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Open Source Science

https://github.com/biocore/microsetta-private-api

A private microservice to support The Microsetta Initiative

https://github.com/biocore/microsetta-private-api

Science Score: 26.0%

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

  • ○
    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 (9.6%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

A private microservice to support The Microsetta Initiative

Basic Info
  • Host: GitHub
  • Owner: biocore
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Size: 46.7 MB
Statistics
  • Stars: 6
  • Watchers: 6
  • Forks: 19
  • Open Issues: 64
  • Releases: 41
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

microsetta-private-api CI

microsetta-private-api

A private microservice to support The Microsetta Initiative

Installation

The private microservice depends on Postgres 9 or higher. For OSX users, we recommend installing Postgres.app and ensuring that path has been configured to allow use of the command line tools delivered with the app. For Linux users, please consult documentation for the Linux distribution in use.

Create a new conda environment containing flask and other necessary packages:

conda create --yes -n microsetta-private-api python=3.7

Once the conda environment is created, activate it:

conda activate microsetta-private-api

Ensure that the conda-forge channel has been added to the conda install and run:

conda install --yes --file ci/conda_requirements.txt

Install additional requirements using pip:

pip install -r ci/pip_requirements.txt

Then install the microsetta-private-api in editable mode:

pip install -e . --no-deps

Test Usage

In the activated conda environment, initialize a test database:

python microsetta_private_api/LEGACY/build_db.py

To run unittests:

make test

Then we'll initiate a Celery worker (Example shown is with embedded Celery Beat scheduler):

celery -A microsetta_private_api.celery_worker.celery worker -B --loglevel=info

*** OR (Allowing for multiple workers)***

celery -A microsetta_private_api.celery_worker.celery worker --loglevel=info (Start 1 worker) celery -A microsetta_private_api.celery_worker.celery beat --loglevel=info (Start the Celery Beat scheduler)

Next, start the microservice using flask's built-in server by running, e.g.,

python ./microsetta_private_api/server.py

which will start the server on http://localhost:8082 . Note that this usage is suitable for development ONLY--real use of the service would require a production-level server.

The Swagger UI should also be available at http://localhost:8082/api/ui .

Owner

  • Name: biocore
  • Login: biocore
  • Kind: organization
  • Location: Cyberspace

Collaboratively developed bioinformatics software.

GitHub Events

Total
  • Create event: 21
  • Release event: 5
  • Issues event: 11
  • Delete event: 1
  • Member event: 1
  • Issue comment event: 11
  • Push event: 57
  • Pull request review comment event: 79
  • Pull request review event: 55
  • Pull request event: 48
Last Year
  • Create event: 21
  • Release event: 5
  • Issues event: 11
  • Delete event: 1
  • Member event: 1
  • Issue comment event: 11
  • Push event: 57
  • Pull request review comment event: 79
  • Pull request review event: 55
  • Pull request event: 48

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 88
  • Total pull requests: 135
  • Average time to close issues: 5 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 8
  • Total pull request authors: 10
  • Average comments per issue: 0.98
  • Average comments per pull request: 0.7
  • Merged pull requests: 113
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 27
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.19
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dhakim87 (37)
  • wasade (25)
  • AmandaBirmingham (15)
  • cassidysymons (6)
  • colts661 (2)
  • b4collinsworth (1)
  • dpromi (1)
  • antgonza (1)
Pull Request Authors
  • cassidysymons (87)
  • ayobi (30)
  • dhakim87 (11)
  • AmandaBirmingham (10)
  • wasade (10)
  • colts661 (8)
  • charles-cowart (2)
  • lmerchant (1)
  • ganeshkumar78 (1)
  • raginirai553 (1)
Top Labels
Issue Labels
enhancement (15) yaml (11) bug (6) codebase quality (5) someday (5) priority (4) documentation (3) invalid (2) question (2) good first issue (1)
Pull Request Labels

Dependencies

ci/conda_requirements.txt pypi
  • flake8 *
  • flask *
  • natsort *
  • pandas *
  • psycopg2 *
  • pycryptodome *
ci/pip_requirements.txt pypi
  • celery *
  • connexion <2.7.1
  • coveralls *
  • flask-babel *
  • html2text *
  • jsonschema <4.0.0
  • openapi-spec-validator <0.2.10
  • pycountry *
  • pyjwt <2.2.0
  • pytest *
  • pytest-cov *
  • python-dateutil *
  • redis *
  • requests *
  • requests_oauthlib *
.github/workflows/python-package-conda.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • conda-incubator/setup-miniconda v2 composite
  • postgres 13.4 docker
setup.py pypi