delete variants by dataset id endpoint

src/api/contexts/contexts.go

@@ -31,6 +31,7 @@ type (
 		Genotype   constants.GenotypeQuery
 		SampleIds  []string
 		Dataset    uuid.UUID
+		DataType   string
 		PositionBounds
 	}
 

src/api/main.go

@@ -185,6 +185,9 @@ func main() {
 	e.GET("/datasets/:dataset/data-types", variantsMvc.GetDatasetDataTypes,
 		// middleware
 		gam.MandateDatasetPathParam)
+	e.DELETE("/datasets/:dataset/data-types/:dataType", variantsMvc.ClearDataset,
+		gam.MandateDatasetPathParam,
+		gam.MandateDataTypePathParam)
 
 	// TODO: refactor (deduplicate) --
 	e.GET("/variants/ingestion/run", variantsMvc.VariantsIngest,

src/api/middleware/datasetMiddleware.go

@@ -56,6 +56,21 @@ func MandateDatasetPathParam(next echo.HandlerFunc) echo.HandlerFunc {
 	}
 }
 
+func MandateDataTypePathParam(next echo.HandlerFunc) echo.HandlerFunc {
+	return func(c echo.Context) error {
+		dataType := c.Param("dataType")
+		if dataType != "variant" {
+			fmt.Printf("Invalid data-type provided: %s\n", dataType)
+			return c.JSON(http.StatusBadRequest, errors.CreateSimpleBadRequest(
+				fmt.Sprintf("invalid data-type %s - please provide a valid data-type (e.g. \"variant\")", dataType),
+			))
+		}
+		gc := c.(*contexts.GohanContext)
+		gc.DataType = dataType
+		return next(gc)
+	}
+}
+
 /*
 Echo middleware to ensure a `dataset` HTTP query parameter is valid if provided
 */

src/api/mvc/variants/main.go

@@ -558,6 +558,41 @@ func GetDatasetSummary(c echo.Context) error {
 	}
 }
 
+func ClearDataset(c echo.Context) error {
+	gc := c.(*contexts.GohanContext)
+	cfg := gc.Config
+	es := gc.Es7Client
+
+	dataset := gc.Dataset
+	dataType := gc.DataType
+	fmt.Printf("[%s] - ClearDataset hit: [%s] - [%s]!\n", time.Now(), dataset.String(), dataType)
+
+	var (
+		deletionCount = 0.0
+		g             = new(errgroup.Group)
+	)
+	// request #1
+	g.Go(func() error {
+		deleteResponse, delErr := esRepo.DeleteVariantsByDatasetId(cfg, es, dataset.String())
+
+		if delErr != nil {
+			fmt.Printf("Failed to delete dataset %s variants\n", dataset)
+			return delErr
+		}
+
+		deletionCount = deleteResponse["deleted"].(float64)
+
+		return nil
+	})
+
+	if err := g.Wait(); err == nil {
+		fmt.Printf("Deleted %f variants from dataset %s\n", deletionCount, dataset)
+		return c.NoContent(http.StatusNoContent)
+	} else {
+		return c.JSON(http.StatusInternalServerError, errors.CreateSimpleInternalServerError("Something went wrong.. Please try again later!"))
+	}
+}
+
 type DataTypeSummary struct {
 	Id        string                 `json:"id"`
 	Label     string                 `json:"label"`

src/api/repositories/elasticsearch/variants.go

@@ -668,6 +668,62 @@ func GetVariantsBucketsByKeywordAndDataset(cfg *models.Config, es *elasticsearch
 	return result, nil
 }
 
+func DeleteVariantsByDatasetId(cfg *models.Config, es *elasticsearch.Client, dataset string) (map[string]interface{}, error) {
+
+	var buf bytes.Buffer
+	query := map[string]interface{}{
+		"query": map[string]interface{}{
+			"match": map[string]interface{}{
+				"dataset": dataset,
+			},
+		},
+	}
+
+	if err := json.NewEncoder(&buf).Encode(query); err != nil {
+		log.Fatalf("Error encoding query: %s\n", query)
+	}
+
+	if cfg.Debug {
+		// view the outbound elasticsearch query
+		myString := string(buf.Bytes()[:])
+		fmt.Println(myString)
+	}
+
+	// Perform the delete request.
+	deleteRes, deleteErr := es.DeleteByQuery(
+		[]string{wildcardVariantsIndex},
+		bytes.NewReader(buf.Bytes()),
+	)
+	if deleteErr != nil {
+		fmt.Printf("Error getting response: %s\n", deleteErr)
+		return nil, deleteErr
+	}
+
+	defer deleteRes.Body.Close()
+
+	resultString := deleteRes.String()
+	if cfg.Debug {
+		fmt.Println(resultString)
+	}
+
+	// Prepare an empty interface
+	result := make(map[string]interface{})
+
+	// Unmarshal or Decode the JSON to the empty interface.
+	// Known bug: response comes back with a preceding '[200 OK] ' which needs trimming
+	bracketString, jsonBodyString := utils.GetLeadingStringInBetweenSquareBrackets(resultString)
+	if !strings.Contains(bracketString, "200") {
+		return nil, fmt.Errorf("failed to get documents by id : got '%s'", bracketString)
+	}
+	umErr := json.Unmarshal([]byte(jsonBodyString), &result)
+	if umErr != nil {
+		fmt.Printf("Error unmarshalling variant deletion response: %s\n", umErr)
+		return nil, umErr
+	}
+
+	return result, nil
+}
+
 // -- internal use only --
 func addAllelesToShouldMap(alleles []string, genotype c.GenotypeQuery, allelesShouldMap []map[string]interface{}) ([]map[string]interface{}, int) {
 	minimumShouldMatch := 0