datacatalog.formats.ginkgo package¶

Submodules¶

datacatalog.formats.ginkgo.convert module¶

class datacatalog.formats.ginkgo.convert.Ginkgo(schemas=[], targetschema=None, options={}, reactor=None)[source]¶

Bases: datacatalog.formats.converter.Converter

Convert Transcriptic samples.json to sample-set schema

FILENAME = 'ginkgo_samples'¶

VERSION = '0.0.2'¶

convert(input_fp, output_fp=None, verbose=True, config={}, enforce_validation=True)[source]¶: Do the conversion by running a method in runner.py

datacatalog.formats.ginkgo.mappings module¶

Implements temporary and/or manual mappings

class datacatalog.formats.ginkgo.mappings.SampleContentsFilter[source]¶

Bases: object

Set of Ginkgo reagents, by lab ID, to exclude from sample.contents

GINKGO_LAB_IDS = [2420, 3170, 2231]¶

datacatalog.formats.ginkgo.runner module¶