chore: update generated Patient models, API files

api/FHIR/Patient/controller/getPatient.js

@@ -3,7 +3,7 @@ const mongodb = require('models/mongodb');
 const {
     createBundle
 } = require('models/FHIR/func');
-const queryBuild = require('../../../../models/FHIR/queryBuild.js');
+const queryBuild = require('models/FHIR/queryBuild.js');
 const {
     handleError
 } = require('models/FHIR/httpMessage');
@@ -22,6 +22,7 @@ const paramsSearch = {
         delete query["_id"];
     }
 }
+
 paramsSearch["_lastUpdated"] = (query) => {
     if (!_.isArray(query["_lastUpdated"])) {
         query["_lastUpdated"] = [query["_lastUpdated"]]
@@ -35,7 +36,6 @@ paramsSearch["_lastUpdated"] = (query) => {
     }
     delete query["_lastUpdated"];
 }
-
 paramsSearchFields["address"] = ["address"];
 paramsSearch["address"] = (query) => {
     if (!_.isArray(query["address"])) {
@@ -164,7 +164,7 @@ paramsSearch["birthdate"] = (query) => {
     }
     delete query["birthdate"];
 }
-paramsSearchFields["email"] = ["telecom.where(system='email')"];
+paramsSearchFields["email"] = ["telecom"];
 paramsSearch["email"] = (query) => {
     if (!_.isArray(query["email"])) {
         query["email"] = [query["email"]]
@@ -240,7 +240,7 @@ paramsSearch["given"] = (query) => {
     }
     delete query['given'];
 }
-paramsSearchFields["phone"] = ["telecom.where(system='phone')"];
+paramsSearchFields["phone"] = ["telecom"];
 paramsSearch["phone"] = (query) => {
     if (!_.isArray(query["phone"])) {
         query["phone"] = [query["phone"]]
@@ -314,7 +314,7 @@ paramsSearch["active"] = (query) => {
     }
     delete query['active'];
 }
-paramsSearchFields["deceased"] = ["deceased.exists() and Patient.deceased != false"];
+paramsSearchFields["deceased"] = "deceased";
 paramsSearch["deceased"] = (query) => {
     if (!_.isArray(query["deceased"])) {
         query["deceased"] = [query["deceased"]]

api/FHIR/Patient/index.js

@@ -29,7 +29,7 @@ router.use((req, res, next) => {
         if (req.headers["content-type"]) {
             if (req.headers["content-type"].includes("xml")) {
                 res.set('Content-Type', 'application/fhir+xml');
-                if (req.method == "POST") {
+                if (req.method == "POST" || req.method == "PUT") {
                     let Fhir = new FHIR();
                     req.body = Fhir.xmlToObj(req.body);
                 }
@@ -50,7 +50,9 @@ router.use((req, res, next) => {
     }
 });
 
-router.use(user.tokenAuthentication);
+if (process.env.ENABLE_TOKEN_AUTH == "true") {
+    router.use(user.tokenAuthentication);
+}
 
 if (_.get(config, "Patient.interaction.search", true)) {
     router.get('/', FHIRValidateParams({

models/mongodb/FHIRDataTypesSchema/Patient_Communication.js

@@ -18,5 +18,9 @@ module.exports = new mongoose.Schema({
     },
     preferred: boolean
 }, {
-    _id: false
+    _id: false,
+    id: false,
+    toObject: {
+        getters: true
+    }
 });

models/mongodb/FHIRDataTypesSchema/Patient_Contact.js

@@ -45,5 +45,9 @@ module.exports = new mongoose.Schema({
         default: void 0
     }
 }, {
-    _id: false
+    _id: false,
+    id: false,
+    toObject: {
+        getters: true
+    }
 });

models/mongodb/FHIRDataTypesSchema/Patient_Link.js

@@ -21,5 +21,9 @@ module.exports = new mongoose.Schema({
         default: void 0
     }
 }, {
-    _id: false
+    _id: false,
+    id: false,
+    toObject: {
+        getters: true
+    }
 });

models/mongodb/model/Patient.js

@@ -11,7 +11,7 @@ const boolean = require('../FHIRDataTypesSchema/boolean');
 const HumanName = require('../FHIRDataTypesSchema/HumanName');
 const ContactPoint = require('../FHIRDataTypesSchema/ContactPoint');
 const date = require('../FHIRDataTypesSchema/date');
-const string = require('../FHIRDataTypesSchema/string');
+const dateTime = require('../FHIRDataTypesSchema/dateTime');
 const Address = require('../FHIRDataTypesSchema/Address');
 const CodeableConcept = require('../FHIRDataTypesSchema/CodeableConcept');
 const Attachment = require('../FHIRDataTypesSchema/Attachment');
@@ -61,7 +61,7 @@ module.exports = function() {
         },
         birthDate: date,
         deceasedBoolean: boolean,
-        deceasedDateTime: string,
+        deceasedDateTime: dateTime,
         address: {
             type: [Address],
             default: void 0
@@ -112,22 +112,36 @@ module.exports = function() {
         ...id,
         index: true
     }
+    Patient.contained = {
+        type: [Object],
+        default: void 0
+    }
     module.exports.schema = Patient;
-    const PatientSchema = new mongoose.Schema(Patient, {
+    let schemaConfig = {
         toObject: {
             getters: true
         },
         toJSON: {
             getters: true
         },
         versionKey: false
-    });
+    };
+    if (process.env.MONGODB_IS_SHARDING_MODE == "true") {
+        schemaConfig["shardKey"] = {
+            id: 1
+        };
+    }
+    const PatientSchema = new mongoose.Schema(Patient, schemaConfig);
 
 
     PatientSchema.methods.getFHIRField = function() {
         let result = this.toObject();
         delete result._id;
         delete result.__v;
+        if (_.get(result, "myCollection")) {
+            let tempCollectionField = _.cloneDeep(result["myCollection"]);
+            _.set(result, "collection", tempCollectionField);
+        }
         return result;
     }
 
@@ -136,7 +150,7 @@ module.exports = function() {
         let storedID = await mongodb.FHIRStoredID.findOne({
             id: this.id
         });
-        if (storedID) {
+        if (storedID && process.env.ENABLE_CHECK_ALL_RESOURCE_ID == "true") {
             if (storedID.resourceType == "Patient") {
                 const docInHistory = await mongodb.Patient_history.findOne({
                         id: this.id
@@ -164,8 +178,8 @@ module.exports = function() {
         let item = result.toObject();
         delete item._id;
         let version = item.meta.versionId;
+        let port = (process.env.FHIRSERVER_PORT == "80" || process.env.FHIRSERVER_PORT == "443") ? "" : `:${process.env.FHIRSERVER_PORT}`;
         if (version == "1") {
-            let port = (process.env.FHIRSERVER_PORT == "80" || process.env.FHIRSERVER_PORT == "443") ? "" : `:${process.env.FHIRSERVER_PORT}`;
             _.set(item, "request", {
                 "method": "POST",
                 url: `http://${process.env.FHIRSERVER_HOST}${port}/${process.env.FHIRSERVER_APIPATH}/Patient/${item.id}/_history/${version}`
@@ -174,6 +188,15 @@ module.exports = function() {
                 status: "201"
             });
             let createdDocs = await mongodb['Patient_history'].create(item);
+        } else {
+            _.set(item, "request", {
+                "method": "PUT",
+                url: `http://${process.env.FHIRSERVER_HOST}${port}/${process.env.FHIRSERVER_APIPATH}/Patient/${item.id}/_history/${version}`
+            });
+            _.set(item, "response", {
+                status: "200"
+            });
+            let createdDocs = await mongodb['Patient_history'].create(item);
         }
         await mongodb.FHIRStoredID.findOneAndUpdate({
             id: result.id
@@ -188,7 +211,7 @@ module.exports = function() {
     PatientSchema.pre('findOneAndUpdate', async function(next) {
         const docToUpdate = await this.model.findOne(this.getFilter());
         let version = Number(docToUpdate.meta.versionId);
-        this._update.$set.meta = {};
+        this._update.$set.meta = docToUpdate.meta;
         this._update.$set.meta.versionId = String(version + 1);
         this._update.$set.meta.lastUpdated = new Date();
         return next();

models/mongodb/model/Patient_history.js

@@ -34,10 +34,6 @@ module.exports = function() {
     PatientHistorySchema.methods.getFHIRField = function() {
         let result = this.toObject();
         delete result._id;
-        let version = result.__v;
-        if (version) {
-            _.set(result, 'meta.versionId', version.toString());
-        }
         delete result.__v;
         delete result['name._id'];
         delete result['request'];
@@ -47,10 +43,6 @@ module.exports = function() {
     PatientHistorySchema.methods.getFHIRBundleField = function() {
         let result = this.toObject();
         delete result._id;
-        let version = result.__v;
-        if (version) {
-            _.set(result, 'meta.versionId', version.toString());
-        }
         delete result.__v;
         delete result['name._id'];
         return result;