Merge branch 'dev' into main

# Conflicts: # package-lock.json
Chinlinlee · Mar 7, 2022 · ac4fbf5 · ac4fbf5
2 parents a476423 + ff6c2b7
commit ac4fbf5
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Showing 85 changed files with 919 additions and 11,105 deletions.
diff --git a/.eslintrc b/.eslintrc
@@ -13,7 +13,8 @@
         "comma-dangle": ["error", "never"], 
         "no-unused-vars": "off",
         "no-console": 0 ,
-        "no-useless-escape": "off"
+        "no-useless-escape": "off",
+        "no-useless-catch": "off"
     },
     "ignorePatterns": ["public/**", "temp/**", "models/FHIR/fhir/**", "docs/**"]
 }
diff --git a/.gitignore b/.gitignore
@@ -27,4 +27,8 @@ models/mongodb/FHIRDataTypesSchema-New
 config/config.js
 
 #ignore apidoc comment files
-docs/apidoc/apidoc-sources
+docs/apidoc/apidoc-sources
+
+#ignore log files
+/log
+/pm2log
diff --git a/Dockerfile b/Dockerfile
@@ -1,19 +1,18 @@
 FROM keymetrics/pm2:latest-alpine
 
-
 WORKDIR /
 RUN mkdir -p /nodejs/fhir-burni/
 WORKDIR /nodejs/fhir-burni/
 # Bundle APP files
-COPY package*.json /nodejs/fhir-burni/
-COPY . /nodejs/fhir-burni/
+COPY --chown=node:node package*.json /nodejs/fhir-burni/
+COPY --chown=node:node . /nodejs/fhir-burni/
 
 # Install app dependencies
 ENV NPM_CONFIG_LOGLEVEL warn
-RUN npm install
-RUN npm rebuild
+ENV NODE_ENV production
+RUN npm ci --only=production
 
 # Show current folder structure in logs
 #RUN ls -al -R
-
+USER node
 CMD [ "pm2-runtime", "start", "ecosystem.config.js" ]
diff --git a/api/FHIR/Patient/index.js b/api/FHIR/Patient/index.js
@@ -4,7 +4,7 @@ const joi = require('joi');
 const {
     FHIRValidateParams
 } = require('api/validator');
-const FHIR = require('../../../models/FHIR/fhir/fhir').Fhir;
+const FHIR = require('fhir').Fhir;
 const {
     handleError
 } = require('../../../models/FHIR/httpMessage');
@@ -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('../../models/FHIR/fhir/fhir').Fhir;
-const fhirVersions = require('../../models/FHIR/fhir/fhir').Versions;
-const ParseConformance = require('../../models/FHIR/fhir/parseConformance').ParseConformance;
-const { handleError, issue, OperationOutcome } = require('../../models/FHIR/httpMessage');
-const { getDeepKeys } = require('../apiService');
+const FHIR = require('fhir').Fhir;
+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 
@@ -21,101 +22,23 @@ module.exports = async function (req, res, resourceType) {
         }
         return res.status(code).send(item);
     };
-    let operationOutcomeMessage;
-    let query = req.query;
-    let resourceBody = req.body;
-    let profile = _.get(query, "profile");
-    if (profile) {
-        try {
-            let fetchProfileRes = await fetch(profile, {
-                headers: {
-                    "accept": "application/fhir+json"
-                }
-            });
-            let profileJson = await fetchProfileRes.json();
-            _.set(profileJson, "id", resourceType);
-            let parser = new ParseConformance(true, fhirVersions.R4);
-
-            let valueSetKeys =
-                getDeepKeys(profileJson)
-                    .filter(v =>
-                        v.includes("binding.valueSet") //&&
-                        //v.includes("snapshot")
-                    );
-            let parsedValueSetsKeys = Object.keys(parser.parsedValueSets);
-            for (let key of valueSetKeys) {
-                let valueSetUri = _.get(profileJson, key);
-                if (!parsedValueSetsKeys.includes(valueSetUri)) {
-                    console.log(`Get valueSet from "${valueSetUri}"`);
-                    let valueSetRes = await fetch(valueSetUri, {
-                        headers: {
-                            "accept": "application/fhir+json"
-                        }
-                    });
-                    let valueSetJson = await valueSetRes.json();
-                    console.log(`Load valueSet "${valueSetJson.id}"`);
-                    parser.parseValueSet(valueSetJson);
-                    console.log(`Success parse valuset "${valueSetJson.id}"`);
-                }
-            }
-
-            parser.parseStructureDefinition(profileJson);
-            console.log(parser.parsedStructureDefinitions[resourceType]);
-            let fhir = new FHIR(parser);
-            let validation = fhir.validate(resourceBody);
-            if (validation.messages.length > 0) {
-                let issueList = [];
-                for (let message of validation.messages) {
-                    let issueObj = new issue(message.severity, "processing", message.message);
-                    _.set(issueObj, "location", [message.location]);
-                    issueList.push(issueObj);
-                }
-                let operationOutcomeError = new OperationOutcome(issueList);
-                if (validation.messages.find(v => v.severity == "error")) {
-                    operationOutcomeMessage = {
-                        code: 412,
-                        msg: operationOutcomeError
-                    };
-                } else {
-                    operationOutcomeMessage = {
-                        code: 200,
-                        msg: operationOutcomeError
-                    };
-                }
-            } else {
-                let operationOutcomeInfo = handleError.informational("No issues detected during validation");
-                operationOutcomeMessage = {
-                    code: 200,
-                    msg: operationOutcomeInfo
-                };
-            }
-        } catch (e) {
-            console.error(e);
-            operationOutcomeMessage = {
-                code: 500,
-                msg: handleError.exception(e)
-            };
-        }
-    } else {
-        let fhir = new FHIR();
-        let validation = fhir.validate(resourceBody);
-        if (validation.messages.length > 0) {
-            for (let message of validation.messages) {
-                let issueObj = new issue(message.severity, "processing", message.message);
-                _.set(issueObj, "Location", [message.location]);
-                let operationOutcomeError = new OperationOutcome(issueObj);
-                operationOutcomeMessage = {
-                    code: 412,
-                    msg: operationOutcomeError
-                };
-            }
+    try {
+        let operationOutcomeMessage;
+        let profileUrl = _.get(req.query, "profile");
+        if (profileUrl) {
+            operationOutcomeMessage = await validateByProfile(profileUrl, req.body);
         } else {
-            let operationOutcomeInfo = handleError.informational("No issues detected during validation");
-            operationOutcomeMessage = {
-                code: 200,
-                msg: operationOutcomeInfo
-            };
+            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);
     }
-    return doRes(operationOutcomeMessage.code, operationOutcomeMessage.msg);
 };
diff --git a/api/FHIRApiService/condition-delete.js b/api/FHIRApiService/condition-delete.js
@@ -3,9 +3,12 @@ const mongodb = require('models/mongodb');
 const {
     handleError
 } = require('../../models/FHIR/httpMessage');
-const FHIR = require('../../models/FHIR/fhir/fhir').Fhir;
+const FHIR = require('fhir').Fhir;
 const { isRealObject } = require('../apiService');
 const user = require('../APIservices/user.service');
+const { logger } = require('../../utils/log');
+const path = require('path');
+const PWD_FILENAME = path.relative(process.cwd(), __filename);
 
 /**
  * 
@@ -16,6 +19,7 @@ const user = require('../APIservices/user.service');
  * @returns 
  */
 module.exports = async function(req, res, resourceType, paramsSearch) {
+    logger.info(`[Info: do condition-delete] [Resource Type: ${resourceType}] [From-File: ${PWD_FILENAME}] [Content-Type: ${res.getHeader("content-type")}] [Url-SearchParam: ${req.url}] `);
     let doRes = function (code , item) {
         if (res.getHeader("content-type").includes("xml")) {
             let fhir = new FHIR();
@@ -25,6 +29,7 @@ module.exports = async function(req, res, resourceType, paramsSearch) {
         return res.status(code).send(item);
     };
     if (!await user.checkTokenPermission(req, resourceType, "delete")) {
+        logger.warn(`[Warn: Request token doesn't have permission with this API] [From-File: ${PWD_FILENAME}] [From-IP: ${req.socket.remoteAddress}]`);
         return doRes(403,handleError.forbidden("Your token doesn't have permission with this API"));
     }
     let queryParameter = _.cloneDeep(req.query);
@@ -45,7 +50,7 @@ module.exports = async function(req, res, resourceType, paramsSearch) {
             paramsSearch[key](queryParameter);
         } catch (e) {
             if (key != "$and") {
-                console.error(e);
+                logger.error(`[Error: Unknown search parameter ${key} or value ${queryParameter[key]}] [Resource Type: ${resourceType}] [From-File: ${PWD_FILENAME}] [${e}]`);
                 return doRes(400 , handleError.processing(`Unknown search parameter ${key} or value ${queryParameter[key]}`));
             }
         }
@@ -59,7 +64,8 @@ module.exports = async function(req, res, resourceType, paramsSearch) {
         let info = handleError.informational(`delete successfully, deleted count : ${deletion.deletedCount}`);
         return doRes(200 , info);
     } catch (e) {
-        console.log(`api ${process.env.FHIRSERVER_APIPATH}/${resourceType}/ has error, `, e);
+        let errorStr = JSON.stringify(e, Object.getOwnPropertyNames(e));
+        logger.error(`[Error: ${errorStr}] [Resource Type: ${resourceType}] [From-File: ${PWD_FILENAME}]`);
         let operationOutcomeError = handleError.exception(e);
         return doRes(500 , operationOutcomeError);
     }