Add initial FHIR endpoint for CodeSystem by OID (#56)

docs/examples.http

@@ -61,4 +61,9 @@ accept: application/json
 GET https://localhost:4000/api/value-set-concepts/code-system/1.0.3166.1
 accept: application/json
 
-###
+###
+
+GET https://localhost:4000/r5/CodeSystem/2.16.840.1.113883.6.238
+accept: application/json
+
+###

go.mod

@@ -1,9 +1,10 @@
 module github.com/skylight-hq/phinvads-go
 
-go 1.23.0
+go 1.23.1
 
 require (
 	github.com/a-h/templ v0.2.771
+	github.com/google/fhir/go v0.7.4
 	github.com/google/uuid v1.6.0
 	github.com/jackc/pgx/v5 v5.6.0
 	github.com/joho/godotenv v1.5.1
@@ -12,11 +13,19 @@ require (
 )
 
 require (
+	bitbucket.org/creachadair/stringset v0.0.9 // indirect
 	github.com/andybalholm/brotli v1.1.0 // indirect
+	github.com/golang/protobuf v1.4.3 // indirect
 	github.com/jackc/pgpassfile v1.0.0 // indirect
 	github.com/jackc/pgservicefile v0.0.0-20221227161230-091c0ba34f0a // indirect
 	github.com/jackc/puddle/v2 v2.2.1 // indirect
+	github.com/json-iterator/go v1.1.10 // indirect
+	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
+	github.com/modern-go/reflect2 v1.0.1 // indirect
+	github.com/pkg/errors v0.9.1 // indirect
+	github.com/serenize/snaker v0.0.0-20201027110005-a7ad2135616e // indirect
 	golang.org/x/crypto v0.17.0 // indirect
 	golang.org/x/sync v0.8.0 // indirect
 	golang.org/x/text v0.14.0 // indirect
+	google.golang.org/protobuf v1.25.0 // indirect
 )

internal/app/fhir/r5/CodeSystem.go

@@ -0,0 +1,64 @@
+package r5
+
+import (
+	"fmt"
+
+	"github.com/google/fhir/go/proto/google/fhir/proto/r5/core/codes_go_proto"
+	datatypespb "github.com/google/fhir/go/proto/google/fhir/proto/r5/core/datatypes_go_proto"
+	r5pb "github.com/google/fhir/go/proto/google/fhir/proto/r5/core/resources/code_system_go_proto"
+	"github.com/skylight-hq/phinvads-go/internal/database/models/xo"
+)
+
+func SerializeCodeSystemToFhir(cs *xo.CodeSystem) (*r5pb.CodeSystem, error) {
+	fhirCS := &r5pb.CodeSystem{
+		Id:           newId(cs.Oid),
+		Status:       &r5pb.CodeSystem_StatusCode{Value: codes_go_proto.PublicationStatusCode_DRAFT},
+		Version:      newString(cs.Version),
+		Name:         newString(cs.Name),
+		Description:  newNullableMarkdown(cs.Definitiontext),
+		Experimental: newBoolean(cs.Legacyflag),
+		Url:          newNullableUri(cs.Sourceurl),
+		Date:         newDateTime(cs.Statusdate),
+		Publisher:    newNullableString(cs.Distributionsourceversionname),
+		Title:        newNullableString(cs.Assigningauthorityversionname),
+		Content:      &r5pb.CodeSystem_ContentCode{Value: 4},
+		// TODO: Count
+		// TODO: Concept
+	}
+
+	fhirCS.Identifier = []*datatypespb.Identifier{
+		{
+			System: newUri("urn:ietf:rfc:3986"), // Assuming this system for oid mapping
+			Value:  newString(fmt.Sprintf("urn:oid:%s", cs.Oid)),
+		},
+	}
+
+	fhirCS.Meta = &datatypespb.Meta{
+		Profile: []*datatypespb.Canonical{
+			{Value: "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"},
+		},
+	}
+
+	fhirCS.Text = &datatypespb.Narrative{
+		Status: &datatypespb.Narrative_StatusCode{Value: codes_go_proto.NarrativeStatusCode_GENERATED},
+		Div:    newXhtml("<div>Your narrative text here</div>"),
+	}
+
+	fhirCS.Contact = []*datatypespb.ContactDetail{
+		{
+			Name: newString("PHIN Vocabulary Services"),
+			Telecom: []*datatypespb.ContactPoint{
+				{
+					System: &datatypespb.ContactPoint_SystemCode{Value: 5},
+					Value:  newString("https://www.cdc.gov/phin/php/phinvads/index.html"),
+				},
+				{
+					System: &datatypespb.ContactPoint_SystemCode{Value: 3},
+					Value:  newString("[email protected]"),
+				},
+			},
+		},
+	}
+
+	return fhirCS, nil
+}

internal/app/fhir/r5/helpers.go

@@ -0,0 +1,66 @@
+package r5
+
+import (
+	"database/sql"
+	"time"
+
+	datatypespb "github.com/google/fhir/go/proto/google/fhir/proto/r5/core/datatypes_go_proto"
+)
+
+func newString(value string) *datatypespb.String {
+	if value == "" {
+		return nil
+	}
+	return &datatypespb.String{Value: value}
+}
+
+func newBoolean(value bool) *datatypespb.Boolean {
+	return &datatypespb.Boolean{Value: value}
+}
+
+func newDateTime(t time.Time) *datatypespb.DateTime {
+	if t.IsZero() {
+		return nil
+	}
+	return &datatypespb.DateTime{
+		ValueUs:   t.UnixMicro(),
+		Precision: datatypespb.DateTime_MICROSECOND,
+	}
+}
+
+func newNullableString(ns sql.NullString) *datatypespb.String {
+	if ns.Valid {
+		return newString(ns.String)
+	}
+	return nil
+}
+
+func newId(value string) *datatypespb.Id {
+	return &datatypespb.Id{Value: value}
+}
+
+func newMarkdown(value string) *datatypespb.Markdown {
+	return &datatypespb.Markdown{Value: value}
+}
+
+func newNullableMarkdown(ns sql.NullString) *datatypespb.Markdown {
+	if ns.Valid {
+		return newMarkdown(ns.String)
+	}
+	return nil
+}
+
+func newUri(value string) *datatypespb.Uri {
+	return &datatypespb.Uri{Value: value}
+}
+
+func newNullableUri(ns sql.NullString) *datatypespb.Uri {
+	if ns.Valid {
+		return newUri(ns.String)
+	}
+	return nil
+}
+
+func newXhtml(value string) *datatypespb.Xhtml {
+	return &datatypespb.Xhtml{Value: value}
+}

internal/app/handlers.go

@@ -9,6 +9,9 @@ import (
 	"net/http"
 	"strconv"
 
+	"github.com/google/fhir/go/fhirversion"
+	"github.com/google/fhir/go/jsonformat"
+	"github.com/skylight-hq/phinvads-go/internal/app/fhir/r5"
 	"github.com/skylight-hq/phinvads-go/internal/database/models"
 	"github.com/skylight-hq/phinvads-go/internal/database/models/xo"
 	customErrors "github.com/skylight-hq/phinvads-go/internal/errors"
@@ -74,6 +77,58 @@ func (app *Application) getCodeSystemByID(w http.ResponseWriter, r *http.Request
 	json.NewEncoder(w).Encode(codeSystem)
 }
 
+func (app *Application) getFHIRCodeSystemByID(w http.ResponseWriter, r *http.Request) {
+	rp := app.repository
+
+	id := r.PathValue("id")
+	id_type, err := determineIdType(id)
+	if err != nil {
+		customErrors.BadRequest(w, r, err, app.logger)
+		return
+	}
+
+	var codeSystem *xo.CodeSystem
+	if id_type == "oid" {
+		codeSystem, err = rp.GetCodeSystemByOID(r.Context(), id)
+	} else {
+		codeSystem, err = rp.GetCodeSystemByID(r.Context(), id)
+	}
+	if err != nil {
+		if errors.Is(err, sql.ErrNoRows) {
+			errorString := fmt.Sprintf("Error: Code System %s not found", id)
+			dbErr := &customErrors.DatabaseError{
+				Err:    err,
+				Msg:    errorString,
+				Method: "getCodeSystemById",
+				Id:     id,
+			}
+			dbErr.NoRows(w, r, err, app.logger)
+		} else {
+			customErrors.ServerError(w, r, err, app.logger)
+		}
+		return
+	}
+
+	w.Header().Set("Content-Type", "application/json")
+
+	fhirCodeSystem, err := r5.SerializeCodeSystemToFhir(codeSystem)
+	if err != nil {
+		customErrors.ServerError(w, r, err, app.logger)
+	}
+
+	marshaller, err := jsonformat.NewMarshaller(false, "", "", fhirversion.R4)
+	if err != nil {
+		customErrors.ServerError(w, r, err, app.logger)
+	}
+
+	fhirJson, err := marshaller.MarshalResource(fhirCodeSystem)
+	if err != nil {
+		customErrors.ServerError(w, r, err, app.logger)
+	}
+
+	w.Write(fhirJson)
+}
+
 func (app *Application) getAllViews(w http.ResponseWriter, r *http.Request) {
 	views, err := models.GetAllViews(r.Context(), app.db)
 	if err != nil {
@@ -420,7 +475,6 @@ func (app *Application) getAllHotTopics(w http.ResponseWriter, r *http.Request)
 	rp := app.repository
 
 	hotTopics, err := rp.GetAllHotTopics(r.Context())
-
 	if err != nil {
 		var (
 			method = r.Method
@@ -477,7 +531,7 @@ func (app *Application) search(w http.ResponseWriter, r *http.Request, searchTer
 	rp := app.repository
 	logger := app.logger
 
-	var result = &models.CodeSystemResultRow{}
+	result := &models.CodeSystemResultRow{}
 	defaultPageCount := 5
 
 	// retrieve code system

internal/app/routes.go

@@ -41,6 +41,8 @@ func (app *Application) routes() http.Handler {
 	mux.HandleFunc("GET /api/value-set-concepts/value-set-version/{valueSetVersionId}", app.getValueSetConceptsByVersionID)
 	mux.HandleFunc("GET /api/value-set-concepts/code-system/{codeSystemOid}", app.getValueSetConceptsByCodeSystemOID)
 
+	mux.HandleFunc("GET /r5/CodeSystem/{id}", app.getFHIRCodeSystemByID)
+
 	mux.HandleFunc("GET /toggle-banner/{action}", app.handleBannerToggle)
 	mux.HandleFunc("GET /load-hot-topics", app.getAllHotTopics)