Merge pull request #60 from fair4health/v1.2.3

V1.2.3

README.md

@@ -68,7 +68,8 @@ The tool writes logs to the following locations:
 - on **Linux**: `~/.config/FAIR4Health Data Curation Tool/logs/log.txt`
 
 ## Terminology Server Connection
-The tool is compatible with FHIR based Terminology Servers, in order to translate values from one system to another. As the sample API https://terminology-service.atosresearch.eu provided by ATOS was used.
+The tool is compatible with FHIR based Terminology Servers, in order to translate values from one system to another.
+ As the sample API `https://health-digital-term.ari-health.eu` provided by ATOS was used.
 
 Currently, in the tool:
 - For the translation operation, the ConceptMap translate API: `/ConceptMap/$translate` is consumed.

package.json

@@ -1,7 +1,7 @@
 {
   "name": "fair4health-data-curation-tool",
   "productName": "FAIR4Health Data Curation Tool",
-  "version": "1.2.2",
+  "version": "1.2.3",
   "private": true,
   "author": "SRDC Corporation <[email protected]>",
   "description": "FAIR4Health | Data Curation and Validation Tool",

src/common/environment.ts

@@ -2,6 +2,10 @@
 const onfhirBase = 'http://localhost:8080/fhir'
 const hl7Base = 'http://hl7.org/fhir'
 
+// The url representing how many resources created during transformation
+// Placed in the extension part of the Provenance and DocumentManifest resources
+const numberOfResourcesUrlBase = `${hl7Base}/f4h/resource-count`
+
 export let environment = {
   toolID: 'data-curation-tool',
   server: {
@@ -19,6 +23,7 @@ export let environment = {
   databaseTypes: ['postgres'],
   hl7: hl7Base,
   FHIRBatchOperationSize: 1000,
+  numberOfResourcesUrlBase,
   codesystems: {
     ATC: 'http://www.whocc.no/atc',
     SNOMED: 'http://snomed.info/sct',

src/common/utils/fhir-util.ts

@@ -197,6 +197,14 @@ export class FHIRUtil {
     }
   }
 
+  /**
+   * Removes the trailing slash in the url
+   * @param url
+   */
+  static trimUrl (url: string): string {
+    return (url || '').replace(/\/$/, '')
+  }
+
   private static readonly secretKey: string = 'E~w*c`r8e?aetZeid]b$y+aIl&p4eNr*a'
 
 }

src/components/BackgroundEngine.ts

@@ -1057,12 +1057,29 @@ export default class BackgroundEngine extends Vue {
    */
   createProvenanceAndLicense (author: string, license: License, provenanceTargets: fhir.Reference[], documentManifestContent: fhir.Reference[]): Promise<void> {
     const currentDate: string = new Date().toISOString()
+    const resourceCounts = provenanceTargets.reduce((acc, currReference) => {
+      const reference = currReference.reference.split('/')[0]
+      if (!acc.hasOwnProperty(reference)) {
+        acc[reference] = 0
+      }
+      acc[reference]++
+      return acc
+    }, {})
+    const extension: fhir.Extension[] = []
+    Object.keys(resourceCounts).map((resourceType: string) => {
+      extension.push({
+        url: `${environment.numberOfResourcesUrlBase}/${resourceType}`,
+        valueInteger: resourceCounts[resourceType]
+      })
+    })
     // Modify provenance resource
+    this.provenance.extension = extension
     this.provenance.target = provenanceTargets
     this.provenance.recorded = currentDate
     this.provenance.signature[0].when = currentDate
     this.provenance.agent[0].who.display = author
     // Modify documentManifest resource
+    this.documentManifest.extension = extension
     this.documentManifest.content = documentManifestContent
     this.documentManifest.created = currentDate
     this.documentManifest.related[0].ref.display = license.display

src/components/CodeSystemSelect.vue

@@ -30,6 +30,7 @@
   import { Component, Vue, Prop } from 'vue-property-decorator'
   import { environment } from '@/common/environment'
   import { VuexStoreUtil as types } from '@/common/utils/vuex-store-util'
+  import {FHIRUtil} from '@/common/utils/fhir-util'
 
   @Component
   export default class CodeSystemSelect extends Vue {
@@ -54,7 +55,7 @@
     }
 
     updateUrl (val: string) {
-      this.url = val?.trim() || ''
+      this.url = FHIRUtil.trimUrl(val?.trim() || '')
       this.$emit('input', this.url)
     }
   }

src/components/OnFHIRConfig.vue

@@ -6,7 +6,7 @@
           <q-item-label class="text-weight-bold q-mb-lg">
             <span class="text-primary"><q-icon name="fas fa-info" size="xs" class="q-mr-xs" /> {{ $t('LABELS.PROVIDE_FHIR_URL') }} </span>
           </q-item-label>
-          <q-input outlined square dense type="url" class="col-10" v-model="onfhirBaseUrl" color="primary"
+          <q-input outlined square dense type="url" class="col-10" v-model.lazy.trim="onfhirBaseUrl" color="primary"
                    @input="fhirBaseVerificationStatus = Status.PENDING"
                    :placeholder="$t('LABELS.FHIR_REPOSITORY_URL')"
                    :disable="isInProgress(fhirBaseVerificationStatus)"
@@ -64,6 +64,7 @@
   import Status from '@/common/Status'
   import StatusMixin from '@/common/mixins/statusMixin'
   import Loading from '@/components/Loading.vue'
+  import {FHIRUtil} from '@/common/utils/fhir-util'
 
   @Component({
     components: {
@@ -96,6 +97,7 @@
 
     verifyFhir () {
       if (this.onfhirBaseUrl) {
+        this.onfhirBaseUrl = FHIRUtil.trimUrl(this.onfhirBaseUrl)
         this.fhirBaseVerificationStatus = Status.IN_PROGRESS
         this.$store.dispatch(types.Fhir.VERIFY_FHIR, this.onfhirBaseUrl)
           .then(() => {

src/components/TerminologyConfig.vue

@@ -4,7 +4,7 @@
       <q-item-label class="text-weight-bold q-mb-lg text-primary text-h6">
         {{ $t('LABELS.ADD_TERMINOLOGY_SERVICE') }}
       </q-item-label>
-      <q-input outlined dense type="url" class="col-10" v-model="terminologyBaseUrl" color="primary"
+      <q-input outlined dense type="url" class="col-10" v-model.lazy.trim="terminologyBaseUrl" color="primary"
                @input="tBaseVerificationStatus = Status.PENDING"
                :placeholder="$t('LABELS.TERMINOLOGY_SERVICE_URL')"
                :disable="isInProgress(tBaseVerificationStatus)"
@@ -40,6 +40,7 @@
   import Status from '@/common/Status'
   import { IpcChannelUtil as ipcChannels } from '@/common/utils/ipc-channel-util'
   import { ipcRenderer } from 'electron'
+  import {FHIRUtil} from '@/common/utils/fhir-util'
 
   @Component
   export default class TerminologyConfig extends Mixins(StatusMixin) {
@@ -58,6 +59,7 @@
 
     verifyTerminology () {
       if (this.terminologyBaseUrl) {
+        this.terminologyBaseUrl = FHIRUtil.trimUrl(this.terminologyBaseUrl)
         this.tBaseVerificationStatus = Status.IN_PROGRESS
         this.$store.dispatch(types.Terminology.VERIFY_TERMINOLOGY, this.terminologyBaseUrl)
           .then(() => {