Tools for validation and storage of JSON data using the NMDC Schema.

Getting Started

pip install nmdc-mongo-tools

Create a .env file in your working directory and add the following lines to it:

NMDC_JSON_SCHEMA_URL=https://raw.githubusercontent.com/microbiomedata/nmdc-metadata/master/schema/nmdc.schema.json
NMDC_MONGO_HOST=<host>
NMDC_MONGO_USERNAME=<username>
NMDC_MONGO_PWD=<password>

, setting appropriate values for connecting to a MongoDB instance. As an alternative to NMDC_JSON_SCHEMA_URL, you may set NMDC_JSON_SCHEMA_FILE to be the path to your local copy of the NMDC Schema JSON file. You may also set your environment variables any other way -- the .env-file approach is supported but not required.

Then, import from the nmdc_mongo package, e.g.

from nmdc_mongo import get_db

db = get_db("dwinston_share")
db.list_collection_names()

# ['metagenome_assembly_set', 'omics_processing_set', 'metaproteomics_analysis_activity_set', 'mags_activity_set',
# 'read_QC_analysis_activity_set', 'nom_analysis_activity_set', 'biosample_set', 'read_based_analysis_activity_set',
# 'study_set', 'metabolomics_analysis_activity_set', 'metagenome_annotation_activity_set', 'data_object_set',
# 'raw.functional_annotation_set']