Merge pull request #10 from bento-platform/qa/v2.3.0

qa/v2.3.0

Makefile

@@ -116,7 +116,7 @@ clean-drs-data:
 ## Tests
 test-api-dev: prepare-test-config
 	@# Run the tests
-	go test tests/integration/...
+	go test tests/integration/... -v
 
 prepare-test-config:
 	@# Prepare environment variables dynamically via a JSON file 

README.md

@@ -296,7 +296,9 @@ Generalized Response Body Structure
 >                            }
 >                        },
 >                        ...
->                    ]
+>                    ],
+>                    "fileId": `string` (UUID),
+>                    "assemblyId": `string` ("GRCh38" | "GRCh37" | "NCBI36" | "Other"),
 >                 },
 >                 ...
 >             ]

docker-compose.yaml

@@ -31,6 +31,7 @@ services:
       - bridge-net
     environment:
       # API
+      - GOHAN_DEBUG=${GOHAN_DEBUG}
       - GOHAN_API_VCF_PATH=${GOHAN_API_CONTAINERIZED_VCF_PATH}
 
       # Elasticsearch

etc/example.env

@@ -1,5 +1,6 @@
 ## Gohan Environment Variables
 
+GOHAN_DEBUG=false
 GOHAN_SERVICES=gateway api elasticsearch kibana drs authorization
 
 # Host

etc/test.config.yml.tpl

@@ -1,3 +1,4 @@
+debug: ${GOHAN_DEBUG}
 api:
   url: "${GOHAN_PUBLIC_URL}"
   port: "${GOHAN_API_INTERNAL_PORT}"

src/api/main.go

@@ -29,6 +29,9 @@ func main() {
 	}
 
 	fmt.Printf("Using : \n"+
+
+		"\tDebug : %t \n\n"+
+
 		"\tVCF Directory Path : %s \n"+
 		"\tElasticsearch Url : %s \n"+
 		"\tElasticsearch Username : %s\n\n"+
@@ -43,6 +46,7 @@ func main() {
 
 		"Running on Port : %s\n",
 
+		cfg.Debug,
 		cfg.Api.VcfPath,
 		cfg.Elasticsearch.Url, cfg.Elasticsearch.Username,
 		cfg.Drs.Url, cfg.Drs.Username,

src/api/models/config.go

@@ -1,21 +1,26 @@
 package models
 
 type Config struct {
+	Debug bool `yaml:"debug" envconfig:"GOHAN_DEBUG"`
+
 	Api struct {
 		Url     string `yaml:"url" envconfig:"GOHAN_PUBLIC_URL"`
 		Port    string `yaml:"port" envconfig:"GOHAN_API_INTERNAL_PORT"`
 		VcfPath string `yaml:"vcfPath" envconfig:"GOHAN_API_VCF_PATH"`
 	} `yaml:"api"`
+
 	Elasticsearch struct {
 		Url      string `yaml:"url" envconfig:"GOHAN_ES_URL"`
 		Username string `yaml:"username" envconfig:"GOHAN_ES_USERNAME"`
 		Password string `yaml:"password" envconfig:"GOHAN_ES_PASSWORD"`
 	} `yaml:"elasticsearch"`
+
 	Drs struct {
 		Url      string `yaml:"url" envconfig:"GOHAN_DRS_URL"`
 		Username string `yaml:"username" envconfig:"GOHAN_DRS_BASIC_AUTH_USERNAME"`
 		Password string `yaml:"password" envconfig:"GOHAN_DRS_BASIC_AUTH_PASSWORD"`
 	} `yaml:"drs"`
+
 	AuthX struct {
 		IsAuthorizationEnabled  bool   `yaml:"isAuthorizationEnabled" envconfig:"GOHAN_AUTHZ_ENABLED"`
 		OidcPublicJwksUrl       string `yaml:"oidcPublicJwksUrl" envconfig:"GOHAN_PUBLIC_AUTHN_JWKS_URL"`

src/api/mvc/variants.go

@@ -244,11 +244,12 @@ func GetVariantsOverview(c echo.Context) error {
 
 	var wg sync.WaitGroup
 	es := c.(*contexts.GohanContext).Es7Client
+	cfg := c.(*contexts.GohanContext).Config
 
 	callGetBucketsByKeyword := func(key string, keyword string, _wg *sync.WaitGroup) {
 		defer _wg.Done()
 
-		results := esRepo.GetBucketsByKeyword(es, keyword)
+		results := esRepo.GetBucketsByKeyword(cfg, es, keyword)
 
 		// retrieve aggregations.items.buckets
 		bucketsMapped := []interface{}{}
@@ -311,6 +312,7 @@ func GetAllVariantIngestionRequests(c echo.Context) error {
 }
 
 func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool) error {
+	cfg := c.(*contexts.GohanContext).Config
 
 	var es, chromosome, lowerBound, upperBound, reference, alternative, genotype, assemblyId = retrieveCommonElements(c)
 
@@ -365,7 +367,7 @@ func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool) error
 
 				fmt.Printf("Executing Get-Variants for VariantId %s\n", _id)
 
-				docs = esRepo.GetDocumentsContainerVariantOrSampleIdInPositionRange(es,
+				docs = esRepo.GetDocumentsContainerVariantOrSampleIdInPositionRange(cfg, es,
 					chromosome, lowerBound, upperBound,
 					_id, "", // note : "" is for sampleId
 					reference, alternative,
@@ -377,7 +379,7 @@ func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool) error
 
 				fmt.Printf("Executing Get-Samples for SampleId %s\n", _id)
 
-				docs = esRepo.GetDocumentsContainerVariantOrSampleIdInPositionRange(es,
+				docs = esRepo.GetDocumentsContainerVariantOrSampleIdInPositionRange(cfg, es,
 					chromosome, lowerBound, upperBound,
 					"", _id, // note : "" is for variantId
 					reference, alternative,
@@ -426,6 +428,7 @@ func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool) error
 }
 
 func executeCountByIds(c echo.Context, ids []string, isVariantIdQuery bool) error {
+	cfg := c.(*contexts.GohanContext).Config
 
 	var es, chromosome, lowerBound, upperBound, reference, alternative, genotype, assemblyId = retrieveCommonElements(c)
 
@@ -448,7 +451,7 @@ func executeCountByIds(c echo.Context, ids []string, isVariantIdQuery bool) erro
 
 				fmt.Printf("Executing Count-Variants for VariantId %s\n", _id)
 
-				docs = esRepo.CountDocumentsContainerVariantOrSampleIdInPositionRange(es,
+				docs = esRepo.CountDocumentsContainerVariantOrSampleIdInPositionRange(cfg, es,
 					chromosome, lowerBound, upperBound,
 					_id, "", // note : "" is for sampleId
 					reference, alternative, genotype, assemblyId)
@@ -458,7 +461,7 @@ func executeCountByIds(c echo.Context, ids []string, isVariantIdQuery bool) erro
 
 				fmt.Printf("Executing Count-Samples for SampleId %s\n", _id)
 
-				docs = esRepo.CountDocumentsContainerVariantOrSampleIdInPositionRange(es,
+				docs = esRepo.CountDocumentsContainerVariantOrSampleIdInPositionRange(cfg, es,
 					chromosome, lowerBound, upperBound,
 					"", _id, // note : "" is for variantId
 					reference, alternative, genotype, assemblyId)