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Fetch plants and animals scientific name information from the internet

License: GNU General Public License v3.0

Python 100.00%

python scientific-names fetcher python3 hacktoberfest biodiversity internet crawler plants animals

scientific-name-fetcher's Introduction

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

Download python from https://www.python.org/downloads/
Install python, follow the instruction
Press Win button (something like window icon on keyboard), search "env", then open Edit the system environment variables
Click Environment Variables
On System Variables section, edit the Path key

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\<YOUR_USERNAME>\AppData\Local\Programs\Python\Python310
C:\Users\<YOUR_USERNAME>\AppData\Local\Programs\Python\Python310\Scripts
C:\Users\<YOUR_USERNAME>\AppData\Roaming\Python\Python310\Scripts

Click OK, then OK
Open cmd, then type python --version, then it should respond with the python version.
Type pip3 install --user pipenv, then it should install pipenv, make sure it's successfully installed.
Type pipenv --version, then it should respond with the pipenv version.
Done! You can continue follow the guide in the "How to run" section.

How to run

Clone

git clone [email protected]: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

scientific-name-fetcher's People

Contributors

Stargazers

Watchers

Forkers

phantsure aldikanugraha pradeepb2505

scientific-name-fetcher's Issues

Implement a CLI for ease of use.

I think this would be more useful and easier to use with a CLI.

For instance, you could have a default behavior that would look up a single organism and print the info to the terminal:
user@host:~$ python3 main.py hydnum repandum
Hydnum is a genus of fungi in the family Hydnaceae. They are notable for their unusual spore-bearing structures of teeth rather than gills...

The current behavior could be invoked with its own command line switch, such as -b, for batch mode.
user@host:~$ python3 main.py -b input.txt

This also lets the user specify a different input file.

Additionally, behavior options could be overwritten on the command line:
user@host:~$ python3 main.py --no-gbif-search --no-auto -b my_long_list_of_names.txt

Or something like that. The Python argparse library could be used to easily implement this.

If you think this would be worthwhile, I can submit a pull request.

Add more information / validity check for each scientific-name

Currently scientific-name-fetcher is using

Wikipedia API to search for scientific name description
GBIF API to check for the validity of the scientific name

It will be good if we add more information or validity checks so that scientific-name-fetcher becomes more useful to the community.

Here are some APIs/Libraries that we may use:

IUCN Redlist: https://apiv3.iucnredlist.org/api/v3/docs
RBGKew POWO: https://github.com/RBGKew/pykew
PyTaxize https://github.com/sckott/pytaxize
Global Names Resolver http://resolver.globalnames.org/api