Data-Cleaning-Framework

We all know how awkward it is to clean data in jupyter notebooks. Multiple cells of exploratory work, trying different transforms, looking up different transforms, adhoc functions that work in one notebook and have to be either copied/pasta-ed to the next notebook, or rewritten from scratch. Data Cleaning Framework (DCF) makes all of that better by providing a visual UI for common cleaning operations AND emitting python code that performs the transformation. Specifically, the DCF is a tool built to interactively explore, clean, and transform pandas dataframes.

How to run DCF

There are two separate repos necessary for running DCF, we will start with this repo, the python server.

Running the dcf server

$ git clone  https://github.com/paddymul/dcf-server 
$ cd dcf-server

create virtual environment using python3 and activate it (keep it outside our project directory)

$ python3 -m venv /path/to/your/virtual/environment
$ source <path/to/venv>/bin/activate

install dependencies in virtualenv

$ pip install -r requirements.txt

setup flask command for our app

$ export FLASK_APP=manage.py
$ export FLASK_ENV=development

create instance folder in /tmp directory (sqlite database, temp files stay here)

$ mkdir /tmp/flaskstarter-instance

initialize database and get two default users (admin & demo), check manage.py for details

$ flask initdb

5. start test server at localhost:5000

$ flask run

At this point the DCF server should properly startup.

Running the UI Server

Start a separate shell from the dcf-server shell to run the UI server. This requires that you have node and npm installed on your system

$ git clone  https://github.com/paddymul/dcf-frontend
$ cd dcf-frontend
$ npm install
$ npm run dev

The UI server should start at this point. Navigate to the local dcf landing page

If you run into errors

The python dcf server is based on the Flask starter project. If you get stuck with these instructions, refer to flaskstarter docs. Also leave a bug report here.

Using DCF

DCF reads a pre-baked dataframe from the server (or an even smaller one baked into typescript if the server isn't available).

Selecting a different csv

By default this is a citibike data dump from 2014. You can specify a different dataframe by setting the environment variable DCF_CSV like this

$ export DCF_CSV=./path-to-your-csv.csv

then restart the dcf server. When you reload the dcf landing page, your dataframe will load in the top pane.

Using commands

At the core DCF commands operate on columns. You must first click on a cell (not a header) in the top pane to select a column.

Next you must click on a command like dropcol, fillna, or groupby to create a new command

After creating a new command, you will see that command in the commands list, now you must edit the details of a command. Select the command by clicking on the bottom cell.

At this point you can either delete the command by clicking the X button or change command parameters.

Writing your own commands

Builtin commands are found in all_transforms.py

Simple example

Here is a simple example command

class DropCol(Transform):
    command_default = [s('dropcol'), s('df'), "col"]
    command_pattern = [None]

    @staticmethod 
    def transform(df, col):
        df.drop(col, axis=1, inplace=True)
        return df

    @staticmethod 
    def transform_to_py(df, col):
        return "    df.drop('%s', axis=1, inplace=True)" % col

command_default is the base configuration of the command when first added, s('dropcol') is a special notation for the function name. s('df') is a symbol notation for the dataframe argument (see LISP section for details). "col" is a placeholder for the selected column.

since dropcol doesn't take any extra arguments, command_pattern is [None]

    def transform(df, col):
        df.drop(col, axis=1, inplace=True)
        return df

This transform is the function that manipulates the dataframe. For dropcol we take two arguments, the dataframe, and the column name.

    def transform_to_py(df, col):
        return "    df.drop('%s', axis=1, inplace=True)" % col

transform_to_py emits equivalent python code for this transform. Code is indented 4 space for use in a function.

Complex example

class GroupBy(Transform):
    command_default = [s("groupby"), s('df'), 'col', {}]
    command_pattern = [[3, 'colMap', 'colEnum', ['null', 'sum', 'mean', 'median', 'count']]]
    @staticmethod 
    def transform(df, col, col_spec):
        grps = df.groupby(col)
        df_contents = {}
        for k, v in col_spec.items():
            if v == "sum":
                df_contents[k] = grps[k].apply(lambda x: x.sum())
            elif v == "mean":
                df_contents[k] = grps[k].apply(lambda x: x.mean())
            elif v == "median":
                df_contents[k] = grps[k].apply(lambda x: x.median())
            elif v == "count":
                df_contents[k] = grps[k].apply(lambda x: x.count())
        return pd.DataFrame(df_contents)

The GroupBy command is complex. it takes a 3rd argument of col_spec. col_spec is an argument of type colEnum. A colEnum argument tells the UI to display a table with all column names, and a drop down box of enum options.

In this case each column can have an operation of either sum, mean, median, or count applied to it.

Note also the leading 3 in the command_pattern. That is telling the UI that these are the specs for the 3rd element of the command. Eventually commands will be able to have multiple configured arguments.

Argument types

Arguments can currently be configured as

• integer - allowing an integer input
• enum - allowing a strict set of options, returned as a string to the transform
• colEnum - allowing a strict set of options per column, returned as a dictionary keyed on column with values of enum options

Order of Operations for data cleaning

The ideal order of operations is as follows

• Column level fixes

  • drop (remove this column)
  • fillna (fill NaN/None with a value)
  • safe int (convert a colum to integers where possible, and nan everywhere else)
  • OneHotEncoding ( create multiple boolean columns from the possible values of this column )
  • MakeCategorical ( change the values of string to a Categorical Data type)
  • Quantize

• DataFrame transformations these transforms largely keep the shape of the data the same

  • Resample
  • ManyColdDecoding (the opposite of OneHotEncoding, take multiple boolean columns and transform into a single categorical
  • Index shift (add a column with the value from previous row's column)

• Dataframe transformations 2 These result in a single new dataframe with a vastly different shape

  • Stack/Unstack columns
  • GroupBy (with UI for sellect group by function for each column)

• DataFrame transformations 2 These transforms emit multiple DataFrames

  • Relational extract (extract one or more columns into a second dataframe that can be joined back to a foreign key column)
  • Split on column (emit separate dataframes for each value of a categorical, no shape editting)

• DataFrame combination

  • concat (concatenate multiple dataframes, with UI affordances to assure a similar shape)
  • join (join two dataframes on a key, with UI affordances)

DCF can only work on a single input dataframe shape at a time. Any newly created columns are visible on output, but not available for manipulation in the same DCF Cell.

Components

• a rich table widget that is embeddable into applications and in the jupyter notebook.
• A UI for selecting and trying transforms interactively
• An output table widget showing the transformed dataframe

What works now, what's coming

Exists now

• React frontend app
  • Displays a datatframe
  • Simple UI for column level functions
  • Shows generated python code
  • Shows transformed data frame
• DCF server
  • Serves up dataframes for use by frontend
  • responds to dcf commands
  • shows generated python code
• Developer User experience
  • define DCF commands in python onloy
• DCF Intepreter
  • Based on Peter Norvig's lispy.py, a simple syntax that is easy for the frontend to generate (no parens, just JSON arrays)
• DCF core (actual transforms supported)
  • dropcol
  • fillna
  • one hot
  • safe int
  • GroupBy

Next major features

• Jupyter Notebook widget
  • embed the same UI from the frontend into a jupyter notebook shell
  • No need to fire up a separate server, commands sent via ipywidgets.comms
  • Add a "send generated python to next cell" function
• React frontend app
  • Styling
    • Server only, some UI for DataFrame selection
  • Pre filtering concept (only operate on first 1000 rows, some sample of all rows)
  • DataFrame joining UI
  • Summary statistics tab for incoming dataframe
  • Multi index columns
  • DateTimeIndex support
• DCF core
  • MakeCategorical
  • Quantize
  • Resample
  • ManyColdDecoding
  • IndexShift
  • Computed
  • Stack/Unstack
  • RelationalExtract
  • Split
  • concat
  • join

FAQ

Why did you use LISP?

This is a problem domain that requried a DSL and intermediate language. I could have written my own or chosen an existing language. I chose LISP because it is simple to interpret and generate, additionally it is well understood. Yes LISP is obscure, but it is less obscure than a custom language I would write myself. I didn't want to expose an entire progrmaming language with all the attendant security risks, I wanted a small safe strict subset of programming features that I explicitly exposed. LISP is easier to manipulate as an AST than any language in PL history. I am not yet using any symbolic manipulation facilities of LISP, and will probably only use them in limited ways.

Do I need to know LISP to use DCF?

No. Users of DCF will never need to know that LISP is at the core of the system.

Do I need to know LISP to contribute to DCF?

Not really. Transfrom functions and their python equivalent are added to the dcf interpreter. Transform functions are very simple and straight forward. Here are the two functions that make fillna work.

def fillna(df, col, val):
    df.fillna({col:val}, inplace=True)
    return df

def fillna_py(df, col, val):
    return "    df.fillna({'%s':%r}, inplace=True)" % (col, val)

If you want to work on code transformations, then a knowledge of lisp and particularly lisp macros are helpful.

What is an example of a code transformation?

Imagine you have a dropcol command which takes a single column to drop, also imagine that there is a function dropcols which takes a list of columns to drop.

It is easier to build the UI to emit individual dropcol commands, you will end up with more readable code when you have a single command that drops all columns.

You could write a transform which reads all dropcol forms and rewrites it to a single dropcols command.

Alternatively, you could write a command that instead of subtractively reducing a dataframe, builds up a new dataframe from an explicit list of columns. That is also a type of transform that could be written.

Is DCF meant to repalce knowledge of python/pandas

No, DCF helps experienced pandas devs quickly build and try the transformations they already know. Transformation names stay very close to the underlying pandas names. DCF makes different transforms more discoverable than reading obscure blogposts and half working stackoverflow submissions. Different transformations can be quickly tried without a lot of reading and tinkering to see if it is the transform you want. Finally, all transformations are emitted as python code. That python code can be a starting point.