cfde-c2m2 0.3.3

Utilities for preparing C2M2 tables

CFDE C2M2 Utilities

A collection of utilities for simplifying the C2M2 submission process. If you prepare your submission with these utilities, you do not need to run the prepare_C2M2_submission.py script or download the CV reference files manually.

Init: Initializes a fresh C2M2 submission in the current working directory, creating blank versions of all tables defined in the current C2M2 datapackage schema (C2M2_datapackage.json).

Prepare: Resolves ontology identifiers and populates the Common Vocabulary (CV) tables.

Validate: Checks validity of C2M2 submission and highlights tables for which corrections, if any, are needed.

Package: Collects metadata tables in a zip file to be submitted to the DRC portal.

Submit: Submits C2M2 datapackage to DRC portal (coming soon)

pipx install 'cfde-c2m2@git+https://github.com/maayanlab/cfde-c2m2'

# create an empty c2m2 submission OR update your existing submission directory
cfde-c2m2 init

# fill in your tables however you like

# finish preparing your package by resolving iris
cfde-c2m2 prepare

# verify integrity of your package
cfde-c2m2 validate

# zip the necessary files for a bare minimum package
cfde-c2m2 package

# Coming Soon: submit to DRC portal
cfde-c2m2 submit