%global _empty_manifest_terminate_build 0
Name: python-cidc-schemas
Version: 0.26.21
Release: 1
Summary: The CIDC data model and tools for working with it.
License: MIT license
URL: https://github.com/CIMAC-CIDC/schemas
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/7a/99/3804acb3cc43059db2e429ba644624a5f866101851113d0aead85db9afcc/cidc_schemas-0.26.21.tar.gz
BuildArch: noarch
Requires: python3-dateparser
Requires: python3-xlsxwriter
Requires: python3-argparse
Requires: python3-pyyaml
Requires: python3-jsonschema
Requires: python3-openpyxl
Requires: python3-jsonmerge
Requires: python3-deepdiff
Requires: python3-jsonpointer
Requires: python3-pandas
Requires: python3-jinja2
Requires: python3-cidc-ngs-pipeline-api
Requires: python3-markupsafe
Requires: python3-regex
%description
# cidc-schemas
| Branch | Status | Maintainability | Test Coverage | Code Style |
| ---------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- |
| [master](https://cimac-cidc.github.io/cidc-schemas/) |  | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/maintainability) | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/test_coverage) | 
|
This repository contains formal definitions of the CIDC metadata model using [json-schema](https://json-schema.org/) syntax and vocabulary.
### View documentation at https://cimac-cidc.github.io/cidc-schemas/
## Installation
To install the latest released version, run:
```bash
pip install cidc-schemas
```
## Development
### Project Structure
- **`cidc_schemas/`** - a python module for generating, validating, and reading manifest and assay templates.
- **`schemas/`** - json specifications defining the CIDC metadata model.
- `templates/` - schemas for generating and validating manifest and assay templates.
- `assays/` - schemas for defining assay data models.
- `artifacts/` - schemas for defining artifacts.
- **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
- **`template_examples/`** - example populated Excel files for template specifications in `schemas/templates`, and `.csv`s auto-generated from those `.xlsx`s that allow to transparently keep track of changes in them.
- **`tests/`** - tests for the `cidc_schemas` module.
- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
### Developer Setup
Install necessary dependencies.
```bash
pip install -r requirements.dev.txt
```
Install and configure pre-commit hooks.
```bash
pre-commit install
```
## JIRA Integration
To set-up the git hook for JIRA integration, run:
```bash
ln -s ../../.githooks/commit-msg .git/hooks/commit-msg
chmod +x .git/hooks/commit-msg
rm .git/hooks/commit-msg.sample
```
This symbolic link is necessary to correctly link files in `.githooks` to `.git/hooks`. Note that setting the `core.hooksPath` configuration variable would lead to [pre-commit failing](https://github.com/pre-commit/pre-commit/issues/1198). The `commit-msg` hook [runs after](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) the `pre-commit` hook, hence the two are de-coupled in this workflow.
To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.
### Running tests
This repository has unit tests in the _tests_ folder. After installing dependencies
the tests can be run via the command
```bash
pytest tests
```
### Building documentation
Pre-commit hooks ensure documentation is automatically up-to date. To build the documentation manually, run the following commands:
```bash
python setup.py install # install helpers from the cidc_schemas library
python docs/generate_docs.py
```
This will output the generated html documents in `docs/docs`. If the updated docs are pushed up and merged into master, they will be viewable at https://cimac-cidc.github.io/cidc-schemas/.
## Using the Command-Line Interface
This project comes with a command-line interface for validating schemas and generating/validating assay and manifest templates.
### Install the CLI
Clone the repository and cd into it
```bash
git clone git@github.com:CIMAC-CIDC/cidc-schemas.git
cd cidc-schemas
```
Install the `cidc_schemas` package (this adds the `cidc_schemas` CLI to your console)
```bash
python setup.py install
```
Run `cidc_schemas --help` to see available options.
If you're making changes to the module and want those changes to be reflected in the CLI without reinstalling the `cidc_schemas` module every time, run
```bash
python3 -m cidc_schemas.cli [args]
```
### Generate templates
Create a template for a given template configuration.
```bash
cidc_schemas generate_template -m templates/manifests/pbmc_template.json -o pbmc.xlsx
```
### Validate filled-out templates
Check that a populated template file is valid with respect to a template specification.
```bash
cidc_schemas validate_template -m templates/manifests/pbmc_template.json -x template_examples/pbmc_template.xlsx
```
### Validate JSON schemas
Check that a JSON schema conforms to the JSON Schema specifications.
```bash
cidc_schemas validate_schema -f shipping_core.json
```
%package -n python3-cidc-schemas
Summary: The CIDC data model and tools for working with it.
Provides: python-cidc-schemas
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-cidc-schemas
# cidc-schemas
| Branch | Status | Maintainability | Test Coverage | Code Style |
| ---------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- |
| [master](https://cimac-cidc.github.io/cidc-schemas/) |  | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/maintainability) | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/test_coverage) | |
This repository contains formal definitions of the CIDC metadata model using [json-schema](https://json-schema.org/) syntax and vocabulary.
### View documentation at https://cimac-cidc.github.io/cidc-schemas/
## Installation
To install the latest released version, run:
```bash
pip install cidc-schemas
```
## Development
### Project Structure
- **`cidc_schemas/`** - a python module for generating, validating, and reading manifest and assay templates.
- **`schemas/`** - json specifications defining the CIDC metadata model.
- `templates/` - schemas for generating and validating manifest and assay templates.
- `assays/` - schemas for defining assay data models.
- `artifacts/` - schemas for defining artifacts.
- **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
- **`template_examples/`** - example populated Excel files for template specifications in `schemas/templates`, and `.csv`s auto-generated from those `.xlsx`s that allow to transparently keep track of changes in them.
- **`tests/`** - tests for the `cidc_schemas` module.
- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
### Developer Setup
Install necessary dependencies.
```bash
pip install -r requirements.dev.txt
```
Install and configure pre-commit hooks.
```bash
pre-commit install
```
## JIRA Integration
To set-up the git hook for JIRA integration, run:
```bash
ln -s ../../.githooks/commit-msg .git/hooks/commit-msg
chmod +x .git/hooks/commit-msg
rm .git/hooks/commit-msg.sample
```
This symbolic link is necessary to correctly link files in `.githooks` to `.git/hooks`. Note that setting the `core.hooksPath` configuration variable would lead to [pre-commit failing](https://github.com/pre-commit/pre-commit/issues/1198). The `commit-msg` hook [runs after](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) the `pre-commit` hook, hence the two are de-coupled in this workflow.
To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.
### Running tests
This repository has unit tests in the _tests_ folder. After installing dependencies
the tests can be run via the command
```bash
pytest tests
```
### Building documentation
Pre-commit hooks ensure documentation is automatically up-to date. To build the documentation manually, run the following commands:
```bash
python setup.py install # install helpers from the cidc_schemas library
python docs/generate_docs.py
```
This will output the generated html documents in `docs/docs`. If the updated docs are pushed up and merged into master, they will be viewable at https://cimac-cidc.github.io/cidc-schemas/.
## Using the Command-Line Interface
This project comes with a command-line interface for validating schemas and generating/validating assay and manifest templates.
### Install the CLI
Clone the repository and cd into it
```bash
git clone git@github.com:CIMAC-CIDC/cidc-schemas.git
cd cidc-schemas
```
Install the `cidc_schemas` package (this adds the `cidc_schemas` CLI to your console)
```bash
python setup.py install
```
Run `cidc_schemas --help` to see available options.
If you're making changes to the module and want those changes to be reflected in the CLI without reinstalling the `cidc_schemas` module every time, run
```bash
python3 -m cidc_schemas.cli [args]
```
### Generate templates
Create a template for a given template configuration.
```bash
cidc_schemas generate_template -m templates/manifests/pbmc_template.json -o pbmc.xlsx
```
### Validate filled-out templates
Check that a populated template file is valid with respect to a template specification.
```bash
cidc_schemas validate_template -m templates/manifests/pbmc_template.json -x template_examples/pbmc_template.xlsx
```
### Validate JSON schemas
Check that a JSON schema conforms to the JSON Schema specifications.
```bash
cidc_schemas validate_schema -f shipping_core.json
```
%package help
Summary: Development documents and examples for cidc-schemas
Provides: python3-cidc-schemas-doc
%description help
# cidc-schemas
| Branch | Status | Maintainability | Test Coverage | Code Style |
| ---------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- |
| [master](https://cimac-cidc.github.io/cidc-schemas/) |  | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/maintainability) | [](https://codeclimate.com/github/CIMAC-CIDC/cidc-schemas/test_coverage) | |
This repository contains formal definitions of the CIDC metadata model using [json-schema](https://json-schema.org/) syntax and vocabulary.
### View documentation at https://cimac-cidc.github.io/cidc-schemas/
## Installation
To install the latest released version, run:
```bash
pip install cidc-schemas
```
## Development
### Project Structure
- **`cidc_schemas/`** - a python module for generating, validating, and reading manifest and assay templates.
- **`schemas/`** - json specifications defining the CIDC metadata model.
- `templates/` - schemas for generating and validating manifest and assay templates.
- `assays/` - schemas for defining assay data models.
- `artifacts/` - schemas for defining artifacts.
- **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
- **`template_examples/`** - example populated Excel files for template specifications in `schemas/templates`, and `.csv`s auto-generated from those `.xlsx`s that allow to transparently keep track of changes in them.
- **`tests/`** - tests for the `cidc_schemas` module.
- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
### Developer Setup
Install necessary dependencies.
```bash
pip install -r requirements.dev.txt
```
Install and configure pre-commit hooks.
```bash
pre-commit install
```
## JIRA Integration
To set-up the git hook for JIRA integration, run:
```bash
ln -s ../../.githooks/commit-msg .git/hooks/commit-msg
chmod +x .git/hooks/commit-msg
rm .git/hooks/commit-msg.sample
```
This symbolic link is necessary to correctly link files in `.githooks` to `.git/hooks`. Note that setting the `core.hooksPath` configuration variable would lead to [pre-commit failing](https://github.com/pre-commit/pre-commit/issues/1198). The `commit-msg` hook [runs after](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) the `pre-commit` hook, hence the two are de-coupled in this workflow.
To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.
### Running tests
This repository has unit tests in the _tests_ folder. After installing dependencies
the tests can be run via the command
```bash
pytest tests
```
### Building documentation
Pre-commit hooks ensure documentation is automatically up-to date. To build the documentation manually, run the following commands:
```bash
python setup.py install # install helpers from the cidc_schemas library
python docs/generate_docs.py
```
This will output the generated html documents in `docs/docs`. If the updated docs are pushed up and merged into master, they will be viewable at https://cimac-cidc.github.io/cidc-schemas/.
## Using the Command-Line Interface
This project comes with a command-line interface for validating schemas and generating/validating assay and manifest templates.
### Install the CLI
Clone the repository and cd into it
```bash
git clone git@github.com:CIMAC-CIDC/cidc-schemas.git
cd cidc-schemas
```
Install the `cidc_schemas` package (this adds the `cidc_schemas` CLI to your console)
```bash
python setup.py install
```
Run `cidc_schemas --help` to see available options.
If you're making changes to the module and want those changes to be reflected in the CLI without reinstalling the `cidc_schemas` module every time, run
```bash
python3 -m cidc_schemas.cli [args]
```
### Generate templates
Create a template for a given template configuration.
```bash
cidc_schemas generate_template -m templates/manifests/pbmc_template.json -o pbmc.xlsx
```
### Validate filled-out templates
Check that a populated template file is valid with respect to a template specification.
```bash
cidc_schemas validate_template -m templates/manifests/pbmc_template.json -x template_examples/pbmc_template.xlsx
```
### Validate JSON schemas
Check that a JSON schema conforms to the JSON Schema specifications.
```bash
cidc_schemas validate_schema -f shipping_core.json
```
%prep
%autosetup -n cidc-schemas-0.26.21
%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-cidc-schemas -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Apr 25 2023 Python_Bot - 0.26.21-1
- Package Spec generated