single gold tool

.gitignore

@@ -13,6 +13,7 @@ googlemaps-api-key.txt
 bin
 
 cachedir
+cache_from_local_mongodb
 examples/outputs
 
 temp/
@@ -63,7 +64,7 @@ sphinx/_build/*
 
 # Cacheing
 tests/cachedir/
-./cachedir/
+cachedir
 
 # https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
 

make-gold-cache.Makefile

@@ -4,7 +4,7 @@
 
 RUN=poetry run
 
-.PHONY: load-gold-biosamples-into-mongo
+.PHONY: gold-to-mongo-all gold-to-mongo-clean load-gold-biosamples-into-mongo rebuild-gold-cache-from-mongodb
 
 gold-to-mongo-all: gold-to-mongo-clean load-gold-biosamples-into-mongo
 
@@ -39,13 +39,31 @@ local/gold-study-ids-with-biosamples.txt: downloads/goldData.xlsx
 #	# 		--purge-diskcache
 #	# 		--env-file
 
+#load-gold-biosamples-into-mongo: local/gold-study-ids-with-biosamples.txt
+#	$(RUN) gold-to-mongo \
+#		--authentication-file config/gold-key.txt \
+#		--cache-dir cache_from_local_mongodb \
+#		--env-file local/.env.27778 \
+#		--log-failures-to-file local/gold-to-mongo-failures.json \
+#		--mongo-uri "mongodb://localhost:27778/staging?directConnection=true&authMechanism=DEFAULT&authSource=admin" \
+#		--study-ids-file $<
+
+
 load-gold-biosamples-into-mongo: local/gold-study-ids-with-biosamples.txt
 	$(RUN) gold-to-mongo \
 		--authentication-file config/gold-key.txt \
+		--cache-dir cache_from_local_mongodb \
 		--log-failures-to-file local/gold-to-mongo-failures.json \
-		--mongo-uri "mongodb://localhost:27017/gold_metadata" \
+		--mongo-uri "mongodb://localhost:27017/gold_metadata_2" \
 		--study-ids-file $<
 
+rebuild-gold-cache-from-mongodb:
+	poetry run rebuild-gold-cache \
+		--mongo-uri "mongodb://localhost:27017/gold_metadata" \
+		--authentication-file config/gold-key.txt \
+		--cache-dir cache_from_local_mongodb
+
+
 local/gold-cache.json: local/gold-studies.tsv
 	# ~ 3 seconds/uncached study
 	# GOLD has ~ 63k studies

pyproject.toml

@@ -77,4 +77,5 @@ cache-gold = "sample_annotator.clients.gold_client:main"
 extract-study-ids-with-biosamples = "sample_annotator.file_utils.extract_study_ids_with_biosamples:main"
 gold-to-mongo = "sample_annotator.gold_to_mongo:main"
 rel_to_oxygen_example = "sample_annotator.rel_to_oxygen_example:cli"
-xlsx-to-tsv = "sample_annotator.file_utils.xlsx_to_tsv:xlsx_to_tsv"
+xlsx-to-tsv = "sample_annotator.file_utils.xlsx_to_tsv:xlsx_to_tsv"
+rebuild-gold-cache = "sample_annotator.rebuild_gold_cache:rebuild_gold_cache"