cidc-schemas
| Branch | Status | Maintainability | Test Coverage | Code Style |
|---|---|---|---|---|
| master |  |
 |
 |
 |
This repository contains formal definitions of the CIDC metadata model using json-schema syntax and vocabulary.
View documentation at https://cimac-cidc.github.io/cidc-schemas/
Installation
To install the latest released version, run:
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 inschemas/templates, and.csvs auto-generated from those.xlsxs that allow to transparently keep track of changes in them.tests/- tests for thecidc_schemasmodule..githooks/- git hooks, e.g. for auto-generating.csvs intemplate_examples/and.htmldocumentation files.
Developer Setup
Install necessary dependencies.
pip install -r requirements.dev.txt
Install and configure pre-commit hooks.
pre-commit install
JIRA Integration
To set-up the git hook for JIRA integration, run:
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. The commit-msg hook runs after 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
pytest tests
Building documentation
Pre-commit hooks ensure documentation is automatically up-to date. To build the documentation manually, run the following commands:
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
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)
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
python3 -m cidc_schemas.cli [args]
Generate templates
Create a template for a given template configuration.
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.
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.
cidc_schemas validate_schema -f shipping_core.json
3 maintainers
Metadata
3 maintainers
Release files for cidc-schemas 0.26.23
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| cidc_schemas-0.26.23.tar.gz | 298.0 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| cidc_schemas-0.26.23-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 490.1 kB
Release files / cidc_schemas-0.26.23.tar.gz
| Download URL | cidc_schemas-0.26.23.tar.gz |
|---|---|
| Size | 298.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
feda4463ba1633e9f610cb3cd977337f7356d39917849808b3a2d4aec6e52a5c
|
|
BLAKE2b-256 checksum How to use checksums |
20991f6fba3b99faff03be9adbdbf997c0b0e2359e1e0d565a52b499fcbbc271
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Release files / cidc_schemas-0.26.23-py2.py3-none-any.whl
| Download URL | cidc_schemas-0.26.23-py2.py3-none-any.whl |
|---|---|
| Size | 192.1 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
b4777b2c6bede95fafe5ada49ca479402ca00eec4489106c8b9b59028767b65e
|
|
BLAKE2b-256 checksum How to use checksums |
50bda3d0df12c33031fb7cf0164de82481b559d3762789502977cf4c36be45f4
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Security for cidc-schemas 0.26.23
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
