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Add more guards to run.sh #22

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83 changes: 50 additions & 33 deletions scripts/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -107,47 +107,64 @@ if [ -f "${DATADIR}"/BL_Species_Elevations_2023.csv ]; then
python3 ./prepare_species/apply_birdlife_data.py --geojsons "${DATADIR}"/species-info/AVES --overrides "${DATADIR}"/BL_Species_Elevations_2023.csv
fi

echo "Generating AoH task list..."
python3 ./utils/aoh_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/aohbatch.csv
if [ ! -d "${DATADIR}"/aohs ]; then
echo "Generating AoH task list..."
python3 ./utils/aoh_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/aohbatch.csv

echo "Generating AoHs..."
littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv "${AOH_CALC_BIN}"
echo "Generating AoHs..."
littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/aohbatch.log -c "${DATADIR}"/aohbatch.csv "${AOH_CALC_BIN}"
fi

# Calculate predictors from AoHs
echo "Generating species richness..."
aoh-species-richness --aohs_folder "${DATADIR}"/aohs/current/ \
--output "${DATADIR}"/summaries/species_richness.tif
echo "Generating endemism..."
aoh-endemism --aohs_folder "${DATADIR}"/aohs/current/ \
--species_richness "${DATADIR}"/summaries/species_richness.tif \
--output "${DATADIR}"/summaries/endemism.tif
if [ ! -f "${DATADIR}"/summaries/species_richness.tif ]; then
echo "Generating species richness..."
aoh-species-richness --aohs_folder "${DATADIR}"/aohs/current/ \
--output "${DATADIR}"/summaries/species_richness.tif
fi
if [ ! -f "${DATADIR}"/summaries/endemism.tif ]; then
echo "Generating endemism..."
aoh-endemism --aohs_folder "${DATADIR}"/aohs/current/ \
--species_richness "${DATADIR}"/summaries/species_richness.tif \
--output "${DATADIR}"/summaries/endemism.tif
fi

# Aoh Validation
echo "Collating validation data..."
aoh-collate-data --aoh_results "${DATADIR}"/aohs/current/ \
--output "${DATADIR}"/validation/aohs.csv
echo "Calculating model validation..."
aoh-validate-prevalence --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--output "${DATADIR}"/validation/model_validation.csv
if [ ! -f "${DATADIR}"/validation/aohs.csv ]; then
echo "Collating validation data..."
aoh-collate-data --aoh_results "${DATADIR}"/aohs/current/ \
--output "${DATADIR}"/validation/aohs.csv
fi
if [ ! -f "${DATADIR}"/validation/model_validation.csv ]; then
echo "Calculating model validation..."
aoh-validate-prevalence --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--output "${DATADIR}"/validation/model_validation.csv
fi

for TAXA in "${TAXALIST[@]}"
do
echo "Fetching GBIF data for ${TAXA}..."
aoh-fetch-gbif-data --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--taxa "${TAXA}" \
--output_dir "${DATADIR}"/validation/occurrences/
echo "Validating occurrences for ${TAXA}..."
aoh-validate-occurrences --gbif_data_path "${DATADIR}"/validation/occurrences/"${TAXA}" \
--species_data "${DATADIR}"/species-info/"${TAXA}"/current/ \
--aoh_results "${DATADIR}"/aohs/current/"${TAXA}"/ \
--output "${DATADIR}"/validation/occurrences/"${TAXA}".csv
if [ ! -f "${DATADIR}"/validation/occurrences/"${TAXA}".csv ]; then
echo "Fetching GBIF data for ${TAXA}..."
aoh-fetch-gbif-data --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--taxa "${TAXA}" \
--output_dir "${DATADIR}"/validation/occurrences/
echo "Validating occurrences for ${TAXA}..."
aoh-validate-occurrences --gbif_data_path "${DATADIR}"/validation/occurrences/"${TAXA}" \
--species_data "${DATADIR}"/species-info/"${TAXA}"/current/ \
--aoh_results "${DATADIR}"/aohs/current/"${TAXA}"/ \
--output "${DATADIR}"/validation/occurrences/"${TAXA}".csv
fi
done

# Threats
echo "Generating threat task list..."
python3 ./utils/threats_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/threatbatch.csv

echo "Generating threat rasters..."
littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/threatbatch.log -c "${DATADIR}"/threatbatch.csv "${PYTHON_BIN}" -- ./threats/threat_processing.py
if [ ! -d "${DATADIR}"/threat_rasters ]; then
echo "Generating threat task list..."
python3 ./utils/threats_generator.py --input "${DATADIR}"/species-info --datadir "${DATADIR}" --output "${DATADIR}"/threatbatch.csv

echo "Summarising threats..."
python3 ./threats/threat_summation.py --threat_rasters "${DATADIR}"/threat_rasters --output "${DATADIR}"/threat_results
echo "Generating threat rasters..."
littlejohn -j "${PROCESS_COUNT}" -o "${DATADIR}"/threatbatch.log -c "${DATADIR}"/threatbatch.csv "${PYTHON_BIN}" -- ./threats/threat_processing.py
fi
if [ ! -d "${DATADIR}"/threat_results ]; then
echo "Summarising threats..."
python3 ./threats/threat_summation.py --threat_rasters "${DATADIR}"/threat_rasters --output "${DATADIR}"/threat_results_tmp
mv "${DATADIR}"/threat_results_tmp "${DATADIR}"/threat_results
fi