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feat: create FHIR resource when doing
STOW-RS
- Add logger for FHIR - Not append await on `dicomToFHIR`, if FHIR is not operate completly, Please check the log. - Add class to operate dicom convert to FHIR ImagingStudy, Patient, Endpoint
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,264 @@ | ||
| const { URL } = require('url'); | ||
| const axios = require('axios').default; | ||
| const _ = require('lodash'); | ||
| const { urlJoin } = require('../../../utils/url'); | ||
| const { fhirLogger } = require('../../../utils/log'); | ||
| const { | ||
| dicomJsonToFHIRImagingStudy | ||
| } = require('./DICOMToFHIRImagingStudy'); | ||
| const { | ||
| dicomJsonToFHIRPatient | ||
| } = require('./DICOMToFHIRPatient'); | ||
| const { | ||
| dicomJsonToFHIREndpoint | ||
| } = require('./DICOMToFHIREndpoint'); | ||
|
|
||
| class DICOMFHIRConverter { | ||
| constructor() { | ||
| this.dicomFHIR = { | ||
| patient: {}, | ||
| endpoint: {}, | ||
| imagingStudy: {} | ||
| }; | ||
| this.fhirPatient = {}; | ||
| this.fhirEndpoint = {}; | ||
| this.fhirImagingStudy = {}; | ||
| this.dicomWeb = { | ||
| retrieveStudiesUrl: "", | ||
| name: "" | ||
| }; | ||
| this.fhir = { | ||
| baseUrl: "" | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * | ||
| * @param {JSON} dicomJson The DICOM Json model | ||
| */ | ||
| dicomJsonToFHIR(dicomJson) { | ||
| let patient = dicomJsonToFHIRPatient(dicomJson); | ||
| let imagingStudy = dicomJsonToFHIRImagingStudy(dicomJson); | ||
| if ( !imagingStudy.subject.reference.includes(patient.id) ) { | ||
| imagingStudy.subject.reference = `Patient/${patient.id}`; | ||
| } | ||
| let endpoint = dicomJsonToFHIREndpoint(this.dicomWeb.retrieveStudiesUrl, this.dicomWeb.name); | ||
| this.dicomFHIR.patient = patient; | ||
| this.dicomFHIR.imagingStudy = imagingStudy; | ||
| this.dicomFHIR.endpoint = endpoint; | ||
| return this.dicomFHIR; | ||
| } | ||
|
|
||
| //#region ImagingStudy | ||
|
|
||
| async getImagingStudyFromFHIRServer() { | ||
| try { | ||
| let getUrl = urlJoin(`/ImagingStudy`, this.fhir.baseUrl); | ||
| let getURLObj = new URL(getUrl); | ||
| let identifier = this.dicomFHIR.imagingStudy.identifier.find(v=> v.system === "urn:dicom:uid"); | ||
| fhirLogger.info(`[FHIR] [Get ImagingStudy from FHIR server, identifier: ${identifier.value}]`); | ||
| getURLObj.searchParams.append("identifier", identifier.value); | ||
| let { data } = await axios.get(getURLObj.href, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json" | ||
| } | ||
| }); | ||
| let fhirBundleEntry = data.entry; | ||
| if (_.isUndefined(fhirBundleEntry)) return undefined; | ||
| else if (_.isArray(data.entry) && data.entry.length === 0) return undefined; | ||
| return data.entry.pop(); | ||
| } catch(e) { | ||
| if (e.isAxiosError) { | ||
| console.log(e.response); | ||
| } else { | ||
| console.error(e); | ||
| } | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * POST the imagingStudy resource to FHIR server | ||
| */ | ||
| async createImagingStudy() { | ||
| try { | ||
| let postUrl = urlJoin(`/ImagingStudy`, this.fhir.baseUrl); | ||
| let { data } = await axios.post(postUrl, this.dicomFHIR.imagingStudy, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json", | ||
| "Accept": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| async updateImagingStudy(existImagingStudy) { | ||
| try { | ||
| let identifier = existImagingStudy.identifier.find(v=> v.system === "urn:dicom:uid"); | ||
| fhirLogger.info(`[FHIR] [ImagingStudy exists, identifier: ${identifier.value}, update it]`); | ||
| this.updateExistSeries(existImagingStudy); | ||
| let putUrl = urlJoin(`/ImagingStudy/${existImagingStudy.id}`, this.fhir.baseUrl); | ||
| let { data } = await axios.put(putUrl, existImagingStudy, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json", | ||
| "Accept": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| updateExistSeries(existImagingStudy) { | ||
| let seriesUID = this.dicomFHIR.imagingStudy.series[0].uid; | ||
| let existSeriesIndex = existImagingStudy.series.findIndex(v=> v.uid === seriesUID); | ||
| if (existSeriesIndex !== -1) { | ||
| let existSeries = existImagingStudy.series[existSeriesIndex]; | ||
| let seriesClone = _.cloneDeep(this.dicomFHIR.imagingStudy.series[0]); | ||
| delete seriesClone.instance; | ||
| existSeries = { | ||
| ...existSeries, | ||
| ...seriesClone | ||
| }; | ||
| this.updateExistInstance(existImagingStudy, existSeriesIndex); | ||
| } else { | ||
| if (existImagingStudy.series) { | ||
| existImagingStudy.series.push(this.dicomFHIR.imagingStudy.series[0]); | ||
| this.updateExistInstance(existImagingStudy, existImagingStudy.series.length - 1); | ||
| } | ||
| else { | ||
| existImagingStudy.series = this.dicomFHIR.imagingStudy.series; | ||
| } | ||
| } | ||
| } | ||
|
|
||
| async updateExistInstance(existImagingStudy, seriesIndex) { | ||
| let series = this.dicomFHIR.imagingStudy.series[0]; | ||
| let existSeries = existImagingStudy.series[seriesIndex]; | ||
| let instanceUID = series.instance[0].uid; | ||
| let existInstanceIndex = existSeries.instance.findIndex(v=> v.uid === instanceUID); | ||
| if (existInstanceIndex !== -1) { | ||
| let existInstance = existSeries.instance[existInstanceIndex]; | ||
| existInstance = { | ||
| ...existInstance, | ||
| ...series.instance[0] | ||
| }; | ||
| } else { | ||
| existSeries.instance.push(series.instance[0]); | ||
| } | ||
| } | ||
|
|
||
| //#endregion | ||
|
|
||
| //#region Patient | ||
| async getPatientFromFHIRServer() { | ||
| try { | ||
| let patientID = this.dicomFHIR.patient.id; | ||
| let getUrl = urlJoin(`/Patient/${patientID}`, this.fhir.baseUrl); | ||
| fhirLogger.info(`[FHIR] [Get Patient from FHIR server, id: ${patientID}]`); | ||
| let { data } = await axios.get(getUrl, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| if (e.isAxiosError) { | ||
| if (e.response.status === 404) return undefined; | ||
| console.log(e.response); | ||
| } else { | ||
| console.error(e); | ||
| } | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
|
|
||
| async createPatientClientId() { | ||
| try { | ||
| let patientID = this.dicomFHIR.patient.id; | ||
| let putUrl = urlJoin(`/Patient/${patientID}`, this.fhir.baseUrl); | ||
| fhirLogger.info(`[FHIR] [The Patient id: ${patientID} not exists, creating it]`); | ||
| let { data } = await axios.put(putUrl, this.dicomFHIR.patient, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json", | ||
| "Accept": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| //#endregion | ||
|
|
||
| //#region Endpoint | ||
|
|
||
| async getEndpointFromFHIRServer() { | ||
| try { | ||
| let endpointID = this.dicomWeb.name; | ||
| let getUrl = urlJoin(`/Endpoint/${endpointID}`, this.fhir.baseUrl); | ||
| fhirLogger.info(`[FHIR] [Get Endpoint from FHIR server, id: ${endpointID}]`); | ||
| let { data } = await axios.get(getUrl, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json", | ||
| "Accept": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| if (e.isAxiosError) { | ||
| if (e.response.status === 404) return undefined; | ||
| console.log(e.response); | ||
| } else { | ||
| console.error(e); | ||
| } | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| async createEndpointClientId() { | ||
| try { | ||
| let endpointID = this.dicomWeb.name; | ||
| let putUrl = urlJoin(`/Endpoint/${endpointID}`, this.fhir.baseUrl); | ||
| fhirLogger.info(`[FHIR] [The Endpoint id: ${endpointID} not exists, creating it]`); | ||
| let { data } = await axios.put(putUrl, this.dicomFHIR.endpoint, { | ||
| headers: { | ||
| "Content-Type": "application/fhir+json", | ||
| "Accept": "application/fhir+json" | ||
| } | ||
| }); | ||
| return data; | ||
| } catch(e) { | ||
| throw e; | ||
| } | ||
| } | ||
|
|
||
| //#endregion | ||
|
|
||
| async postDicomFhir() { | ||
| //Check patient is exists in FHIR server, if not, create it. | ||
| let patientInFHIRServer = await this.getPatientFromFHIRServer(); | ||
| if (!patientInFHIRServer) await this.createPatientClientId(); | ||
|
|
||
| //Check endpoint is exists in FHIR server, if not, create it. | ||
| let endpointInFHIRServer = await this.getEndpointFromFHIRServer(); | ||
| if (!endpointInFHIRServer) await this.createEndpointClientId(); | ||
|
|
||
| //Check endpoint is exists in FHIR server, if not, create it, otherwise update it. | ||
| let imagingStudyInFHIRServer = await this.getImagingStudyFromFHIRServer(); | ||
| if (imagingStudyInFHIRServer) { //update the exist imagingStudy | ||
| await this.updateImagingStudy(imagingStudyInFHIRServer.resource); | ||
| } else { //create a new imagingStudy | ||
| await this.createImagingStudy(); | ||
| } | ||
| } | ||
| } | ||
|
|
||
|
|
||
| module.exports.DICOMFHIRConverter = DICOMFHIRConverter; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| /*connectionType | ||
| dicom-wado-rs | ||
| dicom-qido-rs | ||
| dicom-stow-rs | ||
| dicon-wado-uri | ||
| direct-project | ||
| */ | ||
|
|
||
| /** | ||
| * | ||
| * @param {string} addressUrl The DICOMWeb URL of study level | ||
| * @param {*} id The unique id of this DICOMWeb URL of PACS server. | ||
| * @returns | ||
| */ | ||
| function dicomJsonToFHIREndpoint(addressUrl, id) { | ||
| let endpoint = { | ||
| "resourceType" : "Endpoint" , | ||
| "status": "active", | ||
| "id" : id , | ||
| connectionType : { | ||
| system : "http://terminology.hl7.org/CodeSystem/endpoint-connection-type" , | ||
| code : "dicom-wado-rs" | ||
| }, | ||
| "payloadType": [ | ||
| { | ||
| "text": "DICOM" | ||
| } | ||
| ], | ||
| "payloadMimeType": [ | ||
| "application/dicom" | ||
| ], | ||
| "address": addressUrl | ||
| } | ||
| return endpoint; | ||
| } | ||
|
|
||
| module.exports.dicomJsonToFHIREndpoint = dicomJsonToFHIREndpoint; |
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