Adding logger

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()

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'],
+            y = self.mm_kinetics_function(self.mm['x'],
-                    (self.mm['vmax']*self.mm['x'])/(self.mm['Km']+self.mm['x']), 'b-', label="Michaelis-Menten")
+                                          self.mm['vmax'],
+                                          self.mm['Km'])
+            ax.plot(self.mm['x'], y, 'b-', label="Michaelis-Menten")
         if self.hill:
-            ax.plot(self.hill['x'],
+            y = self.hill_kinetics_function(self.hill['x'],
-                    ((self.hill['vmax']*(self.hill['x']**self.hill['h'])) /
+                                            self.hill['vmax'],
-                        (self.hill['Kprime'] + (self.hill['x']**self.hill['h']))), 'g-', label="Hill")
+                                            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')