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mira

Enabling Access to MIAPPE-compliant ISA Tab archives through BrAPI

https://github.com/ipk-bit/mira

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation ·

Repository

Enabling Access to MIAPPE-compliant ISA Tab archives through BrAPI

Basic Info
  • Host: GitHub
  • Owner: IPK-BIT
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 544 KB
Statistics
  • Stars: 1
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

MIRA

Overview

MIRA is a software solution designed to deploy a BrAPI server on top of a FAIR Digital Object (FDO) that fulfills the MIAPPE requirements. It provides flexibility to run the server either as a Docker container or directly from the source code.

Features

  • Deploys a BrAPI server compliant with MIAPPE standards.
  • Supports deployment via Docker or source code.
  • Supports ARC RO-Crate format for input

Installation

Using Docker

  1. Ensure Docker is installed on your system.
  2. Pull the Docker image: bash docker pull mira:latest
  3. Run the container: bash docker run -p 8000:8000 mira:latest

From Source

  1. Clone the repository: bash git clone https://github.com/IPK-BIT/mira.git cd mira
  2. Install dependencies using Poetry: bash poetry install
  3. Add ./config.yml: ```yml format: data: '' aai:
    • method: basic username: password: server: contact: documentation: location: organization: name: url: description: | name: ```
  4. Start the server: bash cd mira litestar run

Development

Prerequisites

  • Python 3.12 or higher
  • Poetry

Setting Up the Development Environment

  1. Clone the repository: bash git clone https://github.com/IPK-BIT/mira.git cd mira
  2. Install dependencies: bash poetry install
  3. Add ./config.yml: ```yml format: data: '' aai:
    • method: basic username: password: server: contact: documentation: location: organization: name: url: description: | name: ```
  4. Run development server: bash cd mira poetry run litestar run --debug --reload

Usage

Once the server is running, you can access the BrAPI endpoint documentation at http://localhost:8000/schema.

Contributing

Contributions are welcome! Please follow these steps:

  1. Fork the repository.
  2. Create a new branch for your feature or bugfix.
  3. Submit a pull request with a detailed description of your changes.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Owner

  • Name: IPK Gatersleben - Bioinformatics and Information Technology
  • Login: IPK-BIT
  • Kind: organization
  • Location: Germany

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

Citation (CITATIONS.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: MIRA
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Manuel
    family-names: Feser
    email: feser@ipk-gatersleben.de
    affiliation: IPK Gatersleben
    orcid: 'https://orcid.org/0000-0001-6546-1818'
repository-code: 'https://github.com/IPK-BIT/mira'
url: 'https://mira.ipk-gatersleben.de'
abstract: >-
  Enabling Access to MIAPPE-compliant ISA archives
  through BrAPI
keywords:
  - BrAPI
  - MIAPPE
  - Automation
license: MIT

GitHub Events

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Dependencies

Dockerfile docker
  • python 3.11-slim build
docs/requirements.txt pypi
  • mkdocs-material *
poetry.lock pypi
  • aiosqlite 0.21.0
  • annotated-types 0.7.0
  • anyio 4.9.0
  • arctrl 2.5.1
  • babel 2.17.0
  • backrefs 5.8
  • certifi 2025.4.26
  • charset-normalizer 3.4.2
  • click 8.1.8
  • colorama 0.4.6
  • et-xmlfile 2.0.0
  • faker 37.1.0
  • fsspreadsheet 6.3.1
  • ghp-import 2.1.0
  • greenlet 3.2.1
  • h11 0.16.0
  • httpcore 1.0.9
  • httpx 0.28.1
  • idna 3.10
  • jinja2 3.1.6
  • litestar 2.16.0
  • litestar-htmx 0.4.1
  • markdown 3.8
  • markdown-it-py 3.0.0
  • markupsafe 3.0.2
  • mdurl 0.1.2
  • mergedeep 1.3.4
  • mkdocs 1.6.1
  • mkdocs-get-deps 0.2.0
  • mkdocs-material 9.6.13
  • mkdocs-material-extensions 1.3.1
  • msgspec 0.19.0
  • multidict 6.4.3
  • multipart 1.2.1
  • openpyxl 3.1.5
  • packaging 25.0
  • paginate 0.5.7
  • pathspec 0.12.1
  • platformdirs 4.3.8
  • polars 1.29.0
  • polyfactory 2.21.0
  • pydantic 2.11.4
  • pydantic-core 2.33.2
  • pygments 2.19.1
  • pymdown-extensions 10.15
  • python-dateutil 2.9.0.post0
  • python-dotenv 1.1.0
  • pyyaml 6.0.2
  • pyyaml-env-tag 1.0
  • requests 2.32.3
  • rich 14.0.0
  • rich-click 1.8.8
  • six 1.17.0
  • sniffio 1.3.1
  • sqlalchemy 2.0.40
  • typing-extensions 4.13.2
  • typing-inspection 0.4.0
  • tzdata 2025.2
  • urllib3 2.4.0
  • uvicorn 0.34.2
  • watchdog 6.0.0
pyproject.toml pypi
  • mkdocs-material ^9.6.13 develop
  • aiosqlite ^0.21.0
  • arctrl ^2.5.1
  • fsspreadsheet ^6.3.1
  • litestar ^2.16.0
  • polars ^1.29.0
  • pydantic ^2.11.4
  • python ^3.12
  • python-dateutil ^2.9.0.post0
  • python-dotenv ^1.1.0
  • sqlalchemy ^2.0.40
  • uvicorn ^0.34.2