nmdc-mongo-tools 0.0.7

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

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']