qc-service

QC service for checking data for and from OBIS

Source on GitHub at iobis/qc-service

Parameters

There are two endpoints: outlierstaxon and outliersdatasets.

The following parameters are GET request:

• x: longitude of the points
• y: latitude of the points
• mad_coef (optional): Coefficient to multiply the median absolute deviation (MAD) by in order to determine the range of valid values (default is 6)
• iqr_coef (optional): Coefficient to multiply the interquartile range (IQR) by in order to determine the range of valid values (default is 3)
• aphiaid (optional): Taxonomic identifier as provided by the world register of marine species (WoRMS), this is parameter is only used by the outlierstaxon endpoint
• returnvalues (optional): Return the values based on which the outlier analysis is done (default is false).

For a POST request a json or msgpack object with the following attributes is expected:

• points: nested list of longitude/latitude pairs
• mad_coef (optional): Coefficient to multiply the median absolute deviation (MAD) by in order to determine the range of valid values (default is 6)
• iqr_coef (optional): Coefficient to multiply the interquartile range (IQR) by in order to determine the range of valid values (default is 3)
• aphiaid (optional): taxonomic identifier as provided by the world register of marine species (WoRMS), this is parameter is only used by the outlierstaxon endpoint
• returnvalues (optional): Return the values based on which the outlier analysis is done (default is false).

Example usage

GET outlierstaxon: http://api.iobis.org/outlierstaxon?x=50.1936,-170.9961,-80.9894,-99.6441,85.1296,63.6118,141.1846,-148.7020,-28.1081,-169.2730,-101.2903,1.9279,-170.4471,-108.4184,53.9584,16.1789,-100.6414,32.1356,111.3950,-177.6604&y=55.0475,35.6651,-28.7549,-62.0137,82.2984,-29.4130,-73.3057,-72.5911,62.5490,18.6707,55.2831,41.3517,6.5211,85.1608,-21.8638,9.3673,59.2928,21.3336,65.1072,13.9234

GET outliersdataset: http://api.iobis.org/outliersdataset?x=50.1936,-170.9961,-80.9894,-99.6441,85.1296,63.6118,141.1846,-148.7020,-28.1081,-169.2730,-101.2903,1.9279,-170.4471,-108.4184,53.9584,16.1789,-100.6414,32.1356,111.3950,-177.6604&y=55.0475,35.6651,-28.7549,-62.0137,82.2984,-29.4130,-73.3057,-72.5911,62.5490,18.6707,55.2831,41.3517,6.5211,85.1608,-21.8638,9.3673,59.2928,21.3336,65.1072,13.9234

Development environment installation

pipenv --three
pipenv install tox
pipenv install nose
pipenv install requests
pipenv install pandas
pipenv install json-logging-py
pipenv install gunicorn
pipenv install sphinx sphinx-autobuild sphinx_rtd_theme
pipenv install git+https://github.com/iobis/pyxylookup.git#egg=pyxylookup
# enter virtual environment
pipenv shell

Tests

Run tests

pipenv run nosetests --with-coverage --cover-package=service

Run locally

pipenv run gunicorn service.app:api

Call locally

Deploying

1. (Optional) generate requirements.txt

pipenv lock -r > requirements.txt

And remove git+https://github.com/iobis/pyxylookup.git#egg=pyxylookup from it.

2. Use docker-compose or build and start

docker-compose up

Alternative is to build and start the Docker image

docker build -t qc-service .
docker run -e GUNICORN_WORKERS=4 -e GUNICORN_ACCESSLOG=- -p 8000:8000 qc-service

3. Configure the two endpoints (outlierstaxon and outliersdataset) in NGINX

Meta

• License: MIT, see LICENSE file