Merge pull request #45 from bento-platform/qa/v2.6

v2.6.5-rc1

Makefile

@@ -26,7 +26,7 @@ OS_NAME := $(shell uname -s | tr A-Z a-z)
 export OS_NAME
 
 #>>>
-# provide host-level user id as an 
+# provide host-level user id as an
 # environment variable for containers to use
 #<<<
 CURRENT_UID := $(shell id -u)
@@ -47,7 +47,7 @@ export EXECUTED_NOW
 init-chord-services:
 	@echo "-- Initializing CHORD service configuration files  --"
 
-	@# copy services json to the microservices that need it	
+	@# copy services json to the microservices that need it
 	@echo "- Providing a complete chord_services.json to lib/[logging, service-registry, wes]"
 	@envsubst < ${PWD}/etc/templates/chord_services.example.json > $(PWD)/lib/logging/chord_services.json;
 	@envsubst < ${PWD}/etc/templates/chord_services.example.json > $(PWD)/lib/service-registry/chord_services.json;
@@ -60,7 +60,7 @@ init-chord-services:
 # create non-repo directories
 #<<<
 .PHONY: init-dirs
-init-dirs: data-dirs 
+init-dirs: data-dirs
 	@echo "-- Initializing temporary and data directories --"
 	@echo "- Creating temporary secrets dir"
 	mkdir -p $(PWD)/tmp/secrets
@@ -203,7 +203,7 @@ auth-setup:
 #<<<
 run-all:
 	$(foreach SERVICE, $(SERVICES), \
-		$(MAKE) run-$(SERVICE) &) 
+		$(MAKE) run-$(SERVICE) &)
 
 	watch -n 2 'docker ps'
 
@@ -217,7 +217,7 @@ run-all:
 #<<<
 run-web-dev: clean-web
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate web
-run-public-dev: 
+run-public-dev:
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate public
 
 #>>>
@@ -247,22 +247,22 @@ run-katsu-dev: #clean-katsu
 # ...
 #	see docker-compose.dev.yaml
 #<<<
-run-federation-dev: 
+run-federation-dev:
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate federation
 
 #>>>
 # ...
 #	see docker-compose.dev.yaml
 #<<<
-run-wes-dev: 
+run-wes-dev:
 	#clean-wes
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate wes
 
 #>>>
 # ...
 #	see docker-compose.dev.yaml
 #<<<
-run-drs-dev: 
+run-drs-dev:
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate drs
 
 
@@ -271,7 +271,7 @@ run-drs-dev:
 #<<<
 run-%:
 	@# FreeBSD sed -i expects a suffix parameter for a backup file. Empty string
-	@# may be provided after a space which is incompatible with GNU sed (no 
+	@# may be provided after a space which is incompatible with GNU sed (no
 	@# space after -i). The solution here is to create a backup file and remove
 	@# it along with the working copy using a wildcard.
 	@if [[ $* == gateway ]]; then \
@@ -340,8 +340,8 @@ build-common-base:
 #<<<
 build-all:
 	$(foreach SERVICE, $(SERVICES), \
-		$(MAKE) build-$(SERVICE) &) 
-	
+		$(MAKE) build-$(SERVICE) &)
+
 	watch -n 2 'docker ps'
 
 
@@ -355,7 +355,7 @@ build-%:
 		exit 1; \
 	fi
 
-	@mkdir -p tmp/logs/${EXECUTED_NOW}/$* 
+	@mkdir -p tmp/logs/${EXECUTED_NOW}/$*
 	@echo "-- Building $* --" && \
 		docker-compose build --no-cache $* &> tmp/logs/${EXECUTED_NOW}/$*/build.log
 
@@ -418,10 +418,10 @@ clean-all:
 #<<<
 clean-%:
 	@mkdir -p tmp/logs/${EXECUTED_NOW}/$*
-	
+
 	@echo "-- Removing bentov2-$* container --" && \
 		docker rm bentov2-$* --force >> tmp/logs/${EXECUTED_NOW}/$*/clean.log 2>&1
-	
+
 	@# Clean public using native makefile
 	@if [[ $* == public ]]; then \
 		cd lib/bento_public && $(MAKE) clean-public ; \
@@ -495,7 +495,7 @@ run-unit-tests:
 run-integration-tests:
 	@echo "-- Running integration tests! --"
 	@$(PWD)/etc/tests/integration/run_tests.sh 10 firefox False
-	
+
 
 
 # -- Utils --
@@ -520,3 +520,13 @@ clean-dangling-images:
 	docker rmi $(docker images -f "dangling=true" -q)
 clean-exited-containers:
 	docker rm $(docker ps -a -f status=exited -q)
+
+#>>>
+# patch records in DRS database after the change in path from /drs/chord_drs/ to /drs/bento_drs/
+# This needs to be done only once, for installations prior v2.6.5
+#<<<
+patch-drs-db:
+	sqlite3 ${BENTOV2_DRS_PROD_VOL_DIR}/db/db.sqlite3 \
+		"UPDATE drs_object SET location = REPLACE(location, 'chord_drs', 'bento_drs')" && \
+	sqlite3 ${BENTOV2_DRS_DEV_VOL_DIR}/db/db.sqlite3 \
+		"UPDATE drs_object SET location = REPLACE(location, 'chord_drs', 'bento_drs')"

docker-compose.dev.yaml

@@ -16,13 +16,13 @@ services:
         BENTO_WEB_USER: ${CURRENT_UID}
     volumes:
       - ./lib/web/bento_web:/web/bento_web
-    # Execute npm build/install and watch, and 
+    # Execute npm build/install and watch, and
     # nginx "listener" upon container startup
     entrypoint: sh /web/dev_startup.sh
     extends:
       file: docker-compose.yaml
       service: web
-      
+
   public:
     extends:
       file: ./lib/bento_public/docker-compose.yaml
@@ -33,7 +33,7 @@ services:
 
   gateway:
     # Override network aliases, adding BENTOV2_AUTH_DOMAIN
-    networks: 
+    networks:
         bridge-net:
           aliases:
             - ${BENTOV2_DOMAIN}
@@ -47,14 +47,14 @@ services:
     build:
       context: $PWD/lib/katsu
       dockerfile: Dockerfile.dev
-    networks: 
+    networks:
       - bridge-net
     depends_on:
       - katsu-db
     extends:
       file: $PWD/lib/katsu/docker-compose.katsu.yaml
       service: katsu
-    volumes: 
+    volumes:
       - ./lib/katsu/katsu:/app/katsu
       - ${BENTOV2_KATSU_DEV_WES_VOL_TMP_DIR}:/wes/tmp
     environment:
@@ -63,7 +63,7 @@ services:
       - "${BENTOV2_KATSU_EXTERNAL_PORT}:${BENTOV2_KATSU_INTERNAL_PORT}"
 
   katsu-db:
-    networks: 
+    networks:
       - bridge-net
     extends:
       file: $PWD/lib/katsu/docker-compose.katsu.yaml
@@ -76,14 +76,14 @@ services:
     build:
       context: $PWD/lib/federation
       dockerfile: Dockerfile.dev
-    environment: 
+    environment:
       - CHORD_DEBUG=${BENTOV2_FEDERATION_DEV_DEBUG}
-    networks: 
+    networks:
       - bridge-net
     extends:
       file: $PWD/lib/federation/docker-compose.federation.yaml
       service: federation
-    volumes: 
+    volumes:
       - ./lib/federation/bento_federation_service:/federation/bento_federation_service
     ports:
       - "5000:5000"
@@ -94,7 +94,7 @@ services:
     build:
       context: $PWD/lib/wes
       dockerfile: Dockerfile.dev
-    networks: 
+    networks:
       - bridge-net
     environment:
       - CHORD_DEBUG=true
@@ -108,22 +108,27 @@ services:
       - ${BENTOV2_WES_DEV_DROP_BOX_VOL_DIR}:/data
     ports:
       - "5000:5000"
-  
+
   drs:
     build:
       context: $PWD/lib/drs
-      dockerfile: Dockerfile
-    networks: 
+      dockerfile: Dockerfile.dev
+    networks:
       - bridge-net
     extends:
       file: $PWD/lib/drs/docker-compose.drs.yaml
       service: drs
     ports:
       - "${BENTOV2_DRS_EXTERNAL_PORT}:5000"
     volumes:
+      - ./lib/drs/bento_drs:/drs/bento_drs
+      - ./lib/drs/startup.sh:/drs/bento_drs/chord_drs/startup.sh:ro
       # Override main drs data directory
       - ${BENTOV2_DRS_DEV_VOL_DIR}:/drs/bento_drs/data
       - ${BENTOV2_DRS_DEV_WES_VOL_DIR}:/wes/tmp
-networks: 
+    command: >
+      sh -c /drs/bento_drs/chord_drs/startup.sh
+
+networks:
   bridge-net:
     external: true

lib/drs/Dockerfile

@@ -34,7 +34,7 @@ RUN git fetch && \
 RUN ["pip", "install", "-r", "requirements.txt"]
 
 # Run
-WORKDIR /drs/bento_drs/bento_drs
+WORKDIR /drs/bento_drs/chord_drs
 
 COPY startup.sh ./startup.sh
 

lib/drs/Dockerfile.dev

@@ -0,0 +1,24 @@
+ARG BASE_IMAGE
+ARG BASE_IMAGE_VERSION
+
+FROM "${BASE_IMAGE}:${BASE_IMAGE_VERSION}"
+
+# TODO: change USER
+USER root
+
+RUN mkdir /drs && \
+    mkdir /wes;
+
+RUN echo "Building DRS in Development Mode";
+
+RUN mkdir -p /drs/bento_drs/data/obj && \
+    mkdir -p /drs/bento_drs/data/db;
+
+WORKDIR /drs/bento_drs
+
+# Remove comment if custom requirements are needed
+COPY ./bento_drs/requirements.txt ./requirements.txt
+
+RUN ["pip", "install", "-r", "requirements.txt"]
+
+WORKDIR /drs/bento_drs/chord_drs

lib/drs/startup.sh

@@ -2,7 +2,7 @@ cd ../data;
 mkdir db;
 mkdir obj;
 
-cd ../bento_drs;
+cd ../chord_drs;
 flask db upgrade;
 
 # call variant endpoint to trigger init