softfocus

Interact with a database of tidy data tables using Bokeh

objective definition

The purpose of this 'bokeh serve' example is to give a template for visualizing typical measurement databases.

If using the "tidy data" format, a database should be comprising of several tables, each representing a single observational unit (e.g. a sample test in certain experimental conditions). This unit comprises of variables (the columns) recorded in successive observations (the rows). See Wickham's paper

For vizualizing purpose, it is practical to have a dashboard with a main tab or window listing a summary of the information contained in each table. Then select one or several of them and plot/visualize their content. The objective is to be able to compare efficiently variables against each other, but also observational units against each other.

This template produces random csv files in a tests/ folder the first time you start it.

Some functionalities of this template: - list csv files and their info in a main tab - plot the content of a selected csv file, selecting x-axis, y-axis and optionaly a secondary y-axis - download in Excel format the transformed table (javascript implementation) - status text

Getting Started

Prerequisites

You need python 3.6 and to install bokeh, pandas and all their dependencies.

If you use Anaconda, you can also go to the softfocus folder and create a new environment from there:

conda env create -f environment.yml

or make sure your current environment has the necessary packages

conda env update -f environment.yml

Installing

Simply download the folder.

Run it

softfocus uses the "folder" version of bokeh server.

Open a CLI, cd to the top softfocus folder then write:

bokeh serve softfocus

optional arguments:

    --allow-websocket-origin=localhost:5006 \\local access
    --allow-websocket-origin=REMOTE_IP:5006 \\remote access
    --show \\immediately opens a browser tab with the bokeh app
    --args folder/  \\list csv files from designated folder

The first time you run it, a sample data set will be generated in tests/ if you haven't done so yet.

Outlook / Contributing

Things to add/improve in the template:

delete excess xls files in a separate thread without document lock
use Tornado (or anything else) to implement the download method without dummy
make a main class for the main tab/multi tab functionality, then subclasses for the type of database (csv folders, sql, hd5...)
add SQL functionality
filter or use a custom script on a table

Author

Hugues-Yanis Amanieu, hyamani.eu

hyamanieu/softfocus