Refactored logging tools

README.md

-# CP2K
+# CP2K NoMaD Parser
 The NoMaD parser for CP2K. Under development. Will be modified to conform to
 the common parser structure when it is available.
 
+---
 ## QuickStart
 - Clone repository
-- Run setup by running the setup.py script. For local, user specific install
-  without sudo permissions use:
 
     ```shell
-    python setup.py install --user
+    git clone git@gitlab.mpcdf.mpg.de:nomad-lab/parser-cp2k.git
     ```
 
-- For a system-wide install use:
+- Run setup by running the setup.py script. For local, user specific install
+  without sudo permissions use (omit --user for a system-wide install):
 
     ```shell
-    python setup.py install
+    python setup.py install --user
     ```
 
 - You can test if everything is running fine by running the test script in tests folder:
@@ -31,17 +31,19 @@ the common parser structure when it is available.
     ```shell
     python -m cp2kparser
     ```
-
+---
 ## Structure
 Currently the python package is divided into three subpackages:
  - Engines: Classes for parsing different type of files
  - Generics: Generic utility classes and base classes
  - Implementation: The classes that actually define the parser functionality.
 
+---
 ## Reusable components and ideas for other parsers
 
 Some components and ideas could be reused in other parsers as well. If you find
-any of the following useful in you parser, you are welcome to do so.
+any of the following ideas useful in you parser, you are welcome to do reuse
+them.
 
 ### Engines
 Basically all the "engines", that is the modules that parse certain type of
@@ -54,7 +56,7 @@ Currently implemented engines that could be reused (not tested properly yet):
 - RegexEngine: For parsing text files with regular expressions. Uses the re2
   library if available (falls back to default python regex implementation if
   re2 not found).
-- XyzEngine: For parsing XYZ files and files with similar structure. Has a very
+- XYZEngine: For parsing XYZ files and files with similar structure. Has a very
   flexible nature as you can specify comments, column delimiters, column
   indices and the patterns used to separate different configurations.
 
@@ -74,5 +76,13 @@ parsers:
 - Time measurement for performance analysis
 - Providing file contents, sizes and handles
 
+### Logging
+Python has a great [logging package](https://www.google.com) which helps in
+following the program flow and catching different errors and warnings. In
+cp2kparser the file cp2kparser/generics/logconfig.py defines the behaviour of
+the logger. There you can setup the log levels even at a modular level. A more
+easily readable formatting is also provided for the log messages.
+
+---
 ## Lessons learned
 

cp2kparser/__init__.py

 #! /usr/bin/env python
+import cp2kparser.generics.logconfig

cp2kparser/engines/cp2kinputengine.py

 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 from collections import defaultdict
-from cp2kparser.generics.nomadlogging import *
+import logging
+logger = logging.getLogger(__name__)
 
 
 #===============================================================================
@@ -117,14 +118,14 @@ class InputSection(object):
         parts = path.upper().split('/', 1)
         candidates = self.subsections.get(parts[0])    # [s for s in self.subsections if s.name == parts[0]]
         if not candidates:
-            print_debug("Subsection '{}' not found.".format(parts[0]))
+            logger.debug("Subsection '{}' not found.".format(parts[0]))
             return None
         elif len(candidates) > 1:
-            print_warning("Multiple subsections with the same name found with name '{}' If no index is given, the first occurence in the input file is returned.".format(parts[0]))
+            logger.warning("Multiple subsections with the same name found with name '{}' If no index is given, the first occurence in the input file is returned.".format(parts[0]))
         try:
             subsection = candidates[index]
         except IndexError:
-            print_error("Invalid subsection index given.")
+            logger.error("Invalid subsection index given.")
 
         if len(parts) == 1:
             return subsection
@@ -146,17 +147,17 @@ class InputSection(object):
         """
         candidates = self.keywords.get(keyword)    # [s for s in self.subsections if s.name == parts[0]]
         if not candidates:
-            print_debug("No keywords with name '{}' found in subsection '{}'".format(keyword, self.name))
+            logger.debug("No keywords with name '{}' found in subsection '{}'".format(keyword, self.name))
             return None
         elif len(candidates) > 1:
-            print_warning("Multiple keywords with the same name found with name '{}' If no index is given, the first occurence in the input file is returned.".format(parts[0]))
+            logger.warning("Multiple keywords found with name '{}'. If no index is given, the first occurence in the input file is returned.".format(keyword))
         try:
             result = candidates[index]
         except IndexError:
-            print_error("Invalid keyword index given.")
+            logger.error("Invalid keyword index given.")
         return result
 
     def get_parameter(self):
         if self.params is None:
-            print_debug("The section '{}' has no parameters set".format(self.name))
+            logger.debug("The section '{}' has no parameters set".format(self.name))
         return self.params

cp2kparser/engines/regexengine.py

 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 import os
-from cp2kparser.generics.nomadlogging import *
+import logging
+logger = logging.getLogger(__name__)
 
 try:
     import re2 as re
 except ImportError:
     import re
-    print_warning((
+    logger.warning((
         "re2 package not found. Using re package instead. "
         "If you wan't to use re2 please see the following links:"
         "    https://github.com/google/re2"
@@ -71,7 +72,7 @@ class Regex(object):
 
     def check_input(self):
         if self.direction != "down" and self.direction != "up":
-            print_error("Unsupported direction value '{}' in a regex".format(self.direction))
+            logger.error("Unsupported direction value '{}' in a regex".format(self.direction))
 
     def match(self, string):
         return self.compiled_regex.match(string)
@@ -110,13 +111,13 @@ class RegexEngine(object):
         """Use the given regex to parse contents from the given file handle"""
 
         file_name = file_handle.name
-        print_debug("Searching regex in file '{}'".format(file_name))
+        logger.debug("Searching regex in file '{}'".format(file_name))
         result = self.recursive_extraction(regex, file_handle)
         if result:
             return result
 
         # Couldn't find the quantity
-        print_debug("Could not find a result for {}.".format(regex.regex_string))
+        logger.debug("Could not find a result for {}.".format(regex.regex_string))
 
     def recursive_extraction(self, regex, data):
         """Goes through the exctractor tree recursively until the final
@@ -133,16 +134,16 @@ class RegexEngine(object):
 
         # If separator specified, do a blockwise search
         if regex.separator is not None:
-            print_debug("Going into blockwise regex search")
+            logger.debug("Going into blockwise regex search")
             result = self.regex_block_search(data, regex)
         # Regular string search
         else:
-            print_debug("Going into full regex search")
+            logger.debug("Going into full regex search")
             result = self.regex_search_string(data, regex)
 
         # See if the tree continues
         if regex.inner_regex is not None:
-            print_debug("Entering next regex recursion level.")
+            logger.debug("Entering next regex recursion level.")
             return self.recursive_extraction(regex.inner_regex, result)
         else:
             return result
@@ -164,15 +165,15 @@ class RegexEngine(object):
 
         result = None
         if from_beginning:
-            print_debug("Doing full string search from beginning.")
+            logger.debug("Doing full string search from beginning.")
             return regex.match(contents)
         elif index == "all":
-            print_debug("Doing full string search for all results.")
+            logger.debug("Doing full string search for all results.")
             result = regex.findall(contents)
             if not result:
-                print_debug("No matches.")
+                logger.debug("No matches.")
         elif index >= 0:
-            print_debug("Doing full string search with specified index.")
+            logger.debug("Doing full string search with specified index.")
             iter = regex.finditer(contents)
             i = 0
             while i <= index:
@@ -180,9 +181,9 @@ class RegexEngine(object):
                     match = iter.next()
                 except StopIteration:
                     if i == 0:
-                        print_debug("No results.")
+                        logger.debug("No results.")
                     else:
-                        print_debug("Invalid regex index.")
+                        logger.debug("Invalid regex index.")
                     break
                 if i == index:
                     result = match.groups()[0]
@@ -190,12 +191,12 @@ class RegexEngine(object):
         elif index < 0:
             matches = regex.findall(contents)
             if not matches:
-                print_debug("No matches.")
+                logger.debug("No matches.")
             else:
                 try:
                     result = matches[index]
                 except IndexError:
-                    print_debug("Invalid regex index.")
+                    logger.debug("Invalid regex index.")
 
         return result
 
@@ -208,33 +209,30 @@ class RegexEngine(object):
         direction = regex.direction
         index = regex.index
         from_beginning = regex.from_beginning
-        print_debug("Doing blockwise search with separator: '{}', direction: '{}', from_beginning: '{}' and index '{}'".format(separator, direction, from_beginning, index))
+        logger.debug("Doing blockwise search with separator: '{}', direction: '{}', from_beginning: '{}' and index '{}'".format(separator, direction, from_beginning, index))
 
         # Determine the direction in which the blocks are read
         if direction == "up":
-            print_debug("Searching from bottom to up.")
+            logger.debug("Searching from bottom to up.")
             generator = self.reverse_block_generator(file_handle, separator)
         elif direction == "down":
-            print_debug("Searching from up to bottom.")
+            logger.debug("Searching from up to bottom.")
             generator = self.block_generator(file_handle, separator)
         else:
-            print_error("Unknown direction specifier: {}".format(direction))
+            logger.error("Unknown direction specifier: {}".format(direction))
             return
 
         # If all results wanted, just get all results from all blocks
         if index == "all":
-            print_debug("Searchin for all matches.")
+            logger.debug("Searchin for all matches.")
             results = []
             for block in generator:
                 matches = regex.findall(block)
                 if matches:
-                    print_debug("Found match within block.")
                     if isinstance(matches, list):
-                        print_debug("Found multiple matches in a block")
                         for match in matches:
                             results.append(match)
                     else:
-                        print_debug("Found single match in a block")
                         results.append(matches.groups()[0])
             return results
 
@@ -242,12 +240,12 @@ class RegexEngine(object):
         i_result = 0
         counter = 0
         for block in generator:
-            print_debug("Searchin for a specific index.")
+            logger.debug("Searchin for a specific index.")
             counter += 1
             if from_beginning:
                 result = regex.match(block)
                 if result:
-                    print_debug("Found match in beginning of block.")
+                    logger.debug("Found match in beginning of block.")
                     if index + 1 > i_result + 1:
                         i_result += 1
                     else:
@@ -260,7 +258,7 @@ class RegexEngine(object):
                     else:
                         n_results = 1
 
-                    print_debug("Found results within block.")
+                    logger.debug("Found results within block.")
                     if index + 1 > i_result + n_results:
                         i_result += n_results
                     else:

cp2kparser/engines/xyzengine.py

-from cp2kparser.generics.nomadlogging import *
+# from cp2kparser.generics.nomadlogging import *
 import numpy as np
+import logging
+logger = logging.getLogger(__name__)
 from io import StringIO
 try:
     import re2 as re
 except ImportError:
     import re
-    print_warning((
+    logger.warning((
         "re2 package not found. Using re package instead. "
         "If you wan't to use re2 please see the following links:"
         "    https://github.com/google/re2"
@@ -96,12 +98,12 @@ class XYZEngine(object):
                         try:
                             value = vals[column]
                         except IndexError:
-                            print_warning("The given index '{}' could not be found on the line '{}'. The given delimiter or index could be wrong.".format(column, line))
+                            logger.warning("The given index '{}' could not be found on the line '{}'. The given delimiter or index could be wrong.".format(column, line))
                             return
                         try:
                             value = float(value)
                         except ValueError:
-                            print_warning("Could not cast value '{}' to float. Currently only floating point values are accepted".format(value))
+                            logger.warning("Could not cast value '{}' to float. Currently only floating point values are accepted".format(value))
                             return
                         else:
                             line_forces.append(value)

cp2kparser/generics/nomadlogging.py

-#! /usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""Misc. utility functions."""
-import textwrap
-import logging
-logging.basicConfig(format='%(message)s', level=logging.INFO)
-
-
-#===============================================================================
-def make_title(title, width=80):
-    """Styles a title to be printed into console.
-    """
-    space = width-len(title)-4
-    pre_space = space/2-1
-    post_space = space-pre_space
-    line = "|" + str((pre_space)*"=") + " "
-    line += title
-    line += " " + str((post_space)*"=") + "|"
-    return line
-
-
-#===============================================================================
-def print_subtitle(title, width=80):
-    """Styles a title to be printed into console.
-    """
-    space = width-len(title)-4
-    pre_space = space/2-1
-    post_space = space-pre_space
-    line = "|" + str((pre_space)*"-") + " "
-    line += title
-    line += " " + str((post_space)*"-") + "|"
-    print line
-
-
-#===============================================================================
-def make_message(message, width=80, spaces=0):
-    """Styles a message to be printed into console.
-    """
-    wrapper = textwrap.TextWrapper(width=width-6)
-    lines = wrapper.wrap(message)
-    styled_message = ""
-    first = True
-    for line in lines:
-        new_line = spaces*" " + "|  " + line + (width-6-len(line))*" " + "  |"
-        if first:
-            styled_message += new_line
-            first = False
-        else:
-            styled_message += "\n" + new_line
-    styled_message += "\n" + spaces*" " + "|" + (width-2)*"-" + "|"
-    return styled_message
-
-
-#===============================================================================
-def make_titled_message(title, message, width=80, spaces=0):
-    """Styles a message to be printed into console.
-    """
-    wrapper = textwrap.TextWrapper(width=width-6)
-    lines = wrapper.wrap(message)
-    styled_message = ""
-    first = True
-    for line in lines:
-        if first:
-            new_line = spaces*" " + "  >> {}: ".format(title) + line + (width-6-len(line))*" " + "  "
-            styled_message += new_line
-            first = False
-        else:
-            new_line = spaces*" " + "     " + line + (width-6-len(line))*" " + "  "
-            styled_message += "\n" + new_line
-    return styled_message
-
-
-#===============================================================================
-def print_title(title, width=80):
-    """Prints styled title into console.
-    """
-    print make_title(title, width=width)
-
-
-#===============================================================================
-def print_message(title, message, width=80):
-    """Returns a styled warning message to be printed into console.
-    """
-    print make_title(title) + "\n" + make_message(message) + "\n"
-
-
-#===============================================================================
-def print_debug(message, width=80):
-    """Returns a styled warning message to be printed into console.
-    """
-    logging.debug(make_titled_message("DEBUG", message))
-
-
-#===============================================================================
-def print_info(message, width=80):
-    """Returns a styled warning message to be printed into console.
-    """
-    logging.info(make_titled_message("INFO", message))
-
-
-#===============================================================================
-def print_text(text, spaces=0, width=80):
-    """Styles a message to be printed into console. No borders, no footer, no
-    header.
-    """
-    wrapper = textwrap.TextWrapper(width=width-4)
-    lines = wrapper.wrap(text)
-    styled_message = ""
-    first = True
-    for line in lines:
-        new_line = spaces*" " + "  " + line
-        if first:
-            styled_message += new_line
-            first = False
-        else:
-            styled_message += "\n" + new_line
-    print(styled_message)
-
-
-#===============================================================================
-def print_warning(message, width=80):
-    """Returns a styled warning message to be printed into console.
-    """
-    logging.warning("\n        " + make_title("WARNING", width=64) + "\n" + make_message(message, width=64, spaces=8) + "\n")
-
-
-#===============================================================================
-def print_error(message, width=80):
-    """Returns a styled warning message to be printed into console.
-    """
-    logging.error("\n        " + make_title("ERROR", width=64) + "\n" + make_message(message, width=64, spaces=8) + "\n")

cp2kparser/generics/nomadparser.py

@@ -4,8 +4,8 @@ import json
 import os
 import time
 from abc import ABCMeta, abstractmethod
-from cp2kparser.generics.nomadlogging import *
-from pint import UnitRegistry
+import logging
+logger = logging.getLogger(__name__)
 
 
 #===============================================================================
@@ -80,7 +80,7 @@ class NomadParser(object):
             try:
                 handle = open(path, "r")
             except (OSError, IOError):
-                print_error("Could not open file: '{}'".format(path))
+                logger.error("Could not open file: '{}'".format(path))
             else:
                 self.file_handles[file_id] = handle
         handle.seek(0, os.SEEK_SET)
@@ -95,10 +95,10 @@ class NomadParser(object):
         # See if the needed attributes exist
         self.tmp_dir = self.input_json_object.get("tmpDir")
         if self.tmp_dir is None:
-            print_error("No temporary folder specified.")
+            logger.error("No temporary folder specified.")
         self.files = self.input_json_object.get("files")
         if self.files is None:
-            print_error("No files specified.")
+            logger.error("No files specified.")
         self.metainfo_to_keep = self.input_json_object.get("metainfoToKeep")
         self.metainfo_to_skip = self.input_json_object.get("metainfoToSkip")
 
@@ -110,14 +110,14 @@ class NomadParser(object):
         return the value as json.
         """
         # Start timing
-        print_debug(74*'-')
-        print_debug("Getting quantity '{}'".format(name))
+        logger.debug(74*'-')
+        logger.debug("Getting quantity '{}'".format(name))
         start = time.clock()
 
         #Check availability
         available = self.check_quantity_availability(name)
         if not available:
-            print_warning("The quantity '{}' is not available for this parser version.".format(name))
+            logger.warning("The quantity '{}' is not available for this parser version.".format(name))
             return
 
         # Check cache
@@ -127,20 +127,20 @@ class NomadParser(object):
             result = self.get_unformatted_quantity(name)
             self.results[name] = result
         else:
-            print_debug("Using cached result.")
+            logger.debug("Using cached result.")
         if result is None:
-            print_debug("The quantity '{}' is not present or could not be succesfully parsed.".format(name))
+            logger.debug("The quantity '{}' is not present or could not be succesfully parsed.".format(name))
 
         # Check results
         if result is None:
-            print_info("There was an issue in parsing quantity '{}'. It is either not present in the files or could not be succesfully parsed.".format(name))
+            logger.info("There was an issue in parsing quantity '{}'. It is either not present in the files or could not be succesfully parsed.".format(name))
         else:
-            print_info("Succesfully parsed quantity '{}'. Result:\n{}".format(name, result))
+            logger.info("Succesfully parsed quantity '{}'. Result:\n{}".format(name, result))
 
         # Do the conversion to SI units based on the given units
 
         stop = time.clock()
-        print_debug("Elapsed time: {} ms".format((stop-start)*1000))
+        logger.debug("Elapsed time: {} ms".format((stop-start)*1000))
         return result
 
     def get_all_quantities(self):

cp2kparser/implementation/autoparser.py

@@ -42,7 +42,6 @@ def get_parser(path):
 
 #===============================================================================
 if __name__ == '__main__':
-    print __file__
     path = os.path.dirname(os.path.realpath(os.path.dirname(__file__)))
     parser = get_parser(path)
     parser.parse_all()

cp2kparser/implementation/parser.py

@@ -2,13 +2,15 @@
 # -*- coding: utf-8 -*-
 import os
 import re
-from cp2kparser.generics.nomadlogging import *
+# from cp2kparser.generics.nomadlogging import *
 from cp2kparser.generics.nomadparser import NomadParser
 from cp2kparser.implementation.regexs import *
 from cp2kparser.engines.regexengine import RegexEngine
 from cp2kparser.engines.xyzengine import XYZEngine
 from cp2kparser.engines.cp2kinputengine import CP2KInputEngine
 import numpy as np
+import logging
+logger = logging.getLogger(__name__)
 
 
 #===============================================================================
@@ -20,7 +22,6 @@ class CP2KParser(NomadParser):
     implementation. For other versions there should be classes that extend from
     this.
     """
-
     def __init__(self, input_json_string):
         NomadParser.__init__(self, input_json_string)
 
@@ -38,7 +39,6 @@ class CP2KParser(NomadParser):
     def setup_version(self):
         """Inherited from NomadParser.
         """
-
         # Determine the CP2K version from the input file
         beginning = self.read_part_of_file("output", 2048)
         version_regex = re.compile(r"CP2K\|\ version\ string:\s+CP2K\ version\ (\d+\.\d+\.\d+)\n")
@@ -48,20 +48,20 @@ class CP2KParser(NomadParser):
         class_name = "CP2K{}Regexs".format(version_number)
         self.regexs = globals().get(class_name)
         if self.regexs:
-            print_debug("Using version specific regexs '{}'.".format(class_name))
+            logger.debug("Using version specific regexs '{}'.".format(class_name))
             self.regexs = self.regexs()
         else:
-            print_debug("Using default regexs.")
+            logger.debug("Using default regexs.")
             self.regexs = globals()["CP2KRegexs"]()
 
         # Search for a version specific implementation
         class_name = "CP2K{}Implementation".format(version_number)
         class_object = globals().get(class_name)
         if class_object:
-            print_debug("Using version specific implementation '{}'.".format(class_name))
+            logger.debug("Using version specific implementation '{}'.".format(class_name))
             self.implementation = class_object(self)
         else:
-            print_debug("Using default implementation.")
+            logger.debug("Using default implementation.")
             self.implementation = globals()["CP2KImplementation"](self)
 
     def read_part_of_file(self, file_id, size=1024):
@@ -73,7 +73,6 @@ class CP2KParser(NomadParser):
     def determine_file_ids(self):
         """Inherited from NomadParser.
         """
-
         # Determine a list of filepaths that need id resolution
         resolved = {}
         resolvable = []
@@ -103,13 +102,13 @@ class CP2KParser(NomadParser):
 
             # The force path is not typically exactly as written in input
             if force_path.startswith("="):
-                print_debug("Using single force file.")
+                logger.debug("Using single force file.")
                 force_path = force_path[1:]
             elif re.match(r".?/", force_path):
-                print_debug("Using separate force file for each step.")
+                logger.debug("Using separate force file for each step.")
                 force_path = "{}-1_0.xyz".format(force_path)
             else:
-                print_debug("Using separate force file for each step.")
+                logger.debug("Using separate force file for each step.")