From c90c18ee84578004e0fd58935224535a6c59206a Mon Sep 17 00:00:00 2001 From: Alexander Minges Date: Wed, 19 Aug 2015 00:22:15 +0200 Subject: [PATCH] Adding logger --- analyze-cli.py | 52 +++++++++++++++++++++++++++++++++++++---- libkinetics/__init__.py | 33 +++++++++++++++++++------- 2 files changed, 73 insertions(+), 12 deletions(-) diff --git a/analyze-cli.py b/analyze-cli.py index 4dc2045..f66a33c 100755 --- a/analyze-cli.py +++ b/analyze-cli.py @@ -1,4 +1,5 @@ #!/usr/bin/python +# -*- coding: utf-8 -*- import argparse import logging @@ -31,9 +32,39 @@ def parse_arguments(): return args +def initialize_logger(): + """ + Initialization of logging subsystem. Two logging handlers are brought up: + 'fh' which logs to a log file and 'ch' which logs to standard output. + :return logger: returns a logger instance + """ + logger = logging.getLogger('pyKinetics-cli') + logger.setLevel(logging.INFO) + + ch = logging.StreamHandler() + ch.setLevel(logging.INFO) + logger.addHandler(ch) + + try: + log_filename = 'pyKinetics-cli.log' + fh = logging.FileHandler(log_filename, 'w') + fh.setLevel(logging.INFO) + logger.addHandler(fh) + except IOError as error: + logger.warning('WARNING: Cannot create log file! Run pyKinetics-cli' + 'from a directory to which you have write access.') + logger.warning(error.msg) + pass + + return logger + + def main(): # parse command line arguments args = parse_arguments() + # initialize logger + logger = initialize_logger() + if args.with_hill: do_hill = args.with_hill else: @@ -41,25 +72,38 @@ def main(): try: input_path = Path(args.input).resolve() except FileNotFoundError: - print('Path containing input data not found: {}'.format(args.input)) + logger.critical('CRITICAL: Path containing input data ' + 'not found: {}'.format(args.input)) raise try: output_path = Path(args.output).resolve() except FileNotFoundError: - print('Path for writing results not found: {}'.format(args.output)) + logger.critical('CRITICAL: Path for writing results ' + 'not found: {}'.format(args.output)) raise if output_path.is_dir(): if input_path.is_dir(): + logger.info('INFO: Collecting data files') data_files = sorted(input_path.glob('**/*.csv')) + msg = 'Calculating kinetics' + if do_hill: + msg = '{} including Hill kinetics'.format(msg) + logger.info('INFO: {}'.format(msg)) exp = libkinetics.Experiment(data_files, (10, 25), do_hill) + logger.info('INFO: Plotting linear fits to data and kinetics') exp.plot_data(str(output_path)) exp.plot_kinetics(str(output_path)) + logger.info('INFO: Writing results to results.csv') exp.write_data(str(output_path)) else: - raise ValueError('{} is not a directory!'.format(input_path)) + msg = '{} is not a directory!'.format(input_path) + logger.critical('CRITICAL: '.format(msg)) + raise ValueError(msg) else: - raise ValueError('{} is not a directory!'.format(output_path)) + msg = '{} is not a directory!'.format(output_path) + logger.critical('CRITICAL: '.format(msg)) + raise ValueError(msg) if __name__ == "__main__": main() diff --git a/libkinetics/__init__.py b/libkinetics/__init__.py index 57088d5..edd5ae0 100644 --- a/libkinetics/__init__.py +++ b/libkinetics/__init__.py @@ -1,4 +1,5 @@ #!/usr/bin/python +# -*- coding: utf-8 -*- from scipy import stats, optimize import numpy as np @@ -9,6 +10,7 @@ import csv class Replicate(): def __init__(self, x, y, owner): + self.logger = owner.logger self.x = x self.y = y self.owner = owner @@ -36,6 +38,7 @@ class Replicate(): class Measurement(): def __init__(self, x, y, conc, conc_unit, owner): + self.logger = owner.logger self.concentration = float(conc) self.concentration_unit = conc_unit self.x = x @@ -89,7 +92,9 @@ class Measurement(): class Experiment(): - def __init__(self, data_files, xlim, do_hill=False): + def __init__(self, data_files, xlim, do_hill=False, logger=None): + + self.logger = logger # collction of indepentend measurements self.measurements = [] @@ -163,7 +168,11 @@ class Experiment(): 'perr': perr, 'x': x} except: - print('Calculation of Hill kinetics failed!') + msg = 'Calculation of Michaelis-Menten kinetics failed!' + if self.logger: + self.logger.error('ERROR: {}'.format(msg)) + else: + print(msg) return None def do_hill_kinetics(self): @@ -185,7 +194,11 @@ class Experiment(): 'h': h, 'x': x} except: - print('Calculation of Hill kinetics failed!') + msg = 'Calculation of Hill kinetics failed!' + if self.logger: + self.logger.error('ERROR: {}'.format(msg)) + else: + print(msg) return None def plot_kinetics(self, outpath): @@ -200,12 +213,16 @@ class Experiment(): fmt='ok', ms=3, fillstyle='none', label="Data with error") if self.mm: - ax.plot(self.mm['x'], - (self.mm['vmax']*self.mm['x'])/(self.mm['Km']+self.mm['x']), 'b-', label="Michaelis-Menten") + y = self.mm_kinetics_function(self.mm['x'], + self.mm['vmax'], + self.mm['Km']) + ax.plot(self.mm['x'], y, 'b-', label="Michaelis-Menten") if self.hill: - ax.plot(self.hill['x'], - ((self.hill['vmax']*(self.hill['x']**self.hill['h'])) / - (self.hill['Kprime'] + (self.hill['x']**self.hill['h']))), 'g-', label="Hill") + y = self.hill_kinetics_function(self.hill['x'], + self.hill['vmax'], + self.hill['Kprime'], + self.hill['h']) + ax.plot(self.hill['x'], y, 'g-', label="Hill") ax.legend(loc='best', fancybox=True) plt.savefig('{}/kinetics.png'.format(outpath), bbox_inches='tight')