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Myriad python utilities.

Project description

python_utilities

Python utility classes (should work in either Python 2 or 3). Includes the following files:

  • /analysis/

    • /analysis/statistics/confusion_matrix_helper.py - helper class ConfusionMatrixHelperfor working with confusion matrices, usually because you have run a classification model and are trying to assess its quality.
    • /analysis/statistics/stats_helper.py - helper class StatsHelper for help with statistics not implemented in a statistical package. Includes Krippendorff's Alpha, percent agreement, and Potter's Pi, for assessing interrater reliability/agreement.
    • /analysis/statistics/tests.py - unit tests.
  • /bagit/

    • /bagit/bagit_python.ipynb and /bagit/bagit_python.py - bagit python client example code, same code in both files, one is a jupyter notebook, one is a plain Python file.
  • /beautiful_soup/

    • /beautiful_soup/beautiful_soup_helper.py - BeautifulSoupHelper class that implements helper methods for common things you do with BeautifulSoup, like getting child text and encoding HTML entities. Built against BeautifulSoup 3, updated to import BeautifulSoup 4, work just fine far as I can tell...
  • /booleans/

    • /booleans/boolean_helper.py - BooleanHelper class with method to convert non-boolean values to boolean type based on valid known true values (1, 't', 'true', 'y', 'yes').
  • /database

    • /database/database_helper_factory.py - Database_Helper_Factory class provides a class method you can use to pull in either a postgresql or mysql database helper, so you can write code that functions the same way for either, allowing easier switching between the two.
    • /database/database_helper.py - Database_Helper abstract class encapsulates basic logic for dealing with creating connections and cursors using a Python DB API library. Not fancy. Opens, creates cursors and keeps track of all cursors it creates, and closes all related cursors and connection when you call close(). Nothing more.
    • /database/psycopg2_helper.py - psycopg2_Helper class encapsulates basic logic for dealing with creating connections and cursors using the psycopg2 library. Not fancy. Opens and closes, nothing more.
    • /database/MySQLdb_helper.py - MySQLdb_Helper class encapsulates basic logic for dealing with creating connections and cursors using the MySQLdb library. Not fancy. Opens and closes, nothing more.
    • /database/PyMySQL_helper.py - PyMySQL_Helper class encapsulates basic logic for dealing with creating connections and cursors using the PyMySQL library. Not fancy. Opens and closes, nothing more.
  • /dictionaries/

    • /dictionaries/dict_helper.py - DictHelper class contains a function to retrieve a dict values as strings, integers, and lists that also accept a default, so you can convert to types and define default yourself when you look things up in a dict.
  • /django_utils/

    • /django_utils/django_ajax_selects_lookup_helper.py - includes LookupParent class, to allow for easy implementation of robust lookup classes for django_ajax_selects.
    • /django_utils/django\form_helper.py - has a class DjangoFormHelper that includes helper class methods for working with forms: is_form_empty(); is_value_empty(); data_to_html_as_hidden_inputs(), and then classes FormParent and ModelFormParent that correctly apply these methods to forms and model forms, respectively.
    • /django_utils/django_memory_helper.py - has a class DjangoMemoryHelper with a single class method, free_memory(), that does everything I know how to do to free up memory in django while a long-running process is running.
    • /django_utils/django_model_helper.py - has a class DjangoModelHelper with a single class method, copy_m2m_values(), that copies ManyToMany values from one model to another for a field whose name is passed in.
    • /django_utils/django_string_helper.py - extends StringHelper class from strings/string_helper.py, updating the convert_to_unicode() method to use Django's built-in method.
    • /django_utils/django\view_helper.py - has a class DjangoViewHelper with a single class method, get_request_data(), that retrieves data from a request passed in, whether the request is GET or POST.
    • /django_utils/query_filter.py - QueryFilterHelper class, just extends QuerySetHelper for backward compatibility.
    • /django_utils/queryset_helper.py - QuerySetHelper class that contains memory-efficient ways of iterating over large QuerySets, and also a few convenience methods for adding date and primary key filters to a QuerySet.
    • /django_utils/requirements.txt - list of packages required by the code in this folder.
  • /email/

    • /email/email_helper.py - EmailHelper class that contains logic for setting up SMTP server using smtplib, then sending text or HTML email messages.
    • /email/email_test.py - basic email code on which EmailHelper is based, as an example.
  • /exceptions/

    • /exceptions/exception_helper.py - ExceptionHelper class that contains logic for printing exception messages, and also for emailing a summary if email is set up in the isntance.
  • /integers/

    • /integers/integer_helper.py - helper class IntegerHelper with a single class method, is_valid_integer(), that accepts a value and returns True if it contains a valid integer, False if not.
    • /integers/tests.py - unit tests.
  • /json/

    • /json/json_helper.py - JSONHelper class that contains logic for pretty printing JSON and escaping all string values within a JSON object.
  • /lists/

    • /lists/list_helper.py - ListHelper class that contains class method get_value_as_list() that accepts a value, tries to convert it to a list.
  • /logging/

    • /logging/logging_helper.py - LoggingHelper class contains instance variables to hold python logging logger instance and application name used when getting logger, and methods to get and set them. The get_logger() method makes a new one using the application name if none is already present in the instance. Can be used on its own, or as a parent class to add this stuff to an existing class.
    • /logging/summary_helper.py - SummaryHelper class that contains logic for capturing and outputting timing and auditing information.
  • /network

    • /network/http_helper.py - Http_Helper class that contains logic for checking if a URL has been redirected, and if so, storing redirect information including status code and redirect URLs.
    • /network/network_helper.py - Network_Helper class contains instance methods for parsing URL strings and plucking out different known, standard pieces (domain, trimmed domain, just path - no query string, and everything after the domain).
    • /network/openanything.py - Contains SmartRedirectHandler class that keeps track of redirect hops for urllib2, logic to support Http_Helper, from the Dive Into Python site (http://www.diveintopython.net/download/diveintopython-examples-5.4.zip)
  • /objects/

    • /objects/object_helper.py - ObjectHelper class contains logic for detecting attributes in a given class (like the vars() method, only a little fancier).
  • /parameters/

    • /parameters/param_container.py - ParamContainer class contains logic for defining, loading, accessing, and outputting parameters stored in a dictionary.
  • /R/

    • /R/rserve_helper.py - RserveHelper class contains logic for working with the Rserve Python-R integration package.
  • /rate_limited/

    • /rate_limited/basic_rate_limited.py - BasicRateLimited is a non-parallel parent class that contains variables and code for rate-limiting. Details on extending TK below, in Usage Section.
  • /status/

    • /status/status_container.py - StatusContainer class that can be used as a single return-type that contains detailed status information including status code, status message, nested name value pairs (which can include exceptions as values), and a nested status container from a child call.
  • /sequences/

    • /sequences/sequence_helper.py - SequenceHelper class for methods to help with working with Sequences (Lists, etc.). Only method there now is KnuthMorrisPratt(), used to find index in list of places where another list is reproduced in its entirety (looking for subsequences within sequences).
  • /strings/

    • /strings/html_helper.py - HTMLHelper class to help with parsing and dealing with HTML strings. Right now, has one static method, remove_html(), that removes HTML from a string, allowing for a list of HTML elements you want left in, and within those elements, a list of attributes you want left in. If something is not in one of those lists, it will be removed.
    • /strings/string_helper.py - StringHelper class with methods to help with unicode encoding, stripping HTML from strings.
    • /strings/tests.py - unit tests.

Installation

Option 1: pip for stable version

Use pip:

(sudo) pip install python-utilities-jsm

Option 2: latest from github

Clone this repository and place it somewhere in your PYTHON_PATH, including the base "python_utilities" directory. The easiest way to use these libraries with a Django site is to clone this repository into the site's folder alongside other applications, so these utilities are a part of the same python path as other django apps. These utilities are used by other of my django applications, as well. They can also be used outside of django.

Dependencies are listed below. You can install them individually, or you can just use the requirements*.txt files, which lists them all out, to install them all at once using pip. The command to install base packages, without database-specific support:

(sudo) pip install -r python_utilities/requirements.txt

For either option, database packages

For database packages, you'll need to load the requirements file for each database you want to interact with (right now requirements_pgsql.txt for postgresql and rewuirements_mysql.txt for MySQL). Whichever you install, you'll also need to make sure you installed the client and client-dev libraries for each database you use.

/beautiful_soup/*

Requires the Beautiful Soup 4 package, installed via pip:

(sudo) pip install BeautifulSoup4

If you are planning on using Beautiful Soup's "UnicodeDammit" class, you also should install chardet and/or cchardet:

(sudo) pip install chardet
(sudo) pip install cchardet

/strings/html_helper.py

requires bleach, a library for selectively parsing HTML and XML:

(sudo) pip install bleach

and requires the Beautiful Soup 4 package, installed via pip:

(sudo) pip install BeautifulSoup4

/database/MySQLdb_helper.py

Before you can connect to MySQL with this code, you need to do the following:

  • install the MySQL client if it isn't already installed. On linux, you'll also need to install a few dev packages (python-dev, libmysqlclient-dev) ( source ).

  • install the MySQLdb python package. To install, you can either install through your operating system's package manager (ubuntu, for example, has package "python-mysqldb") or using pip (sudo pip install MySQL-python).

/database/psycopg2_helper.py

Before you can connect to Postgresql with this code, you need to do the following (based on http://initd.org/psycopg/install/):

  • install the PostgreSQL client if it isn't already installed. On linux, you'll also need to install a few dev packages (python-dev, libpq-dev) ( source ).

  • install the psycopg2 python package. Install using pip (sudo pip install psycopg2).

/database/PyMySQL_helper.py

Before you can connect to MySQL with this code, you need to do the following:

  • install the PyMySQL python package. To install, use pip (sudo pip install PyMySQL) or conda if you are using anaconda (conda install pymysql).

/network/*

Requires you install mechanize, a library that implements a browser client in python, and requests:

(sudo) pip install mechanize
(sudo) pip install requests

/strings/*

Requires you to install the "six" package, which helps make python code that can run in either python 2 or 3:

(sudo) pip install six

Usage

/exceptions/exception_helper.py

For a class you want to use ExceptionHelper for outputting and potentially emailing exception messages:

# import ExceptionHandler
from python_utilities.exceptions.exception_helper import ExceptionHelper

# import logging
import logging

# make instance
my_exception_helper = ExceptionHelper()

# by default, logs to logger with name "python_utilities.exceptions.exception_helper".
# if you want it to log to a different logger name, initialize that logger,
#    then pass it to the set_logger() method.  Example:
#
# my_logger = logging.getLogger( "logger_name_example" )
# my_exception_helper.set_logger( my_logger )

# By default, ExceptionHelper logs exception information to logging.ERROR.
#    You can set the level at which your exception helper will log messages:
# my_exception_helper.set_logging_level( logging.DEBUG )

# configure mail settings?
'''
smtp_host = 'localhost'
smtp_port = 1234
smtp_use_ssl = True
smtp_username = "smtp_user"
smtp_password = "smtp_pass"
my_exception_helper.email_initialize( smtp_host, smtp_port, smtp_use_ssl, smtp_username, smtp_password ):
'''

# log an exception
try:

    pass

catch Exception as e:

    # log exception.
    exception_message = "Exception caught for article " + str( current_article.id )

    # no email
    my_exception_helper.process_exception( e, exception_message )

    # with email
    # my_exception_helper.process_exception( e, exception_message, True, "email_subject" )        

#-- END try-catch --#

If you are going to be in a long-running or looping process, consider initializing at the beginning and storing instance in a variable, so you can reuse it.

Also, this class extends LoggingHelper, so it can take advantage of that set of functionality as well, outlined below.

/logging/logging_helper.py

The LoggingHelper class can be used two ways:

  1. you can create an instance of it and use that to retrieve a python logger.

     # import logging and LoggingHelper
     import logging
     from python_utilities.logging.logging_helper import LoggingHelper
    
     # make a Logger instance.
     my_logger_factory = LoggingHelper()
    
     # set the logger name
     my_logger_factory.set_logger_name( "test_logger" )
    
     # get a python logging.logger
     my_logger = my_logger_factory.get_logger()
    
  2. You can use it as a parent class for an existing class to add a variable for a logger and a logging application name and methods to get and set each to a class.

     # import logging and Logger
     import logging
     from python_utilities.logging.logging_helper import LoggingHelper
    
     # make Logger the parent class
     class MyClass( LoggingHelper ):
    
         # in your __init__() method, call parent __init__(), then set
         #    self.logger_name to either __name__ or a name you prefer.
         def __init__( self ):
    
             # call parent's __init__()
             super( MyClass, self ).__init__()
    
             # set self.logger_name
             self.set_logger_name( "MyClass" )
    
         #-- END __init__() method --#
    
         # then, to get logger instance, call self.get_logger().
    
     #-- END class MyClass --#        
    

/logging/summary_helper.py

How to use the summary helper:

# import SummaryHelper
from python_utilities.logging.summary_helper import SummaryHelper

# initialize summary helper - this sets start time, as well.
my_summary_helper = SummaryHelper()

# auditing variables
article_counter = -1
exception_counter = -1

# update the variables

# once you are done:

# set stop time
my_summary_helper.set_stop_time()

# add stuff to summary
my_summary_helper.set_prop_value( "article_counter", article_counter )
my_summary_helper.set_prop_desc( "article_counter", "Articles processed" )

my_summary_helper.set_prop_value( "exception_counter", exception_counter )
my_summary_helper.set_prop_desc( "exception_counter", "Exception count" )

# output - set prefix if you want.
summary_string += my_summary_helper.create_summary_string( item_prefix_IN = "==> " )
print( summary_string )

Example output:

==> Articles processed: 46
==> Exception count: 20
==> Start time: 2014-12-31 14:32:28.221066
==> End time: 2014-12-31 14:32:41.982753
==> Duration: 0:00:13.761687

/network/http_helper.py

The Http_Helper class lets you configure an HTTP request in an instance of Http_Helper using its built in storage for request properties and headers, then submit the request using either the urllib2 (https://docs.python.org/2/library/urllib2.html), mechanize (http://wwwsearch.sourceforge.net/mechanize/), or requests (http://docs.python-requests.org/en/latest/) packages. For a given request and package, you can either get the page itself, or just submit a URL to find its final redirected URL.

Example: using requests package to submit a post request.

# create Http_Helper
my_http_helper = Http_Helper()

# set http headers
my_http_helper.set_http_header( "Content-Type", "text/plain" )

# request type
my_http_helper.request_type = Http_Helper.REQUEST_TYPE_POST

# place body of request in a variable.
request_data = "My dog has fleas, figaro, figaro, figaro!"

# make the request using requests package:
requests_response = my_http_helper.load_url_requests( "http://yahoo.com", request_type_IN = Http_Helper.REQUEST_TYPE_POST, data_IN = request_data )

# get raw text response:
requests_raw_text = requests_response.text

# convert to a json object:
requests_response_json = requests_response.json()

# to make request using mechanize (a full-featured web browser):
mechanize_response = my_http_helper.load_url_mechanize( "http://yahoo.com", request_type_IN = Http_Helper.REQUEST_TYPE_POST, data_IN = request_data )

# to make request using urllib2:
urllib2_response = my_http_helper.load_url_urllib2( "http://yahoo.com", request_type_IN = Http_Helper.REQUEST_TYPE_POST, data_IN = request_data )

Troubleshooting:

  • If you are using the requests package and have data that you want to pass to the load_url_requests() method in variable data_IN that is a unicode string, if that unicode string has any non-ascii characters, you must encode the data before passing it in, else somewhere down in a library, something detects that the data is a unicode string and tries to encode it to "ASCII", which fails if there any non-ascii characters. If you encode to UTF-8 before passing the data in, this converts to a byte string, and all works fine.

    • An example of the stack trace and exception message you'll see if you have this problem:

        File "<project_home>/python_utilities/network/http_helper.py", line 638, in load_url_requests
          response_OUT = requests.post( url_IN, headers = headers, data = data_IN )
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/api.py", line 99, in post
          return request('post', url, data=data, json=json, **kwargs)
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/api.py", line 49, in request
          response = session.request(method=method, url=url, **kwargs)
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/sessions.py", line 461, in request
          resp = self.send(prep, **send_kwargs)
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/sessions.py", line 573, in send
          r = adapter.send(request, **kwargs)
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/adapters.py", line 370, in send
          timeout=timeout
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/packages/urllib3/connectionpool.py", line 518, in urlopen
          body=body, headers=headers)
        File "<home_dir>/.virtualenvs/sourcenet/local/lib/python2.7/site-packages/requests/packages/urllib3/connectionpool.py", line 330, in _make_request
          conn.request(method, url, **httplib_request_kw)
        File "/usr/lib/python2.7/httplib.py", line 1001, in request
          self._send_request(method, url, body, headers)
        File "/usr/lib/python2.7/httplib.py", line 1035, in _send_request
          self.endheaders(body)
        File "/usr/lib/python2.7/httplib.py", line 997, in endheaders
          self._send_output(message_body)
        File "/usr/lib/python2.7/httplib.py", line 854, in _send_output
          self.send(message_body)
        File "/usr/lib/python2.7/httplib.py", line 826, in send
          self.sock.sendall(data)
        File "/usr/lib/python2.7/socket.py", line 224, in meth
          return getattr(self._sock,name)(*args)
        UnicodeEncodeError: 'ascii' codec can't encode character u'\u2014' in position 98: ordinal not in range(128)
      
    • An example of encoding using StringHelper:

        encoded_data = StringHelper.encode_string( unicode_string, StringHelper.ENCODING_UTF8 )
      
    • An example of encoding using codecs:

        encoded_data = 
      

/parameters/param_container.py

Usage:

# import ParamContainer
from python_utilities.parameters.param_container import ParamContainer

# make an instance
my_param_container = ParamContainer()

# define parameters (for outputting debug, nothing more at this point)
my_param_container.define_parameter( "test_int", ParamContainer.PARAM_TYPE_INT )
my_param_container.define_parameter( "test_string", ParamContainer.PARAM_TYPE_STRING )
my_param_container.define_parameter( "test_list", ParamContainer.PARAM_TYPE_LIST )

# load parameters in a dict
my_param_container.set_parameters( params )

# load parameters from a django HTTP request
my_param_container.set_request( request )

# get parameter value - pass name and optional default if not present.
test_int = my_param_container.get_param( "test_int", -1 )
test_string = my_param_container.get_param( "test_string", "" )
test_list = my_param_container.get_param( "test_list", [] )

# get param as int
test_int = my_param_container.get_param_as_int( "test_int", -1 )

# get param as str
test_string = my_param_container.get_param_as_str( "test_string", -1 )

# get param as list - pass in name, optional default, list delimiter string (defaults to ",")
test_int = my_param_container.get_param_as_list( "test_int", -1, delimiter_IN = "," )

/rate_limited/basic_rate_limited.py

For a class you want to be rate-limited:

  • have that class import and extend BasicRateLimited.

      # import
      from python_utilities.rate_limited.basic_rate_limited import BasicRateLimited
    
      # class definition
      def class SampleClass( BasicRateLimited ):
    
  • in that class's __init__() method, call the parent __init__() method, then set instance variable rate_limit_in_seconds to the minimum number of seconds you want between requests (can be a decimal).

      def __init__( self ):
    
          # call parent's __init__()
          super( SampleClass, self ).__init__()
    
          # declare variables
    
          # limit to no more than 4 per second
          self.rate_limit_in_seconds = 0.25
    
      #-- END method __init__() --#
    
  • At the start of each transaction, call the self.start_request() method to let the code know you're starting a request.

  • Once the request is done, call continue_collecting = self.may_i_continue() this method will block if you have to wait, will return true if it is OK to continue, will return False if some error occurred.

  • In your control structure, always check the result of may_i_continue() before continuing.

License:

Copyright 2015-present (2019) Jonathan Morgan

This file is part of http://github.com/jonathanmorgan/python_utilities.

python_utilities is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

python_utilities is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with http://github.com/jonathanmorgan/python_utilities. If not, see http://www.gnu.org/licenses/.

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