https://github.com/bigdatabiology/ampspherebackend
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○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 (8.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: BigDataBiology
- License: mit
- Language: Python
- Default Branch: main
- Size: 1.28 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
AMPSphereBackend
This repository contains source code for the backend of AMPSphere website
Deploy instructions
Prepare necessary data
Copy the latest AMPSphere data (should be generated based on Celio's script) to data/originaldata. The folder will be look like. ```text data/originaldata ├── AMPSpheregenerationv.2022-03 │ ├── analysis │ ├── data │ ├── main.py │ ├── README.md │ ├── seqlogo │ └── utils ├── metadataanalysis │ ├── data │ ├── main.py │ ├── outputs │ ├── README.md │ └── utils └── zenodorepo ├── AMPSpherev.2022-03.faa.gz ├── AMPSpherev.2022-03.fna.xz ├── AMPSpherev.2022-03.generalgeneinfo.tsv.gz ├── AMPSpherev.2022-03.qualityassessment.tsv.gz ├── README.md └── SPHEREv.2022-03.levelsassessment.tsv.gz ```
Prepare the environment
```bash conda install -c default -c conda-forge -c bioconda \ fastapi gunicorn sqlalchemy pandas pytest pydantic biopython requests mmseqs2 hmmer uvicorn
For testing
conda install -c default -c conda-forge httpx ```
Generate the backend data and test on dev server
Important: Before executing the data generation step, make sure you have the right VERSION_CODE argument in the script (edit it to modify).
bash
./generate_data.sh
python -m pytest tests
This will cost hours to half a day depends on the available computing resources.
Transfer all the data to the production server
bash
tar zcvf data.tgz --exclude "data/original_data" data
scp data.tgz ampsphere-api.big-data-biology.org:/AMPSphere/website/AMPSphereBackend/
Uncompress the data and do unittest before production
bash
tar zxvf data.tgz
python -m pytest tests/
If everything is Okay, please run the backend in production mode.
Go to its API page and test it manually if necessary: https://ampsphere-api.big-data-biology.org/
Contact
Owner
- Name: Big Data Biology Lab
- Login: BigDataBiology
- Kind: organization
- Email: luis@luispedro.org
- Repositories: 15
- Profile: https://github.com/BigDataBiology
GitHub Events
Total
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Dependencies
- aiofiles *
- biopython *
- datatable *
- fastapi *
- gunicorn *
- httptools *
- living-tree *
- pandas *
- pydantic *
- pytest *
- requests *
- sqlalchemy *
- uvicorn *
- uvloop *