Eubopen compound: adapt sections to use chembl id, hide qt and act profile when no data

components/report_cards/chemical_probe/ActivityProfileComponents/ActivityDataSingleTab.vue

@@ -31,6 +31,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
   data() {
     return {
@@ -60,10 +64,10 @@ export default {
           query: {
             bool: {
               must: [
-                { terms: { molecule_chembl_id: [this.itemID] } },
+                { terms: { molecule_chembl_id: [this.chemblID] } },
                 {
                   terms: {
-                    '_metadata.eubopen_assay_type.aidx_prefix.keyword': [
+                    '_metadata.eubopen_assay_type.aidx_prefix': [
                       this.tabConfig.key,
                     ],
                   },

components/report_cards/chemical_probe/ActivityProfileComponents/ActivityDataTabs.vue

@@ -7,7 +7,11 @@
       </v-alert>
     </template>
     <template v-else>
-      <DownloadButton :item-i-d="itemID" :section-key="sectionKey" />
+      <DownloadButton
+        :item-i-d="itemID"
+        :chembl-i-d="chemblID"
+        :section-key="sectionKey"
+      />
       <v-tabs v-model="tab" show-arrows>
         <v-tab v-for="item in shownSections" :key="item.key">
           {{ item.title }}
@@ -16,7 +20,11 @@
 
       <v-tabs-items v-model="tab">
         <v-tab-item v-for="item in shownSections" :key="item.key">
-          <ActivityDataSingleTab :tab-config="item" :item-i-d="itemID" />
+          <ActivityDataSingleTab
+            :tab-config="item"
+            :item-i-d="itemID"
+            :chembl-i-d="chemblID"
+          />
         </v-tab-item>
       </v-tabs-items>
     </template>
@@ -41,6 +49,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
   data() {
     return {
@@ -146,10 +158,10 @@ export default {
       query: {
         bool: {
           must: [
-            { terms: { molecule_chembl_id: [this.itemID] } },
+            { terms: { molecule_chembl_id: [this.chemblID] } },
             {
               terms: {
-                '_metadata.eubopen_assay_type.aidx_prefix.keyword': aidxPrefixes,
+                '_metadata.eubopen_assay_type.aidx_prefix': aidxPrefixes,
               },
             },
           ],

components/report_cards/chemical_probe/ActivityProfileComponents/DownloadButton.vue

@@ -30,6 +30,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
     sectionKey: {
       type: String,
       default: () => undefined,
@@ -58,12 +62,12 @@ export default {
     },
     starterParams() {
       return {
-        chemblID: this.itemID,
+        chemblID: this.chemblID,
         propertiesGroups: this.propertiesGroups,
         initialQuery: {
           query: {
             bool: {
-              must: [{ terms: { molecule_chembl_id: [this.itemID] } }],
+              must: [{ terms: { molecule_chembl_id: [this.chemblID] } }],
             },
           },
         },

components/report_cards/chemical_probe/CellViabilityAndHealthData.vue

@@ -63,6 +63,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
   data() {
     return {
@@ -72,7 +76,7 @@ export default {
   },
   computed: {
     csvURL() {
-      return `${process.env.esProxyBaseUrl}/eubopen/visualisations/compound/cell_viability_and_health_data/download/CHEMBL180022`
+      return `${process.env.esProxyBaseUrl}/eubopen/visualisations/compound/cell_viability_and_health_data/download/${this.chemblID}`
     },
   },
   mounted() {
@@ -80,7 +84,7 @@ export default {
   },
   methods: {
     loadData() {
-      const visualisationPath = `/eubopen/visualisations/compound/cell_viability_and_health_data/${this.itemID}`
+      const visualisationPath = `/eubopen/visualisations/compound/cell_viability_and_health_data/${this.chemblID}`
 
       ESProxyService.getGenericData(visualisationPath)
         .then((response) => {

components/report_cards/chemical_probe/CompoundActivityProfile.vue

@@ -2,7 +2,11 @@
   <div>
     <v-card>
       <v-card-text>
-        <ActivityDataTabs :item-i-d="itemID" section-key="ActivityProfile" />
+        <ActivityDataTabs
+          :item-i-d="itemID"
+          section-key="ActivityProfile"
+          :chembl-i-d="chemblID"
+        />
       </v-card-text>
     </v-card>
   </div>
@@ -19,6 +23,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
 }
 </script>

components/report_cards/chemical_probe/CompoundCrystalStructures.vue

@@ -41,6 +41,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
   data() {
     return {
@@ -64,7 +68,7 @@ export default {
       const unichemPropertyPath = '_metadata.unichem'
       const docSource = [unichemPropertyPath]
 
-      ESProxyService.getESDocument(indexName, this.itemID, docSource)
+      ESProxyService.getESDocument(indexName, this.chemblID, docSource)
         .then((response) => {
           const sourceObtained = response.data._source
           const unichemRefs = ObjectPropertyAccess.getPropertyPalue(

components/report_cards/chemical_probe/EubopenCompoundReportCard.vue

@@ -40,14 +40,24 @@ export default {
   async mounted() {
     try {
       const paramsFromCompound = await this.getOptionalSectionsParams()
-      const showCellHeatlhAndViabilityData = await this.hasCellHeatlhAndViabilityData()
+      const chemblID = await this.getChEMBLID()
+      const showCellHeatlhAndViabilityData = await this.hasCellHeatlhAndViabilityData(
+        chemblID
+      )
+      const showQualityControlData = await this.hasQualityControlData(chemblID)
+      const showActivityProfileData = await this.hasActivityProfileData(
+        chemblID
+      )
       const reportCardStructure = CompoundReportCardGenerator.generateReportCardStructure(
-        this.itemID,
-        paramsFromCompound.prefName,
         {
+          itemID: this.itemID,
+          chemblID,
+          prefName: paramsFromCompound.prefName,
           isChemicalProbe: paramsFromCompound.isChemicalProbe,
           isNegativeControl: paramsFromCompound.isNegativeControl,
           showCellHeatlhAndViabilityData,
+          showQualityControlData,
+          showActivityProfileData,
         }
       )
 
@@ -107,7 +117,7 @@ export default {
         isNegativeControl,
       }
     },
-    async hasCellHeatlhAndViabilityData() {
+    async getChEMBLID() {
       const chemblIDResponse = await ESProxyService.getESDocument(
         IndexNames.getIndexNameFromEntityID(
           EntityNames.EubopenCompound.entityID
@@ -116,7 +126,9 @@ export default {
         ['molecule_chembl_id']
       )
 
-      const chemblID = chemblIDResponse.data._source.molecule_chembl_id
+      return chemblIDResponse.data._source.molecule_chembl_id
+    },
+    async hasCellHeatlhAndViabilityData(chemblID) {
       const cellHeatlhAndViabilityDataPath = `/eubopen/visualisations/compound/cell_viability_and_health_data/${chemblID}`
       const cellHealthAndViabilityData = await ESProxyService.getGenericData(
         cellHeatlhAndViabilityDataPath
@@ -125,6 +137,68 @@ export default {
       const numDataPoints = cellHealthAndViabilityData.data.num_datapoints
       return numDataPoints > 0
     },
+    async hasQualityControlData(chemblID) {
+      const entityID = EntityNames.EubopenActivity.entityID
+      const indexName = IndexNames.getIndexNameFromEntityID(entityID)
+      const aidxPrefixes = ['MULTI', 'INCU', 'LIABILITY']
+
+      const query = {
+        size: 0,
+        query: {
+          bool: {
+            must: [
+              { terms: { molecule_chembl_id: [chemblID] } },
+              {
+                terms: {
+                  '_metadata.eubopen_assay_type.aidx_prefix': aidxPrefixes,
+                },
+              },
+            ],
+          },
+        },
+      }
+
+      const qtData = await ESProxyService.getESData(indexName, query)
+      const numHits = qtData.data.es_response.hits.total.value
+
+      return numHits > 0
+    },
+    async hasActivityProfileData(chemblID) {
+      const entityID = EntityNames.EubopenActivity.entityID
+      const indexName = IndexNames.getIndexNameFromEntityID(entityID)
+      const aidxPrefixes = [
+        'AB',
+        'AOT',
+        'AP',
+        'S',
+        'ASIC50',
+        'ASSS',
+        'GPCR',
+        'NanoBRET',
+        'ITC',
+        'HTRF',
+      ]
+
+      const query = {
+        size: 0,
+        query: {
+          bool: {
+            must: [
+              { terms: { molecule_chembl_id: [chemblID] } },
+              {
+                terms: {
+                  '_metadata.eubopen_assay_type.aidx_prefix': aidxPrefixes,
+                },
+              },
+            ],
+          },
+        },
+      }
+
+      const qtData = await ESProxyService.getESData(indexName, query)
+      const numHits = qtData.data.es_response.hits.total.value
+      return numHits > 0
+    },
   },
 }
 </script>

components/report_cards/chemical_probe/QualityControl.vue

@@ -2,7 +2,7 @@
   <div>
     <v-card>
       <v-card-text>
-        <ActivityDataTabs :item-i-d="itemID" />
+        <ActivityDataTabs :item-i-d="itemID" :chembl-i-d="chemblID" />
       </v-card-text>
     </v-card>
   </div>
@@ -19,6 +19,10 @@ export default {
       type: String,
       default: () => undefined,
     },
+    chemblID: {
+      type: String,
+      default: () => undefined,
+    },
   },
 }
 </script>

report_cards_structure/CompoundReportCardGenerator.js

@@ -10,11 +10,16 @@ import EntityNames from '~/web-components-submodule/standardisation/EntityNames.
 import CellViabilityAndHealthData from '~/components/report_cards/chemical_probe/CellViabilityAndHealthData.vue'
 
 const methods = {
-  generateReportCardStructure(
+  generateReportCardStructure({
     itemID,
+    chemblID,
     prefName,
-    { isChemicalProbe, isNegativeControl, showCellHeatlhAndViabilityData }
-  ) {
+    isChemicalProbe,
+    isNegativeControl,
+    showCellHeatlhAndViabilityData,
+    showQualityControlData,
+    showActivityProfileData,
+  }) {
     const basePageStructure = [
       {
         id: 'Summary',
@@ -44,18 +49,27 @@ const methods = {
         id: 'QualityControl',
         title: 'Quality Control',
         component: QualityControl,
-        include: true,
+        componentParams: {
+          chemblID,
+        },
+        include: showQualityControlData,
       },
       {
         id: 'ActivityProfile',
         title: 'Activity Profile',
         component: CompoundActivityProfile,
-        include: true,
+        componentParams: {
+          chemblID,
+        },
+        include: showActivityProfileData,
       },
       {
         id: 'CellViabilityAndHealthData',
         title: 'Cell Health Data',
         component: CellViabilityAndHealthData,
+        componentParams: {
+          chemblID,
+        },
         include: showCellHeatlhAndViabilityData,
       },
       {
@@ -71,6 +85,9 @@ const methods = {
         id: 'CrystalStructures',
         title: 'PDB Ligand Codes',
         component: CompoundCrystalStructures,
+        componentParams: {
+          chemblID,
+        },
         include: true,
       },
     ]

web-components-submodule @ 918874fc

-Subproject commit 4a0daf4316804616b68774a5d777c39865cfe599
+Subproject commit 918874fc1fe49e86fd578e0630d8f08cc74be8b0