dbispipeline 0.5.0

should make things more reproducible

DBIS Pipeline

This pipline can be used to run analyses in a structured way.

Usage

the user writes a minimal configuration file which contains only the following information:

• "how do I get the data?", by providing a dataloader
• "what to do with the data?", by providing a scikit pipeline
• "what to do with the result?", by providing output handlers.

Please have a look at the examples for more information.

Requirements

pipenv

everything else should be installed by pipenv.

Installation

1. Create a fresh directory.
2. In that directory, call pipenv install dbispipeline This call will install a virtual environment as well as all dependencies.
3. Write your configuration(s)
4. call pipenv run python -m dbispipeline <yourconfigurationfile.py>

Enjoy!

Configuration

The framework look in multiple directories for its configuration files.

• /usr/local/etc/dbispipeline.ini used for system wide default.
• $HOME/.config/dbispipeline.ini used for user specific configurations.
• ./dbispipeline.ini for project sepcifig configurations.

And example configuration file looks like this:

[database]

# url to your postgres database
host = your.personal.database

# your database user name
user = user

# port of your postgres database, default = 5432
# port = 5432

# password of your database user
password = <secure-password>

# database to use
database = pipelineresults

# table to be used
result_table = my_super_awesome_results

[project]
# this will be stored in the database
name = dbispipeline-test

[mail]
# email address to use as sender
sender = [e-mail]

# recipient. This should probably be set on a home-directory-basis.
recipient = [e-mail]

# smtp server address to use
smtp_server = smtp.yourserver.com

# use smtp authentication, default = no
# authenticate = no

# username for smtp authentication, required if authenticate = yes
# username = foo

# password for smtp authentication, required if authenticate = yes
# password = bar

# port to use for smtp server connection, default = 465
# port = 465