Koza, an ETL framework for the Biolink model
Project description
Koza
Disclaimer: Koza is in beta; we are looking for beta testers
Transform csv, json, yaml, jsonl, and xml and converting them to a target csv, json, or jsonl format based on your dataclass model. Koza also can output data in the KGX format
Documentation: https://koza.monarchinitiative.org/
Highlights
- Author data transforms in semi-declarative Python
- Configure source files, expected columns/json properties and path filters, field filters, and metadata in yaml
- Create or import mapping files to be used in ingests (eg id mapping, type mappings)
- Create and use translation tables to map between source and target vocabularies
Installation
pip install koza
Getting Started
Send a local or remove csv file through Koza to get some basic information (headers, number of rows)
koza validate \
--file https://raw.githubusercontent.com/monarch-initiative/koza/main/examples/data/string.tsv \
--delimiter ' '
Sending a json or jsonl formatted file will confirm if the file is valid json or jsonl
koza validate \
--file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \
--format jsonl
koza validate \
--file ./examples/data/ddpheno.json.gz \
--format json \
--compression gzip
Example: transforming StringDB
koza transform --source examples/string/protein-links-detailed.yaml --global-table examples/translation_table.yaml
koza transform --source examples/string-declarative/protein-links-detailed.yaml --global-table examples/translation_table.yaml
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