['Fake names'])} # + tags=[] name_map # + tags=[] scrubbed_df_consistent_names = df.replace(name_map, regex = True) # + tags=[] scrubbed_df_consistent_names return scrubbed_df_consistent_names def anonymise_script(df, anon_strat, language:str, chosen_redact_entities:List[str], in_allow_list:List[str]=[], progress=Progress(track_tqdm=False)): print("Identifying personal information") analyse_tic = time.perf_counter() key_string = "" # DataFrame to dict df_dict = df.to_dict(orient="list") if in_allow_list: in_allow_list_flat = in_allow_list #[item for sublist in in_allow_list for item in sublist] else: in_allow_list_flat = [] #analyzer = nlp_analyser #AnalyzerEngine() batch_analyzer = BatchAnalyzerEngine(analyzer_engine=nlp_analyser) anonymizer = AnonymizerEngine()#conflict_resolution=ConflictResolutionStrategy.MERGE_SIMILAR_OR_CONTAINED) batch_anonymizer = BatchAnonymizerEngine(anonymizer_engine = anonymizer) #print("Allow list:", in_allow_list) #print("Input data keys:", df_dict.keys()) # Use custom analyzer to be able to track progress with Gradio analyzer_results = analyze_dict(batch_analyzer, df_dict, language=language, entities=chosen_redact_entities, score_threshold=score_threshold, return_decision_process=True, allow_list=in_allow_list_flat) analyzer_results = list(analyzer_results) # Usage in the main function: decision_process_output_str = generate_decision_process_output(analyzer_results, df_dict) #print("decision_process_output_str:\n\n", decision_process_output_str) analyse_toc = time.perf_counter() analyse_time_out = f"Analysing the text took {analyse_toc - analyse_tic:0.1f} seconds." print(analyse_time_out) # Create faker function (note that it has to receive a value) fake = Faker("en_UK") def fake_first_name(x): return fake.first_name() # Set up the anonymization configuration WITHOUT DATE_TIME simple_replace_config = eval('{"DEFAULT": OperatorConfig("replace", {"new_value": "REDACTED"})}') replace_config = eval('{"DEFAULT": OperatorConfig("replace")}') redact_config = eval('{"DEFAULT": OperatorConfig("redact")}') hash_config = eval('{"DEFAULT": OperatorConfig("hash")}') mask_config = eval('{"DEFAULT": OperatorConfig("mask", {"masking_char":"*", "chars_to_mask":100, "from_end":True})}') people_encrypt_config = eval('{"PERSON": OperatorConfig("encrypt", {"key": key_string})}') # The encryption is using AES cypher in CBC mode and requires a cryptographic key as an input for both the encryption and the decryption. fake_first_name_config = eval('{"PERSON": OperatorConfig("custom", {"lambda": fake_first_name})}') if anon_strat == "replace with ": chosen_mask_config = simple_replace_config if anon_strat == "replace with ": chosen_mask_config = replace_config if anon_strat == "redact": chosen_mask_config = redact_config if anon_strat == "hash": chosen_mask_config = hash_config if anon_strat == "mask": chosen_mask_config = mask_config if anon_strat == "encrypt": chosen_mask_config = people_encrypt_config # Generate a 128-bit AES key. Then encode the key using base64 to get a string representation key = secrets.token_bytes(16) # 128 bits = 16 bytes key_string = base64.b64encode(key).decode('utf-8') elif anon_strat == "fake_first_name": chosen_mask_config = fake_first_name_config # I think in general people will want to keep date / times keep_date_config = eval('{"DATE_TIME": OperatorConfig("keep")}') combined_config = {**chosen_mask_config, **keep_date_config} combined_config anonymizer_results = batch_anonymizer.anonymize_dict(analyzer_results, operators=combined_config) scrubbed_df = pd.DataFrame(anonymizer_results) return scrubbed_df, key_string, decision_process_output_str def anon_wrapper_func(anon_file, anon_df, chosen_cols, out_file_paths, out_file_part, out_message, excel_sheet_name, anon_strat, language, chosen_redact_entities, in_allow_list, file_type, anon_xlsx_export_file_name, log_files_output_paths): def check_lists(list1, list2): return any(string in list2 for string in list1) def get_common_strings(list1, list2): """ Finds the common strings between two lists. Args: list1: The first list of strings. list2: The second list of strings. Returns: A list containing the common strings. """ common_strings = [] for string in list1: if string in list2: common_strings.append(string) return common_strings # Check for chosen col, skip file if not found all_cols_original_order = list(anon_df.columns) any_cols_found = check_lists(chosen_cols, all_cols_original_order) if any_cols_found == False: out_message = "No chosen columns found in dataframe: " + out_file_part print(out_message) else: chosen_cols_in_anon_df = get_common_strings(chosen_cols, all_cols_original_order) # Split dataframe to keep only selected columns print("Remaining columns to redact:", chosen_cols_in_anon_df) anon_df_part = anon_df[chosen_cols_in_anon_df] anon_df_remain = anon_df.drop(chosen_cols_in_anon_df, axis = 1) # Anonymise the selected columns anon_df_part_out, key_string, decision_process_output_str = anonymise_script(anon_df_part, anon_strat, language, chosen_redact_entities, in_allow_list) # Rejoin the dataframe together anon_df_out = pd.concat([anon_df_part_out, anon_df_remain], axis = 1) anon_df_out = anon_df_out[all_cols_original_order] # Export file # Rename anonymisation strategy for file path naming if anon_strat == "replace with ": anon_strat_txt = "redact_simple" elif anon_strat == "replace with ": anon_strat_txt = "redact_entity_type" else: anon_strat_txt = anon_strat # If the file is an xlsx, add a new sheet to the existing xlsx. Otherwise, write to csv if file_type == 'xlsx': anon_export_file_name = anon_xlsx_export_file_name # Create a Pandas Excel writer using XlsxWriter as the engine. with pd.ExcelWriter(anon_xlsx_export_file_name, engine='openpyxl', mode='a') as writer: # Write each DataFrame to a different worksheet. anon_df_out.to_excel(writer, sheet_name=excel_sheet_name, index=None) decision_process_log_output_file = anon_xlsx_export_file_name + "_" + excel_sheet_name + "_decision_process_output.txt" with open(decision_process_log_output_file, "w") as f: f.write(decision_process_output_str) else: anon_export_file_name = output_folder + out_file_part + "_anon_" + anon_strat_txt + ".csv" anon_df_out.to_csv(anon_export_file_name, index = None) decision_process_log_output_file = anon_export_file_name + "_decision_process_output.txt" with open(decision_process_log_output_file, "w") as f: f.write(decision_process_output_str) out_file_paths.append(anon_export_file_name) log_files_output_paths.append(decision_process_log_output_file) # As files are created in a loop, there is a risk of duplicate file names being output. Use set to keep uniques. out_file_paths = list(set(out_file_paths)) # Print result text to output text box if just anonymising open text if anon_file=='open_text': out_message = [anon_df_out['text'][0]] return out_file_paths, out_message, key_string, log_files_output_paths def anonymise_data_files(file_paths:List[str], in_text:str, anon_strat:str, chosen_cols:List[str], language:str, chosen_redact_entities:List[str], in_allow_list:List[str]=None, latest_file_completed:int=0, out_message:list=[], out_file_paths:list = [], log_files_output_paths:list = [], in_excel_sheets:list=[], first_loop_state:bool=False, progress=Progress(track_tqdm=True)): tic = time.perf_counter() # If this is the first time around, set variables to 0/blank if first_loop_state==True: latest_file_completed = 0 out_message = [] out_file_paths = [] # Load file # If out message or out_file_paths are blank, change to a list so it can be appended to if isinstance(out_message, str): out_message = [out_message] if not out_file_paths: out_file_paths = [] if in_allow_list: in_allow_list_flat = in_allow_list #[item for sublist in in_allow_list for item in sublist] else: in_allow_list_flat = [] anon_df = pd.DataFrame() #out_file_paths = [] # Check if files and text exist if not file_paths: if in_text: file_paths=['open_text'] else: out_message = "Please enter text or a file to redact." return out_message, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths # If we have already redacted the last file, return the input out_message and file list to the relevant components if latest_file_completed >= len(file_paths): print("Last file reached, returning files:", str(latest_file_completed)) # Set to a very high number so as not to mess with subsequent file processing by the user latest_file_completed = 99 final_out_message = '\n'.join(out_message) return final_out_message, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths file_path_loop = [file_paths[int(latest_file_completed)]] for anon_file in progress.tqdm(file_path_loop, desc="Anonymising files", unit = "file"): if anon_file=='open_text': anon_df = pd.DataFrame(data={'text':[in_text]}) chosen_cols=['text'] sheet_name = "" file_type = "" out_file_part = anon_file out_file_paths, out_message, key_string, log_files_output_paths = anon_wrapper_func(anon_file, anon_df, chosen_cols, out_file_paths, out_file_part, out_message, sheet_name, anon_strat, language, chosen_redact_entities, in_allow_list, file_type, "", log_files_output_paths) else: # If file is an xlsx, we are going to run through all the Excel sheets to anonymise them separately. file_type = detect_file_type(anon_file) print("File type is:", file_type) out_file_part = get_file_path_end(anon_file.name) if file_type == 'xlsx': print("Running through all xlsx sheets") #anon_xlsx = pd.ExcelFile(anon_file) if not in_excel_sheets: out_message.append("No Excel sheets selected. Please select at least one to anonymise.") continue anon_xlsx = pd.ExcelFile(anon_file) # Create xlsx file: anon_xlsx_export_file_name = output_folder + out_file_part + "_redacted.xlsx" from openpyxl import Workbook wb = Workbook() wb.save(anon_xlsx_export_file_name) # Iterate through the sheet names for sheet_name in in_excel_sheets: # Read each sheet into a DataFrame if sheet_name not in anon_xlsx.sheet_names: continue anon_df = pd.read_excel(anon_file, sheet_name=sheet_name) # Process the DataFrame (e.g., print its contents) print(f"Sheet Name: {sheet_name}") print(anon_df.head()) # Print the first few rows out_file_paths, out_message, key_string, log_files_output_paths = anon_wrapper_func(anon_file, anon_df, chosen_cols, out_file_paths, out_file_part, out_message, sheet_name, anon_strat, language, chosen_redact_entities, in_allow_list, file_type, anon_xlsx_export_file_name, log_files_output_paths) else: sheet_name = "" anon_df = read_file(anon_file) out_file_part = get_file_path_end(anon_file.name) out_file_paths, out_message, key_string, log_files_output_paths = anon_wrapper_func(anon_file, anon_df, chosen_cols, out_file_paths, out_file_part, out_message, sheet_name, anon_strat, language, chosen_redact_entities, in_allow_list, file_type, "", log_files_output_paths) # Increase latest file completed count unless we are at the last file if latest_file_completed != len(file_paths): print("Completed file number:", str(latest_file_completed)) latest_file_completed += 1 toc = time.perf_counter() out_time = f"in {toc - tic:0.1f} seconds." print(out_time) if anon_strat == "encrypt": out_message.append(". Your decryption key is " + key_string + ".") out_message.append("Anonymisation of file '" + out_file_part + "' successfully completed in") out_message_out = '\n'.join(out_message) out_message_out = out_message_out + " " + out_time out_message_out = out_message_out + "\n\nGo to to the Redaction settings tab to see redaction logs. Please give feedback on the results below to help improve this app." return out_message_out, out_file_paths, out_file_paths, latest_file_completed, log_files_output_paths, log_files_output_paths