Merge pull request #82 from fair4health/local-definitions

Local definitions

package.json

@@ -1,7 +1,7 @@
 {
   "name": "fair4health-data-curation-tool",
   "productName": "FAIR4Health Data Curation Tool",
-  "version": "1.2.5",
+  "version": "1.2.6",
   "private": true,
   "author": "SRDC Corporation <[email protected]>",
   "description": "FAIR4Health | Data Curation and Validation Tool",
@@ -31,6 +31,7 @@
     "electron-log": "^4.2.2",
     "electron-store": "^5.1.0",
     "es6-promise": "^4.2.8",
+    "extract-zip": "^2.0.1",
     "isomorphic-fetch": "^2.2.1",
     "ng-fhir": "^2.3.0",
     "pg": "^8.5.1",

src/common/environment.ts

@@ -19,6 +19,7 @@ export let environment = {
     },
     compatibleFhirVersions: ['4.0.0', '4.0.1']
   },
+  FHIRDefinitionsZipPath: './fhir-definitions/definitions-r4.zip',
   langs: ['en'],
   databaseTypes: ['postgres'],
   hl7: hl7Base,

src/common/utils/fhir-util.ts

@@ -2,6 +2,10 @@ import HmacSHA256 from 'crypto-js/hmac-md5'
 import { FhirService } from './../services/fhir.service'
 import { environment } from './../environment'
 import { DataTypeFactory } from './../model/factory/data-type-factory'
+import path from 'path'
+import fs from 'fs'
+import { remote } from 'electron'
+import StructureDefinition = fhir.StructureDefinition;
 
 export class FHIRUtil {
 
@@ -61,76 +65,132 @@ export class FHIRUtil {
   }
 
   /**
-   * Parses elements of a StructureDefinition resource (StructureDefinition.snapshot.element)
+   * Filter the StructureDefinition resources from standard profiles-resources.json and save them into
+   * tofhir-structure-definitions.json so that subsequent calls do not need to parse a very large file again and again.
+   *
+   * @return Return an array of #fhir.StructureDefinition objects from the base resource definition files.
+   */
+  static readStructureDefinitionsOfBaseResources (): fhir.StructureDefinition[] {
+    let structureDefinitionsFilePath = localStorage.getItem('structure-definitions-file')
+
+    if (structureDefinitionsFilePath === undefined || structureDefinitionsFilePath === null || !fs.existsSync(structureDefinitionsFilePath)) {
+      const parsedZipPath = path.parse(environment.FHIRDefinitionsZipPath)
+      const resourcesFilePath = path.join(remote.app.getPath('userData'), parsedZipPath.name, 'profiles-resources.json')
+      structureDefinitionsFilePath = path.join(remote.app.getPath('userData'), parsedZipPath.name, 'tofhir-structure-definitions.json')
+
+      const content = fs.readFileSync(resourcesFilePath)
+      const bundle = JSON.parse(content.toString('utf-8')) as fhir.Bundle
+      const structureDefinitionResources = bundle.entry.flatMap<StructureDefinition>(e => e.resource.resourceType === 'StructureDefinition' ? e.resource as StructureDefinition : [])
+      fs.writeFileSync(structureDefinitionsFilePath, JSON.stringify(structureDefinitionResources))
+
+      localStorage.setItem('structure-definitions-file', structureDefinitionsFilePath)
+
+      return structureDefinitionResources
+    }
+
+    return JSON.parse(fs.readFileSync(structureDefinitionsFilePath).toString('utf-8')) as StructureDefinition[]
+  }
+
+  /**
+   * Retrieve the #StructureDefinition of a given resource type from the base FHIR definitions.
+   * @param resourceType
+   */
+  static getStructureDefinitionFromBaseResources (resourceType: string): Promise<StructureDefinition> {
+    return new Promise((resolve, reject) => {
+      const baseResourceDefinition = this.readStructureDefinitionsOfBaseResources().find(sd => sd.url.split('/').pop() === resourceType)
+      if (baseResourceDefinition === undefined || baseResourceDefinition === null) {
+        reject(`Base resource definition file does not include the resourceType: ${resourceType}`)
+      }
+      resolve(baseResourceDefinition)
+    })
+  }
+
+  /**
+   * Retrieve the profile definition from the given FHIR endpoint.
    * @param fhirService
-   * @param parameter - Search parameter
-   * @param profileId
+   * @param profileUrl
    */
-  static parseElementDefinitions (fhirService: FhirService, parameter: string, profileId: string): Promise<any> {
-    return new Promise((resolveParam, rejectParam) => {
+  static getStructureDefinitionOfProfile (fhirService: FhirService, profileUrl: string): Promise<StructureDefinition> {
+    return new Promise((resolve, reject) => {
       const query = {}
-      query[parameter] = profileId
+      query['url'] = profileUrl
 
       fhirService.search('StructureDefinition', query, true)
         .then(res => {
           const bundle = res.data as fhir.Bundle
           if (bundle.entry?.length) {
-            const resource = bundle.entry[0].resource as fhir.StructureDefinition
-            const list: fhir.ElementTree[] = []
-            Promise.all(resource?.snapshot?.element.map((element: fhir.ElementDefinition) => {
-              return new Promise(resolveElement => {
-                // Mark the id field as required field
-                const idSplitted = element.id.split('.')
-                if (idSplitted.length === 2 && idSplitted[1] === 'id') element.min = 1
-                const parts = element.id?.split('.') || []
-                let tmpList = list
-
-                // Fixed code-system uri for code fields
-                const fixedUri = element.fixedUri
-
-                Promise.all(parts.map(part => {
-                  return new Promise((resolveElementPart => {
-                    let match = tmpList.findIndex(_ => _.label === part)
-                    if (match === -1) {
-                      match = 0
-                      const item: fhir.ElementTree = {
-                        value: element.id,
-                        label: part,
-                        definition: element.definition,
-                        comment: element.comment,
-                        short: element.short,
-                        min: element.min,
-                        max: element.max,
-                        type: element.type.map(_ => {
-                          const elementType: fhir.ElementTree = {value: _.code, label: _.code, type: [{value: _.code, label: _.code}], targetProfile: _.targetProfile}
-                          if (_.code !== 'CodeableConcept' && _.code !== 'Coding' && _.code !== 'Reference' && environment.datatypes[_.code])
-                            elementType.lazy = true
-                          return FHIRUtil.cleanJSON(elementType)
-                        }),
-                        children: []
-                      }
-                      tmpList.push(item)
-                      resolveElementPart()
-                    }
-                    if (fixedUri) tmpList[match].fixedUri = fixedUri
-                    tmpList = tmpList[match].children as fhir.ElementTree[]
-                    resolveElementPart()
-                  }))
-                })).then(() => resolveElement()).catch(() => resolveElement())
-              })
-            }) || [])
-              .then(() => {
-                list[0].children.map(_ => {
-                  if (_.type[0].value !== 'BackboneElement') _.children = []
-                  else _.noTick = true
-                  return _
-                })
-                resolveParam(list)
-              })
-              .catch(() => rejectParam([]))
-          } else { resolveParam([]) }
+            resolve(bundle.entry[0].resource as fhir.StructureDefinition)
+          } else {
+            reject(`Returned bundle from the StructureDefinition search endpoint does no include any entries for the profile: ${profileUrl}.`)
+          }
         })
-        .catch(() => rejectParam([]))
+        .catch(() => reject(`Cannot invoke the search under StructureDefinition endpoint of the FHIR service for the profile: ${profileUrl}.`))
+    })
+  }
+
+  /**
+   * Parses elements of a StructureDefinition resource (StructureDefinition.snapshot.element)
+   * @param fhirService
+   * @param parameter - Search parameter
+   * @param profileId
+   */
+  static parseElementDefinitions (fhirService: FhirService, parameter: string, profileId: string): Promise<any> {
+    return new Promise((resolveParam, rejectParam) => {
+      const promise = parameter === 'url' ? this.getStructureDefinitionOfProfile(fhirService, profileId) : this.getStructureDefinitionFromBaseResources(profileId)
+      promise.then(resource => {
+        const list: fhir.ElementTree[] = []
+        Promise.all(resource?.snapshot?.element.map((element: fhir.ElementDefinition) => {
+          return new Promise(resolveElement => {
+            // Mark the id field as required field
+            const idSplitted = element.id.split('.')
+            if (idSplitted.length === 2 && idSplitted[1] === 'id') element.min = 1
+            const parts = element.id?.split('.') || []
+            let tmpList = list
+
+            // Fixed code-system uri for code fields
+            const fixedUri = element.fixedUri
+
+            Promise.all(parts.map(part => {
+              return new Promise((resolveElementPart => {
+                let match = tmpList.findIndex(_ => _.label === part)
+                if (match === -1) {
+                  match = 0
+                  const item: fhir.ElementTree = {
+                    value: element.id,
+                    label: part,
+                    definition: element.definition,
+                    comment: element.comment,
+                    short: element.short,
+                    min: element.min,
+                    max: element.max,
+                    type: element.type.map(_ => {
+                      const elementType: fhir.ElementTree = {value: _.code, label: _.code, type: [{value: _.code, label: _.code}], targetProfile: _.targetProfile}
+                      if (_.code !== 'CodeableConcept' && _.code !== 'Coding' && _.code !== 'Reference' && environment.datatypes[_.code])
+                        elementType.lazy = true
+                      return FHIRUtil.cleanJSON(elementType)
+                    }),
+                    children: []
+                  }
+                  tmpList.push(item)
+                  resolveElementPart()
+                }
+                if (fixedUri) tmpList[match].fixedUri = fixedUri
+                tmpList = tmpList[match].children as fhir.ElementTree[]
+                resolveElementPart()
+              }))
+            })).then(() => resolveElement()).catch(() => resolveElement())
+          })
+        }) || [])
+          .then(() => {
+            list[0].children.map(_ => {
+              if (_.type[0].value !== 'BackboneElement') _.children = []
+              else _.noTick = true
+              return _
+            })
+            resolveParam(list)
+          })
+          .catch(() => rejectParam([]))
+      })
     })
   }
 

src/electron-main.ts

@@ -2,9 +2,13 @@
 
 import { app, protocol, BrowserWindow, dialog, ipcMain, webContents, MessageBoxReturnValue } from 'electron'
 import { createProtocol } from 'vue-cli-plugin-electron-builder/lib'
-import log from 'electron-log'
+import log, {error} from 'electron-log'
 import { IpcChannelUtil as ipcChannels } from './common/utils/ipc-channel-util'
-// import installExtension, { VUEJS_DEVTOOLS } from 'electron-devtools-installer'
+import installExtension, { VUEJS_DEVTOOLS } from 'electron-devtools-installer'
+import path from 'path'
+import fs from 'fs'
+import extract from 'extract-zip'
+import {environment} from '@/common/environment';
 
 const isDevelopment = process.env.NODE_ENV !== 'production'
 
@@ -22,7 +26,7 @@ app.commandLine.appendSwitch('js-flags', '--max-old-space-size=8096')
 
 // Logger settings
 log.transports.file.fileName = 'log.txt'
-log.transports.console.level = false
+// log.transports.console.level = false
 
 // Stack of available background threads
 const availableThreads: webContents[] = []
@@ -39,7 +43,7 @@ function doWork () {
   // win.webContents.send('status', availableThreads.length, taskQueue.length)
 }
 
-function createWindow () {
+async function createWindow () {
   // Create the browser window.
   win = new BrowserWindow({
     minWidth: 800,
@@ -62,7 +66,7 @@ function createWindow () {
   if (process.env.WEBPACK_DEV_SERVER_URL) {
     // Load the url of the dev server if in development mode
     win.loadURL(process.env.WEBPACK_DEV_SERVER_URL as string)
-    // if (!process.env.IS_TEST) win.webContents.openDevTools()
+    if (!process.env.IS_TEST) win.webContents.openDevTools()
   } else {
     createProtocol('fair4health')
     // Load the index.html when not in development
@@ -144,6 +148,28 @@ function createBgWindow (id: number): BrowserWindow {
 
 }
 
+async function extractFHIRDefinitionZip () {
+  const definitionsFilePath = path.resolve(environment.FHIRDefinitionsZipPath)
+  const parsedPath = path.parse(definitionsFilePath)
+  const extractionFolderPath = path.join(app.getPath('userData'), parsedPath.name)
+  log.info('Location of definitions-r4.zip -> ' + definitionsFilePath)
+  log.info('Extracted definitions folder -> ' + extractionFolderPath)
+
+  if (fs.existsSync(path.join(extractionFolderPath, 'profiles-resources.json'))) {
+    // ZIP was previously extracted. Do not extract it again.
+    log.info('Definitions ZIP file already extracted, skipping...')
+    return
+  }
+
+  try {
+    await extract(definitionsFilePath, {dir: extractionFolderPath})
+    log.info(`Extraction of ${definitionsFilePath} completed`)
+  } catch (e) {
+    log.error(`Extraction error: ${e}`)
+    throw e
+  }
+}
+
 // Quit when all windows are closed.
 app.on('window-all-closed', () => {
   // On macOS, quits the app as Cmd + Q does
@@ -164,11 +190,32 @@ app.on('activate', () => {
 app.on('ready', async () => {
   if (isDevelopment && !process.env.IS_TEST) {
     // Install Vue Devtools
-    // try {
-    //   await installExtension(VUEJS_DEVTOOLS)
-    // } catch (e) {
-    //   console.error('Vue Devtools failed to install:', e.toString())
-    // }
+    try {
+      await installExtension(VUEJS_DEVTOOLS)
+    } catch (e) {
+      console.error('Vue Devtools failed to install:', e.toString())
+    }
+  }
+
+  try {
+    await extractFHIRDefinitionZip()
+  } catch (e) {
+    const options = {
+      type: 'info',
+      title: 'FHIR Definitions Zip extraction failed.',
+      message: 'Please consult the project\'s GitHub page.',
+      buttons: ['Close']
+    }
+    dialog.showMessageBox(options)
+      .then((messageBoxReturnValue: MessageBoxReturnValue) => {
+        if (messageBoxReturnValue.response === 0) win?.reload()
+        else win?.destroy()
+      })
+      .catch(err => {
+        log.error(err)
+        win?.destroy()
+      })
+    return
   }
 
   // Create Main renderer window

src/locales/en.json

@@ -76,6 +76,7 @@
     "CANNOT_GET_SAVED_MAPPINGS": "Cannot get saved mappings",
     "CANNOT_LOAD_CREATED_RESOURCES": "Cannot load created resources. Try again",
     "CHOOSE_A_TYPE": "Choose a type for selected items",
+    "COULDNT_EXTRACT_FHIR_DEFINITIONS_ZIP": "Couldn't extract FHIR Definitions zip!",
     "CHUNK_SIZE_CANNOT_BE_X": "Chunk size can not be {chunkSize}.",
     "DATA_COULDNT_BE_IMPORTED": "Data could't be imported",
     "EMPTY_MAPPING_SHEET": "Empty mapping sheet",

src/store/fhirStore/index.ts

@@ -96,9 +96,11 @@ const fhirStore = {
           .then(res => {
             const bundle = res.data as fhir.Bundle
             if (bundle.total > 0) {
-              profileList.push(...(bundle.entry?.map(e => {
+              profileList.push(...(bundle.entry?.flatMap(e => {
                 const structure = e.resource as fhir.StructureDefinition
-                return {id: structure.id, title: structure.title, url: structure.url} as fhir.StructureDefinition
+                if (structure.snapshot) // Add this profile to the list only if it has the snapshot field.
+                  return {id: structure.id, title: structure.title, url: structure.url} as fhir.StructureDefinition
+                else return []
               }) || []))
 
               Promise.all(profileList.map(profile => {
@@ -107,9 +109,11 @@ const fhirStore = {
                     .then(res => {
                       const bundle = res.data as fhir.Bundle
                       if (bundle.total > 0) {
-                        subProfiles.push(...(bundle.entry?.map(e => {
+                        subProfiles.push(...(bundle.entry?.flatMap(e => {
                           const structure = e.resource as fhir.StructureDefinition
-                          return {id: structure.id, title: structure.title, url: structure.url} as fhir.StructureDefinition
+                          if (structure.snapshot) // Add this profile to the list only if it has the snapshot field.
+                            return {id: structure.id, title: structure.title, url: structure.url} as fhir.StructureDefinition
+                          else return []
                         }) || []))
                       }
                       resolveSubProfile(true)

tsconfig.json

@@ -9,6 +9,7 @@
     "noImplicitAny": false,
     "esModuleInterop": true,
     "allowSyntheticDefaultImports": true,
+    "inlineSources": true,
     "sourceMap": true,
     "baseUrl": ".",
     "typeRoots": [

vue.config.js

@@ -26,6 +26,11 @@ module.exports = {
           perMachine: true,
           allowToChangeInstallationDirectory: true,
           createDesktopShortcut: true
+        },
+        extraFiles: {
+          from: 'fhir-definitions',
+          to: 'fhir-definitions',
+          filter: ["**/*"]
         }
       }
     }