dbispipeline 0.6.5

should make things more reproducible

DBIS Pipeline

This pipline can be used to run analyses in a structured way, and stores configurations and results in a database.

Usage

the user writes a minimal plan 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
• "how to process the result?", by providing result handlers.
• "where to additionally store results?" by providing storage handlers.

Please have a look at the examples for more information.

Requirements

• python >= 3.6
• a PostgreSQL database
• an email server if you want to use notification emails

Installation

1. Install dbispipeline in your python. We recommend using pipenv to keep your dependencies clean: pipenv install dbispipeline This call will install a virtual environment as well as all dependencies.
2. Write your plan(s). See the example plan files for guidance.
3. call pipenv run dp <yourplanfile.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 specific 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

# this is used to store backups of the execution
# it is possible to override this by setting the DBISPIPELINE_BACKUP_DIR
# environment variable
# the default is the temp dir of the os if this option is not set.
backup_dir = tmp

[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

Contributing

Please use the pre-commit hooks. Either install it on your system or use the development dependencies.