scientific-name-fetcher (scifetcher)

Fetch plants/animals scientific name information from the internet.

Current supported sources:

MediaWiki. See Docs.
Global Biodiversity Information Facility (GBIF). See Docs.
International Union for Conservation of Nature (IUCN). See Docs. (Need API Token)
Plants of the World Online (POWO). See Docs.

Requirements

python >= 3.7 (you can use pyenv for easier python version management)
pipenv

Detailed Guide for Windows

1. Download python from https://www.python.org/downloads/ 2. Install python, follow the instruction 3. Press Win button (something like window icon on keyboard), search "env", then open `Edit the system environment variables` 4. Click Environment Variables 5. On `System Variables` section, edit the `Path` key 6. Add these paths using the `New` button: ``` # Please replace the username with your windows username, you can see it in C:\Users folder # Please replace the python version with your installed python version C:\Users\\AppData\Local\Programs\Python\Python310 C:\Users\\AppData\Local\Programs\Python\Python310\Scripts C:\Users\\AppData\Roaming\Python\Python310\Scripts ``` 7. Click OK, then OK 8. Open cmd, then type `python --version`, then it should respond with the python version. 9. Type `pip3 install --user pipenv`, then it should install pipenv, make sure it's successfully installed. 10. Type `pipenv --version`, then it should respond with the pipenv version. 11. Done! You can continue follow the guide in the "How to run" section.

How to run

Clone

git clone git@github.com:rizqirizqi/scientific-name-fetcher.git
cd scientific-name-fetcher

Copy env

Linux:
```
cp env.sample .env
```
Windows:
```
copy env.sample .env
```
Install dependencies
```
pipenv --python 3
pipenv install
```
Fill your input in input.txt, please look at samples/input.txt for example. You can also use csv or xlsx if you want.

Run

pipenv run python -m scifetcher -i input.txt

The result will be placed in a file named result.*.txt

Help

pipenv run python -m scifetcher --help

Settings

Edit .env file (see env.sample file for reference)
Change the settings

Available settings:

Setting	Default	Description
AUTO_SEARCH_SIMILAR_SPECIES	True	Search GBIF database with similar name from wikipedia result.
INCLUDE_GBIF_SEARCH	True	Include GBIF search result if it can't find the exact match of the scientific name.
IUCN_API_TOKEN	-	Required token to fetch data from IUCN API. Request a token here.

Contributing

Fork this repo
Develop
Create pull request
Tag @rizqirizqi for review
Merge~~

Run Test

# all
pipenv run python -m unittest
# one file
pipenv run python -m unittest tests
# coverage
pipenv run coverage run -m unittest
coverage report
coverage html && xdg-open ./htmlcov/index.html

Lint

If you're using VSCode:

Open the Command Palette in the View menu (or just Ctrl+Shift+P)
Type Python: Select Interpreter
Select scientific-name-fetcher
Choose pipenv

License

GPL-3.0

rizqirizqi / scientific-name-fetcher

readme