"""waternsw_grabber.py Download bore records from the WaterNSW data portal. """ import os import re import time import shutil import logging import warnings import requests import pandas as pd from tqdm import tqdm from selenium import webdriver from selenium.webdriver.common.by import By from selenium.webdriver.common.keys import Keys from selenium.webdriver.support.ui import WebDriverWait, Select from selenium.webdriver.support import expected_conditions as EC from selenium.common.exceptions import ( TimeoutException, StaleElementReferenceException, NoSuchElementException) def has_admin(): """Check if current user has admin rights. https://stackoverflow.com/questions/2946746 """ if os.name == 'nt': try: # Check if C:/Windows/temp is readable for current user os.listdir(os.path.join(os.environ.get('systemroot'), 'temp')) except PermissionError: return False else: return True else: if 'SUDO_USER' in os.environ and os.geteuid() == 0: return True else: return False def wait_for_element(driver, by, x, timeout=180): """Wait for element on page to load. Args: driver: selenium webdriver object by: locator strategy (e.g. By.ID) x: locator string timeout: maximum wait time (seconds) Raises TimeoutException if element does not load within timeout period """ element_present = EC.presence_of_element_located((by, x)) WebDriverWait(driver, timeout).until(element_present) def get_telemetered_bore(driver, bore_id, start_date, end_date): """Download single record from telemetered bore. Args: driver: selenium webdriver object bore_id: bore ID (string) start_date: start date (string in YYYY-MM-DD format) end_date: end date (string in YYYY-MM-DD format) """ url = 'https://realtimedata.waternsw.com.au/water.stm' driver.get(url) driver.switch_to.default_content() webhyd = driver.find_element_by_id('webhyd') driver.switch_to.frame(webhyd) # Load site specific page driver.execute_script("go('{}','gw', 1)".format(bore_id)) # Wait for results frame to load wait_for_element(driver, By.ID, 'gwgwlf_org') driver.switch_to.frame('gwgwlf_org') # Wait until body text of iframe has loaded body_text = None while not body_text: try: # Get contents of body text body_text = driver.find_element_by_xpath('//*/body').text except (StaleElementReferenceException, NoSuchElementException): pass time.sleep(0.5) # Detect if bore record does not exist if 'No SITE record found for site' in body_text: raise ValueError('No SITE record found for site {}'.format(bore_id)) elif 'No variables data found for this site.' in body_text: raise ValueError('No variables data found for site {}'.format(bore_id)) # Wait for navigation tabs wait_for_element(driver, By.XPATH, '//*[@id="tabstext"]') # Activate outputs tab, and wait for 'Get Output' button driver.execute_script("menuloc.display_frame('gw', 'gwcf_org', '1')") driver.switch_to.parent_frame() wait_for_element(driver, By.ID, 'gwgwcf_org') driver.switch_to.frame('gwgwcf_org') wait_for_element(driver, By.ID, 'submit') # Get output select controls selects = driver.find_elements_by_xpath('//*/select') for select in selects: s = Select(select) label = s.options[0].get_attribute('label') if label == 'All data': period = s elif label == 'Plot': output = s elif label == 'Annual': interval = s # Change period dropdown to 'Custom' period.select_by_visible_text('Custom') # Get date input fields fields = driver.find_elements_by_xpath('//*[starts-with(@id,"cdate")]') # Parse dates start_date = pd.to_datetime(start_date) end_date = pd.to_datetime(end_date) # Update fields with specified dates for field, date in zip(fields, [start_date, end_date]): field.clear() field.send_keys(pd.datetime.strftime(date, '%H:%M_%d/%m/%Y')) # Set output dropdown to 'Download' output.select_by_visible_text('Download') # Set interval dropdown to 'All points' interval.select_by_visible_text('All points') # Make sure 'Groundwater Level - AHD' is selected as an output try: checkbox = driver.find_element_by_xpath( '//*/input[contains(@name, "sel__110.00_115.00")]') if not checkbox.get_attribute('selected'): checkbox.click() except NoSuchElementException: pass # Download data driver.execute_script("get_output()") driver.execute_script("hide_object('confirm');co(level,tab,1)") # Close popup wait_for_element( driver, By.XPATH, "//div[contains(@class, 'lity-container')]", timeout=60) webdriver.ActionChains(driver).send_keys(Keys.ESCAPE).perform() def open_browser(download_dir): """Opens an automated Firefox browser instance. Args: download_dir: path to where downloaded files will be saved Returns: A selenium web browser object """ # Make download directory absolute download_dir = os.path.abspath(download_dir) # Set up Firefox to silently download files to specified folder profile = webdriver.FirefoxProfile() profile.set_preference('browser.download.folderList', 2) profile.set_preference('browser.download.manager.showWhenStarting', False) profile.set_preference('browser.download.dir', download_dir) profile.set_preference('browser.helperApps.neverAsk.saveToDisk', ('application/zip,' 'application/octet-stream,' 'application/x-zip-compressed,' 'multipart/x-zip')) # Create download folder if it does not exist os.makedirs(download_dir, exist_ok=True) # Open browser driver = webdriver.Firefox(firefox_profile=profile) return driver def telemetered_bore_downloader(bore_ids, start_date, end_date, download_dir): """Download multiple records from telemetered bore. Args: bore_ids: bore ID values (array-like) start_date: start date (string YYYY-MM-DD format) end_date: end date (string YYYY-MM-DD format) download_dir: path to where downloaded files will be saved Raises: ValueError when bore ID is invalid """ driver = open_browser(download_dir) # Set up log File log_name = os.path.join(download_dir, 'errors.log') logging.basicConfig(filename=log_name, level=logging.ERROR) # Download bore logs pbar = tqdm(bore_ids) for bore_id in pbar: pbar.set_description(bore_id) try: get_telemetered_bore(driver, bore_id, start_date, end_date) except ValueError as e: logging.error(e) except TimeoutException: e = 'Request timed out on {}. Try again later?'.format(bore_id) logging.error(e) # Tidy up console after tqdm print('\n') # Stop logging logging.shutdown() with open(log_name, 'r') as f: log_data = f.read() # Check contents of log file if log_data: warnings.warn( 'Some files failed to download. See log for details.', stacklevel=2) else: os.remove(log_name) driver.quit() def extract_definitions(input_dir, output_dir): """Extract variable and quality metadata from bore records. Args: input_dir: path to downloaded zip archives output_dir: path to save csv files """ # Get basin info for telemetered site data csv_name = os.path.join( os.path.dirname(os.path.dirname(__file__)), 'data', 'telemetered-sites.csv') basins = pd.read_csv(csv_name, index_col=0) # Find zip files zip_names = [f for f in os.listdir(input_dir) if f.endswith('.zip')] # Prepare output directory os.makedirs(output_dir, exist_ok=True) for zip_name in zip_names: # Skip duplicate downloads if re.search(r'\([0-9]+\)', zip_name): continue # Rename '.part' file if zip was not correctly downloaded if os.path.getsize(os.path.join(input_dir, zip_name)) == 0: shutil.move( os.path.join(input_dir, zip_name) + '.part', os.path.join(input_dir, zip_name)) # Read csv file inside zip archive df = pd.read_csv( os.path.join(input_dir, zip_name), header=2, skiprows=[3], parse_dates=['Date'], compression='zip', dayfirst=True, nrows=100) # Extract metadata from last column keys = ['Sites:', 'Variables:', 'Qualities:'] meta = {k: [] for k in keys} for i, row in df.iterrows(): line = row.values[-1] if line in keys: header = True var = line elif line == ' ': continue else: meta[var].append(line) # Get bore specifics site_data = meta['Sites:'][0] lat = float(re.search(r'(?<=Lat:)\S+', site_data).group()) lon = float(re.search(r'(?<=Long:)\S+', site_data).group()) elev = float(re.search(r'(?<=Elev:).+(?=m)', site_data).group()) address = re.search(r'(?<=\d\.\d\.\d - ).+(?=\sLat)', site_data).group() bore_id = re.search(r'^\S+', site_data).group() site, hole, pipe = bore_id.split('.') sites = pd.DataFrame() sites['ID'] = [bore_id] sites['Site'] = [site] sites['Hole'] = [hole] sites['Pipe'] = [pipe] sites['Lat'] = [lat] sites['Lon'] = [lon] sites['Elev'] = [elev] sites['Address'] = [address] sites = sites.set_index('ID') # Get basin from master site dataframe sites['Basin name'] = basins.loc[sites.index, 'Basin name'] sites['Basin code'] = basins.loc[sites.index, 'Basin code'] # Save variable definitions variables = pd.DataFrame( [v.split(' - ', 1) for v in meta['Variables:']]) variables.columns = ['Code', 'Description'] variables['Code'] = variables['Code'].astype(int) variables = variables.set_index('Code') # Save quality definitions qualities = pd.DataFrame( [q.split(' - ', 1) for q in meta['Qualities:']]) qualities.columns = ['Code', 'Description'] qualities['Code'] = qualities['Code'].astype(int) qualities = qualities.set_index('Code') # Update existing values csv_name_s = os.path.join(output_dir, 'sites.csv') csv_name_v = os.path.join(output_dir, 'variables.csv') csv_name_q = os.path.join(output_dir, 'qualities.csv') try: sites = sites.append(pd.read_csv(csv_name_s, index_col=0)) sites = sites.drop_duplicates().sort_index() except FileNotFoundError: pass try: variables = variables.append(pd.read_csv(csv_name_v, index_col=0)) variables = variables.drop_duplicates().sort_index() except FileNotFoundError: pass try: variables = variables.append(pd.read_csv(csv_name_q, index_col=0)) qualities = qualities.drop_duplicates().sort_index() except FileNotFoundError: pass # Export updated tables sites.to_csv(csv_name_s) variables.to_csv(csv_name_v) qualities.to_csv(csv_name_q) sites = sites[~sites.index.duplicated(keep='first')] return sites def extract_records(input_dir, output_dir, clean_up=False): """Extract downloaded bore records. Args: input_dir: path to downloaded zip archives output_dir: path to save csv files clean_up: delete original zip archive after extracting it """ # Update definition tables sites = extract_definitions(input_dir, output_dir) # Keep unique basin codes basin_codes = sites['Basin code'].unique() # Find zip files zip_names = [f for f in os.listdir(input_dir) if f.endswith('.zip')] # Prepare output directory os.makedirs(output_dir, exist_ok=True) # Create master dataframe periods = ['all', 'daily', 'weekly'] master = {} for basin_code in basin_codes: master[basin_code] = {} for period in periods: master[basin_code][period] = pd.DataFrame() for zip_name in tqdm(zip_names): # Skip duplicate downloads if re.search(r'\([0-9]+\)', zip_name): continue # Rename '.part' file if zip was not correctly downloaded if os.path.getsize(os.path.join(input_dir, zip_name)) == 0: shutil.move( os.path.join(input_dir, zip_name) + '.part', os.path.join(input_dir, zip_name)) # Read header header = pd.read_csv( os.path.join(input_dir, zip_name), compression='zip', nrows=3) # Remove comments header = header.iloc[:, 1:-1].T # Apply product codes to all columns header.iloc[1::2, 0] = header.iloc[::2, 0].values header[0] = header[0].astype(float).astype(int).astype(str) # Move quality label header.iloc[1::2, 1] = header.iloc[1::2, 2] # Combine labels columns = [' '.join(c) for c in header.iloc[:, :-1].values] # Read csv file inside zip archive df = pd.read_csv( os.path.join(input_dir, zip_name), header=2, skiprows=[3], parse_dates=['Date'], index_col=['Date'], compression='zip', dayfirst=True) # Convert quality codes to integers for col in df.columns: if 'Quality' in col: df[col] = df[col].astype(int) # Update column names df.columns = columns + ['Metadata'] # Get bore specifics meta = df['Metadata'].iloc[1] bore_id = re.search(r'^\S+', meta).group() site, hole, pipe = bore_id.split('.') df = df.drop(columns='Metadata') # Get basin ID basin_code = sites.loc[bore_id, 'Basin code'] # Resample if necessary for period in periods: if period == 'daily': # Resample to daily timestamps df = df.resample('1d').mean() elif period == 'weekly': # Resample to weekly timestamps df = df.resample('1w').mean() # Add specific borehole details df['Site'] = sites.loc[bore_id, 'Site'] df['Hole'] = sites.loc[bore_id, 'Hole'] df['Pipe'] = sites.loc[bore_id, 'Pipe'] df['Basin'] = sites.loc[bore_id, 'Basin code'] df = df[['Site', 'Hole', 'Pipe', 'Basin'] + columns] # Remove empty rows df = df.dropna() # Add to master dataframe master[basin_code][period] = pd.concat( [master[basin_code][period], df]) if clean_up: # Remove original zip archive os.remove(os.path.join(input_dir, zip_name)) for basin_code in basin_codes: for period in periods: # Get latest date from dataframe latest_date = master[basin_code][period].index[-1].strftime( '%Y-%m-%d') csv_name = os.path.join( output_dir, '{}-{}-{}.csv'.format(basin_code, latest_date, period)) # Export to csv master[basin_code][period].to_csv( csv_name, index=True, float_format='%0.3f')