Merge branch 'nih-sparc:main' into main

nih-sparc · Jul 18, 2024 · 04c5580 · 04c5580
2 parents 942f921 + ed419db
commit 04c5580
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diff --git a/.github/workflows/quality_control_cypress.yml b/.github/workflows/quality_control_cypress.yml
@@ -98,29 +98,22 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      latest-sha: ${{ steps.latest-deployment-sha.outputs.sha }}
+      latest-sha: ${{ steps.latest-deployment-sha.outputs.deployment-sha }}
 
-    permissions:
-      deployments: read
-      contents: read
     steps:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
 
       - name: Get sha of latest deployment in main branch
         id: latest-deployment-sha
-        uses: vrnithinkumar/latest-deployment-sha@v1.0.0
+        uses: go-fjords/get-active-deployment-action@v0.0.3
         with:
-          repo_owner: nih-sparc
-          repo_name: sparc-app-2
           environment: sparc-app-prod
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Print latest deployment sha
         id: output
-        run: echo "${{ steps.latest-deployment-sha.outputs.sha }}"
+        run: echo "${{ steps.latest-deployment-sha.outputs.deployment-sha }}"
 
   quality-control-cypress-run:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/scheduled_production_cypress.yml b/.github/workflows/scheduled_production_cypress.yml
@@ -56,29 +56,22 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      latest-sha: ${{ steps.latest-deployment-sha.outputs.sha }}
+      latest-sha: ${{ steps.latest-deployment-sha.outputs.deployment-sha }}
 
-    permissions:
-      deployments: read
-      contents: read
     steps:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
 
       - name: Get sha of latest deployment in main branch
         id: latest-deployment-sha
-        uses: vrnithinkumar/latest-deployment-sha@v1.0.0
+        uses: go-fjords/get-active-deployment-action@v0.0.3
         with:
-          repo_owner: nih-sparc
-          repo_name: sparc-app-2
           environment: sparc-app-prod
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Print latest deployment sha
         id: output
-        run: echo "${{ steps.latest-deployment-sha.outputs.sha }}"
+        run: echo "${{ steps.latest-deployment-sha.outputs.deployment-sha }}"
 
   scheduled-cypress-run-production:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/scheduled_staging_cypress.yml b/.github/workflows/scheduled_staging_cypress.yml
@@ -56,29 +56,22 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      latest-sha: ${{ steps.latest-deployment-sha.outputs.sha }}
+      latest-sha: ${{ steps.latest-deployment-sha.outputs.deployment-sha }}
 
-    permissions:
-      deployments: read
-      contents: read
     steps:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
 
       - name: Get sha of latest deployment in main branch
         id: latest-deployment-sha
-        uses: vrnithinkumar/latest-deployment-sha@v1.0.0
+        uses: go-fjords/get-active-deployment-action@v0.0.3
         with:
-          repo_owner: nih-sparc
-          repo_name: sparc-app-2
           environment: sparc-app-2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Print latest deployment sha
         id: output
-        run: echo "${{ steps.latest-deployment-sha.outputs.sha }}"
+        run: echo "${{ steps.latest-deployment-sha.outputs.deployment-sha }}"
 
   scheduled-cypress-run-staging:
     runs-on: ubuntu-latest

diff --git a/app.vue b/app.vue
@@ -16,16 +16,9 @@ import { successMessage } from './utils/notification-messages'
 export default {
   async setup() {
     const nuxtApp = useNuxtApp()
-    const loading = ref(false)
+    const loading = ref(true)
     const loaded = ref(false)
     const logo = sparcLogoFast
-    nuxtApp.hook("page:start", () => {
-      setTimeout(() => {
-        if (!loaded.value) {
-          loading.value = true
-        }
-      }, 1000)
-    })
     nuxtApp.hook("page:finish", () => {
       loading.value = false
       loaded.value = true

diff --git a/components/DatasetDetails/DatasetActionBox.vue b/components/DatasetDetails/DatasetActionBox.vue
@@ -24,6 +24,19 @@
           Cite Scaffold
         </el-button>
       </template>
+      <template v-else-if="datasetTypeName === 'device'">
+        <template v-if="hasFiles">
+          <el-button
+            class="dataset-button"
+            @click="actionButtonClicked('files')"
+          >
+            Get Device
+          </el-button>
+        </template>
+        <el-button class="secondary" @click="actionButtonClicked('cite')">
+          Cite Device
+        </el-button>
+      </template>
       <template v-else-if="datasetTypeName === 'computational model'">
         <el-button v-if="canViewSimulation" @click="openSimulationViewer()">
           View Simulation
@@ -68,15 +81,17 @@
           </sparc-tooltip>
         </a>
       </template>
-      <el-button
-        v-if="hasFiles"
-        @click="actionButtonClicked('files')"
-      >
-        Get Dataset
-      </el-button>
-      <el-button class="secondary" @click="actionButtonClicked('cite')">
-        Cite Dataset
-      </el-button>
+      <template v-else>
+        <el-button
+          v-if="hasFiles"
+          @click="actionButtonClicked('files')"
+        >
+          Get Dataset
+        </el-button>
+        <el-button class="secondary" @click="actionButtonClicked('cite')">
+          Cite Dataset
+        </el-button>
+      </template>
       <template v-if="sdsViewer">
         <a
           :href="sdsViewer"

diff --git a/components/DatasetDetails/DatasetDescriptionInfo.vue b/components/DatasetDetails/DatasetDescriptionInfo.vue
@@ -13,32 +13,42 @@
     <div class="heading2 mb-8">
       Metadata
     </div>
-    <p class="mb-8"><strong>Experimental Design: </strong></p>
+    <template v-if="isDevice">
+      <p class="mb-8"><strong>Intended Use: </strong>{{ intendedUseText }}</p>
+      <p class="mb-8"><strong>Current Use: </strong>{{ currentUse }}</p>
+      <p class="mb-8"><strong>Device Type: </strong>{{ deviceType }}</p>
+      <p class="mb-8"><strong>Application: </strong>{{ deviceApplication }}</p>
+      <p class="mb-8"><strong>Device Target (disease or disorder): </strong> {{ deviceTarget }}</p>
+      <p class="mb-8"><strong>Target Population: </strong></p>
+    </template>
+    <template v-else>
+      <p class="mb-8"><strong>Experimental Design: </strong></p>
+      <div class="experimental-design-container mb-8">
+        <span class="experimental-design-section-text-column"><strong>Protocol Links: </strong></span>
+        <span v-if="datasetRecords.length !== 0">
+          <div v-for="record in datasetRecords" :key="record.id">
+            <a
+              class="link2"
+              :href="record.url"
+              target="_blank"
+            >
+              {{ record.url }}
+            </a>
+          </div> 
+        </span>
+        <span
+          v-else
+        >
+          N/A
+        </span>
+      </div>
+      <div class="experimental-design-container mb-16">
+        <span><strong>Experimental Approach: </strong>{{experimentalApproachText}}</span>
+      </div>
+      <p class="mb-8"><strong>Subject Information: </strong></p>
+    </template>
     <div class="experimental-design-container mb-8">
-      <span class="experimental-design-section-text-column"><strong>Protocol Links: </strong></span>
-      <span v-if="datasetRecords.length !== 0">
-        <div v-for="record in datasetRecords" :key="record.id">
-          <a
-            class="link2"
-            :href="record.url"
-            target="_blank"
-          >
-            {{ record.url }}
-          </a>
-        </div> 
-      </span>
-      <span
-        v-else
-      >
-        n/a
-      </span>
-    </div>
-    <div class="experimental-design-container mb-16">
-      <span><strong>Experimental Approach: </strong>{{experimentalApproachText}}</span>
-    </div>
-    <p class="mb-8"><strong>Subject Information: </strong></p>
-    <div class="experimental-design-container mb-8">
-      <span><strong>Anatomical structure: </strong>{{anatomicalStructureText}}</span>
+      <span><strong>Anatomical Structure: </strong>{{anatomicalStructureText}}</span>
     </div>
     <div class="experimental-design-container mb-8">
       <span><strong>Species: </strong>{{speciesText}}</span>
@@ -47,10 +57,10 @@
       <span><strong>Sex: </strong>{{sexText}}</span>
     </div>
     <div class="experimental-design-container mb-8">
-      <span><strong>Age range: </strong>{{ageRangeText}}</span>
+      <span><strong>Age Range: </strong>{{ageRangeText}}</span>
     </div>
-    <div class="experimental-design-container mb-16">
-      <span><strong>Number of samples: </strong>{{samplesMetadataText}}</span>
+    <div v-if="!isDevice" class="experimental-design-container mb-16">
+      <span><strong>Number of Samples: </strong>{{samplesMetadataText}}</span>
     </div>
     <div class="mb-16">
       <sparc-tooltip
@@ -101,7 +111,7 @@
       </span>
     </span>
     <span v-else>
-      <p>n/a</p>
+      <p>N/A</p>
     </span>
   </div>
 </template>
@@ -146,7 +156,7 @@ export default {
   },
 
   computed: {
-    ...mapState(useMainStore, ['datasetFacetsData','datasetInfo', 'userToken']),
+    ...mapState(useMainStore, ['datasetFacetsData', 'datasetTypeName', 'datasetInfo', 'userToken']),
     EMBARGO_ACCESS() {
       return EMBARGO_ACCESS
     },
@@ -182,7 +192,37 @@ export default {
       {
         return `${this.numberSamples} samples from ${this.numberSubjects} subjects`
       }
-      return 'n/a'
+      return 'N/A'
+    },
+    intendedUseText() {
+      let intendedUse = _.get(this.datasetMetadataInfo, 'device.intendedUse[0].name', 'N/A')
+      if (intendedUse.length > 0)
+        intendedUse = intendedUse.charAt(0).toUpperCase() + intendedUse.slice(1)
+      return intendedUse
+    },
+    currentUse() {
+      let currentUse = _.get(this.datasetMetadataInfo, 'device.currentUse[0].name', 'N/A')
+      if (currentUse.length > 0)
+        currentUse = currentUse.charAt(0).toUpperCase() + currentUse.slice(1)
+      return currentUse
+    },
+    deviceType() {
+      let deviceType = _.get(this.datasetMetadataInfo, 'device.type[0].name', 'N/A')
+      if (deviceType.length > 0)
+        deviceType = deviceType.charAt(0).toUpperCase() + deviceType.slice(1)
+      return deviceType
+    },
+    deviceApplication() {
+      let deviceApplication = _.get(this.datasetMetadataInfo, 'device.application[0].description', 'N/A')
+      if (deviceApplication.length > 0)
+        deviceApplication = deviceApplication.charAt(0).toUpperCase() + deviceApplication.slice(1)
+      return deviceApplication
+    },
+    deviceTarget() {
+      let deviceTarget = _.get(this.datasetMetadataInfo, 'device.target[0].name', 'N/A')
+      if (deviceTarget.length > 0)
+        deviceTarget = deviceTarget.charAt(0).toUpperCase() + deviceTarget.slice(1)
+      return deviceTarget
     },
     /**
      * Gets dataset id
@@ -208,6 +248,9 @@ export default {
         url += `?api_key=${this.userToken}`
       }
       return url
+    },
+    isDevice() {
+      return this.datasetTypeName == 'device'
     }
   },
 
@@ -228,7 +271,7 @@ export default {
       const facet = this.datasetFacetsData.find(item => item.key === facetKey)
       if (facet === undefined || !facet.children)
       {
-        return 'n/a'
+        return 'N/A'
       }
       facet.children.forEach(child => {
         let childLabel = child.label.charAt(0).toUpperCase() + child.label.slice(1)

diff --git a/components/DatasetDetails/DatasetHeader.vue b/components/DatasetDetails/DatasetHeader.vue
@@ -187,10 +187,10 @@ export default {
       return !this.embargoed && this.numCitations !== 0
     },
     numCitationsText: function() {
-      return this.showCitations ? `${this.numCitations}` : 'n/a'
+      return this.showCitations ? `${this.numCitations}` : 'N/A'
     },
     numDownloadsText: function() {
-      return this.embargoed ? 'n/a' : `${this.numDownloads}`
+      return this.embargoed ? 'N/A' : `${this.numDownloads}`
     }
   },
 

diff --git a/components/FacetMenu/ProjectsFacetMenu.vue b/components/FacetMenu/ProjectsFacetMenu.vue
@@ -80,6 +80,9 @@ export default {
     if (this.$route.query.selectedProjectsAnatomicalFocusIds) {
       this.defaultCheckedAnatomicalFocusIds = this.$route.query.selectedProjectsAnatomicalFocusIds.split(",")
     }
+    else {
+      this.$emit('projects-selections-changed')
+    }
   },
 
   methods: {

diff --git a/components/FeaturedData/FeaturedData.vue b/components/FeaturedData/FeaturedData.vue
@@ -99,6 +99,9 @@ export default {
           (contentfulFields.containsSearch && contentfulFields.containsSearch.some(keyword => normStr(organ.label).includes(normStr(keyword))))
       )
       organFacets.forEach(organFacet => {
+        if (organFacet == undefined || organFacet.children == undefined) {
+          return
+        }
         if (organFacet.children.length == 0) {
           return
         }

diff --git a/components/Gallery/Gallery.vue b/components/Gallery/Gallery.vue
@@ -21,6 +21,8 @@
                 :width="cardWidth" show-card-details @card-clicked="cardClicked" />
               <component v-else-if="galleryItemType === 'featuredData'" :is="galleryItemComponent" :item="item" 
                 :width="cardWidth" @card-clicked="cardClicked" />
+              <component v-else-if="galleryItemType === 'inProgressDatasets'" :is="galleryItemComponent" :width="cardWidth"
+                :key="item" :item="item" />
             </template>
           </span>
         </template>
@@ -40,6 +42,7 @@ import HighlightCard from '~/components/Gallery/GalleryItems/HighlightCard.vue'
 import DatasetCard from '~/components/Gallery/GalleryItems/DatasetCard.vue'
 import FileViewerCard from '~/components/Gallery/GalleryItems/FileViewerCard.vue'
 import FeaturedDataCard from '~/components/Gallery/GalleryItems/FeaturedDataCard.vue'
+import PennsieveDatasetCard from '~/components/Gallery/GalleryItems/PennsieveDatasetCard.vue'
 
 import { defaultTo } from 'ramda'
 import { ref } from 'vue'
@@ -50,7 +53,8 @@ const galleryItemComponents = {
   highlights: HighlightCard,
   datasets: DatasetCard,
   fileViewer: FileViewerCard,
-  featuredData: FeaturedDataCard
+  featuredData: FeaturedDataCard,
+  inProgressDatasets: PennsieveDatasetCard
 }
 
 function convertRemToPixels(rem) {