Merge branch 'master' into releases/v4.0

etc/example.env

@@ -2,7 +2,7 @@
 
 GOHAN_DEBUG=false
 GOHAN_SERVICE_CONTACT=[email protected]
-GOHAN_SEMVER=3.8.0
+GOHAN_SEMVER=3.9.0
 GOHAN_SERVICES="gateway api elasticsearch kibana drs authorization"
 
 # GOOS=linux

src/api/contexts/contexts.go

@@ -2,6 +2,7 @@ package contexts
 
 import (
 	"gohan/api/models"
+	"gohan/api/models/constants"
 	"gohan/api/services"
 	variantsService "gohan/api/services/variants"
 
@@ -14,9 +15,25 @@ type (
 	//  an elasticsearch client and other variables
 	GohanContext struct {
 		echo.Context
+		QueryParameters
 		Es7Client        *es7.Client
 		Config           *models.Config
 		IngestionService *services.IngestionService
 		VariantService   *variantsService.VariantService
 	}
+
+	// Convenient storage for relevant http context data
+	QueryParameters struct {
+		AssemblyId constants.AssemblyId
+		Alleles    []string
+		Chromosome string
+		Genotype   constants.GenotypeQuery
+		SampleIds  []string
+		PositionBounds
+	}
+
+	PositionBounds struct {
+		LowerBound int
+		UpperBound int
+	}
 )

src/api/main.go

@@ -162,22 +162,24 @@ func main() {
 		gam.MandateCalibratedBounds,
 		gam.MandateCalibratedAlleles,
 		gam.MandateAssemblyIdAttribute,
-		gam.MandateSampleIdsPluralAttribute,
+		gam.CalibrateOptionalSampleIdsPluralAttribute,
 		gam.ValidatePotentialGenotypeQueryParameter)
 	e.GET("/variants/get/by/documentId", variantsMvc.VariantsGetByDocumentId)
 
 	e.GET("/variants/count/by/variantId", variantsMvc.VariantsCountByVariantId,
 		// middleware
 		gam.ValidateOptionalChromosomeAttribute,
 		gam.MandateCalibratedBounds,
+		gam.MandateCalibratedAlleles,
 		gam.MandateAssemblyIdAttribute,
 		gam.ValidatePotentialGenotypeQueryParameter)
 	e.GET("/variants/count/by/sampleId", variantsMvc.VariantsCountBySampleId,
 		// middleware
 		gam.ValidateOptionalChromosomeAttribute,
 		gam.MandateCalibratedBounds,
+		gam.MandateCalibratedAlleles,
 		gam.MandateAssemblyIdAttribute,
-		gam.MandateSampleIdsSingularAttribute,
+		gam.CalibrateOptionalSampleIdsSingularAttribute,
 		gam.ValidatePotentialGenotypeQueryParameter)
 
 	// TODO: refactor (deduplicate) --

src/api/middleware/assemblyMiddleware.go

@@ -1,6 +1,8 @@
 package middleware
 
 import (
+	"gohan/api/contexts"
+	"gohan/api/models/constants"
 	assid "gohan/api/models/constants/assembly-id"
 	"net/http"
 
@@ -19,6 +21,10 @@ func MandateAssemblyIdAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 			return echo.NewHTTPError(http.StatusBadRequest, "Missing or unknown assemblyId!")
 		}
 
-		return next(c)
+		// forward a type-safe value down the pipeline
+		gc := c.(*contexts.GohanContext)
+		gc.AssemblyId = constants.AssemblyId(assemblyId)
+
+		return next(gc)
 	}
 }

src/api/middleware/calibratedAllelesMiddleware.go

@@ -1,7 +1,10 @@
 package middleware
 
 import (
+	"fmt"
+	"gohan/api/contexts"
 	"gohan/api/models/dtos/errors"
+	"gohan/api/utils"
 	"net/http"
 	"strings"
 
@@ -10,24 +13,48 @@ import (
 
 func MandateCalibratedAlleles(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
-		if len(c.QueryParam("alleles")) > 0 {
-			allelesQP := strings.Split(c.QueryParam("alleles"), ",")
+		gc := c.(*contexts.GohanContext)
+
+		var alleles []string
+		var allelesQP string = c.QueryParam("alleles")
+		if len(allelesQP) > 0 {
+			alleles = strings.Split(allelesQP, ",")
 
 			// ensure the allele query is properly formatted
-			if allelesQP[len(allelesQP)-1] == "" {
+			if alleles[len(alleles)-1] == "" {
 				return echo.NewHTTPError(
 					http.StatusBadRequest,
 					errors.CreateSimpleBadRequest("Found an empty allele! Please double check your request!"))
 			}
 
 			// ensure no more than 2 alleles are provided at once
-			if len(allelesQP) > 2 {
+			if len(alleles) > 2 {
 				return echo.NewHTTPError(
 					http.StatusBadRequest,
 					errors.CreateSimpleBadRequest("Too many alleles! Please only provide 1 or 2"))
 			}
+
+			// check validity of each provided character
+			for i, allele := range alleles {
+				// - accept lower cases, but transform to upper for elasticsearch (case sensitive)
+				upperAllele := strings.ToUpper(allele)
+				// - check validity of the rest
+				for _, nuc := range upperAllele {
+					if !utils.StringInSlice(string(nuc), utils.AcceptedNucleotideCharacters) {
+						// return status 400 if any allele is incorrect
+						return echo.NewHTTPError(
+							http.StatusBadRequest,
+							errors.CreateSimpleBadRequest(fmt.Sprintf("Nucleotide %s unacceptable! Please double check and try again.", string(nuc))))
+					}
+				}
+				// - replace 'N' with uppercase '?' for elasticsearch
+				upperAllele = strings.Replace(upperAllele, "N", "?", -1)
+
+				alleles[i] = upperAllele
+			}
 		}
 
-		return next(c)
+		gc.Alleles = alleles
+		return next(gc)
 	}
 }

src/api/middleware/calibratedBoundsMiddleware.go

@@ -1,6 +1,7 @@
 package middleware
 
 import (
+	"gohan/api/contexts"
 	"net/http"
 	"strconv"
 
@@ -9,6 +10,8 @@ import (
 
 func MandateCalibratedBounds(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		gc := c.(*contexts.GohanContext)
+
 		var (
 			lowerBound int
 			upperBound int
@@ -50,6 +53,8 @@ func MandateCalibratedBounds(next echo.HandlerFunc) echo.HandlerFunc {
 			return echo.NewHTTPError(http.StatusBadRequest, "Invalid lower and upper bounds!")
 		}
 
-		return next(c)
+		gc.LowerBound = lowerBound
+		gc.UpperBound = upperBound
+		return next(gc)
 	}
 }

src/api/middleware/chromosomeMiddleware.go

@@ -1,6 +1,7 @@
 package middleware
 
 import (
+	"gohan/api/contexts"
 	"gohan/api/models/constants/chromosome"
 	"net/http"
 
@@ -12,6 +13,8 @@ Echo middleware to ensure a valid `chromosome` HTTP query parameter was provided
 */
 func ValidateOptionalChromosomeAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		gc := c.(*contexts.GohanContext)
+
 		// check for chromosome query parameter
 		chromQP := c.QueryParam("chromosome")
 
@@ -22,6 +25,13 @@ func ValidateOptionalChromosomeAttribute(next echo.HandlerFunc) echo.HandlerFunc
 			return echo.NewHTTPError(http.StatusBadRequest, "Please provide a valid 'chromosome' (either 1-23, X, Y, or M)")
 		}
 
-		return next(c)
+		if len(chromQP) == 0 {
+			// if no chromosome is provided, assume "wildcard" search
+			gc.Chromosome = "*"
+		} else {
+			gc.Chromosome = chromQP
+		}
+
+		return next(gc)
 	}
 }

src/api/middleware/genotypeMiddleware.go

@@ -4,6 +4,8 @@ import (
 	"fmt"
 	"net/http"
 
+	"gohan/api/contexts"
+	"gohan/api/models/constants"
 	gq "gohan/api/models/constants/genotype-query"
 
 	"github.com/labstack/echo"
@@ -14,18 +16,25 @@ Echo middleware to ensure the validity of the optionally provided `genotype` HTT
 */
 func ValidatePotentialGenotypeQueryParameter(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		gc := c.(*contexts.GohanContext)
+
 		// check for a genotype query parameter
+		var (
+			genotype    constants.GenotypeQuery
+			genotypeErr error
+		)
 		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)
+			genotype, genotypeErr = gq.CastToGenoType(genotypeQP)
 			if genotypeErr != nil {
 				return echo.NewHTTPError(http.StatusBadRequest, fmt.Sprintf("Invalid genotype query %s, %s", genotypeQP, genotypeErr))
 			}
 		}
 
-		return next(c)
+		gc.Genotype = genotype
+		return next(gc)
 	}
 }

src/api/middleware/sampleMiddleware.go

@@ -1,40 +1,49 @@
 package middleware
 
 import (
-	"net/http"
+	"gohan/api/contexts"
 	"strings"
 
 	"github.com/labstack/echo"
 )
 
 /*
-	Echo middleware to ensure a singular `id` HTTP query parameter was provided
+Echo middleware to prepare the context for an optionall provided singular `id` HTTP query parameter
 */
-func MandateSampleIdsSingularAttribute(next echo.HandlerFunc) echo.HandlerFunc {
+func CalibrateOptionalSampleIdsSingularAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		gc := c.(*contexts.GohanContext)
+
 		// check for id query parameter
 		sampleId := c.QueryParam("id")
 		if len(sampleId) == 0 {
-			// if no id was provided return an error
-			return echo.NewHTTPError(http.StatusBadRequest, "Missing 'id' query parameter for sample id querying!")
+			sampleId = "*" // wildcard
 		}
 
-		return next(c)
+		gc.SampleIds = append(gc.SampleIds, sampleId)
+		return next(gc)
 	}
 }
 
 /*
-	Echo middleware to ensure a pluralized `id` (spelled `ids`) HTTP query parameter was provided
+Echo middleware to prepare the context for an optionally provided pluralized `id` (spelled `ids`) HTTP query parameter
 */
-func MandateSampleIdsPluralAttribute(next echo.HandlerFunc) echo.HandlerFunc {
+func CalibrateOptionalSampleIdsPluralAttribute(next echo.HandlerFunc) echo.HandlerFunc {
 	return func(c echo.Context) error {
+		gc := c.(*contexts.GohanContext)
+
 		// check for id's query parameter
-		sampleIds := strings.Split(c.QueryParam("ids"), ",")
-		if len(sampleIds) == 0 {
-			// if no ids were provided return an error
-			return echo.NewHTTPError(http.StatusBadRequest, "Missing 'ids' query parameter for sample id querying!")
+		var (
+			sampleIdQP = c.QueryParam("ids")
+			sampleIds  []string
+		)
+		if len(sampleIdQP) > 0 {
+			sampleIds = strings.Split(sampleIdQP, ",")
+		} else {
+			sampleIds = append(sampleIds, "*") // wildcard
 		}
 
-		return next(c)
+		gc.SampleIds = append(gc.SampleIds, sampleIds...)
+		return next(gc)
 	}
 }

src/api/mvc/genes/main.go

@@ -322,26 +322,23 @@ func GetAllGeneIngestionRequests(c echo.Context) error {
 
 func GenesGetByNomenclatureWildcard(c echo.Context) error {
 	fmt.Printf("[%s] - GenesGetByNomenclatureWildcard hit!\n", time.Now())
-	cfg := c.(*contexts.GohanContext).Config
-	es := c.(*contexts.GohanContext).Es7Client
+	gc := c.(*contexts.GohanContext)
+	cfg := gc.Config
+	es := gc.Es7Client
 
 	// Chromosome search term
-	chromosomeSearchTerm := c.QueryParam("chromosome")
-	if len(chromosomeSearchTerm) == 0 {
-		// if no chromosome is provided, assume "wildcard" search
-		chromosomeSearchTerm = "*"
-	}
+	chromosomeSearchTerm := gc.Chromosome
 
 	// Name search term
 	term := c.QueryParam("term")
 
 	// Assembly ID
 	// perform wildcard search if empty/random parameter is passed
 	// - set to Unknown to trigger it
-	assId := assemblyId.Unknown
-	if assemblyId.CastToAssemblyId(c.QueryParam("assemblyId")) != assemblyId.Unknown {
+	var assId constants.AssemblyId
+	if gc.AssemblyId != assemblyId.Unknown {
 		// retrieve passed parameter if is valid
-		assId = assemblyId.CastToAssemblyId(c.QueryParam("assemblyId"))
+		assId = gc.AssemblyId
 	}
 
 	// Size