%global _empty_manifest_terminate_build 0 Name: python-koza Version: 0.3.1 Release: 1 Summary: Data transformation framework for LinkML data models License: BSD License URL: https://pypi.org/project/koza/ Source0: https://mirrors.aliyun.com/pypi/web/packages/b1/dd/8620d2612ca2c6b8a942760358e79cac25939d6761e68411694c2d781cb6/koza-0.3.1.tar.gz BuildArch: noarch Requires: python3-linkml-validator Requires: python3-pydantic Requires: python3-pyyaml Requires: python3-requests Requires: python3-ordered-set Requires: python3-typer Requires: python3-typer-cli Requires: python3-loguru %description # Koza - a data transformation framework [![Pyversions](https://img.shields.io/pypi/pyversions/koza.svg)](https://pypi.python.org/pypi/koza) [![PyPi](https://img.shields.io/pypi/v/koza.svg)](https://pypi.python.org/pypi/koza) ![Github Action](https://github.com/monarch-initiative/koza/actions/workflows/build.yml/badge.svg) ![pupa](docs/img/pupa.png) [**Documentation**](https://koza.monarchinitiative.org/ ) _Disclaimer_: Koza is in beta; we are looking for beta testers ### Overview - 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](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md#kgx-format-as-tsv) - Write 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 Koza is available on PyPi and can be installed via pip/pipx: ``` [pip|pipx] install koza ``` ### Usage **NOTE: As of version 0.2.0, there is a new method for getting your ingest's `KozaApp` instance. Please see the [updated documentation](https://koza.monarchinitiative.org/Usage/configuring_ingests/#transform-code) for details.** See the [Koza documentation](https://koza.monarchinitiative.org/) for usage information ### Try the Examples #### Validate Give Koza a local or remote csv file, and get some basic information (headers, number of rows) ```bash 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 ```bash koza validate \ --file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \ --format jsonl ``` ```bash koza validate \ --file ./examples/data/ddpheno.json.gz \ --format json \ --compression gzip ``` #### Transform Run the example ingest, "string/protein-links-detailed" ```bash 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 ``` note: koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml) %package -n python3-koza Summary: Data transformation framework for LinkML data models Provides: python-koza BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-koza # Koza - a data transformation framework [![Pyversions](https://img.shields.io/pypi/pyversions/koza.svg)](https://pypi.python.org/pypi/koza) [![PyPi](https://img.shields.io/pypi/v/koza.svg)](https://pypi.python.org/pypi/koza) ![Github Action](https://github.com/monarch-initiative/koza/actions/workflows/build.yml/badge.svg) ![pupa](docs/img/pupa.png) [**Documentation**](https://koza.monarchinitiative.org/ ) _Disclaimer_: Koza is in beta; we are looking for beta testers ### Overview - 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](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md#kgx-format-as-tsv) - Write 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 Koza is available on PyPi and can be installed via pip/pipx: ``` [pip|pipx] install koza ``` ### Usage **NOTE: As of version 0.2.0, there is a new method for getting your ingest's `KozaApp` instance. Please see the [updated documentation](https://koza.monarchinitiative.org/Usage/configuring_ingests/#transform-code) for details.** See the [Koza documentation](https://koza.monarchinitiative.org/) for usage information ### Try the Examples #### Validate Give Koza a local or remote csv file, and get some basic information (headers, number of rows) ```bash 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 ```bash koza validate \ --file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \ --format jsonl ``` ```bash koza validate \ --file ./examples/data/ddpheno.json.gz \ --format json \ --compression gzip ``` #### Transform Run the example ingest, "string/protein-links-detailed" ```bash 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 ``` note: koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml) %package help Summary: Development documents and examples for koza Provides: python3-koza-doc %description help # Koza - a data transformation framework [![Pyversions](https://img.shields.io/pypi/pyversions/koza.svg)](https://pypi.python.org/pypi/koza) [![PyPi](https://img.shields.io/pypi/v/koza.svg)](https://pypi.python.org/pypi/koza) ![Github Action](https://github.com/monarch-initiative/koza/actions/workflows/build.yml/badge.svg) ![pupa](docs/img/pupa.png) [**Documentation**](https://koza.monarchinitiative.org/ ) _Disclaimer_: Koza is in beta; we are looking for beta testers ### Overview - 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](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md#kgx-format-as-tsv) - Write 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 Koza is available on PyPi and can be installed via pip/pipx: ``` [pip|pipx] install koza ``` ### Usage **NOTE: As of version 0.2.0, there is a new method for getting your ingest's `KozaApp` instance. Please see the [updated documentation](https://koza.monarchinitiative.org/Usage/configuring_ingests/#transform-code) for details.** See the [Koza documentation](https://koza.monarchinitiative.org/) for usage information ### Try the Examples #### Validate Give Koza a local or remote csv file, and get some basic information (headers, number of rows) ```bash 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 ```bash koza validate \ --file ./examples/data/ZFIN_PHENOTYPE_0.jsonl.gz \ --format jsonl ``` ```bash koza validate \ --file ./examples/data/ddpheno.json.gz \ --format json \ --compression gzip ``` #### Transform Run the example ingest, "string/protein-links-detailed" ```bash 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 ``` note: koza expects a directory structure as described in the above example (examples/ingest_name/ingest.yaml) %prep %autosetup -n koza-0.3.1 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-koza -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Fri Jun 09 2023 Python_Bot - 0.3.1-1 - Package Spec generated