moving the logger to common module (#8)

README.md

@@ -32,7 +32,7 @@ on your system
 In the opened command prompt, run:
 
 ```
-pip3 install guizero numpy pandas xlrd xlsxwriter matplotlib openpyxl nested_dict h5py scipy pathlib
+pip3 install guizero numpy pandas xlrd xlsxwriter matplotlib openpyxl nested_dict h5py scipy pathlib bcolors==1.0.2
 ```
 
 ## Update the code:

binary.py

@@ -48,7 +48,7 @@
 OUTPUT_NO_PARAMETERS = "_Not"
 OUTPUT_ZERO_TO_ONE_CSV_NAME = "01"
 OUTPUT_ONE_TO_ZERO_CSV_NAME = "10"
-OUTPUT_LOG_FILE = "output.txt"
+OUTPUT_LOG_FILE = "binary_output.log"
 
 # UI related constants
 INPUT_FOLDER_NAME_BOX_MAX_WIDTH = 26
@@ -211,7 +211,7 @@ def format_out_name_with_param_val(
 ):
     global param_file_exists
 
-    if param_file_exists == False or (
+    if param_file_exists is False or (
         param_min_time_duration_before == 0 and param_min_time_duration_after == 0
     ):
         return ""
@@ -668,7 +668,7 @@ def process_input_file(input_file, output_folder):
 
     # Get a base output DataFrame without any criteria's applied
     result, out_df = process_input_df(df)
-    if result == False or out_df.empty:
+    if result is False or out_df.empty:
         return False
 
     out_base_file = out_base(input_file, output_folder)
@@ -806,32 +806,6 @@ def get_input_files(input_dir):
     return input_files
 
 
-class loghandler(logging.StreamHandler):
-    """
-    Custom logging handler
-    """
-
-    def emit(self, record):
-        """
-        Writes the message to the output file (or the default logger stream),
-        stdout and the UI result text box
-        """
-        try:
-            # TODO: Have different log format for input depending on whether
-            # it is the file output or anything else. And, also based on the
-            # log level. Ex: error logs can be prepend with some string like
-            # "ERROR:: "
-            msg = self.format(record)
-            if r_log_box is not None:
-                r_log_box.value += msg
-            print(msg)
-            self.flush()
-        except (KeyboardInterrupt, SystemExit):
-            raise
-        except:
-            self.handleError(record)
-
-
 def main(input_folder_or_file, separate_files, output_folder):
     global output_dir, create_output_folder_with_file_name
 
@@ -1267,13 +1241,13 @@ def csv_file_name_to_output():
     Main entry point
     """
 
-    progress = loghandler()
+    custom_log_handler = common.loghandler()
     logging.basicConfig(filename=OUTPUT_LOG_FILE,
                         level=logging.INFO, format="")
     common.logger = logging.getLogger(__name__)
     formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
-    progress.setFormatter(formatter)
-    common.logger.addHandler(progress)
+    custom_log_handler.setFormatter(formatter)
+    common.logger.addHandler(custom_log_handler)
     argv = sys.argv[1:]
     console_mode = False
     separate_files = False
@@ -1519,6 +1493,9 @@ def csv_file_name_to_output():
     r_log_box = TextBox(
         rwin, text="", height=200, width=500, multiline=True, scrollbar=True
     )
+
+    custom_log_handler.set_result_log_ui_box(r_log_box)
+
     # Non editable
     r_log_box.disable()
 

colorsort.py

@@ -20,7 +20,7 @@
 from nested_dict import nested_dict
 
 # constants
-OUTPUT_LOG_FILE = "output.txt"
+OUTPUT_LOG_FILE = "colorsort_output.log"
 
 # globals
 output_file = ""

common.py

@@ -1,10 +1,12 @@
 #!/usr/bin/python
 
+import logging
 import os
 import subprocess
 import sys
 from csv import reader
 
+import bcolors
 import pandas as pd
 from pandas.api.types import is_numeric_dtype
 
@@ -22,6 +24,10 @@
 OUTPUT_DIR_NAME = "_output"
 CSV_EXT = ".csv"
 
+# Colors
+LIGHT_RED_COLOR = "#FFCCCB"
+LIGHT_YELLOW_COLOR = "#FFFFED"
+
 # globals
 logger = None
 input_dir = ""
@@ -179,3 +185,46 @@ def compare_csv_files(self, expected_csv_file, actual_file):
                     else:
                         self.assertEqual(exp_w, actual_w)
                 x += 1
+
+
+class loghandler(logging.StreamHandler):
+    """
+    Custom logging handler
+    """
+
+    def __init__(self):
+        self.result_log_ui_box = None
+        logging.StreamHandler.__init__(self=self)
+
+    def set_result_log_ui_box(self, result_log_ui_box):
+        self.result_log_ui_box = result_log_ui_box
+
+    def emit(self, record):
+        """
+        Writes the message to the output file (or the default logger stream),
+        stdout and the UI result text box
+        """
+        try:
+            msg = self.format(record)
+            match record.levelno:
+                case logging.WARNING:
+                    p_msg = bcolors.WARN + msg + bcolors.ENDC
+                case logging.CRITICAL | logging.ERROR:
+                    p_msg = bcolors.ERR + msg + bcolors.ENDC
+                case _:
+                    p_msg = msg
+            if self.result_log_ui_box is not None:
+                match record.levelno:
+                    case logging.WARNING:
+                        # If it wasn't previously set to higher attention.
+                        if not self.result_log_ui_box.bg == LIGHT_RED_COLOR:
+                            self.result_log_ui_box.bg = LIGHT_YELLOW_COLOR
+                    case logging.CRITICAL | logging.ERROR:
+                        self.result_log_ui_box.bg = LIGHT_RED_COLOR
+                self.result_log_ui_box.value += msg
+            print(p_msg)
+            self.flush()
+        except (KeyboardInterrupt, SystemExit):
+            raise
+        except:
+            self.handleError(record)

dff.py

@@ -35,7 +35,7 @@
 PARAM_UI_TIME_WINDOW_DURATION_TEXT = "Time window duration (secs): "
 
 # Other constants
-OUTPUT_LOG_FILE = "output.txt"
+OUTPUT_LOG_FILE = "dff_output.log"
 OUTPUT_COL0_TS = "Start time (sec)"
 OUTPUT_COL1_LEN = "Bout length (sec)"
 OUTPUT_COL2_MI_AVG = "Motion Index (avg)"
@@ -134,7 +134,7 @@ def main(input_dir: str, parameter_obj: Parameters):
             )
             for idx, v in enumerate(nan):
                 # Discard NaN
-                if v == False:
+                if v is False:
                     cleaned_z_score.append(z_score[idx])
                     cleaned_ts.append(ts[idx])
             z_score = cleaned_z_score
@@ -217,7 +217,7 @@ def main(input_dir: str, parameter_obj: Parameters):
                 out_df_not = results[17]
 
                 param_ext = ""
-                if param == None:
+                if param is None:
                     param_ext = "_outside-parameters"
                 elif not param == "":
                     param_ext = "_" + param
@@ -598,28 +598,6 @@ def process(
     ]
 
 
-class loghandler(logging.StreamHandler):
-    """
-    Custom logging handler
-    """
-
-    def emit(self, record):
-        """
-        Writes the message to the output file (or the default logger stream),
-        stdout and the UI result text box
-        """
-        try:
-            msg = self.format(record)
-            if r_log_box is not None:
-                r_log_box.value += msg
-            print(msg)
-            self.flush()
-        except (KeyboardInterrupt, SystemExit):
-            raise
-        except:
-            self.handleError(record)
-
-
 def print_help():
     """
     Display help
@@ -843,13 +821,13 @@ def line_r(rwin):
     Main entry point
     """
 
-    progress = loghandler()
+    custom_log_handler = common.loghandler()
     logging.basicConfig(filename=OUTPUT_LOG_FILE,
                         level=logging.INFO, format="")
     common.logger = logging.getLogger(__name__)
     formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
-    progress.setFormatter(formatter)
-    common.logger.addHandler(progress)
+    custom_log_handler.setFormatter(formatter)
+    common.logger.addHandler(custom_log_handler)
     argv = sys.argv[1:]
     console_mode = False
     separate_files = False
@@ -1034,6 +1012,9 @@ def line_r(rwin):
     r_log_box = TextBox(
         rwin, text="", height=200, width=500, multiline=True, scrollbar=True
     )
+
+    custom_log_handler.set_result_log_ui_box(r_log_box)
+
     # Non editable
     r_log_box.disable()
 

test_binary.py

@@ -98,8 +98,7 @@ def setUp(self):
                             level=logging.DEBUG, format="")
         common.logger = logging.getLogger(__name__)
         if not common.logger.handlers:
-            progress = b.loghandler()
-            common.logger.addHandler(progress)
+            common.logger.addHandler(common.loghandler())
 
     def validate_df(self, df, expected_data):
         expected_df = pd.DataFrame(expected_data)

test_dff.py

@@ -28,8 +28,7 @@ def setUp(self):
                             level=logging.INFO, format="")
         common.logger = logging.getLogger(__name__)
         if not common.logger.handlers:
-            progress = dff.loghandler()
-            common.logger.addHandler(progress)
+            common.logger.addHandler(common.loghandler())
 
     def test_bvt(self):
         # Whole duration parameter

test_parameter.py

@@ -71,7 +71,7 @@ def validate_min_t_duration(self, input_dir):
             min_time_duration_before,
             min_time_duration_after,
         ) = expected_param.get_min_time_duration_values()
-        self.assertEqual(param_file_exists == False, True)
+        self.assertFalse(param_file_exists, False)
         self.assertEqual(
             min_time_duration_before == Parameters.MIN_TIME_DURATION_BEFORE_DEFAULT,
             True,