- ADD: Added support for remote URL tokens for more security.

- CHG: Changes to BrAPI interactions. -
cropgeeks · Sep 3, 2024 · 29e4328 · 29e4328
1 parent 0fe8f62
commit 29e4328
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Showing 18 changed files with 280 additions and 67 deletions.
diff --git a/src/components/BrapiExportSection.vue b/src/components/BrapiExportSection.vue
@@ -49,7 +49,7 @@
           </b-col>
         </b-row>
 
-        <b-button type="submit" variant="primary" :disabled="!canProceed"><IBiCloudUpload /> {{ $t('buttonSendData') }}</b-button>
+        <b-button class="mb-3" type="submit" variant="primary" :disabled="!canProceed"><IBiCloudUpload /> {{ $t('buttonSendData') }}</b-button>
       </div>
     </b-form>
   </div>
@@ -59,7 +59,7 @@
 import { mapState, mapStores } from 'pinia'
 import { coreStore } from '@/store'
 
-import { brapiGetPrograms, brapiGetTrials, brapiGetStudies, brapiGetStudyTypes, brapiPostGermplasmSearch, brapiPostObservationVariables, brapiPostObservationVariableSearch, brapiDefaultCatchHandler, brapiPostObservationUnits, brapiPostObservations } from '@/plugins/brapi'
+import { brapiGetPrograms, brapiGetTrials, brapiGetStudies, brapiGetStudyTypes, brapiPostGermplasmSearch, brapiPostObservationVariables, brapiPostObservationVariableSearch, brapiDefaultCatchHandler, brapiPostObservationUnits, brapiPostObservations, brapiGetObservationUnits } from '@/plugins/brapi'
 import { getTrialDataCached } from '@/plugins/datastore'
 import { updateGermplasmBrapiIds, updateTraitBrapiIds } from '@/plugins/idb'
 
@@ -224,7 +224,7 @@ export default {
             case 'float':
             case 'int':
             case 'range':
-              scale.dataType = 'Numeric'
+              scale.dataType = 'Numerical'
               break
             case 'categorical':
               scale.dataType = 'Ordinal'
@@ -266,6 +266,34 @@ export default {
       if (trialData) {
         emitter.emit('set-loading', true)
 
+        // Generate a mapping based on display row and column for lookup
+        const displayMapping = {}
+        for (let y = 0; y < this.trial.layout.rows; y++) {
+          // And each field column
+          for (let x = 0; x < this.trial.layout.columns; x++) {
+            // Get the data cell
+            const cell = trialData[`${y}|${x}`]
+
+            if (cell) {
+              displayMapping[`${cell.displayRow}|${cell.displayColumn}`] = `${y}|${x}`
+            }
+          }
+        }
+
+        // First, search for observation units from this study, save the observationUnitDbId for those that have local matches
+        brapiGetObservationUnits(this.selectedStudy.studyDbId)
+          .then(ous => {
+            if (ous && ous.length > 0) {
+              ous.forEach(ou => {
+                const match = displayMapping[`${ou.observationUnitPosition.positionCoordinateY}|${ou.observationUnitPosition.positionCoordinateX}`]
+
+                if (match) {
+                  trialData[match].observationUnitDbId = ou.observationUnitDbId
+                }
+              })
+            }
+          })
+
         // For legacy reasons we now need to send the observations as part of the ObservationUnit, then check if what we get back is what we sent.
         // If so, then the Germinate BrAPI backend is the old (wrong) version. However, that's all that's required in that case. If not, we need
         // to go on and actually send the observations separately using the observationunits we got back.
@@ -298,9 +326,9 @@ export default {
                 entryType: cell.categories && cell.categories.includes(CELL_CATEGORY_CONTROL) ? 'CHECK' : 'TEST',
                 geoCoordinates: geoCoordinates,
                 positionCoordinateXType: 'GRID_COL',
-                positionCoordinateX: cell.displayColumn,
+                positionCoordinateX: `${cell.displayColumn}`,
                 positionCoordinateYType: 'GRID_ROW',
-                positionCoordinateY: cell.displayRow,
+                positionCoordinateY: `${cell.displayRow}`,
                 observationLevel: (cell.rep !== undefined && cell.rep !== null)
                   ? {
                       levelName: 'rep',
@@ -365,6 +393,19 @@ export default {
       const data = []
       const observationUnitMap = {}
 
+      // Get the locally know ids first from the GET observationunits call
+      for (let y = 0; y < this.trial.layout.rows; y++) {
+        // And each field column
+        for (let x = 0; x < this.trial.layout.columns; x++) {
+          // Get the data cell
+          const cell = trialData[`${y}|${x}`]
+          if (cell.observationUnitDbId) {
+            observationUnitMap[`${cell.displayRow}|${cell.displayColumn}`] = cell.observationUnitDbId
+          }
+        }
+      }
+
+      // Then write the remote ones as well
       observationUnits.forEach(ou => {
         observationUnitMap[`${ou.observationUnitPosition.positionCoordinateY}|${ou.observationUnitPosition.positionCoordinateX}`] = ou.observationUnitDbId
       })
@@ -455,11 +496,13 @@ export default {
                   matches = t.dataType === 'text'
                   break
                 case 'Numeric':
+                case 'Numerical':
                   matches = t.dataType === 'float' || t.dataType === 'int' || t.dataType === 'range'
                   break
                 case 'Duration':
                   matches = t.dataType === 'int'
                   break
+                case 'Nominal':
                 case 'Ordinal':
                   matches = t.dataType === 'categorical'
                   break

diff --git a/src/components/BrapiTrialImportSection.vue b/src/components/BrapiTrialImportSection.vue
@@ -38,7 +38,15 @@
 
         <TrialLayoutDimensionComponent class="mt-3" :editLabelsAllowed="false" :editValuesAllowed="false" :layout="layout" @layout-changed="updateLayout" ref="trialDimensionComponent" />
 
-        <b-button @click="importData" variant="primary" :disabled="!canProceed"><IBiCloudDownload /> {{ $t('buttonImportData') }}</b-button>
+        <div v-if="errors && errors.length > 0" class="my-3">
+          <h3>{{ $t('widgetBrapiTrialImportErrorsTitle') }}</h3>
+
+          <b-list-group class="import-errors">
+            <b-list-group-item variant="danger" v-for="(error, index) in errors" :key="`import-error-${index}`">{{ error }}</b-list-group-item>
+          </b-list-group>
+        </div>
+
+        <b-button @click="importData" variant="primary" :disabled="!canImport"><IBiCloudDownload /> {{ $t('buttonImportData') }}</b-button>
       </template>
     </b-form>
   </b-container>
@@ -80,7 +88,8 @@ export default {
         columnLabels: [],
         columnOrder: DISPLAY_ORDER_LEFT_TO_RIGHT,
         rowOrder: DISPLAY_ORDER_TOP_TO_BOTTOM
-      }
+      },
+      errors: []
     }
   },
   watch: {
@@ -108,6 +117,9 @@ export default {
     canProceed: function () {
       return this.selectedProgram && this.selectedTrial && this.selectedStudyType && this.selectedStudy
     },
+    canImport: function () {
+      return this.canProceed && this.errors.length < 1 && this.layoutValid
+    },
     programOptions: function () {
       if (this.programs) {
         return this.programs.map(t => {
@@ -162,6 +174,7 @@ export default {
       this.layout = JSON.parse(JSON.stringify(layout))
     },
     importData: function () {
+      this.errors = []
       const plotMapping = {}
 
       this.cells.forEach(c => {
@@ -206,16 +219,24 @@ export default {
                 if (ou.observationUnitPosition.positionCoordinateXType === 'GRID_COL') {
                   columnIndex = +ou.observationUnitPosition.positionCoordinateX
                   columns.add(columnIndex)
+                } else {
+                  this.errors.push(this.$t('widgetBrapiTrialImportErrorNoColumnInformation', { germplasm: ou.germplasmName || ou.observationUnitDbId }))
                 }
                 if (ou.observationUnitPosition.positionCoordinateYType === 'GRID_ROW') {
                   rowIndex = +ou.observationUnitPosition.positionCoordinateY
                   rows.add(rowIndex)
+                } else {
+                  this.errors.push(this.$t('widgetBrapiTrialImportErrorNoRowInformation', { germplasm: ou.germplasmName || ou.observationUnitDbId }))
                 }
                 if (ou.germplasmName) {
                   germplasmIdentifier = ou.germplasmName
+                } else {
+                  this.errors.push(this.$t('widgetBrapiTrialImportErrorNoGermplasmName', { germplasm: ou.observationUnitDbId }))
                 }
                 if (ou.germplasmDbId) {
                   brapiId = ou.germplasmDbId
+                } else {
+                  this.errors.push(this.$t('widgetBrapiTrialImportErrorNoGermplasmDbId', { germplasm: ou.observationUnitDbId }))
                 }
                 if (ou.observationUnitPosition.observationLevel) {
                   if (ou.observationUnitPosition.observationLevel.levelName === 'rep') {
@@ -342,6 +363,9 @@ export default {
 }
 </script>
 
-<style>
-
+<style scoped>
+.import-errors {
+  max-height: min(300px, 50vh);
+  overflow-y: auto;
+}
 </style>
diff --git a/src/components/TraitDefinitionComponent.vue b/src/components/TraitDefinitionComponent.vue
@@ -372,11 +372,13 @@ export default {
                 type = 'text'
                 break
               case 'Numeric':
+              case 'Numerical':
                 type = 'float'
                 break
               case 'Duration':
                 type = 'int'
                 break
+              case 'Nominal':
               case 'Ordinal':
                 type = 'categorical'
                 break
@@ -395,7 +397,7 @@ export default {
               restrictions.max = +t.scale.validValues.maximumValue
             }
             if (t.scale.validValues.categories && t.scale.validValues.categories.length > 0) {
-              restrictions.categories = t.scale.validValues.categories.map(c => c.value)
+              restrictions.categories = t.scale.validValues.categories.map(c => c.label)
             }
           }
 

diff --git a/src/components/TrialCard.vue b/src/components/TrialCard.vue
@@ -11,12 +11,12 @@
       </template>
     </a>
     <TrialInformation :trial="trial" @on-share-clicked="$emit('showShareCodes')" />
-    <b-button v-if="selectable" :variant="selectedToEdit ? 'info' : 'secondary'" @click="selectedToEdit = !selectedToEdit">
-      <IBiCheckSquare v-if="selectedToEdit" /><IBiSquare v-else /> {{ selectedToEdit ? $t('buttonDeselect') : $t('buttonSelect') }}
-    </b-button>
     <b-button v-if="trial.remoteUrl" class="button-disabled" variant="secondary" v-b-tooltip.hover="trial.remoteUrl">
       <IBiCloudPlusFill /> {{ $t('buttonTrialRemoteUrl') }}
     </b-button>
+    <b-button v-if="selectable" :variant="selectedToEdit ? 'info' : 'secondary'" @click="selectedToEdit = !selectedToEdit">
+      <IBiCheckSquare v-if="selectedToEdit" /><IBiSquare v-else /> {{ selectedToEdit ? $t('buttonDeselect') : $t('buttonSelect') }}
+    </b-button>
     <b-button @click="$emit('handleTrialExpiration')" v-if="trial.showExpiryWarning === true" variant="danger" v-b-tooltip.hover="$t('tooltipTrialSelectorTrialExpiryWarning', { date: new Date(trial.expiresOn).toLocaleDateString() })">
       <IBiCalendarXFill />
     </b-button>

diff --git a/src/components/modals/BrapiTraitImportModal.vue b/src/components/modals/BrapiTraitImportModal.vue
@@ -97,12 +97,13 @@ export default {
                 case 'Text':
                   type = this.$t('traitTypeShortText')
                   break
-                case 'Numeric':
+                case 'Numerical':
                   type = this.$t('traitTypeShortFloat')
                   break
                 case 'Duration':
                   type = this.$t('traitTypeShortInt')
                   break
+                case 'Nominal':
                 case 'Ordinal':
                   type = this.$t('traitTypeShortCategorical')
                   break
@@ -112,18 +113,18 @@ export default {
               }
 
               if (type && type.length > 0) {
-                type = `<span class="badge badge-primary ms-2">${type}</span>`
+                type = `<span class="badge text-bg-primary ms-2">${type}</span>`
               }
 
               if (t.scale.validValues) {
                 if (t.scale.validValues.minimumValue !== undefined && t.scale.validValues.minimumValue !== null) {
-                  restrictions += `<span class="badge badge-secondary ms-2">&ge;${t.scale.validValues.minimumValue}</span>`
+                  restrictions += `<span class="badge text-bg-secondary ms-2">&ge;${t.scale.validValues.minimumValue}</span>`
                 }
                 if (t.scale.validValues.maximumValue !== undefined && t.scale.validValues.maximumValue !== null) {
-                  restrictions += `<span class="badge badge-secondary ms-2">&le;${t.scale.validValues.maximumValue}</span>`
+                  restrictions += `<span class="badge text-bg-secondary ms-2">&le;${t.scale.validValues.maximumValue}</span>`
                 }
                 if (t.scale.validValues.categories) {
-                  restrictions += `<span class="badge badge-secondary ms-2">${t.scale.validValues.categories.map(tr => tr.value).join(', ')}</span>`
+                  restrictions += `<span class="badge text-bg-secondary ms-2">${t.scale.validValues.categories.map(tr => tr.label).join(', ')}</span>`
                 }
               }
             }

diff --git a/src/components/modals/MissingTrialModal.vue b/src/components/modals/MissingTrialModal.vue
@@ -63,7 +63,16 @@ export default {
   },
   methods: {
     checkArchiveExists: function () {
-      checkTrialArchiveExists((this.trial && this.trial.remoteUrl) ? this.trial.remoteUrl : null, this.shareCode)
+      let remoteConfig = null
+
+      if (this.trial && this.trial.remoteUrl) {
+        remoteConfig = {
+          url: this.trial.remoteUrl,
+          token: this.trial.remoteToken || null
+        }
+      }
+
+      checkTrialArchiveExists(remoteConfig, this.shareCode)
         .then(result => {
           this.archiveExists = true
           this.archiveInformation = result

diff --git a/src/components/modals/TrialExpirationModal.vue b/src/components/modals/TrialExpirationModal.vue
@@ -71,7 +71,17 @@ export default {
     },
     sendCaptcha: function () {
       emitter.emit('show-loading', true)
-      extendTrialPeriod((this.trial && this.trial.remoteUrl) ? this.trial.remoteUrl : null, this.shareCode, { captcha: this.captcha })
+
+      let remoteConfig = null
+
+      if (this.trial && this.trial.remoteUrl) {
+        remoteConfig = {
+          url: this.trial.remoteUrl,
+          token: this.trial.remoteToken || null
+        }
+      }
+
+      extendTrialPeriod(remoteConfig, this.shareCode, { captcha: this.captcha })
         .then(() => {
           this.hide()
           emitter.emit('trials-updated')

diff --git a/src/components/modals/TrialShareCodeModal.vue b/src/components/modals/TrialShareCodeModal.vue
@@ -45,6 +45,13 @@
                 <span v-html="$t('formDescriptionTrialShareRemoteUrl')" />
               </template>
             </b-form-group>
+
+            <b-form-group v-if="shareWithRemote" :label="$t('formLabelTrialShareRemoteToken')" label-for="remoteToken">
+              <b-form-input v-model="remoteToken" id="remoteToken" />
+              <template #description>
+                <span v-html="$t('formDescriptionTrialShareRemoteToken')" />
+              </template>
+            </b-form-group>
           </div>
 
           <b-button @click="getShareCodes" :disabled="isOnline === false || buttonDisabled === true" variant="primary"><IBiQrCodeScan /> {{ $t('buttonGenerateShareCodes') }}</b-button>
@@ -83,7 +90,8 @@ export default {
       TRIAL_STATE_OWNER,
       TRIAL_STATE_VIEWER,
       shareWithRemote: false,
-      remoteUrl: null
+      remoteUrl: null,
+      remoteToken: null
     }
   },
   computed: {
@@ -100,7 +108,7 @@ export default {
   methods: {
     getShareCodes: function () {
       emitter.emit('show-loading', true)
-      shareTrial(this.shareWithRemote ? this.remoteUrl : null, this.trial.localId)
+      shareTrial({ url: this.shareWithRemote ? this.remoteUrl : null, token: this.remoteToken }, this.trial.localId)
         .then(() => emitter.emit('plausible-event', { key: 'trial-shared' }))
         .catch(error => {
           console.error(error)

diff --git a/src/components/modals/TrialSynchronizationModal.vue b/src/components/modals/TrialSynchronizationModal.vue
@@ -230,7 +230,17 @@ export default {
     askToSynchronize: function () {
       if (!this.trial.shareCodes.ownerCode && !this.trial.shareCodes.editorCode) {
         emitter.emit('show-loading', true)
-        getTrialByCode((this.trial && this.trial.remoteUrl) ? this.trial.remoteUrl : null, this.trial.shareCodes.viewerCode)
+
+        let remoteConfig = null
+
+        if (this.trial && this.trial.remoteUrl) {
+          remoteConfig = {
+            url: this.trial.remoteUrl,
+            token: this.trial.remoteToken || null
+          }
+        }
+
+        getTrialByCode(remoteConfig, this.trial.shareCodes.viewerCode)
           .then(result => {
             return deleteTrial(this.trial.localId)
               .then(() => {
@@ -270,7 +280,17 @@ export default {
     },
     synchronize: function () {
       emitter.emit('show-loading', true)
-      synchronizeTrial((this.trial && this.trial.remoteUrl) ? this.trial.remoteUrl : null, this.trial.shareCodes.ownerCode || this.trial.shareCodes.editorCode, this.transaction)
+
+      let remoteConfig = null
+
+      if (this.trial && this.trial.remoteUrl) {
+        remoteConfig = {
+          url: this.trial.remoteUrl,
+          token: this.trial.remoteToken || null
+        }
+      }
+
+      synchronizeTrial(remoteConfig, this.trial.shareCodes.ownerCode || this.trial.shareCodes.editorCode, this.transaction)
         .then(result => {
           if (this.trial.group && this.trial.group.name) {
             result.group = {