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Cope with no species excludes #8

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Merged
mdales merged 1 commit into from
May 8, 2025
Merged

Cope with no species excludes #8

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2 changes: 1 addition & 1 deletion aoh-calculator
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Submodule aoh-calculator updated 4 files
+26 −8 aohcalc.py
+23 −10 habitat_process.py
+1 −1 summaries/species_richness.py
+17 −12 validation/collate_data.py
12 changes: 9 additions & 3 deletions prepare_species/extract_species_data_psql.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,6 @@
LEFT JOIN red_list_category_lookup ON red_list_category_lookup.id = assessments.red_list_category_id
WHERE
assessments.latest = true
AND assessments.sis_taxon_id NOT IN %s
AND assessment_scopes.scope_lookup_id = 15 -- global assessments only
AND taxons.class_name = %s
AND taxons.infra_type is NULL -- no subspecies
Expand Down Expand Up @@ -435,7 +434,7 @@ def extract_data_per_species(
connection = psycopg2.connect(DB_CONFIG)
cursor = connection.cursor()

excludes = []
excludes = tuple([])
if excludes_path is not None:
try:
df = pd.read_csv(excludes_path)
Expand All @@ -449,7 +448,14 @@ def extract_data_per_species(
for era, presence in [("current", (1, 2))]:
era_output_directory_path = os.path.join(output_directory_path, era)

cursor.execute(MAIN_STATEMENT, (excludes, class_name,))
# You can't do NOT IN on an empty list in SQL
if excludes:
exclude_statement = "AND assessments.sis_taxon_id NOT IN %s"
statement = MAIN_STATEMENT + exclude_statement
cursor.execute(statement, (class_name, excludes))
else:
cursor.execute(MAIN_STATEMENT, (class_name,))

# This can be quite big (tens of thousands), but in modern computer term is quite small
# and I need to make a follow on DB query per result.
results = cursor.fetchall()
Expand Down
2 changes: 1 addition & 1 deletion scripts/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ python3 ./prepare_layers/convert_crosswalk.py --original ${PWD}/data/crosswalk_b
# Get species data per taxa from IUCN data
for TAXA in "${TAXALIST[@]}"
do
python3 ./prepare_species/extract_species_data_psql.py --class ${TAXA} --output ${DATADIR}/species-info/${TAXA}/ --projection "ESRI:54009"
python3 ./prepare_species/extract_species_data_psql.py --class ${TAXA} --output ${DATADIR}/species-info/${TAXA}/ --projection "ESRI:54009" --excludes ${DATADIR}/SpeciesList_generalisedRangePolygons.csv
done

if [ -f data/BL_Species_Elevations_2023.csv ]; then
Expand Down