koza

pupa Data transformation framework

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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