Merge pull request #34 from bento-platform/releases/v3.7

[WIP] v3.7 rc-1

.github/workflows/api.build.yml

@@ -6,6 +6,7 @@ on:
   pull_request:
     branches:
       - master
+      - "releases/**" # temp
   push:
     branches:
       - master

.gitignore

@@ -1,4 +1,5 @@
 .vscode
+.DS_store
 
 */bin
 */obj
@@ -31,7 +32,7 @@ authorization/policy.rego
 authorization/*.policy.rego
 
 # temp test file
-src/tests/common/test.config.yml
+src/api/tests/common/test.config.yml
 
 # executables
 

Makefile

@@ -1,22 +1,25 @@
 # Makefile for Gohan
 
-# import global variables
-env ?= .env
-
 #>>>
 # set default shell
 #<<<
 SHELL = bash
 
-include $(env)
-export $(shell sed 's/=.*//' $(env))
-
 # export host user IDs for more secure
 # containerization and volume mounting
 export HOST_USER_UID=$(shell id -u)
 export HOST_USER_GID=$(shell id -g)
 export OS_NAME=$(shell uname -s | tr A-Z a-z)
 
+export GOOS=${OS_NAME}
+export GOARCH=$(shell if [ "$(uname -m)" == "aarch64" ]; then echo arm64; else echo $(uname -m); fi | tr A-Z a-z)
+
+# import global variables
+env ?= .env
+
+include $(env)
+export $(shell sed 's/=.*//' $(env))
+
 
 # initialize services
 init:
@@ -43,8 +46,7 @@ init-networks:
 
 init-vendor:
 	@echo "Initializing Go Module Vendor"
-	cd src/api && go mod vendor
-	cd src/tests && go mod tidy && go mod vendor
+	cd src/api && go mod tidy && go mod vendor
 
 init-data-dirs:
 	mkdir -p ${GOHAN_API_DRS_BRIDGE_HOST_DIR}
@@ -76,7 +78,7 @@ init-data-dirs:
 
 # Run
 run-all:
-	docker-compose -f docker-compose.yaml up -d --force-recreate
+	docker-compose -f docker-compose.yaml up -d
 
 run-dev-all:
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate
@@ -85,8 +87,7 @@ run-dev-%:
 	docker-compose -f docker-compose.dev.yaml up -d --force-recreate $*
 
 run-%:
-	docker-compose -f docker-compose.yaml up -d --force-recreate $*
-
+	docker-compose -f docker-compose.yaml up -d $*
 
 
 # Build
@@ -111,10 +112,6 @@ build-api: stop-api clean-api
 	@echo "-- Building Golang-Api-Alpine Container --"
 	docker-compose -f docker-compose.yaml build api
 
-build-drs: stop-drs clean-drs
-	@echo "-- Building DRS Container --"
-	docker-compose -f docker-compose.yaml build drs
-
 build-authz: stop-authz clean-authz
 	@echo "-- Building Authorization Container --"
 	docker-compose -f docker-compose.yaml build authorization
@@ -130,7 +127,7 @@ stop-%:
 
 
 # Clean up
-clean-all: clean-networks clean-api clean-gateway clean-drs
+clean-all: clean-networks clean-api clean-gateway
 
 clean-networks:
 	docker network remove ${GOHAN_DOCKER_NET} &
@@ -144,10 +141,6 @@ clean-api:
 	docker rm ${GOHAN_API_CONTAINER_NAME} --force; \
 	docker rmi ${GOHAN_API_IMAGE}:${GOHAN_API_VERSION} --force;
 
-clean-drs:
-	docker rm ${GOHAN_DRS_CONTAINER_NAME} --force; \
-	docker rmi ${GOHAN_DRS_IMAGE}:${GOHAN_DRS_VERSION} --force;
-
 clean-authz:
 	docker rm ${GOHAN_AUTHZ_OPA_CONTAINER_NAME} --force; \
 	docker rmi ${GOHAN_AUTHZ_OPA_IMAGE}:${GOHAN_AUTHZ_OPA_IMAGE_VERSION} --force;
@@ -205,14 +198,15 @@ clean-api-drs-bridge-data:
 ## Tests
 test-api-dev: prepare-test-config
 	@# Run the tests
+	cd src/api && \
 	go clean -cache && \
-	go test tests/integration/... -v
+	go test ./tests/integration/... -v
 
 prepare-test-config:
 	@# Prepare environment variables dynamically via a JSON file 
 	@# since xUnit doens't support loading env variables natively
-	envsubst < ./etc/test.config.yml.tpl > ./src/tests/common/test.config.yml
+	envsubst < ./etc/test.config.yml.tpl > ./src/api/tests/common/test.config.yml
 
 clean-tests:
 	@# Clean up
-	rm ./src/tests/common/test.config.yml
+	rm ./src/api/tests/common/test.config.yml

README.md

@@ -58,7 +58,6 @@
 
   # build services
   make build-gateway 
-  make build-drs
   make build-api 
 
   # run services
@@ -148,7 +147,6 @@ make run-kibana
 
 Run 
 ```
-make build-drs
 make run-drs
 ```
 
@@ -320,6 +318,7 @@ Requests
 >   - upperBound : **number**
 >   - reference : **string** `an allele ( "A" | "C" | "G" | "T" | "N" or some combination thereof )`
 >   - alternative : **string** `an allele`
+>   - alleles : **string** `ordered comma-deliminated list of alleles (max: 2)`
 >   - ids : **string** `(a comma-deliminated list of variant ID alphanumeric codes)`
 >   - size : **number** `(maximum number of results per id)`
 >   - sortByPosition : **string** `(<empty> | asc | desc)`
@@ -334,6 +333,7 @@ Requests
 >   - upperBound : **number**
 >   - reference : **string** `an allele`
 >   - alternative : **string** `an allele`
+>   - alleles : **string** `ordered comma-deliminated list of alleles (max: 2)`
 >   - ids : **string** `(a comma-deliminated list of variant ID alphanumeric codes)`
 >   - genotype : **string** `( "HETEROZYGOUS" | "HOMOZYGOUS_REFERENCE" | "HOMOZYGOUS_ALTERNATE" )`
 
@@ -344,6 +344,7 @@ Requests
 >   - upperBound : **number**
 >   - reference : **string** `an allele`
 >   - alternative : **string** `an allele`
+>   - alleles : **string** `ordered comma-deliminated list of alleles (max: 2)`
 >   - ids : **string** `(comma-deliminated list of sample ID alphanumeric codes)`
 >   - size : **number** `(maximum number of results per id)`
 >   - sortByPosition : **string** `(<empty> | asc | desc)`
@@ -357,6 +358,7 @@ Requests
 >   - upperBound : **number**
 >   - reference : **string** `an allele`
 >   - alternative : **string** `an allele`
+>   - alleles : **string** `ordered comma-deliminated list of alleles (max: 2)`
 >   - ids : **string** `(comma-deliminated list of sample ID alphanumeric codes)`
 >   - genotype : **string** `( "HETEROZYGOUS" | "HOMOZYGOUS_REFERENCE" | "HOMOZYGOUS_ALTERNATE" )`
 >
@@ -384,6 +386,7 @@ Generalized Response Body Structure
 >                    "pos": `number`,
 >                    "ref": `[]string`,  // list of alleles
 >                    "alt": `[]string`,  // list of alleles
+>                    "alleles": `[]string`,  // ordereed list of alleles
 >                    "info": [
 >                        {
 >                            "id": `string`,

docker-compose.yaml

@@ -134,16 +134,6 @@ services:
       retries: 3
 
   drs:
-    build:
-      context: $PWD/drs
-      args:
-        BASE_IMAGE: ${GOHAN_DRS_BASE_IMAGE}
-        BASE_IMAGE_VERSION: ${GOHAN_DRS_BASE_IMAGE_VERSION}
-        REPO: ${GOHAN_DRS_REPO}
-        BRANCH: ${GOHAN_DRS_BRANCH}
-        TAG: ${GOHAN_DRS_TAG}
-        HOST_USER_UID: ${HOST_USER_UID}
-        HOST_USER_GID: ${HOST_USER_GID}
     mem_limit: ${GOHAN_DRS_MEM_LIM} # for mem_limit to work, make sure docker-compose is v2.4
     cpus: ${GOHAN_DRS_CPUS}
     cpu_shares: 512
@@ -159,7 +149,6 @@ services:
       - DATA=/drs/bento_drs/data/obj/  # DRS file objects, vs. the database
       - INTERNAL_PORT=${GOHAN_DRS_INTERNAL_PORT}
     volumes:
-      - ./drs/startup.sh:/drs/bento_drs/startup.sh
       - ${GOHAN_DRS_DATA_DIR}:/drs/bento_drs/data
       - ${GOHAN_API_DRS_BRIDGE_HOST_DIR}:${GOHAN_DRS_API_DRS_BRIDGE_DIR_CONTAINERIZED}
     healthcheck:

etc/example.env

@@ -2,11 +2,11 @@
 
 GOHAN_DEBUG=false
 GOHAN_SERVICE_CONTACT=[email protected]
-GOHAN_SEMVER=3.6.0
+GOHAN_SEMVER=3.6.1
 GOHAN_SERVICES="gateway api elasticsearch kibana drs authorization"
 
-GOOS=linux
-GOARCH=amd64
+# GOOS=linux
+# GOARCH=amd64
 
 # Host
 GOHAN_PUBLIC_PROTO=https
@@ -38,7 +38,7 @@ GOHAN_GATEWAY_CPUS=2
 GOHAN_API_IMAGE=gohan-api
 GOHAN_API_VERSION=latest
 
-GOHAN_API_BUILDER_BASE_IMAGE=golang:1.15.15-alpine3.14
+GOHAN_API_BUILDER_BASE_IMAGE=golang:1.19-alpine
 GOHAN_API_BASE_IMAGE=alpine
 
 GOHAN_API_CONTAINER_NAME=gohan-api
@@ -111,13 +111,8 @@ GOHAN_KB_ES_PORT=9200
 
 
 # DRS
-GOHAN_DRS_REPO=https://github.com/bento-platform/bento_drs
-GOHAN_DRS_BRANCH=master
-GOHAN_DRS_TAG=v0.5.1
-GOHAN_DRS_BASE_IMAGE=python
-GOHAN_DRS_BASE_IMAGE_VERSION=3.6-alpine
-GOHAN_DRS_IMAGE=gohan-drs
-GOHAN_DRS_VERSION=0.0.1
+GOHAN_DRS_IMAGE=ghcr.io/bento-platform/bento_drs
+GOHAN_DRS_VERSION=0.7.0
 GOHAN_DRS_CONTAINER_NAME=gohan-drs
 GOHAN_DRS_INTERNAL_PORT=5000
 GOHAN_DRS_EXTERNAL_PORT=6000

src/api/Dockerfile

@@ -43,7 +43,7 @@ RUN apk --update add ncurses-dev && \
     rm -rf htslib samtools
 
 # Build gohan api
-RUN CGO_ENABLED=0 && \
+RUN go mod vendor && \
     go build -ldflags="-s -w" -o gohan_api 
     # Temporarily disabling: 
     #&& \

src/api/contexts/contexts.go

@@ -1,9 +1,9 @@
 package contexts
 
 import (
-	"api/models"
-	"api/services"
-	variantsService "api/services/variants"
+	"gohan/api/models"
+	"gohan/api/services"
+	variantsService "gohan/api/services/variants"
 
 	es7 "github.com/elastic/go-elasticsearch/v7"
 	"github.com/labstack/echo"