Library to extract information collected in the Minka API. This library is part of MECODA (ModulE for Citizen Observatory Data Analysis), aimed to facilitate analysis and viewing of citizen science data.

This repository is part of the work made by the EMBIMOS Reseach Group, at Marine Sciences Institute (CSIC) of Barcelona.

Installation

pip install mecoda-minka

Use

Get observations

With get_obs you can extract data from the observations collected in the API. The function supports combinations of these arguments, which act as filters, getting the observations in descending order of id, with a maximum of 20,000 (API limitation):

For the taxon argument the possible values are: chromista, protozoa, animalia, mollusca, arachnida, insecta, aves, mammalia, amphibia, reptilia, actinopterygii, fungi, plantae, cnidaria, annelida, platyhelminthes, echinodermata, bryozoa, porifera, elasmobranchii, crustacea y ctenophora.

Example of use:

from mecoda_minka import get_obs

observations = get_obs(year=2018, taxon='fungi')

observations is an object list Observation.

Get projects

With get_project you can get the information of the projects collected in the API. The function supports a single argument, which can be the project identification number or the name of the project. In case the name does not correspond exclusively to a project, it returns the information from the list of projects that include that word.

Example of use:

from mecoda_minka import get_project

projects = get_project("urbamar")

projects es siempre una lista de objetos Project.

Get count of observations by taxonomic family

With get_count_by_taxon we can know the number of observations that correspond to each of the taxonomic families. The function does not take any argument.

Example of use:

from mecoda_minka import get_count_by_taxon

count = get_count_by_taxon()

count is a dictionary with the structure {taxonomy: number of observations}

Models

The models are defined using objects from [Pydantic] (https://pydantic-docs.helpmanual.io/). Type validation of all attributes is done and data can be extracted with the dict or json method.

Observation

The object Observation contains the information of each of the observations registered in [Minka] (https://minka-sdg.org/observations) and has the following attributes:

Project

The Project object contains the information of each of the projects registered in [Minka] (https://minka-sdg.org/observations) and has the following attributes:

Photo

The Photo object contains the information of each photography linked to an observation and has the following attributes.

Contributions

To contribute to this library, follow the steps below.

• You need to have Python 3.7 or higher, virtualenv and git installed.

• Create a github fork of this project.

• Clone your fork and enter the directory

  git clone git@github.com:<your_username>/mecoda_minka.git
  cd mecoda_minka
  

• Configure your virtualenv to run the tests:

  virtualenv -p `which python3.7` env
  source env/bin/activate
  

• Install mecoda_minka and its dependencies.

  pip3 install -e .
  pip3 install -r requirements-dev.txt
  

• Create a new branch and make your changes:

  git checkout -b mi-nueva-rama
  

• Run the tests with:

  python -m pytest --cov-report term-missing --cov src tests
  

  If you need to pass a specific test, you can use pytest -k <test-name>.

• Update the documentation.

• Make commit, push and create your pull request.

Upload a new version

• Switch to master and update:

  git checkout master
  git pull
  

• Create a new branch:

  git checkout -b <branch-name>
  git pull
  

• Make changes to the code

• Run the tests:

  python -m pytest --cov-report term-missing --cov src tests
  

• Edit the setup.py file to upload the version, which means changing the version argument in the setup function. The convention is 0.1.0 == major.minor.patch. major is to introduce changes that break the existing code. minor refers to changes that add functionality but do not break existing code. patch refers to changes that fix bugs but do not add functionality.

• Make commit and push:

  git add .
  git commit -m "<comment>"
  git push --set-upstream origin <branch-name>
  

• Follow the link to github returned by the push and merge.

• Update master:

  git checkout master
  git pull
  

• Create tag with the new version:

  git tag <new-version>
  git push --tags
  

• Build the package:

  rm dist/ build/ -r
  python setup.py -q bdist_wheel
  python setup.py -q sdist
  

• Upload package to pypi:

  twine upload -r pypi dist/*
  

Thanks for contributing to this project!