Add basin code and bore details to output

waternsw_grabber/waternsw_grabber.py

@@ -363,6 +363,9 @@ def extract_definitions(input_dir, output_dir):
         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.
@@ -374,26 +377,14 @@ def extract_records(input_dir, output_dir, clean_up=False):
     """
 
     # Update definition tables
-    extract_definitions(input_dir, output_dir)
+    sites = extract_definitions(input_dir, output_dir)
 
-    # 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)
+    # 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')]
 
-    # Get basin IDs for all zip files
-    basin_codes = []
-    for zip_name in zip_names:
-        bore_id = os.path.splitext(zip_name)[0].replace('cf', '')
-        basin_codes.append(basins.loc[bore_id, 'Basin code'])
-
-    # Keep uniue basin codes
-    basin_codes = list(set(basin_codes))
-
     # Prepare output directory
     os.makedirs(output_dir, exist_ok=True)
 
@@ -441,13 +432,15 @@ def extract_records(input_dir, output_dir, clean_up=False):
             parse_dates=['Date'],
             index_col=['Date'],
             compression='zip',
-            dayfirst=True,
-            nrows=100)
+            dayfirst=True)
 
-        # FIXME: convert quality codes to integers
+        # 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']
+        df.columns = columns + ['Metadata']
 
         # Get bore specifics
         meta = df['Metadata'].iloc[1]
@@ -456,21 +449,31 @@ def extract_records(input_dir, output_dir, clean_up=False):
         df = df.drop(columns='Metadata')
 
         # Get basin ID
-        basin_code = basins.loc[bore_id, 'Basin code']
+        basin_code = sites.loc[bore_id, 'Basin code']
 
-        # Append to master dataframe
+        # Resample if necessary
         for period in periods:
             if period == 'daily':
                 # Resample to daily timestamps
                 df = df.resample('1d').mean()
-                # FIXME: add bore IDs
 
             elif period == 'weekly':
                 # Resample to weekly timestamps
                 df = df.resample('1w').mean()
-                # FIXME: add bore IDs
 
-            master[basin_code][period] = pd.concat([master[basin_code][period], df])
+            # 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
@@ -479,9 +482,12 @@ def extract_records(input_dir, output_dir, clean_up=False):
     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')
+            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))
+                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')
+            master[basin_code][period].to_csv(
+                csv_name, index=True, float_format='%0.3f')