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Open Source Science

https://github.com/biocore/microsetta-interface

The Microsetta participant facing user interface

https://github.com/biocore/microsetta-interface

Science Score: 26.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .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
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

The Microsetta participant facing user interface

Basic Info
  • Host: GitHub
  • Owner: biocore
  • License: bsd-3-clause
  • Language: Jinja
  • Default Branch: master
  • Size: 11.3 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 17
  • Open Issues: 49
  • Releases: 33
Created almost 6 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

microsetta-interface

The Microsetta participant facing user interface

Installation

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

conda create --yes -n microsetta-interface python=3.7 conda install --yes -n microsetta-interface --file ci/conda_requirements.txt conda activate microsetta-interface pip install -r ci/pip_requirements.txt

Then install the microsetta-interface in editable mode:

pip install -e .

Test Usage

In the activated conda environment, start the microservice using flask's built-in server by running, e.g.,

python microsetta_interface/server.py

which will start the server on http://localhost:8083. Note that this usage is suitable for development ONLY--real use of the service would require a production-level server.

In order for the interface to be functional, it needs to be able to communicate with an instance of microsetta_private_api. Details for installing and running the private API can be found here.

Integration tests

An integration test suite is available which exercises the interaction between microsetta-interface and microsetta-private-api. These tests are only run if the private API appears online and accessible, and if custom public/private keys are available for managing JWTs.

To execute the integration suite:

  • modify the server_config.json of microsetta-private-api, adding "disable_authentication": true".
  • start microsetta-private-api
  • construct new public/private keys and make them available with source keys_for_testing.sh
  • run the integration suite with python microsetta_interface/tests/test_integration.py.

If communication with the private API is working, and if public/private keys are accessible, the tests will run. Otherwise, the test suite will skip all tests.

Owner

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

Collaboratively developed bioinformatics software.

GitHub Events

Total
  • Create event: 18
  • Release event: 1
  • Issues event: 1
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 31
  • Push event: 62
  • Pull request review event: 48
  • Pull request review comment event: 58
  • Pull request event: 32
Last Year
  • Create event: 18
  • Release event: 1
  • Issues event: 1
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 31
  • Push event: 62
  • Pull request review event: 48
  • Pull request review comment event: 58
  • Pull request event: 32

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 61
  • Total pull requests: 176
  • Average time to close issues: 4 months
  • Average time to close pull requests: 21 days
  • Total issue authors: 7
  • Total pull request authors: 13
  • Average comments per issue: 0.8
  • Average comments per pull request: 0.8
  • Merged pull requests: 139
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 41
  • Average time to close issues: 4 months
  • Average time to close pull requests: 17 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.05
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wasade (28)
  • specsdom (14)
  • AmandaBirmingham (7)
  • cassidysymons (7)
  • eadiaz73 (3)
  • ayobi (1)
  • gwarmstrong (1)
Pull Request Authors
  • cassidysymons (85)
  • dhakim87 (32)
  • ayobi (19)
  • lmerchant (14)
  • wasade (8)
  • colts661 (6)
  • charles-cowart (5)
  • AmandaBirmingham (5)
  • raginirai553 (5)
  • Ram6911 (3)
  • specsdom (3)
  • ragini7913 (2)
  • gwarmstrong (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Dependencies

microsetta_interface/static/vendor/jquery-ui-1.12.1/package.json npm
  • commitplease 2.3.0 development
  • grunt 0.4.5 development
  • grunt-bowercopy 1.2.4 development
  • grunt-cli 0.1.13 development
  • grunt-compare-size 0.4.0 development
  • grunt-contrib-concat 0.5.1 development
  • grunt-contrib-csslint 0.5.0 development
  • grunt-contrib-jshint 0.12.0 development
  • grunt-contrib-qunit 1.0.1 development
  • grunt-contrib-requirejs 0.4.4 development
  • grunt-contrib-uglify 0.11.1 development
  • grunt-git-authors 3.1.0 development
  • grunt-html 6.0.0 development
  • grunt-jscs 2.1.0 development
  • load-grunt-tasks 3.4.0 development
  • rimraf 2.5.1 development
  • testswarm 1.1.0 development
ci/conda_requirements.txt pypi
  • flake8 *
  • flask *
  • flask-babel *
  • natsort *
  • pandas *
  • pycryptodome *
  • pytest *
  • redis *
  • redis-py *
ci/pip_requirements.txt pypi
  • connexion *
  • coveralls *
  • pycountry *
  • pyjwt *
  • pytest <5.3.4
  • pytest-cov *
  • python-dateutil *