From 153b7bc8eb7fd193e847ef7d99d789f81d795bbb Mon Sep 17 00:00:00 2001
From: Brennan Brouillette <brennan.brouillette@computationalgenomics.ca>
Date: Wed, 14 Jun 2023 01:04:49 -0400
Subject: [PATCH] patch: - temp file ownership setting, testing only - check
 for failed flushed files

---
 Makefile                                 | 10 +++++-----
 src/api/tests/build/api/variants_test.go |  9 ++++++---
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index 367ffde..de2a311 100644
--- a/Makefile
+++ b/Makefile
@@ -51,27 +51,27 @@ init-vendor:
 init-data-dirs:
 	mkdir -p ${GOHAN_API_DRS_BRIDGE_HOST_DIR}
 	chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_DRS_BRIDGE_HOST_DIR}
-	chmod -R 770 ${GOHAN_API_DRS_BRIDGE_HOST_DIR}
+	chmod -R 777 ${GOHAN_API_DRS_BRIDGE_HOST_DIR}
 
 	mkdir -p ${GOHAN_DRS_DATA_DIR}
 	chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_DRS_DATA_DIR}
-	chmod -R 770 ${GOHAN_DRS_DATA_DIR}
+	chmod -R 777 ${GOHAN_DRS_DATA_DIR}
 
 	mkdir -p ${GOHAN_ES_DATA_DIR}
 	chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_ES_DATA_DIR}
-	chmod -R 770 ${GOHAN_ES_DATA_DIR}
+	chmod -R 777 ${GOHAN_ES_DATA_DIR}
 
 	@# tmp:
 	@# (setup for when gohan needs to preprocess vcf's at ingestion time):
 	mkdir -p ${GOHAN_API_VCF_PATH}
 	mkdir -p ${GOHAN_API_VCF_PATH}/tmp
 	chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_VCF_PATH}
-	chmod -R 770 ${GOHAN_API_VCF_PATH}/tmp
+	chmod -R 777 ${GOHAN_API_VCF_PATH}/tmp
 
 	mkdir -p ${GOHAN_API_GTF_PATH}
 	mkdir -p ${GOHAN_API_GTF_PATH}/tmp
 	chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_GTF_PATH}
-	chmod -R 770 ${GOHAN_API_GTF_PATH}/tmp
+	chmod -R 777 ${GOHAN_API_GTF_PATH}/tmp
 	
 	@echo ".. done!"
 
diff --git a/src/api/tests/build/api/variants_test.go b/src/api/tests/build/api/variants_test.go
index d5cff9c..d5eff4d 100644
--- a/src/api/tests/build/api/variants_test.go
+++ b/src/api/tests/build/api/variants_test.go
@@ -166,10 +166,13 @@ func TestIngest(t *testing.T) {
 		if stats.NumAdded == stats.NumFlushed {
 			fmt.Println("Done, moving on..")
 			break
-		} else {
-			// pause
-			time.Sleep(3 * time.Second)
 		}
+		if stats.NumFailed > 0 {
+			log.Fatal("More than one variant failed to flush")
+		}
+
+		// pause
+		time.Sleep(3 * time.Second)
 	}
 
 	// todo: verify demo vcf was properly ingested