A library designed to automate the ingestion of raw data and metadata schema generation.
Documentation about available functions and helpful usage notes can be found at https://microbiomedata.github.io/nmdc_mass_spectrometry_metadata_generation/.
To install run the following pip command pip install -e git+https://github.com/microbiomedata/nmdc_mass_spectrometry_metadata_generation.git#egg=src
This will install the package through the git repository. Each module can be accessed through its name. For example:
import metadata_generator
To utilize the CLI, first download the source code. Then run the script with the required flags. More details on the flags can be found in the documentation. Credentials to reach the NMDC API for necessary functions can either be passed in a .toml file OR read in from .env variables. Examples on format for these can be found under src/example_data.
python3 /path/to/main.py --generator lcms_lipid --metadata_file /path/to/csv --database_dump_json_path /path/to/dump --raw_data_url https://example.com/raw/ --process_data_url https://example.com/results/To use the CLI with toml credentials:
python3 /path/to/main.py --generator lcms_lipid --metadata_file /path/to/csv --database_dump_json_path /path/to/dump --raw_data_url https://example.com/raw/ --process_data_url https://example.com/results/ --minting_config_creds path/to/config_creds.toml