Merge pull request #12 from bento-platform/qa/v3.0.0

qa/v3.0.0

.gitignore

@@ -49,4 +49,7 @@ bin/*
 *.vcf.gz
 
 */*/*.csv
+
+# ignore .gtf files
+*/*.gtf*
 */*/*.gtf*

docker-compose.yaml

@@ -33,6 +33,7 @@ services:
       # API
       - GOHAN_DEBUG=${GOHAN_DEBUG}
       - GOHAN_API_VCF_PATH=${GOHAN_API_CONTAINERIZED_VCF_PATH}
+      - GOHAN_API_GTF_PATH=${GOHAN_API_CONTAINERIZED_GTF_PATH}
 
       # Elasticsearch
       - GOHAN_ES_URL=${GOHAN_PRIVATE_ES_URL}
@@ -51,6 +52,7 @@ services:
       - GOHAN_DRS_BASIC_AUTH_PASSWORD=${GOHAN_DRS_BASIC_AUTH_PASSWORD}
     volumes: 
       - ${GOHAN_API_VCF_PATH}:${GOHAN_API_CONTAINERIZED_VCF_PATH}
+      - ${GOHAN_API_GTF_PATH}:${GOHAN_API_CONTAINERIZED_GTF_PATH}
 
   elasticsearch:
     image: ${GOHAN_ES_BASE_IMAGE}:${GOHAN_ES_BASE_VERSION}

etc/example.env

@@ -37,6 +37,9 @@ GOHAN_API_INTERNAL_PORT=5000
 GOHAN_API_VCF_PATH=/path/to/vcfs/on/host/machine
 GOHAN_API_CONTAINERIZED_VCF_PATH=/app/vcfs
 
+GOHAN_API_GTF_PATH=/path/to/gtfs/on/host/machine
+GOHAN_API_CONTAINERIZED_GTF_PATH=/app/gtfs
+
 GOHAN_API_ES_PI=variants
 GOHAN_API_ES_PROTO=http
 GOHAN_API_ES_HOST=elasticsearch

src/api/main.go

@@ -33,6 +33,7 @@ func main() {
 		"\tDebug : %t \n\n"+
 
 		"\tVCF Directory Path : %s \n"+
+		"\tGTF Directory Path : %s \n"+
 		"\tElasticsearch Url : %s \n"+
 		"\tElasticsearch Username : %s\n\n"+
 
@@ -48,6 +49,7 @@ func main() {
 
 		cfg.Debug,
 		cfg.Api.VcfPath,
+		cfg.Api.GtfPath,
 		cfg.Elasticsearch.Url, cfg.Elasticsearch.Username,
 		cfg.Drs.Url, cfg.Drs.Username,
 		cfg.AuthX.IsAuthorizationEnabled,
@@ -160,6 +162,8 @@ func main() {
 	e.GET("/genes/search", mvc.GenesGetByNomenclatureWildcard,
 		// middleware
 		gam.ValidateOptionalChromosomeAttribute)
+	e.GET("/genes/ingestion/requests", mvc.GetAllGeneIngestionRequests)
+	e.GET("/genes/ingestion/run", mvc.GenesIngest)
 
 	// Run
 	e.Logger.Fatal(e.Start(":" + cfg.Api.Port))

src/api/models/config.go

@@ -7,6 +7,7 @@ type Config 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"`
+		GtfPath string `yaml:"gtfPath" envconfig:"GOHAN_API_GTF_PATH"`
 	} `yaml:"api"`
 
 	Elasticsearch struct {

src/api/models/ingest/ingest.go

@@ -7,13 +7,14 @@ import (
 type State string
 
 const (
-	Queued  State = "Queued"
-	Running       = "Running"
-	Done          = "Done"
-	Error         = "Error"
+	Queued      State = "Queued"
+	Downloading       = "Downloading"
+	Running           = "Running"
+	Done              = "Done"
+	Error             = "Error"
 )
 
-type IngestRequest struct {
+type VariantIngestRequest struct {
 	Id        uuid.UUID `json:"id"`
 	Filename  string    `json:"filename"`
 	State     State     `json:"state"`
@@ -22,6 +23,14 @@ type IngestRequest struct {
 	UpdatedAt string    `json:"updatedAt"`
 }
 
+type GeneIngestRequest struct {
+	Filename  string `json:"filename"`
+	State     State  `json:"state"`
+	Message   string `json:"message"`
+	CreatedAt string `json:"createdAt"`
+	UpdatedAt string `json:"updatedAt"`
+}
+
 type IngestResponseDTO struct {
 	Id       uuid.UUID `json:"id"`
 	Filename string    `json:"filename"`