fix: incorrect way to convert 00080061 to FHIR

- Refactor, functional `getModalitiesInStudy`
- Fix, set modalities in study when processing DICOM to FHIR
- Fix, missing set endpoint of FHIR ImagingStudy
- Remove read value of 00080061 and set `study.modality`
in `DICOM2FHIRImagingStudy.js` file
> The 00080061 may not present in DICOM instance,
> it is calculate from DB and use for querying

api/dicom-web/controller/STOW-RS/storeInstance.js

@@ -196,7 +196,7 @@ async function dicomToFHIR(req, dicomJson, uidObj) {
         let protocol = req.secure ? "https" : "http";
         dicomFHIRConverter.dicomWeb.retrieveStudiesUrl = `${protocol}://${req.headers.host}/${process.env.DICOMWEB_API}/studies`;
 
-        dicomFHIRConverter.dicomJsonToFHIR(dicomJson);
+        await dicomFHIRConverter.dicomJsonToFHIR(dicomJson);
 
         dicomFHIRConverter.fhir.baseUrl = process.env.FHIRSERVER_BASE_URL;
         await dicomFHIRConverter.postDicomFhir();

models/FHIR/DICOM/DICOMToFHIR.js

@@ -6,6 +6,7 @@ const { fhirLogger } = require("../../../utils/log");
 const { dicomJsonToFHIRImagingStudy } = require("./DICOMToFHIRImagingStudy");
 const { dicomJsonToFHIRPatient } = require("./DICOMToFHIRPatient");
 const { dicomJsonToFHIREndpoint } = require("./DICOMToFHIREndpoint");
+const { getModalitiesInStudy } = require("../../../models/mongodb/models/dicom");
 
 class DICOMFHIRConverter {
     constructor() {
@@ -30,7 +31,7 @@ class DICOMFHIRConverter {
      *
      * @param {JSON} dicomJson The DICOM Json model
      */
-    dicomJsonToFHIR(dicomJson) {
+    async dicomJsonToFHIR(dicomJson) {
         let patient = dicomJsonToFHIRPatient(dicomJson);
         let imagingStudy = dicomJsonToFHIRImagingStudy(dicomJson);
         if (!imagingStudy.subject.reference.includes(patient.id)) {
@@ -42,10 +43,35 @@ class DICOMFHIRConverter {
         );
         this.dicomFHIR.patient = patient;
         this.dicomFHIR.imagingStudy = imagingStudy;
+        await this.setModalitiesInStudy(dicomJson);
         this.dicomFHIR.endpoint = endpoint;
+        this.dicomFHIR.imagingStudy.endpoint = [
+            {
+                reference: `Endpoint/${this.dicomFHIR.endpoint.id}`,
+                type: "Endpoint"
+            }
+        ];
         return this.dicomFHIR;
     }
 
+    async setModalitiesInStudy(dicomJson) {
+        let studyModalities = [];
+        let modalitiesInStudy = await getModalitiesInStudy({
+            studyUID: dicomJson["0020000D"].Value[0]
+        });
+        if (modalitiesInStudy.length > 0) {
+            let modalitiesInStudyValue = modalitiesInStudy[0]["00080061"].Value;
+            for(let i = 0 ; i < modalitiesInStudyValue.length; i++) {
+                let modality = {
+                    system: "http://dicom.nema.org/resources/ontology/DCM",
+                    code: modalitiesInStudyValue[i]
+                };
+                studyModalities.push(modality);
+            }
+            this.dicomFHIR.imagingStudy.modality = studyModalities;
+        }
+    }
+
     //#region ImagingStudy
 
     async getImagingStudyFromFHIRServer() {

models/FHIR/DICOM/DICOMToFHIRImagingStudy.js

@@ -213,7 +213,6 @@ function dicomJsonToFHIRImagingStudy(dicomJson) {
         dcm2jsonV8.dcmString(dicomJson, "00200010")
     ];
     studyObj.identifier = getStudyIdentifiers(identifiers);
-    studyObj.modality = dcm2jsonV8.dcmString(dicomJson, "00080061");
 
     let patientId = dcm2jsonV8.dcmString(dicomJson, "00100020");
     studyObj.subject.identifier = new Identifier();

models/mongodb/models/dicom.js

@@ -127,39 +127,44 @@ dicomModelSchema.post("findOneAndUpdate", async function (doc) {
     });
 });
 
-async function updateStudyModalitiesInStudy(doc) {
-    try {
-        let modalitiesInStudy = await mongoose.model("dicom").aggregate([
-            {
-                $match: {
-                    studyUID: doc.studyUID
-                }
-            },
-            {
-                $group: {
-                    _id: "$studyUID",
-                    modalitiesInStudy: {
-                        $addToSet: "$00080060.Value"
-                    }
+async function getModalitiesInStudy(doc) {
+    let modalitiesInStudy = await mongoose.model("dicom").aggregate([
+        {
+            $match: {
+                studyUID: doc.studyUID
+            }
+        },
+        {
+            $group: {
+                _id: "$studyUID",
+                modalitiesInStudy: {
+                    $addToSet: "$00080060.Value"
                 }
-            },
-            {
-                $project: {
-                    "00080061": {
-                        vr: "CS",
-                        Value: {
-                            $reduce: {
-                                input: "$modalitiesInStudy",
-                                initialValue: [],
-                                in: {
-                                    $concatArrays: ["$$value", "$$this"]
-                                }
+            }
+        },
+        {
+            $project: {
+                "00080061": {
+                    vr: "CS",
+                    Value: {
+                        $reduce: {
+                            input: "$modalitiesInStudy",
+                            initialValue: [],
+                            in: {
+                                $concatArrays: ["$$value", "$$this"]
                             }
                         }
                     }
                 }
             }
-        ]);
+        }
+    ]);
+    return modalitiesInStudy;
+}
+
+async function updateStudyModalitiesInStudy(doc) {
+    try {
+        let modalitiesInStudy = await getModalitiesInStudy(doc);
         await mongoose.model("dicomStudy").findOneAndUpdate(
             {
                 studyUID: doc.studyUID
@@ -301,3 +306,4 @@ async function updateStudyNumberOfStudyRelatedInstance(doc) {
 
 let dicomModel = mongoose.model("dicom", dicomModelSchema, "dicom");
 module.exports = dicomModel;
+module.exports.getModalitiesInStudy = getModalitiesInStudy;