gbifSpecieLinkContructor

• This tool is to build the species url of the GBIF web page that describes it.
• The program expect an excel file with two columns named named: "Nombre científico" and "ID del nombre científico". Where "Nombre científico" correspond to the column with the species and "ID del nombre científico" an empty column where the species url from the GBIF will be stored. You can find an example in the folder "Dataset_examples -> "DwC_D&L_EGF_Mutata-Carepa_20230608.xlsx".

Installation

First step: Install miniconda and Python.

You must have installed Python (tested on Python >= 3.9.16). The recommended option is through Conda.

• Get conda for mac:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh

• Run conda:

bash Miniconda3-latest-MacOSX-arm64.sh

• Using Conda:

conda create -n gbif pip && conda activate gbif

Second step: Clone this repository and install requirements.

git clone https://github.com/juanjo255/gbifSpecieLinkContructor.git && cd gbifSpecieLinkContructor

• After you install Python by your method of preference install requirements:

pip install -r requirements.txt

Third step: Run the program

• To run the program is just as simple as:

python gbifSpecieLinkContructor.py path_to_dataset

The default path to save the output file is the working directory.

• To print the help message on the options available

python gbifSpecieLinkContructor.py --help