| """ |
| Users dataset processor for Psi survey data. |
| |
| Processes two types of user survey files: |
| 1. users14.dat (2000-2015): Fixed format with variable commas in username/location fields |
| 2. questions.dat (2014-2022): Similar format with email field and different timestamp format |
| |
| Common schema: |
| - Username, Timestamp, Email, City, State, Coordinates, Country |
| - Psi1-15: Psi test responses (15 questions) |
| - Hemi1-10: Hemispheric dominance questions (10 questions) |
| - HowFind: How user found the survey (text field) |
| - na_count_Psi_and_Hemi: Count of NAs in Psi and Hemi columns |
| |
| Data cleaning rules: |
| - Usernames and location fields can contain commas (dirty data before Psi1) |
| - Remove duplicate usernames: keep row with fewest NAs, then prefer oldest date |
| - Column 32 (HowFind) format changed in Sept 2002 from yes/no to descriptive text |
| """ |
|
|
| from pathlib import Path |
| from typing import List, Dict, Any, Optional |
| from datetime import datetime |
| import pandas as pd |
| import re |
| import csv |
| from io import StringIO |
|
|
| from ..core.base_classes import BaseProcessor |
| from ..core.config import Config |
| from ..core.exceptions import ProcessorError |
| from ..cleaners.encoding_cleaner import EncodingCleaner |
| from ..cleaners.delimiter_cleaner import DelimiterCleaner |
| from ..cleaners.temporal_parser import TemporalParser |
| from ..cleaners.location_parser import LocationParser |
|
|
|
|
| class UsersProcessor(BaseProcessor): |
| """ |
| Processes user survey data from two time periods. |
| |
| Handles: |
| - users14.dat: 2000-2015 data with basic timestamp format |
| - questions.dat: 2014-2022 data with Wed Jan 1 format and email field |
| |
| Both formats have extremely dirty user-entered data before Psi1 column. |
| Username and location fields can contain commas. |
| """ |
|
|
| BATCH_DELIMITER_CLEAN = False |
|
|
| |
| FILE_PATTERNS = ['users14*.dat', 'questions*.dat'] |
|
|
| |
| COLUMNS_UNIFIED = [ |
| 'username', 'timestamp', 'email', 'city', 'state', |
| 'coordinates', 'country' |
| ] + [f'psi_{i:02d}' for i in range(1, 16)] + [ |
| f'hemi_{i:02d}' for i in range(1, 11) |
| ] + ['how_find', 'na_count_psi_and_hemi', 'source_file', 'source_row_number', 'file_type'] |
|
|
| |
| PSI_COLUMNS = [f'psi_{i:02d}' for i in range(1, 16)] |
| HEMI_COLUMNS = [f'hemi_{i:02d}' for i in range(1, 11)] |
|
|
| def __init__(self, config: Config): |
| """Initialize Users processor. |
| |
| Args: |
| config: Configuration object |
| """ |
| super().__init__(config, 'users') |
|
|
| |
| self.encoding_cleaner = EncodingCleaner(config, self.errata_logger) |
| self.delimiter_cleaner = DelimiterCleaner(config, self.errata_logger) |
| self.temporal_parser = TemporalParser(config, self.errata_logger) |
| self.location_parser = LocationParser(config, self.errata_logger) |
|
|
| |
| self.stats = { |
| 'files_processed': 0, |
| 'files_failed': 0, |
| 'rows_total': 0, |
| 'rows_valid': 0, |
| 'rows_invalid': 0, |
| 'users14_rows': 0, |
| 'questions_rows': 0, |
| 'duplicates_removed': 0, |
| 'na_usernames_count': 0 |
| } |
|
|
| def detect_file_type(self, file_path: Path) -> str: |
| """ |
| Detect whether file is users14 or questions format. |
| |
| Args: |
| file_path: Path to file |
| |
| Returns: |
| 'users14' or 'questions' |
| """ |
| if 'users14' in file_path.name.lower(): |
| return 'users14' |
| elif 'questions' in file_path.name.lower(): |
| return 'questions' |
| else: |
| |
| with open(file_path, 'r', encoding='utf-8', errors='replace') as f: |
| first_line = f.readline() |
| |
| if 'Wed ' in first_line or 'Mon ' in first_line or 'Tue ' in first_line: |
| return 'questions' |
| else: |
| return 'users14' |
|
|
| def parse_dirty_csv_line(self, line: str, expected_clean_cols: int = 25) -> tuple: |
| """ |
| Parse CSV line by finding clean numeric data working backwards. |
| |
| Strategy: |
| 1. Split by comma |
| 2. Work backwards to find 25 contiguous numeric columns (Psi1-15, Hemi1-10) |
| 3. Everything before = dirty user data (username, timestamp, location fields) |
| 4. Everything after = HowFind + na_count (for users14 only) |
| |
| The Psi and Hemi columns should only contain values 1-5 or be empty. |
| We use this as an anchor to identify where the clean data starts. |
| |
| Args: |
| line: Raw CSV line |
| expected_clean_cols: Number of expected columns from Psi1 onwards (default 25) |
| |
| Returns: |
| Tuple of (dirty_part, clean_part, tail_part) |
| - dirty_part: List of user-entered fields before Psi1 |
| - clean_part: List of 25 Psi/Hemi columns |
| - tail_part: List of fields after Hemi10 (HowFind, na_count) |
| """ |
| def is_valid_response(val: str) -> bool: |
| """Check if value is valid Psi/Hemi response (1-5 or empty).""" |
| val = val.strip() |
| return val == '' or val in ['1', '2', '3', '4', '5'] |
|
|
| |
| parts = line.split(',') |
|
|
| |
| if len(parts) < expected_clean_cols: |
| return parts, [], [] |
|
|
| |
| |
| min_dirty_fields = 2 |
|
|
| for i in range(len(parts) - expected_clean_cols, min_dirty_fields - 1, -1): |
| window = parts[i:i + expected_clean_cols] |
|
|
| |
| if len(window) == expected_clean_cols and all(is_valid_response(v) for v in window): |
| |
| dirty_part = parts[:i] |
| clean_part = parts[i:i + expected_clean_cols] |
| tail_part = parts[i + expected_clean_cols:] |
|
|
| return dirty_part, clean_part, tail_part |
|
|
| |
| |
| return parts, [], [] |
|
|
| def process_users14_file(self, file_path: Path, pre_cleaned_text: Optional[str] = None) -> Optional[pd.DataFrame]: |
| """ |
| Process users14.dat format file (2000-2015). |
| |
| Format: Username, Timestamp, City, State, Coordinates, Country, |
| Psi1-15, Hemi1-10, HowFind, na_count |
| |
| Args: |
| file_path: Path to file |
| pre_cleaned_text: Pre-cleaned text from parallel batch cleaning. |
| |
| Returns: |
| DataFrame or None |
| """ |
| try: |
| |
| if pre_cleaned_text is not None: |
| text = pre_cleaned_text |
| else: |
| text = self.encoding_cleaner.clean(file_path) |
|
|
| |
| lines = text.strip().split('\n') |
|
|
| parsed_rows = [] |
| for line_num, line in enumerate(lines, 1): |
| if not line.strip(): |
| continue |
|
|
| |
| |
| dirty_part, clean_part, tail_part = self.parse_dirty_csv_line(line, expected_clean_cols=25) |
|
|
| |
| if len(clean_part) != 25: |
| self.errata_logger.log_error( |
| 'parse_failed', |
| f'Line {line_num}: Could not identify clean Psi/Hemi section', |
| file_path=str(file_path), |
| line_number=line_num |
| ) |
| continue |
|
|
| |
| |
| |
| username = dirty_part[0].strip() if len(dirty_part) > 0 else None |
| timestamp = dirty_part[1].strip() if len(dirty_part) > 1 else None |
|
|
| |
| location_str = ','.join(dirty_part[2:]) if len(dirty_part) > 2 else None |
|
|
| |
| location = self.location_parser.parse_location(location_str) if location_str else { |
| 'city': None, 'state': None, 'coordinates': None, 'country': None |
| } |
|
|
| row = { |
| 'username': username, |
| 'timestamp': timestamp, |
| 'email': None, |
| 'city': location['city'], |
| 'state': location['state'], |
| 'coordinates': location['coordinates'], |
| 'country': location['country'], |
| } |
|
|
| |
| for i in range(15): |
| row[f'psi_{i+1:02d}'] = clean_part[i].strip() if clean_part[i].strip() else None |
|
|
| |
| for i in range(10): |
| row[f'hemi_{i+1:02d}'] = clean_part[15 + i].strip() if clean_part[15 + i].strip() else None |
|
|
| |
| row['how_find'] = tail_part[0].strip() if len(tail_part) > 0 else None |
| row['na_count_psi_and_hemi'] = tail_part[1].strip() if len(tail_part) > 1 else None |
|
|
| |
| if len(tail_part) > 2: |
| row['how_find'] = ','.join([t.strip() for t in tail_part[:-1]]) |
| row['na_count_psi_and_hemi'] = tail_part[-1].strip() |
|
|
| row['source_file'] = file_path.name |
| row['source_row_number'] = line_num |
| row['file_type'] = 'users14' |
|
|
| parsed_rows.append(row) |
|
|
| if not parsed_rows: |
| self.errata_logger.log_error( |
| 'empty_file', |
| 'No valid rows parsed', |
| file_path=str(file_path) |
| ) |
| return None |
|
|
| df = pd.DataFrame(parsed_rows) |
| return df |
|
|
| except Exception as e: |
| import traceback |
| self.errata_logger.log_error( |
| 'file_processing_failed', |
| f'{type(e).__name__}: {e} - entire file omitted', |
| file_path=str(file_path), |
| scope='file', |
| context={'traceback': traceback.format_exc()}, |
| ) |
| return None |
|
|
| def process_questions_file(self, file_path: Path, pre_cleaned_text: Optional[str] = None) -> Optional[pd.DataFrame]: |
| """ |
| Process questions.dat format file (2014-2022). |
| |
| Format: Username, Timestamp, Email, City, State, Coordinates, Country, |
| Psi1-15, Hemi1-10, HowFind |
| |
| Timestamp format: "Wed Jan 1 00:33:44 2014" |
| |
| Args: |
| file_path: Path to file |
| pre_cleaned_text: Pre-cleaned text from parallel batch cleaning. |
| |
| Returns: |
| DataFrame or None |
| """ |
| try: |
| |
| if pre_cleaned_text is not None: |
| text = pre_cleaned_text |
| else: |
| text = self.encoding_cleaner.clean(file_path) |
|
|
| |
| lines = text.strip().split('\n') |
|
|
| parsed_rows = [] |
| for line_num, line in enumerate(lines, 1): |
| if not line.strip(): |
| continue |
|
|
| |
| |
| dirty_part, clean_part, tail_part = self.parse_dirty_csv_line(line, expected_clean_cols=25) |
|
|
| |
| if len(clean_part) != 25: |
| self.errata_logger.log_error( |
| 'parse_failed', |
| f'Line {line_num}: Could not identify clean Psi/Hemi section', |
| file_path=str(file_path), |
| line_number=line_num |
| ) |
| continue |
|
|
| |
| |
| |
| username = dirty_part[0].strip() if len(dirty_part) > 0 else None |
| timestamp = dirty_part[1].strip() if len(dirty_part) > 1 else None |
| email = dirty_part[2].strip() if len(dirty_part) > 2 else None |
|
|
| |
| location_str = ','.join(dirty_part[3:]) if len(dirty_part) > 3 else None |
|
|
| |
| location = self.location_parser.parse_location(location_str) if location_str else { |
| 'city': None, 'state': None, 'coordinates': None, 'country': None |
| } |
|
|
| row = { |
| 'username': username, |
| 'timestamp': timestamp, |
| 'email': email, |
| 'city': location['city'], |
| 'state': location['state'], |
| 'coordinates': location['coordinates'], |
| 'country': location['country'], |
| } |
|
|
| |
| for i in range(15): |
| row[f'psi_{i+1:02d}'] = clean_part[i].strip() if clean_part[i].strip() else None |
|
|
| |
| for i in range(10): |
| row[f'hemi_{i+1:02d}'] = clean_part[15 + i].strip() if clean_part[15 + i].strip() else None |
|
|
| |
| row['how_find'] = ','.join([t.strip() for t in tail_part]) if tail_part else None |
|
|
| |
| row['na_count_psi_and_hemi'] = None |
|
|
| row['source_file'] = file_path.name |
| row['source_row_number'] = line_num |
| row['file_type'] = 'questions' |
|
|
| parsed_rows.append(row) |
|
|
| if not parsed_rows: |
| self.errata_logger.log_error( |
| 'empty_file', |
| 'No valid rows parsed', |
| file_path=str(file_path) |
| ) |
| return None |
|
|
| df = pd.DataFrame(parsed_rows) |
| return df |
|
|
| except Exception as e: |
| import traceback |
| self.errata_logger.log_error( |
| 'file_processing_failed', |
| f'{type(e).__name__}: {e} - entire file omitted', |
| file_path=str(file_path), |
| scope='file', |
| context={'traceback': traceback.format_exc()}, |
| ) |
| return None |
|
|
| def process_file(self, file_path: Path, pre_cleaned_text: Optional[str] = None) -> Optional[pd.DataFrame]: |
| """ |
| Process a single user data file. |
| |
| Args: |
| file_path: Path to file |
| pre_cleaned_text: Pre-cleaned text from parallel batch cleaning. |
| If None, cleans the file inline (backward compat). |
| |
| Returns: |
| DataFrame or None |
| """ |
| file_type = self.detect_file_type(file_path) |
|
|
| if file_type == 'users14': |
| df = self.process_users14_file(file_path, pre_cleaned_text=pre_cleaned_text) |
| else: |
| df = self.process_questions_file(file_path, pre_cleaned_text=pre_cleaned_text) |
|
|
| if df is None or df.empty: |
| self.stats['files_failed'] += 1 |
| return None |
|
|
| |
| df = self.validate_dataframe(df, file_path) |
|
|
| if df.empty: |
| self.stats['files_failed'] += 1 |
| return None |
|
|
| |
| self.stats['files_processed'] += 1 |
| if file_type == 'users14': |
| self.stats['users14_rows'] += len(df) |
| else: |
| self.stats['questions_rows'] += len(df) |
|
|
| return df |
|
|
| def validate_dataframe(self, df: pd.DataFrame, file_path: Path) -> pd.DataFrame: |
| """ |
| Validate and clean DataFrame. |
| |
| Args: |
| df: Input DataFrame |
| file_path: Source file path |
| |
| Returns: |
| Cleaned DataFrame |
| """ |
| initial_count = len(df) |
|
|
| |
| if 'username' in df.columns: |
| na_usernames = df['username'].isna() | (df['username'].str.lower().str.strip() == 'na') |
| self.stats['na_usernames_count'] += na_usernames.sum() |
|
|
| |
| if 'timestamp' in df.columns: |
| df['timestamp'] = self.temporal_parser.parse_dates_vectorized( |
| df['timestamp'], file_path=str(file_path) |
| ) |
|
|
| |
| for col in self.PSI_COLUMNS: |
| if col in df.columns: |
| df[col] = self.to_numeric_logged(df[col], col, str(file_path)) |
|
|
| |
| for col in self.HEMI_COLUMNS: |
| if col in df.columns: |
| df[col] = self.to_numeric_logged(df[col], col, str(file_path)) |
|
|
| |
| if 'na_count_psi_and_hemi' not in df.columns or df['na_count_psi_and_hemi'].isna().all(): |
| psi_hemi_cols = self.PSI_COLUMNS + self.HEMI_COLUMNS |
| existing_cols = [col for col in psi_hemi_cols if col in df.columns] |
| df['na_count_psi_and_hemi'] = df[existing_cols].isna().sum(axis=1) |
| else: |
| df['na_count_psi_and_hemi'] = self.to_numeric_logged(df['na_count_psi_and_hemi'], 'na_count_psi_and_hemi', str(file_path)) |
|
|
| |
| for col in self.COLUMNS_UNIFIED: |
| if col not in df.columns: |
| df[col] = None |
|
|
| |
| df = df[self.COLUMNS_UNIFIED] |
|
|
| invalid_count = initial_count - len(df) |
| if invalid_count > 0: |
| self.errata_logger.log_file_summary( |
| str(file_path), |
| 'partial', |
| initial_count, |
| len(df), |
| invalid_count |
| ) |
|
|
| return df |
|
|
| def remove_duplicates(self, df: pd.DataFrame) -> pd.DataFrame: |
| """ |
| Remove duplicate usernames using deduplication rules: |
| 1. Keep row with fewest NAs in Psi and Hemi columns |
| 2. If tied on NAs, keep oldest timestamp |
| |
| Args: |
| df: Input DataFrame |
| |
| Returns: |
| Deduplicated DataFrame |
| """ |
| initial_count = len(df) |
|
|
| |
| print("\nPer-file duplicate analysis:") |
| print("-" * 50) |
|
|
| |
| if 'file_type' in df.columns: |
| for file_type in df['file_type'].unique(): |
| file_df = df[df['file_type'] == file_type] |
| file_dupes = len(file_df) - file_df['username'].nunique() |
| print(f" {file_type}: {len(file_df):,} rows, {file_dupes:,} internal duplicates") |
|
|
| |
| total_rows = len(df) |
| unique_usernames = df['username'].nunique() |
| total_dupes = total_rows - unique_usernames |
|
|
| print(f"\nCross-file analysis:") |
| print(f" Total rows: {total_rows:,}") |
| print(f" Unique usernames: {unique_usernames:,}") |
| print(f" Total duplicates to remove: {total_dupes:,}") |
| print() |
|
|
| |
| df_sorted = df.sort_values( |
| by=['username', 'na_count_psi_and_hemi', 'timestamp'], |
| ascending=[True, True, True] |
| ) |
|
|
| |
| |
| kept_indices = df_sorted.groupby('username').head(1).index |
| df_dedup = df_sorted.loc[kept_indices].reset_index(drop=True) |
|
|
| |
| if 'file_type' in df.columns: |
| print("Deduplication results by file type:") |
| removed_df = df[~df.index.isin(kept_indices)] |
|
|
| for file_type in df['file_type'].unique(): |
| kept_count = (df_dedup['file_type'] == file_type).sum() |
| removed_count = (removed_df['file_type'] == file_type).sum() |
| original_count = (df['file_type'] == file_type).sum() |
| print(f" {file_type}: kept {kept_count:,} / {original_count:,}, removed {removed_count:,}") |
| print() |
|
|
| duplicates_removed = initial_count - len(df_dedup) |
| self.stats['duplicates_removed'] = duplicates_removed |
|
|
| if duplicates_removed > 0: |
| self.errata_logger.log_error( |
| 'duplicates_removed', |
| f'Removed {duplicates_removed} duplicate username entries', |
| file_path='combined_data' |
| ) |
|
|
| |
| |
| removed_df = df_sorted[~df_sorted.index.isin(kept_indices)] |
| compare_cols = self.PSI_COLUMNS + self.HEMI_COLUMNS + ['timestamp', 'city', 'state', 'country'] |
| compare_cols = [c for c in compare_cols if c in df.columns] |
|
|
| sample_users = removed_df['username'].unique()[:50] |
| for uname in sample_users: |
| kept_row = df_dedup[df_dedup['username'] == uname] |
| removed_rows = removed_df[removed_df['username'] == uname] |
| if kept_row.empty or removed_rows.empty: |
| continue |
| kept_vals = kept_row[compare_cols].iloc[0] |
| for _, rem_row in removed_rows.iterrows(): |
| diffs = {} |
| for col in compare_cols: |
| k, r = kept_vals[col], rem_row[col] |
| if str(k) != str(r): |
| diffs[col] = {'kept': str(k), 'removed': str(r)} |
| if diffs: |
| self.errata_logger.log_error( |
| 'duplicate_detail', |
| f"Discarded row for '{uname}' differs in {len(diffs)} field(s)", |
| file_path='combined_data', |
| scope='row', |
| context={'differing_fields': diffs}, |
| ) |
|
|
| return df_dedup |
|
|
| def process(self, max_files: Optional[int] = None) -> pd.DataFrame: |
| """ |
| Process all user data files. |
| |
| Args: |
| max_files: Optional limit on number of files to process |
| |
| Returns: |
| Combined DataFrame |
| """ |
| files = self.get_file_list() |
|
|
| if max_files: |
| files = files[:max_files] |
|
|
| print(f"Processing {len(files)} user data files...") |
|
|
| |
| cleaned_texts = self._batch_clean_files(files, use_delimiter_cleaner=False) |
| print(f"Successfully cleaned {len(cleaned_texts)}/{len(files)} files") |
|
|
| dfs = [] |
|
|
| try: |
| from tqdm import tqdm |
| iterator = tqdm(files, desc="Processing user files") |
| except ImportError: |
| iterator = files |
|
|
| for file_path in iterator: |
| pre_cleaned = cleaned_texts.get(file_path) |
| if pre_cleaned is None: |
| continue |
| df = self.process_file(file_path, pre_cleaned_text=pre_cleaned) |
| if df is not None and not df.empty: |
| dfs.append(df) |
|
|
| if not dfs: |
| raise ProcessorError("No valid data processed") |
|
|
| print("Combining files...") |
| combined = pd.concat(dfs, ignore_index=True) |
|
|
| self.stats['rows_total'] = len(combined) |
|
|
| |
| unique_usernames_before = combined['username'].nunique() |
| print(f"\nBefore deduplication:") |
| print(f" Total rows: {len(combined):,}") |
| print(f" Unique usernames: {unique_usernames_before:,}") |
| print() |
|
|
| |
| print("Removing duplicate usernames...") |
| combined = self.remove_duplicates(combined) |
|
|
| |
| unique_usernames_after = combined['username'].nunique() |
| print(f"After deduplication:") |
| print(f" Total rows: {len(combined):,}") |
| print(f" Unique usernames: {unique_usernames_after:,}") |
| print() |
|
|
| self.stats['rows_valid'] = len(combined) |
|
|
| |
| audit_mode = self.config.get('processing.audit_mode', False) |
| if not audit_mode: |
| audit_cols = ['source_file', 'source_row_number'] |
| cols_to_drop = [col for col in audit_cols if col in combined.columns] |
| if cols_to_drop: |
| combined = combined.drop(columns=cols_to_drop) |
| print(f"Audit mode disabled: Removed columns {cols_to_drop}") |
| print() |
|
|
|
|
| |
| self.errata_logger.close() |
|
|
| return combined |
|
|
| def get_stats(self) -> Dict[str, Any]: |
| """Get processing statistics.""" |
| return self.stats.copy() |
|
|