Metadata-Version: 1.0
Name: DancingPeasant
Version: 0.1.4
Summary: Utilities that allow a batch of CSV files to be passed as a single SQLITE db
Home-page: http://pypi.python.org/pypi/DancingPeasant/
Author: Michael Imelfort
Author-email: mike@mikeimelfort.com
License: GPLv3
Description: # DancingPeasant
        
        ## Overview
        
        This is a living / functional experiment in moving bioinformatics workflows away from multiple CSV files and towards SQL (specifically SQLite).
        DancingPeasant consists of two main classes: BaseFile and Interface
        
        BaseFile is a base class that enables packaging of several csv-type files into one SQLite database. It supports creation, addition of tables, versioning and history.
        Interface is a base class that provides access (currently insert / select / update) to the tables in BaseFile.
        
        ## Installation
        
        DancingPeasant depends only on Python core libraries and it's on PIP. so just:
        
            $ pip install DancingPeasant
        
        ## Example usage
        
        You should make your classes derive from BaseFile and Interface. Suppose you want to make a new db-based file format called a foofile (*.ff). First you need to extend the BaseClass:
        
        Somewhere within your "foo" package you should make a file called "db.py" with the following contents:
        
            # Always version your files!
            __FOO_DB_VERSION__ = "1.0.0"
        
            from dancingPeasant.baseFile import BaseFile
            from dancingPeasant.exceptions import *
        
            class FooDB(BaseFile):
                def __init__(self, verbosity=0):
                    BaseFile.__init__(self, verbosity)
        
                def createNewFile(self,
                                  fileName,             # name of the new file
                                  force=False,          # should we check to see if this is a wise move?
                                  ):
                    """Create a new Foo database file"""
                    # make a basic file
                    BaseFile.createNewFile(self,
                                           fileName,
                                           type="Foo_DB",
                                           version=__FOO_DB_VERSION__,
                                           force=force)
        
                    # add Foo specific tables
                    self._addTable("bars",                  # the name of the table
                                   {
                                    "length" : "INT",       # Specify column names and
                                    "diameter" : "INT",     # standard SQL syntax for the type
                                    "material" : "TEXT",    # As may as you like
                                   },
                                   force=True)
        
                    # Keep adding tables
                    ...
        
        
        To read and write from this file you'll need to extend the Interface class.
        Make a file called importer.py with the following contents:
        
            from dancingPeasant.exceptions import *
            from dancingPeasant.interface import Interface
            from dancingPeasant.interface import Condition
            from foo.db import FooDB                        # <--- NOTE: foo is the name of your package and FooDB is the name of your file class
        
        class FooInterface(Interface):
            """Use this interface for importing data stored in csv
            files into the TrackM DB"""
        
            def __init__(self,
                         dbFileName,        # file name to connect to
                         verbosity=-1       # turn off all DP chatter
                         ):
                Interface.__init__(self, dbFileName, verbosity)
                self.db = FooDB(verbosity=verbosity)            # <-- This line is important!
        
            def addBars(self, bars):
                """Add bars to the database"""
                # connect to the database
                self.connect()
        
                # bars is an array of tuples. All ordered in the same way
                # EX:
                # [(10, 1, "iron"), (20, 15, "wax"), ... ]
                #
                self.insert("bars",
                            ["length",
                             "diameter",
                             "material"],
                             bars)
        
                # disconnect once done
                self.disconnect()
        
            def getBars(self, length):
                """Get bars longer tha a set length"""
        
                # connect to the database
                self.connect()
        
                # set the select condition
                C = Condition("length", ">", length)
        
                # access the database and get rows
                rows = self.select('bars', ["material", "diameter"], C)
        
                # disconnect once done
                self.disconnect()
        
                # do something with the results
        
        This is just a starter. Hopefully I'll add some more examples here soon but I'm still busy writing it and trying to learn how to use it.
        In the meantime check out the unit tests in dancngpeasant and the various interfaces and dbs used in TrackM and StoreM for more examples on how I use this class.
        
        ## Help
        
        If you experience any problems using DancingPeasant, open an [issue](https://github.com/minillinim/DancingPeasant/issues) on GitHub and tell us about it.
        
        ## Licence
        
        GPL3, with love.
        
        Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/DancingPeasant
        
        ## Copyright
        
        Copyright (c) 2014 Michael Imelfort. See LICENSE.txt for further details.
        
Platform: UNKNOWN
