Merge branch 'qa/v2.2.0'

Makefile

@@ -44,7 +44,7 @@ build-gateway: stop-gateway clean-gateway
 	echo "-- Building Gateway Container --"
 	docker-compose -f docker-compose.yaml build gateway
 
-build-api-go-alpine-binaries:
+build-api-binaries:
 	@echo "-- Building Golang-Api-Alpine Binaries --"
 
 	cd src/api && \
@@ -55,10 +55,10 @@ build-api-go-alpine-binaries:
 	cd ../.. && \
 	upx --brute bin/api_${GOOS}_${GOARCH}
 
-build-api-go-alpine-container: stop-api-go-alpine clean-api-go-alpine build-api-go-alpine-binaries
+build-api-container: stop-api clean-api build-api-binaries
 	@echo "-- Building Golang-Api-Alpine Container --"
 	cp bin/api_${GOOS}_${GOARCH} src/api
-	docker-compose -f docker-compose.yaml build api-go-alpine
+	docker-compose -f docker-compose.yaml build api
 	rm src/api/api_${GOOS}_${GOARCH}
 
 build-drs: stop-drs clean-drs
@@ -86,15 +86,7 @@ clean-gateway:
 	docker rm ${GOHAN_GATEWAY_CONTAINER_NAME} --force; \
 	docker rmi ${GOHAN_GATEWAY_IMAGE}:${GOHAN_GATEWAY_VERSION} --force;
 
-# clean-api:
-# 	docker rm ${GOHAN_API_CONTAINER_NAME} --force; \
-# 	docker rmi ${GOHAN_API_IMAGE}:${GOHAN_API_VERSION} --force;
-
-# clean-api-alpine:
-# 	docker rm ${GOHAN_API_CONTAINER_NAME} --force; \
-# 	docker rmi ${GOHAN_API_IMAGE}:${GOHAN_API_VERSION} --force;
-
-clean-api-go-alpine:
+clean-api:
 	rm -f bin/api_${GOOS}_${GOARCH}
 	docker rm ${GOHAN_API_CONTAINER_NAME} --force; \
 	docker rmi ${GOHAN_API_IMAGE}:${GOHAN_API_VERSION} --force;
@@ -108,6 +100,7 @@ clean-authz:
 	docker rmi ${GOHAN_AUTHZ_OPA_IMAGE}:${GOHAN_AUTHZ_OPA_IMAGE_VERSION} --force;
 
 
+
 ## -- WARNING: DELETES ALL LOCAL ELASTICSEARCH DATA
 clean-elastic-data:
 	docker-compose -f docker-compose.yaml down

README.md

@@ -388,7 +388,7 @@ Local Release:
  From the project root, run 
 
 ```
-make build-api-go-alpine-binaries
+make build-api-binaries
 ```
 
 
@@ -427,8 +427,8 @@ Containerized Alpine Release:
  When ready, build the `docker image` and spawn the `container` by running
 
 ```
-make build-api-go-alpine-container
-make run-api-go-alpine
+make build-api-container
+make run-api
 ```
 
  and the `docker-compose.yaml` file will handle the configuration.
@@ -445,7 +445,7 @@ All in all, run
 make run-elasticsearch 
 make run-drs
 make build-gateway && make run-gateway 
-make build-api-go-alpine && make run-api-go-alpine
+make build-api && make run-api
 
 # and optionally
 make run-kibana

docker-compose.dev.yaml

@@ -1,12 +1,12 @@
 version: '2.4'
 
 services:
-    api-go-alpine:
+    api:
         ports:
             - "${GOHAN_API_EXTERNAL_PORT}:${GOHAN_API_INTERNAL_PORT}"
         extends:
             file: docker-compose.yaml
-            service: api-go-alpine
+            service: api
 
 
     elasticsearch:

docker-compose.yaml

@@ -17,15 +17,15 @@ services:
       - "80:80"
       - "443:443"  
 
-  api-go-alpine:
+  api:
     build:
       context: $PWD/src/api
       args:
-        BASE_IMAGE: ${GOHAN_API_ALPINE_BASE_IMAGE}
+        BASE_IMAGE: ${GOHAN_API_BASE_IMAGE}
         API_EXECUTABLE_FILENAME: api_linux_amd64
         # also passed in as an ENV from within Dockerfile :
         GOHAN_API_INTERNAL_PORT: ${GOHAN_API_INTERNAL_PORT} 
-    image: ${GOHAN_API_GO_IMAGE}:${GOHAN_API_GO_VERSION}
+    image: ${GOHAN_API_IMAGE}:${GOHAN_API_VERSION}
     container_name: ${GOHAN_API_CONTAINER_NAME}
     networks:
       - bridge-net

etc/example.env

@@ -1,6 +1,6 @@
 ## Gohan Environment Variables
 
-GOHAN_SERVICES=gateway api-go-alpine elasticsearch kibana drs authorization
+GOHAN_SERVICES=gateway api elasticsearch kibana drs authorization
 
 # Host
 GOHAN_PUBLIC_PROTO=https
@@ -26,14 +26,8 @@ GOHAN_GATEWAY_CONTAINER_NAME=gohan-gateway
 GOHAN_API_IMAGE=gohan-api
 GOHAN_API_VERSION=latest
 
-GOHAN_API_GO_IMAGE=gohan-api
-GOHAN_API_GO_VERSION=latest
+GOHAN_API_BASE_IMAGE=alpine
 
-GOHAN_API_BASE_IMAGE=mcr.microsoft.com/dotnet/aspnet:3.1.13-buster-slim
-GOHAN_API_ALPINE_BASE_IMAGE=alpine
-
-GOHAN_API_SRC_DIR=./bin/Release/netcoreapp3.1/linux-x64/publish
-GOHAN_API_ALPINE_SRC_DIR=./bin/ReleaseAlpine/netcoreapp3.1/linux-musl-x64/publish
 GOHAN_API_CONTAINER_NAME=gohan-api
 GOHAN_API_SERVICE_HOST=0.0.0.0
 GOHAN_API_EXTERNAL_PORT=5000
@@ -57,9 +51,6 @@ GOHAN_API_AUTHZ_REQHEADS=X-CUSTOM-1,X-CUSTOM-2
 GOHAN_ES_USERNAME=elastic
 GOHAN_ES_PASSWORD=changeme!
 
-GOHAN_ES_PUBLIC_GATEWAY_PATH=/es
-GOHAN_ES_GATEWAY_PATH=/
-
 GOHAN_ES_BASE_IMAGE=elasticsearch
 GOHAN_ES_BASE_VERSION=7.10.1
 GOHAN_ES_CONTAINER_NAME=elasticsearch
@@ -108,8 +99,6 @@ GOHAN_DRS_BASIC_AUTH_PASSWORD=drspasswordchangeme!
 
 GOHAN_DRS_DATA_DIR=./data/drs
 
-GOHAN_DRS_PUBLIC_GATEWAY_PATH=/drs
-
 
 
 # AUTHORIZATION

src/api/middleware/calibratedBoundsMiddleware.go

@@ -17,17 +17,21 @@ func MandateCalibratedBounds(next echo.HandlerFunc) echo.HandlerFunc {
 			upperBoundPointer *int
 		)
 
+		// check for a 'lowerBound' query paramter
 		lowerBoundQP := c.QueryParam("lowerBound")
 		if len(lowerBoundQP) > 0 {
+			// try to convert to an integer
 			lb, conversionErr := strconv.Atoi(lowerBoundQP)
 			if conversionErr == nil {
 				lowerBound = lb
 				lowerBoundPointer = &lowerBound
 			}
 		}
 
+		// check for an 'upperBoundQP' query paramter
 		upperBoundQP := c.QueryParam("upperBound")
 		if len(upperBoundQP) > 0 {
+			// try to convert to an integer
 			ub, conversionErr := strconv.Atoi(upperBoundQP)
 			if conversionErr == nil {
 				upperBound = ub

src/api/middleware/chromosomeMiddleware.go

@@ -7,6 +7,9 @@ import (
 	"github.com/labstack/echo"
 )
 
+/*
+	Echo middleware to ensure a valid `chromosome` HTTP query parameter was provided
+*/
 func MandateChromosomeAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
 		// check for chromosome query parameter
@@ -16,6 +19,7 @@ func MandateChromosomeAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 			return echo.NewHTTPError(http.StatusBadRequest, "Missing 'chromosome' query parameter for querying!")
 		}
 
+		// verify:
 		i, conversionErr := strconv.Atoi(chromQP)
 		if conversionErr != nil {
 			// if invalid chromosome

src/api/middleware/genotypeMiddleware.go

@@ -9,11 +9,17 @@ import (
 	"github.com/labstack/echo"
 )
 
+/*
+	Echo middleware to ensure the validity of the optionally provided `genotype` HTTP query parameter
+*/
 func ValidatePotentialGenotypeQueryParameter(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		// check for a genotype query parameter
 		genotypeQP := c.QueryParam("genotype")
-
 		if len(genotypeQP) > 0 {
+			// validate that the genotype string
+			// converts to a valid GenotypeQuery
+			// (skips "UNCALLED" values)
 			_, genotypeErr := gq.CastToGenoType(genotypeQP)
 			if genotypeErr != nil {
 				return echo.NewHTTPError(http.StatusBadRequest, fmt.Sprintf("Invalid genotype query %s, %s", genotypeQP, genotypeErr))

src/api/middleware/sampleMiddleware.go

@@ -7,6 +7,9 @@ import (
 	"github.com/labstack/echo"
 )
 
+/*
+	Echo middleware to ensure a singular `id` HTTP query parameter was provided
+*/
 func MandateSampleIdsSingularAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
 		// check for id query parameter
@@ -20,6 +23,9 @@ func MandateSampleIdsSingularAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	}
 }
 
+/*
+	Echo middleware to ensure a pluralized `id` (spelled `ids`) HTTP query parameter was provided
+*/
 func MandateSampleIdsPluralAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
 		// check for id's query parameter

src/api/models/constants/main.go

@@ -1,9 +1,13 @@
 package constants
 
-type enumString string
-type enumInt int
+/*
+	Defines a set of base level
+	constants and enums to be used
+	throughout Gohan and it's
+	associated services.
+*/
+type GenotypeQuery string
+type SearchOperation string
+type SortDirection string
 
-type GenotypeQuery enumString
-type SearchOperation enumString
-
-type Zygosity enumInt
+type Zygosity int

src/api/models/constants/sort/main.go

@@ -0,0 +1,23 @@
+package sort
+
+import (
+	"api/models/constants"
+	"strings"
+)
+
+const (
+	Undefined  constants.SortDirection = ""
+	Ascending  constants.SortDirection = "asc"
+	Descending constants.SortDirection = "desc"
+)
+
+func CastToSortDirection(text string) constants.SortDirection {
+	switch strings.ToLower(text) {
+	case "asc":
+		return Ascending
+	case "desc":
+		return Descending
+	default:
+		return Undefined
+	}
+}

src/api/mvc/variants.go

@@ -17,6 +17,7 @@ import (
 	"api/models"
 	"api/models/constants"
 	gq "api/models/constants/genotype-query"
+	s "api/models/constants/sort"
 	"api/models/ingest"
 	esRepo "api/repositories/elasticsearch"
 	"api/utils"
@@ -322,7 +323,7 @@ func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool) error
 		}
 	}
 
-	sortByPosition := c.QueryParam("sortByPosition")
+	sortByPosition := s.CastToSortDirection(c.QueryParam("sortByPosition"))
 
 	includeSamplesInResultSetQP := c.QueryParam("includeSamplesInResultSet")
 	var (

src/api/repositories/elasticsearch/main.go

@@ -12,6 +12,7 @@ import (
 
 	c "api/models/constants"
 	gq "api/models/constants/genotype-query"
+	s "api/models/constants/sort"
 	z "api/models/constants/zygosity"
 
 	"github.com/elastic/go-elasticsearch"
@@ -21,7 +22,7 @@ func GetDocumentsContainerVariantOrSampleIdInPositionRange(es *elasticsearch.Cli
 	chromosome string, lowerBound int, upperBound int,
 	variantId string, sampleId string,
 	reference string, alternative string,
-	size int, sortByPosition string,
+	size int, sortByPosition c.SortDirection,
 	includeSamplesInResultSet bool, genotype c.GenotypeQuery) map[string]interface{} {
 
 	// begin building the request body.
@@ -163,28 +164,14 @@ func GetDocumentsContainerVariantOrSampleIdInPositionRange(es *elasticsearch.Cli
 	}
 
 	// set up sorting
-	sortDirection := "asc"
-	if sortByPosition != "" {
-		switch sortByPosition {
-		case "asc":
-			fmt.Println("Already set 'sortByPosition' keyword 'asc' to query")
-			break
-		case "desc":
-			fmt.Println("Setting 'sortByPosition' keyword 'desc' to query")
-			sortDirection = "desc"
-			break
-		default:
-			fmt.Printf("Found unknown 'sortByPosition' keyword : %s -- ignoring\n", sortByPosition)
-			break
-		}
-
-	} else {
-		fmt.Println("Found empty 'sortByPosition' keyword -- defaulting to 'asc'")
+	if sortByPosition == s.Undefined {
+		// default to ascending order
+		sortByPosition = s.Ascending
 	}
 
 	// append sorting components
 	query["sort"] = map[string]string{
-		"pos": sortDirection,
+		"pos": string(sortByPosition),
 	}
 
 	// encode the query