def main(radial_file, save_path, qc_values): """ Main function to parse and qc radial files :param radial_file: Path to radial file :param save_path: Path to save quality controlled radial file :param qc_values: Dictionary containing thresholds for each QC test """ try: r = Radial(radial_file) except Exception as err: logging.error('{} - {}'.format(radial_file, err)) return if r.is_valid(): # run high frequency radar qartod tests on open radial file r.initialize_qc() r.qc_qartod_syntax() r.qc_qartod_maximum_velocity(**qc_values['qc_qartod_maximum_velocity']) r.qc_qartod_valid_location() r.qc_qartod_radial_count(**qc_values['qc_qartod_radial_count']) r.qc_qartod_spatial_median(**qc_values['qc_qartod_spatial_median']) # r.qc_qartod_avg_radial_bearing(qc_values['average_bearing_threshold']) # Export radial file to either a radial or netcdf try: r.export(os.path.join(save_path, r.file_name), 'radial') except ValueError as err: logging.error('{} - {}'.format(radial_file, err)) pass
def main(file_list): client = MongoClient() db = client.codar db.radials.create_indexes([index1, index2]) bulk_info = [] for radial in file_list: # TODO Add multiprocessing here. # print(radial) r = Radial(radial) # print(r) if r.is_valid(): r.metadata['Site'] = r.metadata['Site'] try: r.metadata['PatternType'] = r.metadata['PatternType'].lower() except KeyError: pass # print(r.file_name) r.clean_header(split_origin=True) r.metadata['filename'] = r.file_name # assign a system type so we can sort on this r.metadata['SystemType'] = frequency_check( r.metadata['TransmitCenterFreqMHz']) r.metadata['RadialSolutions'] = r.data.__len__() # Try statements in case a radial file doesn't contain a diagnostic table. try: r.metadata[ 'diagnostics_hardware'] = r.diagnostics_hardware.to_dict( orient='r') except AttributeError as ae: logging.error(ae) try: r.metadata[ 'diagnostics_radial'] = r.diagnostics_radial.to_dict( orient='r') except AttributeError as ae: logging.error(ae) bulk_info.append(InsertOne(r.metadata)) try: db.radials.bulk_write(bulk_info, ordered=False) logging.info( 'Bulk radial insert successful. {} radials inserted.'.format( len(bulk_info))) except BulkWriteError as bwe: logging.error(bwe.details)
def main(radial_file, save_path): """ Main function to parse and qc radial files :param radial_file: Path to radial file :param save_path: Path to save quality controlled radial file """ try: r = Radial(radial_file) except Exception: return if r.is_valid(): try: r.export( os.path.join(save_path, r.file_name.replace('.ruv', '.nc')), 'netcdf') except ValueError: pass
def parse_radial_file(radial_file): """ Parse CODAR radial files utilizing the Radial class and upload to MySQL database. :param radial_file: Path to CODAR Radial File """ basename = os.path.basename(radial_file).split('.')[0] logging.debug( '{} - Checking if file is uploaded to MySQL database.'.format( basename)) uploaded = db.check_file_upload(session, basename, RadialMetadata) if not uploaded: # Check if the file has been uploaded already. If it hasn't, upload it completely. logging.debug('{} - Loading'.format(radial_file)) try: r = Radial(radial_file) if not r.is_valid(): return r.clean_header( ) # Clean up header information for entry into mysql database r.metadata['filename'] = os.path.splitext( os.path.basename(radial_file))[0] r.metadata['fileModTime'] = dt.datetime.fromtimestamp( os.stat(radial_file).st_mtime) # Fill certain table columns with relational ids # Check to see if the site has been uploaded to the HfrSites table of the MySQL database try: site_info = sites[sites.site == r.metadata['Site']] site_id = int(site_info.id.iloc[0]) except IndexError: logging.info( '{} not found. Uploading site to hfrSites table'.format( r.metadata['Site'])) site_info = db.update_site_table( session, r.metadata['Site'], r.metadata['TransmitCenterFreqMHz'], r.metadata['Origin']) site_id = int(site_info) r.metadata['Site'] = site_id try: patt_type = pattern_types[pattern_types.type == r.metadata['PatternType']] pattern_id = int(patt_type.id.iloc[0]) except IndexError: logging.error('{} not found. Pattern type invalid'.format( r.metadata['PatternType'])) return r.metadata['PatternType'] = pattern_id # Add extra information to header r.metadata['TableType'] = r._tables['1']['TableType'] r.metadata['TableColumns'] = r._tables['1']['TableColumns'] r.metadata['TableColumnTypes'] = r._tables['1']['TableColumnTypes'] r.metadata['TableRows'] = r._tables['1']['TableRows'] # Upload radial header information and update latest radials table r.metadata = dbr.upload_radial_header(session, r.metadata) dbr.update_latest_radials(session, r.metadata) try: # Upload radial diagnostic data r.diagnostics_radial = r.diagnostics_radial.drop( ['TIME', 'TYRS', 'TMON', 'TDAY', 'THRS', 'TMIN', 'TSEC'], axis=1) r.diagnostics_radial['id_site'] = r.metadata['Site'] r.diagnostics_radial['id_radial'] = r.metadata['radial_id'] dbr.upload_diagnostics(session, RadialDiagnostics, r.diagnostics_radial, r.metadata['Site']) logging.debug( '{} - Table `{}` - Diagnostic data uploaded '.format( r.metadata['filename'], 'hfrRadialDiagnostics')) except: pass try: # Upload hardware diagnostic data r.diagnostics_hardware = r.diagnostics_hardware.drop( ['TIME', 'TYRS', 'TMON', 'TDAY', 'THRS', 'TMIN', 'TSEC'], axis=1) r.diagnostics_hardware['id_site'] = r.metadata['Site'] r.diagnostics_hardware['id_radial'] = r.metadata['radial_id'] dbr.upload_diagnostics(session, HardwareDiagnostics, r.diagnostics_hardware, r.metadata['Site']) logging.debug( '{} - Table `{}` - Diagnostic data uploaded '.format( r.metadata['filename'], 'hfrHardwareDiagnostics')) except: pass logging.info('{} - File uploaded successfully'.format(radial_file)) except: logging.error('{} - File failed to upload'.format(radial_file))