feat: add new method for $validate API

- add `fhir-validator` - add `refreshResourceResolver` to call C# API to reload profiles - add `storeValidationFile` to store `StructureDefinition`, `ValueSet`, `CodeSystem` - add `fetchValueSet` to get `ValueSet` resource by URL - add `fetchCodeSystem` to get `CodeSystem` resource by URL - add `validateByProfile` to validate resource by specific profile URL in URL path - add `validateByMetaProfile` to validate resource by profiles URL from meta.profile - add `FHIRValidationFiles` MongoDB schema to store data about validation files - add schedule to update validation files in MongoDB - The validation workflow note can retrieve from https://imgur.com/a/SjklQTR > feat: 新增新的方法處理 `$validate` API > - 新增 `fhir-validator` > - 新增`refreshResourceResolver`呼叫 C# API讓Server重新讀取profiles > - 新增`storedValidationFile` 儲存`StructureDefinition`, `ValueSet`, `CodeSystem` > - 新增 `fetchValueSet` 將指定 URL 的 `ValueSet` 爬下來並轉為JSON > - 新增 `fetchCodeSystem` 將指定 URL 的 `CodeSystem` 爬下來並轉為JSON > - 新增 `validateByProfile` 使用在URL指定的 profile 驗證 resource > - 新增 `validateByMetaProfile` 使用 resource 當中的 meta.profile 進行驗證 > - 新增 `FHIRValidationFiles` MongoDB schema 儲存與驗證相關的資料 > - 驗證流程 https://imgur.com/a/SjklQTR
Chinlinlee · Mar 6, 2022 · 5b82908 · 5b82908
1 parent 9c59674
commit 5b82908
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diff --git a/api/FHIR/Patient/index.js b/api/FHIR/Patient/index.js
@@ -82,7 +82,7 @@ if (_.get(config, "Patient.interaction.create", true)) {
     router.post('/', require('./controller/postPatient'));
 }
 
-//router.post('/([\$])validate', require('./controller/postPatientValidate'));
+router.post('/([\$])validate', require('./controller/postPatientValidate'));
 
 if (_.get(config, "Patient.interaction.update", true)) {
     router.put('/:id', require("./controller/putPatient"));

diff --git a/api/FHIRApiService/$validate.js b/api/FHIRApiService/$validate.js
@@ -1,10 +1,11 @@
 const _ = require('lodash');
-const fetch = require('node-fetch');
 const FHIR = require('fhir').Fhir;
-const fhirVersions = require('fhir').Versions;
-const ParseConformance = require('fhir/parseConformance').ParseConformance;
-const { handleError, issue, OperationOutcome } = require('../../models/FHIR/httpMessage');
-const { getDeepKeys } = require('../apiService');
+const { handleError } = require('../../models/FHIR/httpMessage');
+const { validateByProfile, validateByMetaProfile } = require('../../models/FHIR/fhir-validator');
+const { logger } = require('../../utils/log');
+const path = require('path');
+const PWD_FILENAME = path.relative(process.cwd(), __filename);
+
 /**
  * 
  * @param {import('express').Request} req 
@@ -21,15 +22,23 @@ module.exports = async function (req, res, resourceType) {
         }
         return res.status(code).send(item);
     };
-    let operationOutcomeMessage;
-    return doRes(400, {
-        "resourceType": "OperationOutcome",
-        "issue": [
-            {
-                "severity": "processing",
-                "code": "processing",
-                "diagnostics": "$validate is not support"
-            }
-        ]
-    });
+    try {
+        let operationOutcomeMessage;
+        let profileUrl = _.get(req.query, "profile");
+        if (profileUrl) {
+            operationOutcomeMessage = await validateByProfile(profileUrl, req.body);
+        } else {
+            operationOutcomeMessage = await validateByMetaProfile(req.body);
+        }
+        let haveError = (_.get(operationOutcomeMessage, "issue")) ? operationOutcomeMessage.issue.find(v=> v.severity === "error") : false;
+        if (haveError) {
+            return doRes(412, operationOutcomeMessage);
+        }
+        return doRes(200, operationOutcomeMessage);
+    } catch(e) {
+        let errorStr = JSON.stringify(e, Object.getOwnPropertyNames(e));
+        logger.error(`[Error: ${errorStr}] [From-File: ${PWD_FILENAME}]`);
+        let operationOutcomeError = handleError.exception(errorStr);
+        return doRes(500, operationOutcomeError);
+    }
 };
diff --git a/api_generator/API_Generator_V2.js b/api_generator/API_Generator_V2.js
@@ -317,7 +317,7 @@ function generateAPI(option) {
             router.post('/', require('./controller/post${res}'));
         }
 
-        //router.post('/([\\$])validate', require('./controller/post${res}Validate'));
+        router.post('/([\\$])validate', require('./controller/post${res}Validate'));
 
         if (_.get(config, "${res}.interaction.update", true)) {
             router.put('/:id', require("./controller/put${res}"));

diff --git a/models/FHIR/fhir-validator.js b/models/FHIR/fhir-validator.js
@@ -0,0 +1,182 @@
+const _ = require('lodash');
+const fetch = require('node-fetch');
+const mongodb = require('../mongodb');
+const { handleError, issue, OperationOutcome } = require('./httpMessage');
+const flatten = require('flat');
+const hash = require('object-hash');
+const fs = require('fs');
+const nodeUrl = require('url');
+const https = require('https');
+const { logger } = require('../../utils/log');
+const path = require('path');
+const PWD_FILENAME = path.relative(process.cwd(), __filename);
+const VALIDATION_API_URL = process.env.VALIDATION_API_URL;
+
+/**
+ * @param {string} profileUrl 
+ */
+async function validateByProfile(profileUrl, resourceContent) {
+    try {
+        await storeValidationFile(profileUrl);
+        await refreshResourceResolver();
+        let validation = await validate([profileUrl], resourceContent);
+        if (validation.status) {
+            return JSON.parse(validation.data);
+        } else {
+            throw new Error(validation.data);
+        }
+    } catch(e) {
+        throw e;
+    }
+}
+
+async function validateByMetaProfile(resourceContent) {
+    try {
+        let metaProfile = _.get(resourceContent, "meta.profile");
+        if (metaProfile) {
+            for (let i = 0 ; i< metaProfile.length; i++) {
+                let profileUrl = metaProfile[i];
+                await storeValidationFile(profileUrl);
+            }
+            await refreshResourceResolver();
+            let validation = await validate(metaProfile, resourceContent);
+            if (validation.status) {
+                return JSON.parse(validation.data);
+            } else {
+                throw new Error(validation.data);
+            }
+        }
+    } catch(e) {
+        throw e;
+    }
+}
+
+/**
+ * Store StructureDefinition, ValueSet, CodeSystem json when not exists in MongoDB.
+ * @param {string} url 
+ */
+ async function storeValidationFile(url) {
+    try {
+        let validationFile = await mongodb.FHIRValidationFiles.findOne({
+            url: url
+        });
+        if (!validationFile) {
+            logger.info(`[Info: Fetch Profile From URL: ${url}]`);
+            let fetchRes = await fetch(url, {
+                headers: {
+                    "accept": "application/fhir+json"
+                }
+            });
+            let resJson = await fetchRes.json();
+            if (resJson.resourceType === "StructureDefinition") {
+                await fetchValueSet(resJson);
+            } else if (resJson.resourceType === "ValueSet") {
+                await fetchCodeSystem(resJson);
+            }
+            let contentHash = hash(resJson);
+            let storePath = path.join(process.env.VALIDATION_FILES_ROOT_PATH, hash({url:url}) + ".json");
+            fs.writeFile(path.resolve(storePath), JSON.stringify(resJson), ()=> {});
+            let validationFileObj = {
+                url: url,
+                hash: contentHash,
+                path: storePath,
+                id: resJson.id
+            };
+            await mongodb.FHIRValidationFiles.findOneAndUpdate({
+                url: url
+            }, { $set: validationFileObj}, {
+                upsert: true
+            });
+        }
+    } catch(e) {
+        throw e;
+    }
+}
+
+/**
+ * Store value set json when not exists in MongoDB.
+ * @param {JSON} content 
+ */
+ async function fetchValueSet(content) {
+    let flattenContent = flatten(content);
+    let valueSetKeys = Object.keys(flattenContent).filter( 
+        key=> key.includes("binding.valueSet")
+    );
+    for (let key of valueSetKeys) {
+        let valueSetUri = _.get(content, key);
+        await storeValidationFile(valueSetUri);
+    }
+}
+
+/**
+ * Store code system json when not exists in MongoDB.
+ * @param {JSON} valueSet 
+ */
+async function fetchCodeSystem(valueSet) {
+    let flattenValueSet= flatten(valueSet);
+    let codeSystemKeys = Object.keys(flattenValueSet).filter( 
+        key=> key.endsWith(".system")
+    );
+    for (let key of codeSystemKeys) {
+        let codeSystemUri = _.get(valueSet, key);
+        if (codeSystemUri.includes("CodeSystem"))
+        await storeValidationFile(codeSystemUri);
+    }
+}
+
+/**
+ * Call C# validator API server to reload profiles.
+ */
+async function refreshResourceResolver() {
+    try {
+        const httpsAgent = new https.Agent({
+            rejectUnauthorized: false
+        }); 
+        let APIUrl = new nodeUrl.URL("/api/refreshresourceresolver" , VALIDATION_API_URL).href;
+        let fetchRes = await fetch(APIUrl, {
+            method: "POST",
+            agent: httpsAgent
+        });
+        logger.info(`[Info: Refresh C# Validator Resource Resolver] [Content: ${JSON.stringify(await fetchRes.json())}]`);
+    } catch(e) {
+        throw e;
+    }
+}
+
+/**
+ * Call C# API server to validate with profiles.
+ * @param {Array<string>} profile The string array of profiles URL.
+ * @param {JSON} resourceContent The FHIR resource JSON object.
+ * @return {JSON}
+ */
+async function validate(profile, resourceContent) {
+    try {
+        const httpsAgent = new https.Agent({
+            rejectUnauthorized: false
+        });      
+        let APIUrl = new nodeUrl.URL("/api/validate" , VALIDATION_API_URL).href;
+        let body = {
+            profile: profile,
+            resourceJson: JSON.stringify(resourceContent)
+        };
+        let fetchRes = await fetch(APIUrl, {
+            method: "POST",
+            body: JSON.stringify(body),
+            agent: httpsAgent,
+            headers: {
+                'content-type': 'application/json'
+            }
+        });
+        let fetchResJson = await fetchRes.json();
+        logger.info(`[Info: Call Validation function from C# successfully] [URL: ${APIUrl}]`);
+        return fetchResJson;
+    } catch(e) {
+        throw e;
+    }
+}
+
+module.exports.validateByProfile = validateByProfile;
+module.exports.validateByMetaProfile = validateByMetaProfile;
+module.exports.refreshResourceResolver = refreshResourceResolver;
+module.exports.fetchValueSet = fetchValueSet;
+module.exports.fetchCodeSystem = fetchCodeSystem;
diff --git a/models/FHIR/schedule-update-validation-files.js b/models/FHIR/schedule-update-validation-files.js
@@ -0,0 +1,78 @@
+require('dotenv').config({
+    path: `${process.cwd()}/.env`
+});
+const _ = require('lodash');
+const fetch = require('node-fetch');
+const mongodb = require('../mongodb');
+const hash = require('object-hash');
+const fs = require('fs');
+const { fetchCodeSystem, fetchValueSet, refreshResourceResolver } = require('./fhir-validator');
+const { logger } = require('../../utils/log');
+const path = require('path');
+const PWD_FILENAME = path.relative(process.cwd(), __filename);
+const schedule = require('node-schedule');
+
+/**
+ * Store StructureDefinition, ValueSet, CodeSystem json when not exists in MongoDB.
+ * @param {JSON} structureDefinition
+ */
+ async function updateValidationFile(url, resJson, contentHash) {
+    try {
+        if (resJson.resourceType === "StructureDefinition") {
+            await fetchValueSet(resJson);
+        } else if (resJson.resourceType === "ValueSet") {
+            await fetchCodeSystem(resJson);
+        }
+        let storePath = path.join(process.env.VALIDATION_FILES_ROOT_PATH, hash({url:url}) + ".json");
+        fs.writeFile(path.resolve(storePath), JSON.stringify(resJson), ()=> {});
+        let validationFileObj = {
+            url: url,
+            hash: contentHash,
+            path: storePath,
+            id: resJson.id
+        };
+        await mongodb.FHIRValidationFiles.findOneAndUpdate({
+            url: url
+        }, { $set: validationFileObj}, {
+            upsert: true
+        });
+    } catch(e) {
+        throw e;
+    }
+}
+
+async function iterateUpdateValidationFiles() {
+    try {
+        let validationFiles = await mongodb.FHIRValidationFiles.find({}).limit(10);
+        while(validationFiles.length > 0) {
+            for(let validationFileObj of validationFiles) {
+                let url = validationFileObj.url;
+                logger.info(`[Info: Fetch Profile From URL: ${url}]`);
+                let fetchRes = await fetch(url, {
+                    headers: {
+                        "accept": "application/fhir+json"
+                    }
+                });
+                let resJson = await fetchRes.json();
+                let contentHash = hash(resJson);
+                if (validationFileObj.hash != contentHash) {
+                    await updateValidationFile(url, resJson, contentHash);
+                }
+            }
+            let lastId = validationFiles[validationFiles.length - 1]._id;
+            validationFiles = await mongodb.FHIRValidationFiles.find({
+                _id: {
+                    $gt: lastId
+                }
+            })
+            .limit(10);
+        }
+    } catch(e) {
+        logger.error(e);
+    }
+}
+
+const updateValidationFileJob = schedule.scheduleJob('0 0 0 * *', async function(){
+    await iterateUpdateValidationFiles();
+    await refreshResourceResolver();
+});
diff --git a/models/mongodb/staticModel/FHIRValidationFiles.js b/models/mongodb/staticModel/FHIRValidationFiles.js
@@ -0,0 +1,35 @@
+module.exports = function (mongodb) {
+    let FHIRValidationFilesSchema = mongodb.Schema({
+        url: {
+            type: String,
+            default: void 0
+        },
+        hash: {
+            type: String ,
+            default : void 0
+        },
+        path: {
+            type: String,
+            default : void 0
+        },
+        id: {
+            type: String,
+            default : void 0
+        }
+    } , {
+        versionKey : false
+    });
+    FHIRValidationFilesSchema.index({
+        "url": 1,
+        "hash": 1
+    }, {
+        background: true
+    });
+    FHIRValidationFilesSchema.index({
+        "id": 1
+    }, {
+        background: true
+    });
+    let FHIRValidationFilesModel = mongodb.model('FHIRValidationFiles', FHIRValidationFilesSchema, 'FHIRValidationFiles');
+    return FHIRValidationFilesModel;
+};