Merge pull request #16 from bento-platform/qa/v3.1

qa/v3.1.1
bento-platform · Dec 16, 2021 · c2f71a4 · c2f71a4
2 parents 7ae43be + 0916b95
commit c2f71a4
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Showing 8 changed files with 273 additions and 249 deletions.
diff --git a/Makefile b/Makefile
@@ -51,6 +51,12 @@ init-data-dirs:
 		chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_ES_DATA_DIR} && \
 		chmod -R 770 ${GOHAN_ES_DATA_DIR} && \
 	chmod -R 770 ./data && \
+	# tmp: \
+	# (setup for when gohan needs to preprocess vcf's at ingestion time): \
+	mkdir -p ${GOHAN_API_VCF_PATH}/tmp && \
+		chown -R ${HOST_USER_UID}:${HOST_USER_GID}  ${GOHAN_API_VCF_PATH}/tmp && \
+		chmod -R 770 ${GOHAN_API_VCF_PATH}/tmp && \
+	chmod -R 770 ${GOHAN_API_VCF_PATH}/tmp && \
 	echo ".. done!"
 
 

diff --git a/src/api/Dockerfile b/src/api/Dockerfile
@@ -35,9 +35,10 @@ RUN apk --update add ncurses-dev && \
 
 # Build gohan api
 RUN CGO_ENABLED=0 && \
-    go build -ldflags="-s -w" -o gohan_api && \
+    go build -ldflags="-s -w" -o gohan_api 
+    #&& \
     # Compress the final binary :
-    upx --brute gohan_api
+    #upx --brute gohan_api
 
 
 # Stage two - executioner

diff --git a/src/api/main.go b/src/api/main.go
@@ -130,6 +130,10 @@ func main() {
 	e.GET("/data-types/variant/schema", mvc.GetVariantDataTypeSchema)
 	e.GET("/data-types/variant/metadata_schema", mvc.GetVariantDataTypeMetadataSchema)
 
+	// -- TEMP (simulating bento_variants)
+	e.GET("/tables/fake", mvc.FakeBentoTableSchema)
+	// --
+
 	// -- Variants
 	e.GET("/variants/overview", mvc.GetVariantsOverview)
 

diff --git a/src/api/models/dtos.go b/src/api/models/dtos.go
@@ -1,17 +1,32 @@
 package models
 
+import "api/models/constants"
+
+type BentoV2CompatibleVariantsResponseDTO struct {
+	Results []BentoV2CompatibleVariantResponseCallsModel `json:"results"`
+}
+type BentoV2CompatibleVariantResponseCallsModel struct {
+	AssemblyId constants.AssemblyId                        `json:"assembly_id"`
+	Calls      []BentoV2CompatibleVariantResponseDataModel `json:"calls"`
+	Chromosome string                                      `json:"chromosome"`
+	Start      int                                         `json:"start"`
+	End        int                                         `json:"end"`
+}
+type BentoV2CompatibleVariantResponseDataModel struct {
+	SampleId     string `json:"sample_id"`
+	GenotypeType string `json:"genotype_type"`
+}
+
 type VariantsResponseDTO struct {
 	Status  int                        `json:"status"`
 	Message string                     `json:"message"`
 	Data    []VariantResponseDataModel `json:"data"`
 }
-
 type VariantResponseDataModel struct {
-	VariantId string    `json:"variantId"`
-	SampleId  string    `json:"sampleId"`
-	Count     int       `json:"count"`
-	Results   []Variant `json:"results"`   // []Variant
-	SampleIds []string  `json:"sampleIds"` // []string
+	VariantId string      `json:"variantId"`
+	SampleId  string      `json:"sampleId"`
+	Count     int         `json:"count"`
+	Results   interface{} `json:"results"` // i.e.: []Variant or []string
 }
 
 type GenesResponseDTO struct {

diff --git a/src/api/models/schemas/schemas.go b/src/api/models/schemas/schemas.go
@@ -2,7 +2,6 @@ package schemas
 
 import (
 	c "api/models/constants"
-	gq "api/models/constants/genotype-query"
 	so "api/models/constants/search"
 )
 
@@ -31,101 +30,36 @@ var VARIANT_SCHEMA Schema = map[string]interface{}{
 	"$schema":     "http://json-schema.org/draft-07/schema#",
 	"description": "Bento variant data type",
 	"type":        "object",
-	"required":    []string{"assembly_id", "chromosome", "start", "end", "ref", "alt", "calls"},
+	"required": []string{
+		"assembly_id",
+		"chromosome",
+		"start",
+		"end",
+		"calls",
+	},
 	"search": map[string]interface{}{
 		"operations": []c.SearchOperation{},
 	},
 	"properties": map[string]interface{}{
 		"assembly_id": map[string]interface{}{
-			"type":        "string",
-			"enum":        []string{"GRCh38", "GRCh37", "NCBI36", "Other"},
 			"description": "Reference genome assembly ID.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "all",
-				"canNegate":  false,
-				"required":   true,
-				"type":       "single",
-				"order":      0,
-			},
-		},
-		"chromosome": map[string]interface{}{
-			"type": "string",
-			// TODO: Choices
-			"description": "Reference genome chromosome identifier (e.g. 17 or X)",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "all",
-				"canNegate":  false,
-				"required":   true,
-				"type":       "single", // single / unlimited
-				"order":      1,
-			},
-		},
-		"start": map[string]interface{}{
-			"type":        "integer",
-			"description": "1-indexed start location of the variant on the chromosome.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ, so.SEARCH_OP_LT, so.SEARCH_OP_LE, so.SEARCH_OP_GT, so.SEARCH_OP_GE},
-				"queryable":  "all",
-				"canNegate":  false,
-				"required":   true,        // TODO: Shouldn't be "required" here; but should show up by default anyway
-				"type":       "unlimited", // single / unlimited
-				"order":      2,
+			"enum": []string{
+				"GRCh38",
+				"GRCh37",
+				"NCBI36",
+				"Other",
 			},
-		},
-		"end": map[string]interface{}{
-			"type": "integer",
-			"description": ("1-indexed end location (exclusive) of the variant on the chromosome, in terms of the " +
-				"number of bases in the reference sequence for the variant."),
 			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ, so.SEARCH_OP_LT, so.SEARCH_OP_LE, so.SEARCH_OP_GT, so.SEARCH_OP_GE},
-				"queryable":  "all",
-				"canNegate":  true,
-				"required":   false,
-				"type":       "unlimited", // single / unlimited
-				"order":      3,
-			},
-		},
-		"ref": map[string]interface{}{
-			"type":        "string",
-			"description": "Reference base sequence for the variant.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "all",
-				"canNegate":  true,
-				"required":   false,
-				"type":       "single", // single / unlimited
-				"order":      4,
-			},
-		},
-		"alt": map[string]interface{}{
-			"type":        "array",
-			"description": "Alternate (non-reference) base sequences for the variant.",
-			"items": map[string]interface{}{
-				"type":        "string",
-				"description": "Alternate base sequence for the variant.",
-				"search": map[string]interface{}{
-					"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-					"queryable":  "all",
-					"canNegate":  true,
-					"required":   false,
-					"type":       "single", // single / unlimited
-					"order":      0,
+				"canNegate": false,
+				"operations": []string{
+					"eq",
 				},
+				"order":     0,
+				"queryable": "all",
+				"required":  true,
+				"type":      "single",
 			},
-			"search": map[string]interface{}{
-				"order": 5,
-			},
-		},
-		"qual": map[string]interface{}{
-			"type":        []string{"integer", "null"},
-			"description": "Phred-scaled quality score for the assertion made by the alt field.",
-			"search": map[string]interface{}{
-				"required": false,
-				"type":     "unlimited",
-				"order":    6,
-			},
+			"type": "string",
 		},
 		"calls": map[string]interface{}{
 			"type":        "array",
@@ -137,27 +71,55 @@ var VARIANT_SCHEMA Schema = map[string]interface{}{
 				"order":    7,
 			},
 		},
-		"_extra": map[string]interface{}{
-			"type": "object",
-			"properties": map[string]interface{}{
-				"file_uri": map[string]interface{}{
-					"type": "string",
-					"search": map[string]interface{}{
-						"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-						"queryable":  "internal",
-						"canNegate":  true,
-						"required":   false,
-						"type":       "single", // single / unlimited
-						"order":      0,
-					},
+		"chromosome": map[string]interface{}{
+			"description": "Reference genome chromosome identifier (e.g. 17 or X)",
+			"search": map[string]interface{}{
+				"canNegate": false,
+				"operations": []string{
+					"eq",
+				},
+				"order":     1,
+				"queryable": "all",
+				"required":  true,
+				"type":      "single",
+			},
+			"type": "string",
+		},
+		"start": map[string]interface{}{
+			"description": "1-indexed start location of the variant on the chromosome.",
+			"search": map[string]interface{}{
+				"canNegate": false,
+				"operations": []string{
+					"eq",
+					"lt",
+					"le",
+					"gt",
+					"ge",
 				},
+				"order":     2,
+				"queryable": "all",
+				"required":  true,
+				"type":      "unlimited",
 			},
+			"type": "integer",
+		},
+		"end": map[string]interface{}{
+			"description": "1-indexed end location (exclusive) of the variant on the chromosome, in terms of the number of bases in the reference sequence for the variant.",
 			"search": map[string]interface{}{
-				"queryable": "internal",
+				"canNegate": true,
+				"operations": []string{
+					"eq",
+					"lt",
+					"le",
+					"gt",
+					"ge",
+				},
+				"order":     3,
+				"queryable": "all",
 				"required":  false,
 				"type":      "unlimited",
-				"order":     8,
 			},
+			"type": "integer",
 		},
 	},
 }
@@ -166,7 +128,10 @@ var VARIANT_CALL_SCHEMA Schema = map[string]interface{}{
 	"id":          "variant:variant_call", // TODO: Real ID
 	"type":        "object",
 	"description": "An object representing a called instance of a variant.",
-	"required":    []string{"sample_id", "genotype_bases"},
+	"required": []string{
+		"sample_id",
+		"genotype_type",
+	},
 	"properties": map[string]interface{}{
 		"sample_id": map[string]interface{}{
 			"type":        "string",
@@ -180,87 +145,28 @@ var VARIANT_CALL_SCHEMA Schema = map[string]interface{}{
 				"order":      0,
 			},
 		},
-		"genotype_bases": map[string]interface{}{
-			"type":        "array",
-			"description": "Variant call genotype.",
-			"items": map[string]interface{}{
-				"type":        []string{"string", "null"},
-				"description": "Variant call bases on a chromosome.",
-				"search": map[string]interface{}{
-					"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-					"queryable":  "all",
-					"canNegate":  true,
-					"required":   false,
-					"type":       "single",
-					"order":      0,
-				},
-			},
-			// TODO: Is this search block really needed
-			"search": map[string]interface{}{
-				"required": false,
-				"type":     "unlimited",
-				"order":    1,
-			},
-		},
 		"genotype_type": map[string]interface{}{
-			"type":        "string",
 			"description": "Variant call genotype type.",
-			"enum": []c.GenotypeQuery{
-				// No call
-				gq.UNCALLED,
-
-				// Haploid
-				gq.REFERENCE,
-				gq.ALTERNATE,
-
-				// Diploid or higher
-				gq.HOMOZYGOUS_REFERENCE,
-				gq.HETEROZYGOUS,
-				gq.HOMOZYGOUS_ALTERNATE,
+			"enum": []string{
+				"MISSING",
+				"MISSING_UPSTREAM_DELETION",
+				"REFERENCE",
+				"ALTERNATE",
+				"HOMOZYGOUS_REFERENCE",
+				"HETEROZYGOUS",
+				"HOMOZYGOUS_ALTERNATE",
 			},
 			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "all",
-				"canNegate":  true,
-				"required":   true, // TODO: Shouldn't be "required" here; but should show up by default anyway
-				"type":       "single",
-				"order":      2.0,
-			},
-		},
-		"phased": map[string]interface{}{
-			"type":        "boolean",
-			"description": "Whether the called genotype is phased.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "all",
-				"canNegate":  true,
-				"required":   false,
-				"type":       "single",
-				"order":      3,
-			},
-		},
-		"phase_set": map[string]interface{}{
-			"type":        []string{"number", "null"},
-			"description": "Genotype phase set, if any.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ},
-				"queryable":  "internal",
-				"canNegate":  true,
-				"required":   false,
-				"type":       "single",
-				"order":      4,
-			},
-		},
-		"read_depth": map[string]interface{}{
-			"type":        []string{"integer", "null"},
-			"description": "Read depth at this position for this sample.",
-			"search": map[string]interface{}{
-				"operations": []c.SearchOperation{so.SEARCH_OP_EQ, so.SEARCH_OP_GT, so.SEARCH_OP_GE, so.SEARCH_OP_LT, so.SEARCH_OP_LE},
-				"queryable":  "all",
-				"canNegate":  true,
-				"required":   false,
-				"order":      5,
+				"canNegate": true,
+				"operations": []string{
+					"eq",
+				},
+				"order":     2.0,
+				"queryable": "all",
+				"required":  true,
+				"type":      "single",
 			},
+			"type": "string",
 		},
 	},
 }