Partner metadata handling for BIOSCAN and ANOSPP projects
To set up, execute in terminal
git clone [email protected]:amakunin/bioscan_anospp_metadata.git
cd bioscan_anospp_metadata
conda env create -f work/env.yml
conda activate bioscan_metadata_dev
mkdir resultsCopy 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.ipynborwork/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
fnvalue 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