bioscan_anospp_metadata

Partner metadata handling for BIOSCAN and ANOSPP projects

Setup

To set up, execute in terminal

git clone git@github.com:amakunin/bioscan_anospp_metadata.git
cd bioscan_anospp_metadata
conda env create -f work/env.yml
conda activate bioscan_metadata_dev
mkdir results

Copy manifest to validate somewhere in results directory

To run, execute in terminal

jupyter notebook

Then, in browser at localhost:8888,

• navigate to work/validate_bioscan.ipynb or work/validate_anospp.ipynb
• run all cells - note this will take a while on the first time as NCBI Taxonomy is downloaded to work/taxdump.tar.gz
• in the first cell of "Validation" section, replace fn value with path to your manifest
• running the cell should yield the validation report

NB keep track of user_agent value in Nominatim function for geocoding