koza

Koza, an ETL framework for the Biolink model

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Maintainers

glass-ships kevinschaper kshefchek tputman

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Project links

Project description

pupa Data transformation framework

Disclaimer: Koza is in pre-alpha

Transform csv, json, and jsonl 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

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/dev/tests/resources/source-files/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/metadata.yaml 

koza transform --source examples/string-declarative/metadata.yaml

Project details

These details have been verified by PyPI

Maintainers

glass-ships kevinschaper kshefchek tputman

These details have not been verified by PyPI

Project links

Release history Release notifications | RSS feed

0.7.2

Oct 5, 2024

0.7.1

Oct 5, 2024

0.7.0

Oct 4, 2024

0.6.1

Aug 7, 2024

0.6.0

May 13, 2024

0.5.4

Apr 2, 2024

0.5.3

Dec 13, 2023

0.5.2

Dec 8, 2023

0.5.1

Nov 22, 2023

0.5.0

Nov 10, 2023

0.3.1

Apr 18, 2023

0.3.0

Apr 3, 2023

0.2.5

Dec 1, 2022

0.2.3

Nov 11, 2022

0.2.2

Nov 4, 2022

0.2.1

Jul 16, 2022

0.1.14

Jun 4, 2022

0.1.13

Apr 25, 2022

0.1.11

Apr 8, 2022

0.1.9

Mar 22, 2022

0.1.8

Mar 22, 2022

0.1.7

Feb 15, 2022

0.1.6

Nov 10, 2021

0.1.5

Nov 3, 2021

0.1.4

Oct 29, 2021

0.1.3

Oct 27, 2021

0.1.2

Oct 11, 2021

0.1.1

Sep 28, 2021

0.1.0

Sep 27, 2021

This version

0.0.1a6 pre-release

Jul 8, 2021

0.0.1a5 pre-release

Jul 8, 2021

0.0.1a4 pre-release

Jun 24, 2021

0.0.1a3 pre-release

Jun 23, 2021

0.0.1a2 pre-release

Feb 25, 2021

0.0.1a1 pre-release

Feb 25, 2021

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