Merge pull request #59 from fair4health/v1.2.2

V1.2.2

package.json

@@ -1,7 +1,7 @@
 {
   "name": "fair4health-data-curation-tool",
   "productName": "FAIR4Health Data Curation Tool",
-  "version": "1.2.1",
+  "version": "1.2.2",
   "private": true,
   "author": "SRDC Corporation <[email protected]>",
   "description": "FAIR4Health | Data Curation and Validation Tool",
@@ -25,7 +25,7 @@
   "dependencies": {
     "@quasar/extras": "^1.0.0",
     "@types/lodash": "^4.14.150",
-    "axios": "^0.19.0",
+    "axios": "^0.21.1",
     "core-js": "^3.3.2",
     "crypto-js": "^4.0.0",
     "electron-log": "^4.2.2",
@@ -34,7 +34,7 @@
     "isomorphic-fetch": "^2.2.1",
     "ng-fhir": "^2.3.0",
     "pg": "^8.5.1",
-    "quasar": "^1.9.12",
+    "quasar": "^1.15.10",
     "readline-sync": "^1.4.10",
     "spectron": "^11.1.0",
     "typeorm": "^0.2.29",

src/common/environment.ts

@@ -18,6 +18,7 @@ export let environment = {
   langs: ['en'],
   databaseTypes: ['postgres'],
   hl7: hl7Base,
+  FHIRBatchOperationSize: 1000,
   codesystems: {
     ATC: 'http://www.whocc.no/atc',
     SNOMED: 'http://snomed.info/sct',

src/common/model/data-table.ts

@@ -4,41 +4,59 @@
 
 import { QTable } from 'quasar'
 
+interface FAIRTable extends QTable {
+  columns: Array<{
+    name: string
+    label: string
+    field: string | (() => void)
+    required?: boolean
+    icon?: string
+    align?: string
+    sortable?: boolean
+    style?: string
+    classes?: string
+    headerStyle?: string
+    headerClasses?: string
+    format? (): void
+    sort? (): void
+  }>
+}
+
 export const cellType = {
   s: 'Text',
   b: 'Boolean',
   d: 'Date',
   n: 'Number'
 }
-export const savedMappingTable: QTable = {
+export const savedMappingTable: FAIRTable = {
   columns: [
     { name: 'date', label: 'TABLE.DATE_MODIFIED', align: 'left', field: 'date', icon: 'today', sortable: true },
-    { name: 'action', label: 'TABLE.ACTIONS', align: 'right' }
+    { name: 'action', label: 'TABLE.ACTIONS', align: 'right', field: 'action' }
   ],
   pagination: { sortBy: 'date', descending: true, page: 1, rowsPerPage: 5 }
-} as QTable
+} as FAIRTable
 
-export const sourceDataTable: QTable = {
+export const sourceDataTable: FAIRTable = {
   columns: [
     { name: 'attr', required: true, label: 'TABLE.ATTRIBUTE', align: 'left', field: 'value', icon: 'fas fa-bars', sortable: true },
     { name: 'type', required: true, label: 'TABLE.TYPE', align: 'left', field: 'type', icon: 'fas fa-spell-check' },
     { name: 'target', label: 'TABLE.TARGET', align: 'left', field: 'target' },
     { name: 'conceptMap', label: 'TABLE.CONCEPT_MAP', align: 'right', field: 'conceptMap' }
   ],
   pagination: { page: 1, rowsPerPage: 10 }
-} as QTable
+} as FAIRTable
 
-export const validatorTable: QTable = {
+export const validatorTable: FAIRTable = {
   columns: [
     { name: 'status', align: 'center', label: 'TABLE.STATUS', field: 'status', icon: 'fas fa-info-circle', classes: 'bg-grey-2', headerClasses: 'bg-primary text-white' },
     { name: 'file', align: 'left', label: 'TABLE.FILE', field: 'file', icon: 'fas fa-file', sortable: true },
     { name: 'sheet', align: 'left', label: 'TABLE.SHEET', field: 'sheet', icon: 'far fa-file-alt', sortable: true },
     { name: 'targets', align: 'center', label: 'TABLE.TARGET_MAPPINGS', field: 'targets', icon: 'fas fa-hashtag', sortable: true }
   ],
   pagination: { page: 1, rowsPerPage: 0 }
-} as QTable
+} as FAIRTable
 
-export const transformerTable: QTable = {
+export const transformerTable: FAIRTable = {
   columns: [
     { name: 'status', label: 'TABLE.STATUS', field: 'status', align: 'left', icon: 'fas fa-info-circle', classes: 'bg-grey-2' },
     { name: 'resourceType', label: 'TABLE.RESOURCE_TYPE', field: 'resourceType', align: 'left', sortable: true },
@@ -47,9 +65,9 @@ export const transformerTable: QTable = {
     { name: 'action', label: 'TABLE.ACTIONS', align: 'right' }
   ],
   pagination: { page: 1, rowsPerPage: 0 }
-} as QTable
+} as FAIRTable
 
-export const mappingDetailTable: QTable = {
+export const mappingDetailTable: FAIRTable = {
   columns: [
     { name: 'sourceField', label: 'TABLE.SOURCE_FIELD', field: 'value', align: 'left', sortable: true },
     { name: 'targetField', label: 'TABLE.TARGET_FIELD', field: 'targetField', align: 'left', sortable: true },
@@ -59,9 +77,9 @@ export const mappingDetailTable: QTable = {
     { name: 'conceptMap', label: 'TABLE.CONCEPT_MAP', field: 'conceptMap', align: 'left', sortable: true }
   ],
   pagination: { page: 1, rowsPerPage: 5 }
-} as QTable
+} as FAIRTable
 
-export const outcomeDetailTable: QTable = {
+export const outcomeDetailTable: FAIRTable = {
   columns: [
     { name: 'status', label: 'TABLE.STATUS', field: 'status', align: 'center', icon: 'fas fa-info-circle',
       classes: 'bg-grey-2', headerClasses: 'bg-primary text-white col-1 outcome-table-column' },
@@ -70,4 +88,4 @@ export const outcomeDetailTable: QTable = {
     { name: 'message', label: 'TABLE.DETAILS', field: 'message', align: 'left', sortable: true }
   ],
   pagination: { page: 1, rowsPerPage: 10 }
-} as QTable
+} as FAIRTable

src/common/model/resource-generators/Observation.ts

@@ -210,6 +210,9 @@ export class Observation implements Generator {
       if (resource.has('Observation.value[x].boolean')) {
         observation.valueBoolean = String(resource.get('Observation.value[x].boolean').value).toLowerCase() === 'true'
       }
+      if (resource.has('Observation.value[x].integer')) {
+        observation.valueInteger = Number(resource.get('Observation.value[x].integer').value)
+      }
       if (resource.has('Observation.value[x].dateTime')) {
         const item = resource.get('Observation.value[x].dateTime')
         try {