feat: Integrate more V2 API queries (#1174)

#1101 Also temporarily disables automatic querying of `__typename` due to a bug in the new API.
chanzuckerberg · Sep 26, 2024 · 92f80a7 · 92f80a7
1 parent d21ffd9
commit 92f80a7
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Showing 6 changed files with 48 additions and 40 deletions.
diff --git a/frontend/packages/data-portal/app/apollo.server.ts b/frontend/packages/data-portal/app/apollo.server.ts
@@ -22,7 +22,7 @@ export const apolloClientV2 = new ApolloClient({
       fetchPolicy: 'no-cache',
     },
   },
-  cache: new InMemoryCache(),
+  cache: new InMemoryCache({ addTypename: false }), // TODO(bchu): Re-enable __typename when fixed in BE.
   link: createHttpLink({
     uri: process.env.API_URL_V2 ?? ENVIRONMENT_CONTEXT_DEFAULT_VALUE.API_URL_V2,
   }),

diff --git a/frontend/packages/data-portal/app/components/Run/RunHeader.tsx b/frontend/packages/data-portal/app/components/Run/RunHeader.tsx
@@ -50,6 +50,7 @@ export function RunHeader() {
     resolutions,
     annotationFilesAggregates,
     tomogramsCount,
+    alignmentsCount,
   } = useRunById()
   const { toggleDrawer } = useMetadataDrawer()
   const { t } = useI18n()
@@ -142,8 +143,9 @@ export function RunHeader() {
                         : 'text-sds-color-primitive-gray-500',
                   },
                   {
-                    key: t('alignmentFile'),
-                    value: '', // TODO(bchu): Confirm how this should be counted.
+                    key: t('alignment'),
+                    value:
+                      alignmentsCount > 0 ? t('available') : t('notSubmitted'),
                   },
                   {
                     key: t('tomograms'),

diff --git a/frontend/packages/data-portal/app/graphql/getRunByIdDiffer.ts b/frontend/packages/data-portal/app/graphql/getRunByIdDiffer.ts
@@ -10,32 +10,33 @@ import {
   Tomogram_Reconstruction_Method_Enum,
 } from 'app/__generated_v2__/graphql'
 
-/* eslint-disable no-console */
+/* eslint-disable no-console, no-param-reassign */
 export function logIfHasDiff(
   url: string,
   v1: GetRunByIdQuery,
   v2: GetRunByIdV2Query,
 ): void {
   console.log('Checking for run query diffs')
 
-  // eslint-disable-next-line no-param-reassign
   v2 = structuredClone(v2)
+  // There are no alignments in V1.
+  delete v2.alignmentsAggregate.aggregate
   // Tomogram deposition relations in V1 are incomplete.
   for (const tomogram of v2.tomograms) {
     delete tomogram.deposition
   }
+  // Frames are not populated in V2 yet.
+  for (const run of v2.runs) {
+    delete run.framesAggregate
+  }
 
   const v1Transformed: GetRunByIdV2Query = {
     runs: v1.runs.map((run) => ({
-      __typename: 'Run',
       id: run.id,
       name: run.name,
       tiltseries: {
-        __typename: 'TiltseriesConnection',
         edges: run.tiltseries.map((runTiltseries) => ({
-          __typename: 'TiltseriesEdge',
           node: {
-            __typename: 'Tiltseries',
             accelerationVoltage: runTiltseries.acceleration_voltage,
             alignedTiltseriesBinning: runTiltseries.aligned_tiltseries_binning,
             binningFromFrames: runTiltseries.binning_from_frames,
@@ -67,7 +68,6 @@ export function logIfHasDiff(
         })),
       },
       dataset: {
-        __typename: 'Dataset',
         cellComponentName: run.dataset.cell_component_name,
         cellComponentId: run.dataset.cell_component_id,
         cellName: run.dataset.cell_name,
@@ -95,22 +95,16 @@ export function logIfHasDiff(
         tissueId: run.dataset.tissue_id,
         title: run.dataset.title,
         fundingSources: {
-          __typename: 'DatasetFundingConnection',
           edges: run.dataset.funding_sources.map((source) => ({
-            __typename: 'DatasetFundingEdge',
             node: {
-              __typename: 'DatasetFunding',
               fundingAgencyName: source.funding_agency_name,
               grantId: source.grant_id,
             },
           })),
         },
         authors: {
-          __typename: 'DatasetAuthorConnection',
           edges: run.dataset.authors.map((author) => ({
-            __typename: 'DatasetAuthorEdge',
             node: {
-              __typename: 'DatasetAuthor',
               correspondingAuthorStatus: author.corresponding_author_status,
               email: author.email,
               name: author.name,
@@ -121,19 +115,13 @@ export function logIfHasDiff(
         },
       },
       tomogramVoxelSpacings: {
-        __typename: 'TomogramVoxelSpacingConnection',
         edges: run.tomogram_voxel_spacings.map((tomogramVoxelSpacing) => ({
-          __typename: 'TomogramVoxelSpacingEdge',
           node: {
-            __typename: 'TomogramVoxelSpacing',
             id: tomogramVoxelSpacing.id,
             s3Prefix: tomogramVoxelSpacing.s3_prefix!,
             tomograms: {
-              __typename: 'TomogramConnection',
               edges: tomogramVoxelSpacing.tomograms.map((tomogram) => ({
-                __typename: 'TomogramEdge',
                 node: {
-                  __typename: 'Tomogram',
                   ctfCorrected: tomogram.ctf_corrected,
                   fiducialAlignmentStatus:
                     tomogram.fiducial_alignment_status as Fiducial_Alignment_Status_Enum,
@@ -153,7 +141,6 @@ export function logIfHasDiff(
                   sizeZ: tomogram.size_z,
                   voxelSpacing: tomogram.voxel_spacing,
                   alignment: {
-                    __typename: 'Alignment',
                     affineTransformationMatrix: JSON.stringify(
                       tomogram.affine_transformation_matrix,
                     ).replaceAll(',', ', '),
@@ -164,9 +151,20 @@ export function logIfHasDiff(
           },
         })),
       },
+      tiltseriesAggregate: {
+        aggregate: [
+          {
+            count: run.tiltseries_aggregate.aggregate?.count,
+            avg: {
+              tiltSeriesQuality:
+                run.tiltseries_aggregate.aggregate?.avg?.tilt_series_quality,
+            },
+          },
+        ],
+      },
     })),
+    alignmentsAggregate: {},
     tomograms: v1.tomograms.map((tomogram) => ({
-      __typename: 'Tomogram',
       ctfCorrected: tomogram.ctf_corrected,
       fiducialAlignmentStatus:
         tomogram.fiducial_alignment_status as Fiducial_Alignment_Status_Enum,
@@ -193,17 +191,13 @@ export function logIfHasDiff(
       tomogramVoxelSpacing:
         tomogram.tomogram_voxel_spacing != null
           ? {
-              __typename: 'TomogramVoxelSpacing',
               id: tomogram.tomogram_voxel_spacing.id,
               s3Prefix: tomogram.tomogram_voxel_spacing.s3_prefix!,
             }
           : undefined,
       authors: {
-        __typename: 'TomogramAuthorConnection',
         edges: tomogram.authors.map((author) => ({
-          __typename: 'TomogramAuthorEdge',
           node: {
-            __typename: 'TomogramAuthor',
             primaryAuthorStatus: author.primary_author_status,
             correspondingAuthorStatus: author.corresponding_author_status,
             name: author.name,

diff --git a/frontend/packages/data-portal/app/graphql/getRunByIdV2.server.ts b/frontend/packages/data-portal/app/graphql/getRunByIdV2.server.ts
@@ -151,17 +151,26 @@ const GET_RUN_BY_ID_QUERY_V2 = gql(`
         }
 
         # Header
-        # tiltseriesAggregate { # TODO(bchu): Uncomment when __typename bug is fixed.
-        #   aggregate {
-        #     count
-        #     avg {
-        #       tiltSeriesQuality
-        #     }
-        #     # sum {
-        #     #   tiltseriesFramesCount # TODO(bchu): Uncomment when populated.
-        #     # }
-        #   }
-        # }
+        framesAggregate {
+          aggregate {
+            count
+          }
+        }
+        tiltseriesAggregate {
+          aggregate {
+            count
+            avg {
+              tiltSeriesQuality
+            }
+          }
+        }
+      }
+
+      # Header
+      alignmentsAggregate(where: {run: {id: {_eq: $id}}}) {
+        aggregate {
+          count
+        }
       }
 
       # Annotations table

diff --git a/frontend/packages/data-portal/app/hooks/useRunById.ts b/frontend/packages/data-portal/app/hooks/useRunById.ts
@@ -47,6 +47,8 @@ export function useRunById() {
 
   const tomogramsCount = v1.tomograms_aggregate.aggregate?.count ?? 0
 
+  const alignmentsCount = v2.alignmentsAggregate.aggregate?.[0]?.count ?? 0
+
   const { deposition } = v1
 
   return {
@@ -60,6 +62,7 @@ export function useRunById() {
     resolutions,
     annotationFilesAggregates,
     tomogramsCount,
+    alignmentsCount,
     deposition,
   }
 }
diff --git a/frontend/packages/data-portal/e2e/apollo.ts b/frontend/packages/data-portal/e2e/apollo.ts
@@ -19,7 +19,7 @@ export function getApolloClient() {
 export function getApolloClientV2() {
   return new apollo.ApolloClient({
     ssrMode: true,
-    cache: new apollo.InMemoryCache(),
+    cache: new apollo.InMemoryCache({ addTypename: false }), // TODO(bchu): Re-enable __typename when fixed in BE.
     link: apollo.createHttpLink({
       uri:
         process.env.API_URL_V2 ?? ENVIRONMENT_CONTEXT_DEFAULT_VALUE.API_URL_V2,