fix: remove all mentions of constants.AssemblyId

bento-platform · Dec 11, 2023 · fa12ae3 · fa12ae3
1 parent 8c3c6bc
commit fa12ae3
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Showing 7 changed files with 35 additions and 42 deletions.
diff --git a/src/api/models/constants/assembly-id/main.go b/src/api/models/constants/assembly-id/main.go
@@ -1,10 +1,6 @@
 package assemblyId
 
-import (
-	"gohan/api/models/constants"
-)
-
 const (
-	GRCh38 constants.AssemblyId = "GRCh38"
-	GRCh37 constants.AssemblyId = "GRCh37"
+	GRCh38 string = "GRCh38"
+	GRCh37 string = "GRCh37"
 )
diff --git a/src/api/models/dtos/main.go b/src/api/models/dtos/main.go
@@ -1,7 +1,6 @@
 package dtos
 
 import (
-	"gohan/api/models/constants"
 	"gohan/api/models/indexes"
 	"time"
 )
@@ -21,11 +20,11 @@ type VariantCountReponse struct {
 }
 
 type VariantResult struct {
-	Query      string               `json:"query,omitempty"`
-	AssemblyId constants.AssemblyId `json:"assembly_id"`
-	Chromosome string               `json:"chromosome"`
-	Start      int                  `json:"start"`
-	End        int                  `json:"end"`
+	Query      string `json:"query,omitempty"`
+	AssemblyId string `json:"assembly_id"`
+	Chromosome string `json:"chromosome"`
+	Start      int    `json:"start"`
+	End        int    `json:"end"`
 }
 
 type VariantGetResult struct {
@@ -54,9 +53,9 @@ type VariantCall struct {
 	Alleles      []string `json:"alleles,omitempty"`
 	// TODO: GenotypeProbability, PhredScaleLikelyhood ?
 
-	AssemblyId constants.AssemblyId `json:"assemblyId,omitempty"`
-	Dataset    string               `json:"dataset,omitempty"`
-	DocumentId string               `json:"documentId,omitempty"`
+	AssemblyId string `json:"assemblyId,omitempty"`
+	Dataset    string `json:"dataset,omitempty"`
+	DocumentId string `json:"documentId,omitempty"`
 }
 
 // --- Dataset

diff --git a/src/api/models/indexes/main.go b/src/api/models/indexes/main.go
@@ -18,10 +18,10 @@ type Variant struct {
 
 	Sample Sample `json:"sample"`
 
-	FileId      string       `json:"fileId"`
-	Dataset     string       `json:"dataset"`
-	AssemblyId  c.AssemblyId `json:"assemblyId"`
-	CreatedTime time.Time    `json:"createdTime"`
+	FileId      string    `json:"fileId"`
+	Dataset     string    `json:"dataset"`
+	AssemblyId  string    `json:"assemblyId"`
+	CreatedTime time.Time `json:"createdTime"`
 }
 
 type Info struct {
@@ -51,9 +51,9 @@ type Genotype struct {
 }
 
 type Gene struct {
-	Name       string       `json:"name"`
-	Chrom      string       `json:"chrom"`
-	Start      int          `json:"start"`
-	End        int          `json:"end"`
-	AssemblyId c.AssemblyId `json:"assemblyId"`
+	Name       string `json:"name"`
+	Chrom      string `json:"chrom"`
+	Start      int    `json:"start"`
+	End        int    `json:"end"`
+	AssemblyId string `json:"assemblyId"`
 }
diff --git a/src/api/mvc/genes/main.go b/src/api/mvc/genes/main.go
@@ -6,7 +6,6 @@ import (
 	"crypto/tls"
 	"fmt"
 	"gohan/api/contexts"
-	"gohan/api/models/constants"
 	assemblyId "gohan/api/models/constants/assembly-id"
 	"gohan/api/models/constants/chromosome"
 	"gohan/api/models/dtos"
@@ -51,15 +50,15 @@ func GenesIngest(c echo.Context) error {
 			http.DefaultTransport.(*http.Transport).TLSClientConfig = &tls.Config{InsecureSkipVerify: true}
 		}
 
-		assemblyIdMap := map[constants.AssemblyId]string{
+		assemblyIdMap := map[string]string{
 			assemblyId.GRCh38: "gencode.v38.annotation.gtf",
 			assemblyId.GRCh37: "gencode.v19.annotation.gtf",
 			// SKIP
 			// assemblyId.NCBI36: "hg18",
 			// assemblyId.NCBI35: "hg17",
 			// assemblyId.NCBI34: "hg16",
 		}
-		assemblyIdGTFUrlMap := map[constants.AssemblyId]string{
+		assemblyIdGTFUrlMap := map[string]string{
 			assemblyId.GRCh38: "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz",
 			assemblyId.GRCh37: "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz",
 			// SKIP
@@ -79,7 +78,7 @@ func GenesIngest(c echo.Context) error {
 				CreatedAt: fmt.Sprintf("%v", time.Now()),
 			}
 
-			go func(_assId constants.AssemblyId, _fileName string, _assemblyWg *sync.WaitGroup, reqStat *ingest.GeneIngestRequest) {
+			go func(_asmId string, _fileName string, _assemblyWg *sync.WaitGroup, reqStat *ingest.GeneIngestRequest) {
 				defer _assemblyWg.Done()
 
 				var (
@@ -89,7 +88,7 @@ func GenesIngest(c echo.Context) error {
 				gtfFile, err := os.Open(fmt.Sprintf("%s/%s", gtfPath, _fileName))
 				if err != nil {
 					// Download the file
-					fullURLFile := assemblyIdGTFUrlMap[_assId]
+					fullURLFile := assemblyIdGTFUrlMap[_asmId]
 
 					handleHardErr := func(err error) {
 						msg := "Something went wrong:  " + err.Error()
@@ -193,13 +192,13 @@ func GenesIngest(c echo.Context) error {
 				defer gtfFile.Close()
 
 				// clean out genes currently in elasticsearch by assembly id
-				fmt.Printf("Cleaning out %s gene documents from genes index (if any)\n", string(_assId))
-				esRepo.DeleteGenesByAssemblyId(cfg, es7Client, _assId)
+				fmt.Printf("Cleaning out %s gene documents from genes index (if any)\n", string(_asmId))
+				esRepo.DeleteGenesByAssemblyId(cfg, es7Client, _asmId)
 
 				fileScanner := bufio.NewScanner(gtfFile)
 				fileScanner.Split(bufio.ScanLines)
 
-				fmt.Printf("Ingesting %s\n", string(_assId))
+				fmt.Printf("Ingesting %s\n", string(_asmId))
 				reqStat.State = ingest.Running
 				iz.GeneIngestRequestChan <- reqStat
 
@@ -222,7 +221,7 @@ func GenesIngest(c echo.Context) error {
 					go func(rowText string, _chromHeaderKey int,
 						_startKey int, _endKey int,
 						_nameHeaderKeys []int, _geneNameHeaderKeys []int,
-						_assId constants.AssemblyId,
+						_assId string,
 						_gwg *sync.WaitGroup) {
 						// fmt.Printf("row : %s\n", row)
 
@@ -276,19 +275,19 @@ func GenesIngest(c echo.Context) error {
 							Chrom:      chromosomeClean,
 							Start:      start,
 							End:        end,
-							AssemblyId: _assId,
+							AssemblyId: _asmId,
 						}
 
 						iz.GeneIngestionBulkIndexingQueue <- &structs.GeneIngestionQueueStructure{
 							Gene:      discoveredGene,
 							WaitGroup: _gwg,
 						}
-					}(rowText, chromHeaderKey, startKey, endKey, nameHeaderKeys, geneNameHeaderKeys, _assId, &geneWg)
+					}(rowText, chromHeaderKey, startKey, endKey, nameHeaderKeys, geneNameHeaderKeys, _asmId, &geneWg)
 				}
 
 				geneWg.Wait()
 
-				fmt.Printf("%s ingestion done!\n", _assId)
+				fmt.Printf("%s ingestion done!\n", _asmId)
 				fmt.Printf("Deleting %s\n", unzippedFileName)
 				err = os.Remove(fmt.Sprintf("%s/%s", gtfPath, unzippedFileName))
 				if err != nil {

diff --git a/src/api/repositories/elasticsearch/genes.go b/src/api/repositories/elasticsearch/genes.go
@@ -12,7 +12,6 @@ import (
 	"time"
 
 	"gohan/api/models"
-	"gohan/api/models/constants"
 	"gohan/api/utils"
 
 	"github.com/elastic/go-elasticsearch/v7"
@@ -216,7 +215,7 @@ func GetGeneDocumentsByTermWildcard(cfg *models.Config, es *elasticsearch.Client
 	return result, nil
 }
 
-func DeleteGenesByAssemblyId(cfg *models.Config, es *elasticsearch.Client, assId constants.AssemblyId) (map[string]interface{}, error) {
+func DeleteGenesByAssemblyId(cfg *models.Config, es *elasticsearch.Client, asmId string) (map[string]interface{}, error) {
 
 	if cfg.Debug {
 		http.DefaultTransport.(*http.Transport).TLSClientConfig = &tls.Config{InsecureSkipVerify: true}
@@ -226,7 +225,7 @@ func DeleteGenesByAssemblyId(cfg *models.Config, es *elasticsearch.Client, assId
 	query := map[string]interface{}{
 		"query": map[string]interface{}{
 			"match": map[string]interface{}{
-				"assemblyId": string(assId),
+				"assemblyId": asmId,
 			},
 		},
 	}

diff --git a/src/api/repositories/elasticsearch/variants.go b/src/api/repositories/elasticsearch/variants.go
@@ -109,7 +109,7 @@ func GetDocumentsContainerVariantOrSampleIdInPositionRange(cfg *models.Config, e
 	reference string, alternative string, alleles []string,
 	size int, sortByPosition c.SortDirection,
 	includeInfoInResultSet bool,
-	genotype c.GenotypeQuery, assemblyId c.AssemblyId,
+	genotype c.GenotypeQuery, assemblyId string,
 	getSampleIdsOnly bool) (map[string]interface{}, error) {
 
 	// begin building the request body.
@@ -404,7 +404,7 @@ func CountDocumentsContainerVariantOrSampleIdInPositionRange(cfg *models.Config,
 	chromosome string, lowerBound int, upperBound int,
 	variantId string, sampleId string, datasetString string,
 	reference string, alternative string, alleles []string,
-	genotype c.GenotypeQuery, assemblyId c.AssemblyId) (map[string]interface{}, error) {
+	genotype c.GenotypeQuery, assemblyId string) (map[string]interface{}, error) {
 
 	// begin building the request body.
 	mustMap := []map[string]interface{}{{

diff --git a/src/api/services/ingestion.go b/src/api/services/ingestion.go
@@ -350,7 +350,7 @@ func (i *IngestionService) UploadVcfGzToDrs(cfg *models.Config, drsBridgeDirecto
 
 func (i *IngestionService) ProcessVcf(
 	gzippedFilePath string, drsFileId string, dataset uuid.UUID,
-	assemblyId constants.AssemblyId, filterOutReferences bool,
+	assemblyId string, filterOutReferences bool,
 	lineProcessingConcurrencyLevel int) {
 
 	// ---   reopen gzipped file after having been copied to the temporary api-drs