Merge pull request #8 from bento-platform/releases/v2.2.0

releases/v2.2.0

README.md

@@ -210,12 +210,13 @@ Requests
 >   - chromosome : **number**
 >   - lowerBound : **number**
 >   - upperBound : **number**
->   - reference : **string** `an allele ( "A" | "C" | "G" | "T"  or some combination thereof)`
+>   - reference : **string** `an allele ( "A" | "C" | "G" | "T"  or some combination thereof )`
 >   - alternative : **string** `an allele`
 >   - ids : **string** `(a comma-deliminated list of variant ID alphanumeric codes)`
 >   - size : **number** `(maximum number of results per id)`
 >   - sortByPosition : **string** `(<empty> | asc | desc)`
 >   - includeSamplesInResultSet : **boolean** `(true | false)`
+>   - genotype : **string** `( "HOMOZYGOUS" | "HETEROZYGOUS_REFERENCE" | "HETEROZYGOUS_ALTERNATE" )`
 >
 > &nbsp;&nbsp;**GET** `/variants/count/by/variantId`<br/>
 > &nbsp;&nbsp;&nbsp;params: 
@@ -225,6 +226,7 @@ Requests
 >   - reference : **string** `an allele`
 >   - alternative : **string** `an allele`
 >   - ids : **string** `(a comma-deliminated list of variant ID alphanumeric codes)`
+>   - genotype : **string** `( "HOMOZYGOUS" | "HETEROZYGOUS_REFERENCE" | "HETEROZYGOUS_ALTERNATE" )`
 
 > &nbsp;&nbsp;**GET** `/variants/get/by/sampleId`<br/>
 > &nbsp;&nbsp;&nbsp;params: 
@@ -237,6 +239,7 @@ Requests
 >   - size : **number** `(maximum number of results per id)`
 >   - sortByPosition : **string** `(<empty> | asc | desc)`
 >   - includeSamplesInResultSet : **boolean** `(true | false)`
+>   - genotype : **string** `( "HOMOZYGOUS" | "HETEROZYGOUS_REFERENCE" | "HETEROZYGOUS_ALTERNATE" )`
 >
 > &nbsp;&nbsp;**GET** `/variants/count/by/sampleId`<br/>
 > &nbsp;&nbsp;&nbsp;params: 
@@ -246,6 +249,7 @@ Requests
 >   - reference : **string** `an allele`
 >   - alternative : **string** `an allele`
 >   - ids : **string** `(comma-deliminated list of sample ID alphanumeric codes)`
+>   - genotype : **string** `( "HOMOZYGOUS" | "HETEROZYGOUS_REFERENCE" | "HETEROZYGOUS_ALTERNATE" )`
 >
 
 <br />
@@ -265,12 +269,8 @@ Generalized Response Body Structure
 >                 {
 >                    "filter": `string`,
 >                    "pos": `number`,
->                    "ref": [
->                        `string`,  // an allele
->                    ],
->                    "alt": [
->                         `string`,  // an allele
->                    ],
+>                    "ref": `[]string`,  // list of alleles
+>                    "alt": `[]string`,  // list of alleles
 >                    "info": [
 >                        {
 >                            "id": `string`,
@@ -283,8 +283,17 @@ Generalized Response Body Structure
 >                    "id": `string`,
 >                    "samples": [
 >                        {
->                            "sampleId": `string`,
->                            "variation": `string`,
+>                            "id": `string`,
+>                            "variation": {
+>                                "genotype": {
+>                                    "phased": `boolean`,
+>                                    "alleleLeft": `number`,
+>                                    "alleleRight": `number`,
+>                                    "zygosity": `number` (0 : "Unknown" | 1 : "Homozygous" | 2 : "Heterozygous")
+>                                },
+>                                "genotypeProbability": `[]float` | null,
+>                                "phredScaleLikelyhood": `[]float` | null,
+>                            }
 >                        },
 >                        ...
 >                    ]

src/api/main.go

@@ -117,24 +117,31 @@ func main() {
 
 	// -- Variants
 	e.GET("/variants/overview", mvc.GetVariantsOverview)
+
 	e.GET("/variants/get/by/variantId", mvc.VariantsGetByVariantId,
 		// middleware
 		gam.MandateChromosomeAttribute,
-		gam.MandateCalibratedBounds)
+		gam.MandateCalibratedBounds,
+		gam.ValidatePotentialGenotypeQueryParameter)
 	e.GET("/variants/get/by/sampleId", mvc.VariantsGetBySampleId,
 		// middleware
 		gam.MandateChromosomeAttribute,
 		gam.MandateCalibratedBounds,
-		gam.MandateSampleIdsPluralAttribute)
+		gam.MandateSampleIdsPluralAttribute,
+		gam.ValidatePotentialGenotypeQueryParameter)
+
 	e.GET("/variants/count/by/variantId", mvc.VariantsCountByVariantId,
 		// middleware
 		gam.MandateChromosomeAttribute,
-		gam.MandateCalibratedBounds)
+		gam.MandateCalibratedBounds,
+		gam.ValidatePotentialGenotypeQueryParameter)
 	e.GET("/variants/count/by/sampleId", mvc.VariantsCountBySampleId,
 		// middleware
 		gam.MandateChromosomeAttribute,
 		gam.MandateCalibratedBounds,
-		gam.MandateSampleIdsSingularAttribute)
+		gam.MandateSampleIdsSingularAttribute,
+		gam.ValidatePotentialGenotypeQueryParameter)
+
 	e.GET("/variants/ingestion/run", mvc.VariantsIngest)
 	e.GET("/variants/ingestion/requests", mvc.GetAllVariantIngestionRequests)
 

src/api/middleware/genotypeMiddleware.go

@@ -0,0 +1,25 @@
+package middleware
+
+import (
+	"fmt"
+	"net/http"
+
+	gq "api/models/constants/genotype-query"
+
+	"github.com/labstack/echo"
+)
+
+func ValidatePotentialGenotypeQueryParameter(next echo.HandlerFunc) echo.HandlerFunc {
+	return func(c echo.Context) error {
+		genotypeQP := c.QueryParam("genotype")
+
+		if len(genotypeQP) > 0 {
+			_, genotypeErr := gq.CastToGenoType(genotypeQP)
+			if genotypeErr != nil {
+				return echo.NewHTTPError(http.StatusBadRequest, fmt.Sprintf("Invalid genotype query %s, %s", genotypeQP, genotypeErr))
+			}
+		}
+
+		return next(c)
+	}
+}

src/api/models/constants/genotype-query/main.go

@@ -0,0 +1,39 @@
+package genotypeQuery
+
+import (
+	"api/models/constants"
+	"errors"
+	"strings"
+)
+
+const (
+	UNCALLED constants.GenotypeQuery = ""
+
+	// # Haploid
+	REFERENCE constants.GenotypeQuery = "REFERENCE"
+	ALTERNATE constants.GenotypeQuery = "ALTERNATE"
+
+	// # Diploid or higher
+	HOMOZYGOUS_REFERENCE constants.GenotypeQuery = "HOMOZYGOUS_REFERENCE"
+	HETEROZYGOUS         constants.GenotypeQuery = "HETEROZYGOUS"
+	HOMOZYGOUS_ALTERNATE constants.GenotypeQuery = "HOMOZYGOUS_ALTERNATE"
+)
+
+func CastToGenoType(text string) (constants.GenotypeQuery, error) {
+	switch strings.ToLower(text) {
+	case "":
+		return UNCALLED, nil
+	case "reference":
+		return REFERENCE, nil
+	case "alternate":
+		return ALTERNATE, nil
+	case "homozygous_reference":
+		return HOMOZYGOUS_REFERENCE, nil
+	case "heterozygous":
+		return HETEROZYGOUS, nil
+	case "homozygous_alternate":
+		return HOMOZYGOUS_ALTERNATE, nil
+	default:
+		return UNCALLED, errors.New("unable to parse genotype query")
+	}
+}

src/api/models/constants/main.go

@@ -0,0 +1,9 @@
+package constants
+
+type enumString string
+type enumInt int
+
+type GenotypeQuery enumString
+type SearchOperation enumString
+
+type Zygosity enumInt

src/api/models/constants/search/main.go

@@ -0,0 +1,15 @@
+package search
+
+import (
+	"api/models/constants"
+)
+
+const (
+	SEARCH_OP_EQ constants.SearchOperation = "eq"
+	SEARCH_OP_LT constants.SearchOperation = "lt"
+	SEARCH_OP_LE constants.SearchOperation = "le"
+	SEARCH_OP_GT constants.SearchOperation = "gt"
+	SEARCH_OP_GE constants.SearchOperation = "ge"
+
+	SEARCH_OP_CO constants.SearchOperation = "co"
+)

src/api/models/constants/zygosity/main.go

@@ -0,0 +1,20 @@
+package zygosity
+
+import (
+	"api/models/constants"
+)
+
+const (
+	Empty constants.Zygosity = iota - 1
+	Unknown
+	Homozygous
+	Heterozygous
+)
+
+func IsValid(value int) bool {
+	return value <= int(Heterozygous)
+}
+
+func IsValidQuery(value int) bool {
+	return value > int(Empty) && IsValid(value)
+}

src/api/models/elasticsearch.go

@@ -1,5 +1,9 @@
 package models
 
+import (
+	c "api/models/constants"
+)
+
 var VcfHeaders = []string{"chrom", "pos", "id", "ref", "alt", "qual", "filter", "info", "format"}
 
 type Variant struct {
@@ -8,7 +12,7 @@ type Variant struct {
 	Id     string   `json:"id"`
 	Ref    []string `json:"ref"`
 	Alt    []string `json:"alt"`
-	Format string   `json:"format"`
+	Format []string `json:"format"`
 	Qual   int      `json:"qual"`
 	Filter string   `json:"filter"`
 	Info   []Info   `json:"info"`
@@ -23,6 +27,19 @@ type Info struct {
 }
 
 type Sample struct {
-	SampleId  string `json:"sampleId"`
-	Variation string `json:"variation"`
+	Id        string    `json:"id"`
+	Variation Variation `json:"variation"`
+}
+
+type Variation struct {
+	Genotype             Genotype  `json:"genotype"`
+	GenotypeProbability  []float64 `json:"genotypeProbability"`  // -1 = no call (equivalent to a '.')
+	PhredScaleLikelyhood []float64 `json:"phredScaleLikelyhood"` // -1 = no call (equivalent to a '.')
+}
+
+type Genotype struct {
+	Phased      bool       `json:"phased"`
+	AlleleLeft  int        `json:"alleleLeft"`  // -1 = no call (equivalent to a '.')
+	AlleleRight int        `json:"alleleRight"` // -1 = no call (equivalent to a '.')
+	Zygosity    c.Zygosity `json:"zygosity"`
 }