cherita-flask-api
A web service designed to provide a robust and scalable interface for managing and analyzing biological data
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary
Repository
A web service designed to provide a robust and scalable interface for managing and analyzing biological data
Basic Info
- Host: GitHub
- Owner: haniffalab
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://cherita-flask-api-dot-haniffa-lab.nw.r.appspot.com
- Size: 292 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 6
- Releases: 17
Metadata Files
README.md
Cherita Flask API
A web service designed to provide a robust and scalable interface for managing and analyzing biological data. This API leverages Flask, a lightweight WSGI web application framework in Python, to deliver high-performance endpoints for data retrieval, processing, and visualization.
Development
Create a development environment with the requirements.txt file
sh
python -m venv .venv
source .venv/bin/activate
python -m pip install -r requirements.txt
Set the FLASK_APP environment variable to the cherita directory
sh
export FLASK_APP=cherita
Run the API
sh
python -m flask run
You can enable debugging mode with
sh
python -m flask run --debug
You can set a specific port for the API with the -p flag
sh
python -m flask run -p 8001
Caching
The API is setup to use Redis for caching (supported by Flask-Caching).
The app will attempt to connect to a Redis instance if the environment variable REDIS_HOST is set to the instance's IP address. REDIS_PORT and CACHE_KEY_PREFIX can also be set.
If REDIS_HOST is set and the app cannot connect to the Redis instance it will throw an "Redis connection error" on each attempt to access the cache.
When updating the API's responses you will have to flush the cache to avoid getting outdated data. You need to connect to the redis instance, we recommend using redis-cli. You can install it with
sh
sudo apt-get install redis-tools
You can send the FLUSHALL command directly like
sh
redis-cli -h instance-ip-address -p port FLUSHALL
Alternatively, you can connect to the instance and then execute the command
sh
redis-cli -h instance-ip-address -p port
FLUSHALL
GCP Memorystore
Note that when using a Memorystore Redis instance you will need to connect from a VM that is within the instance's authorized network. Refer to the official documentation for more information.
Owner
- Name: Haniffa Lab
- Login: haniffalab
- Kind: organization
- Location: Newcastle upon Tyne
- Website: https://haniffalab.com/
- Twitter: haniffalab
- Repositories: 26
- Profile: https://github.com/haniffalab
Based in the Newcastle University Biosciences Institute, we apply disruptive techniques to understand how the immune system develops and maintains health
Citation (CITATION.cff)
cff-version: 1.2.0
type: software
message: "If you use this repo, please cite it"
title: "Cherita Flask API"
abstract: "A web service designed to provide a robust and scalable interface for managing and analyzing biological data."
version: "1.2.6"
url: "https://github.com/haniffalab/cherita-flask-api"
repository-code: "git@github.com:haniffalab/cherita-flask-api.git"
doi: 10.5281/zenodo.14772563
license: "MIT"
authors:
- family-names: "Basurto-Lozada"
given-names: "Daniela"
orcid: "https://orcid.org/0000-0003-3943-8424"
- family-names: "Horsfall"
given-names: "David"
orcid: "https://orcid.org/0000-0002-8086-812X"
GitHub Events
Total
- Create event: 30
- Issues event: 10
- Release event: 15
- Delete event: 19
- Issue comment event: 8
- Push event: 83
- Public event: 1
- Pull request review comment event: 2
- Pull request review event: 18
- Pull request event: 39
Last Year
- Create event: 30
- Issues event: 10
- Release event: 15
- Delete event: 19
- Issue comment event: 8
- Push event: 83
- Public event: 1
- Pull request review comment event: 2
- Pull request review event: 18
- Pull request event: 39
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 9
- Total pull requests: 24
- Average time to close issues: 3 months
- Average time to close pull requests: 9 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 0.33
- Average comments per pull request: 0.04
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 4
Past Year
- Issues: 8
- Pull requests: 24
- Average time to close issues: about 2 months
- Average time to close pull requests: 9 days
- Issue authors: 2
- Pull request authors: 3
- Average comments per issue: 0.38
- Average comments per pull request: 0.04
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 4
Top Authors
Issue Authors
- dannda (5)
- davehorsfall (4)
Pull Request Authors
- dannda (14)
- davehorsfall (6)
- dependabot[bot] (4)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- peaceiris/actions-gh-pages v3 composite
- Flask ==2.3.2
- aiohttp ==3.10.11
- anndata ==0.9.1
- flask-cors ==4.0.2
- flask-restx ==1.3.0
- fsspec ==2023.5.0
- gcsfs ==2023.5.0
- gunicorn ==22.0.0
- kaleido ==0.2.1
- plotly ==5.14.1
- requests ==2.32.2
- s3fs ==2023.5.0
- scipy ==1.14.0
- zarr ==2.16.1
- actions/checkout v3 composite
- google-github-actions/auth v2 composite
- google-github-actions/deploy-cloudrun v2 composite