provbug

Supporting infrastructure to debug scientific experiments with noworkflow


Keywords
scientific, experiments, provenance, debug
License
MIT
Install
pip install provbug==0.2.3

Documentation

Provbug

Copyright (c) 2018 Universidade Federal Fluminense (UFF). All rights reserved.

Provbug is a tool that consumes provenance data collected by noWorkFlow to allow a post-execution inspection of a script. The post-execution inspection can be useful to allow the developer to have a better understanding of what happened during an execution, and also to identify, understand and correct defects in the source code, without forcing the developer to re-execute the script. We expect that this approach can be helpful to allow script developers to debug, even if the developer does not have a computer science background.

Provbug was designed to work together with noWorkFlow, so in order to use Provbug to inspect the script past execution, the script developer must use noWorkFlow to capture the provenance of the script execution.

Always run provbug with python 3.5 or 3.6

Developers:
Henrique Linhares (UFF)
Rômulo Ponciano (UFF)

Install

  1. Clone the repository from https://github.com/linharesh/provbug.git
git clone https://github.com/linharesh/provbug.git
  1. Enter the 'provbug' directory
cd provbug
  1. Call 'python setup.py install'
python setup.py install

If you encounter any problems, just clone this repository, get the file "provbug.py" inside the provbug folder and put this file on the same right where the .noworkflow folder (the folder containing the data) is located. Then, execute:

python provbug.py trial <id>

Basic Usage

To use the functions of Provbug you must execute your script with noWorkflow. Then, in the same directory that contains the '.noworkflow' folder, you could call:

provbug trial <id> 

Passing directly the number of trial that he wants to inspect. After that, the Provbug will connect to the SQLite relational database created by noWorkFlow, and will use the information available in that database to perform the queries over variables and functions

To see all commands:
To see all possible commands provided by Provbug, just type:

-h

To inspect variables:
In this way, the developer will not be forced to re-execute the script every time he wants to make a variable inspection.

var <name_of_var_inside_script>

You can inspect the variables with conditions:

var <name_of_var_inside_script> <conditional_symbol> <value>
var a < 10

To inspect functions:
By inspecting function calls, we allow the developer to have a better understanding about which where the functions that were called during the script execution, how many times a function was called, in which line the function was called, and the call stack.

func <name_of_function_inside_script_without_parentheses()>

To exit of Provbug:

exit

License Terms

The MIT License (MIT)

Copyright (c) 2018 Universidade Federal Fluminense (UFF). All rights reserved.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.