get NLCD values and nearby OSM features for Alaska air study

.gitignore

@@ -13,6 +13,9 @@ googlemaps-api-key.txt
 bin
 
 cachedir
+
+sample_annotator/cache/
+
 examples/outputs
 
 temp/

make-gold-cache.Makefile

@@ -13,6 +13,12 @@ local/gold-studies.tsv: downloads/goldData.xlsx
 		--sheet-name Study \
 		--output-file $@
 
+local/gold-biosamples.tsv: downloads/goldData.xlsx
+	poetry run python sample_annotator/file_utils/xlsx_to_tsv.py \
+		--excel-file $< \
+		--sheet-name Study \
+		--output-file $@
+
 local/gold-study-ids.txt: local/gold-studies.tsv
 	# without the grep filter, this introduces some noise (non-id rows)
 	tail -n +2 $< | cut -f 1 | sort | grep 'Gs' > $@
@@ -49,4 +55,26 @@ load-gold-biosamples-into-mongo: local/gold-study-ids-subset.txt
 #		--biosample-output-file local/gold-biosamples-only.json \
 #		--project-output-file local/gold-projects-only.json \
 #		--remove-contacts \
-#		--remove-nulls
+#		--remove-nulls
+
+local/gold-emp500-study-id.txt:
+	echo "Gs0154244" > $@
+	sleep 1
+
+local/gold-emp500-cache.json: local/gold-emp500-study-id.txt
+	# ~ 3 seconds/uncached study
+	# GOLD has ~ 63k studies
+	# < 2 days to fetch all studies ?
+	poetry run python sample_annotator/clients/gold_client.py \
+		--verbose \
+		fetch-studies \
+		--output-format json \
+		--output $@ \
+		--include-biosamples \
+		--authentication-file config/gold-key.txt \
+		$<
+
+local/gold-emp500-cache.tsv: local/gold-emp500-cache.json
+	poetry run python sample_annotator/parse_biosample_metadata_from_gold_study.py \
+		--input-file $< \
+		--output-file $@