feat: search allergy

- searches for allegy by the provided name

Signed-off-by: Kathurima Kimathi <kathurimakimathi415@gmail.com>

pkg/clinical/application/dto/output.go

@@ -134,3 +134,10 @@ type Condition struct {
 	PatientID   string `json:"patientID"`
 	EncounterID string `json:"encounterID"`
 }
+
+// Terminology models the OCL terminology output
+type Terminology struct {
+	Code   string            `json:"code"`
+	System TerminologySource `json:"system"`
+	Name   string            `json:"name"`
+}

pkg/clinical/domain/concept.go

@@ -1,29 +1,27 @@
 package domain
 
-import "time"
-
 // Concept models a concept type from OpenConceptLab
 type Concept struct {
-	ConceptClass     string     `mapstructure:"concept_class" json:"concept_class"`
-	DataType         string     `mapstructure:"datatype" json:"datatype"`
-	DisplayLocale    string     `mapstructure:"display_locale" json:"display_locale"`
-	DisplayName      string     `mapstructure:"display_name" json:"display_name"`
-	ExternalID       string     `mapstructure:"external_id" json:"external_id"`
-	ID               string     `mapstructure:"id" json:"id"`
-	IsLatestVersion  bool       `mapstructure:"is_latest_version" json:"is_latest_version"`
-	Locale           *string    `mapstructure:"locale" json:"locale"`
-	Owner            string     `mapstructure:"owner" json:"owner"`
-	OwnerType        string     `mapstructure:"owner_type" json:"owner_type"`
-	OwnerURL         string     `mapstructure:"owner_url" json:"owner_url"`
-	Retired          bool       `mapstructure:"retired" json:"retired"`
-	Source           string     `mapstructure:"source" json:"source"`
-	Type             string     `mapstructure:"type" json:"type"`
-	UpdateComment    string     `mapstructure:"update_comment" json:"update_comment"`
-	URL              string     `mapstructure:"url" json:"url"`
-	UUID             string     `mapstructure:"uuid" json:"uuid"`
-	Version          string     `mapstructure:"version" json:"version"`
-	VersionCreatedBy string     `mapstructure:"version_created_by" json:"version_created_by"`
-	VersionCreatedOn *time.Time `mapstructure:"version_created_on" json:"version_created_on"`
-	VersionURL       string     `mapstructure:"version_url" json:"version_url"`
-	VersionsURL      string     `mapstructure:"versions_url" json:"versions_url"`
+	ConceptClass     string  `mapstructure:"concept_class" json:"concept_class"`
+	DataType         string  `mapstructure:"datatype" json:"datatype"`
+	DisplayLocale    string  `mapstructure:"display_locale" json:"display_locale"`
+	DisplayName      string  `mapstructure:"display_name" json:"display_name"`
+	ExternalID       string  `mapstructure:"external_id" json:"external_id"`
+	ID               string  `mapstructure:"id" json:"id"`
+	IsLatestVersion  bool    `mapstructure:"is_latest_version" json:"is_latest_version"`
+	Locale           *string `mapstructure:"locale" json:"locale"`
+	Owner            string  `mapstructure:"owner" json:"owner"`
+	OwnerType        string  `mapstructure:"owner_type" json:"owner_type"`
+	OwnerURL         string  `mapstructure:"owner_url" json:"owner_url"`
+	Retired          bool    `mapstructure:"retired" json:"retired"`
+	Source           string  `mapstructure:"source" json:"source"`
+	Type             string  `mapstructure:"type" json:"type"`
+	UpdateComment    string  `mapstructure:"update_comment" json:"update_comment"`
+	URL              string  `mapstructure:"url" json:"url"`
+	UUID             string  `mapstructure:"uuid" json:"uuid"`
+	Version          string  `mapstructure:"version" json:"version"`
+	VersionCreatedBy string  `mapstructure:"version_created_by" json:"version_created_by"`
+	VersionCreatedOn string  `mapstructure:"version_created_on" json:"version_created_on"`
+	VersionURL       string  `mapstructure:"version_url" json:"version_url"`
+	VersionsURL      string  `mapstructure:"versions_url" json:"versions_url"`
 }

pkg/clinical/infrastructure/infrastructure.go

@@ -21,10 +21,10 @@ type ServiceOCL interface {
 		ctx context.Context, org string, source string, verbose bool, q *string,
 		sortAsc *string, sortDesc *string, conceptClass *string, dataType *string,
 		locale *string, includeRetired *bool,
-		includeMappings *bool, includeInverseMappings *bool) ([]map[string]interface{}, error)
+		includeMappings *bool, includeInverseMappings *bool) ([]*domain.Concept, error)
 	GetConcept(
 		ctx context.Context, org string, source string, concept string,
-		includeMappings bool, includeInverseMappings bool) (map[string]interface{}, error)
+		includeMappings bool, includeInverseMappings bool) (*domain.Concept, error)
 }
 
 // BaseExtension is an interface that represents some methods in base

pkg/clinical/infrastructure/services/openconceptlab/mock/service_mock.go

@@ -5,6 +5,8 @@ import (
 	"io"
 	"net/http"
 	"net/url"
+
+	"github.com/savannahghi/clinical/pkg/clinical/domain"
 )
 
 // FakeOCL is an mock of the Open concept lab
@@ -14,10 +16,10 @@ type FakeOCL struct {
 		ctx context.Context, org string, source string, verbose bool, q *string,
 		sortAsc *string, sortDesc *string, conceptClass *string, dataType *string,
 		locale *string, includeRetired *bool,
-		includeMappings *bool, includeInverseMappings *bool) ([]map[string]interface{}, error)
+		includeMappings *bool, includeInverseMappings *bool) ([]*domain.Concept, error)
 	MockGetConceptFn func(
 		ctx context.Context, org string, source string, concept string,
-		includeMappings bool, includeInverseMappings bool) (map[string]interface{}, error)
+		includeMappings bool, includeInverseMappings bool) (*domain.Concept, error)
 }
 
 // NewFakeOCLMock initializes a new instance of ocl mock
@@ -28,25 +30,24 @@ func NewFakeOCLMock() *FakeOCL {
 				StatusCode: 200,
 			}, nil
 		},
-		MockListConceptsFn: func(
-			ctx context.Context, org string, source string, verbose bool, q *string,
-			sortAsc *string, sortDesc *string, conceptClass *string, dataType *string,
-			locale *string, includeRetired *bool,
-			includeMappings *bool, includeInverseMappings *bool) ([]map[string]interface{}, error) {
-			m := map[string]interface{}{
-				"concept": "C00001",
-			}
-			return []map[string]interface{}{
-				m,
+		MockListConceptsFn: func(ctx context.Context, org, source string, verbose bool, q, sortAsc, sortDesc, conceptClass, dataType, locale *string, includeRetired, includeMappings, includeInverseMappings *bool) ([]*domain.Concept, error) {
+			return []*domain.Concept{
+				{
+					ConceptClass:  "CIEL",
+					DataType:      "N/A",
+					DisplayLocale: "en/us",
+					DisplayName:   "test",
+					ExternalID:    "1234",
+					ID:            "1234",
+				},
 			}, nil
 		},
 		MockGetConceptFn: func(
 			ctx context.Context, org string, source string, concept string,
-			includeMappings bool, includeInverseMappings bool) (map[string]interface{}, error) {
-			m := map[string]interface{}{
-				"id": "C12345",
-			}
-			return m, nil
+			includeMappings bool, includeInverseMappings bool) (*domain.Concept, error) {
+			return &domain.Concept{
+				ID: "1234",
+			}, nil
 		},
 	}
 }
@@ -61,13 +62,13 @@ func (o *FakeOCL) ListConcepts(
 	ctx context.Context, org string, source string, verbose bool, q *string,
 	sortAsc *string, sortDesc *string, conceptClass *string, dataType *string,
 	locale *string, includeRetired *bool,
-	includeMappings *bool, includeInverseMappings *bool) ([]map[string]interface{}, error) {
+	includeMappings *bool, includeInverseMappings *bool) ([]*domain.Concept, error) {
 	return o.MockListConceptsFn(ctx, org, source, verbose, q, sortAsc, sortDesc, conceptClass, dataType, locale, includeRetired, includeMappings, includeInverseMappings)
 }
 
 // GetConcept is a mock implementation of getting a concept
 func (o *FakeOCL) GetConcept(
 	ctx context.Context, org string, source string, concept string,
-	includeMappings bool, includeInverseMappings bool) (map[string]interface{}, error) {
+	includeMappings bool, includeInverseMappings bool) (*domain.Concept, error) {
 	return o.MockGetConceptFn(ctx, org, source, concept, includeMappings, includeInverseMappings)
 }

pkg/clinical/infrastructure/services/openconceptlab/service.go

@@ -13,6 +13,8 @@ import (
 	"strconv"
 	"time"
 
+	"github.com/mitchellh/mapstructure"
+	"github.com/savannahghi/clinical/pkg/clinical/domain"
 	"github.com/savannahghi/serverutils"
 )
 
@@ -82,7 +84,7 @@ func (s Service) MakeRequest(method string, path string, params url.Values, body
 // e.g GET /orgs/WHO/sources/ICD-10-2010/concepts/A15.1/?includeInverseMappings=true
 func (s Service) GetConcept(
 	_ context.Context, org string, source string, concept string,
-	includeMappings bool, includeInverseMappings bool) (map[string]interface{}, error) {
+	includeMappings bool, includeInverseMappings bool) (*domain.Concept, error) {
 	s.enforcePreconditions()
 
 	path := fmt.Sprintf("orgs/%s/sources/%s/concepts/%s", org, source, concept)
@@ -117,7 +119,14 @@ func (s Service) GetConcept(
 		return nil, fmt.Errorf("failed to get %v concept with id %v", source, concept)
 	}
 
-	return output, nil
+	var terminologyConcept *domain.Concept
+
+	err = mapstructure.Decode(output, &terminologyConcept)
+	if err != nil {
+		return nil, err
+	}
+
+	return terminologyConcept, nil
 }
 
 // ListConcepts searches for matching concepts on OpenConceptLab
@@ -127,7 +136,7 @@ func (s Service) ListConcepts(
 	_ context.Context, org string, source string, verbose bool, q *string,
 	sortAsc *string, sortDesc *string, conceptClass *string, dataType *string,
 	locale *string, includeRetired *bool,
-	includeMappings *bool, includeInverseMappings *bool) ([]map[string]interface{}, error) {
+	includeMappings *bool, includeInverseMappings *bool) ([]*domain.Concept, error) {
 	s.enforcePreconditions()
 
 	path := fmt.Sprintf("orgs/%s/sources/%s/concepts", org, source)
@@ -182,18 +191,31 @@ func (s Service) ListConcepts(
 
 	defer resp.Body.Close()
 
-	output := []map[string]interface{}{}
+	terminologyConcepts := []map[string]interface{}{}
 
 	data, err := io.ReadAll(resp.Body)
 	if err != nil {
 		return nil, fmt.Errorf("unable to read OCL API response body: %w", err)
 	}
 
-	err = json.Unmarshal(data, &output)
+	err = json.Unmarshal(data, &terminologyConcepts)
 	if err != nil {
 		return nil, fmt.Errorf(
 			"unable to marshal OCL get concept response %s to JSON: %w", string(data), err)
 	}
 
-	return output, nil
+	var concepts []*domain.Concept
+
+	for _, terminologyConcept := range terminologyConcepts {
+		var concept *domain.Concept
+
+		err := mapstructure.Decode(terminologyConcept, &concept)
+		if err != nil {
+			return nil, err
+		}
+
+		concepts = append(concepts, concept)
+	}
+
+	return concepts, nil
 }

pkg/clinical/presentation/graph/clinical.graphql

@@ -18,6 +18,9 @@ extend type Query {
   getPatientPulseRateEntries(patientID: String!): [Observation!]
   getPatientBMIEntries(patientID: String!): [Observation!]
   getPatientWeightEntries(patientID: String!): [Observation!]
+
+  # Allergy
+   searchAllergyTerminology(name: String!): [Terminology]
 }
 
 extend type Mutation {