feat: Start writing run query for new API

frontend/packages/data-portal/app/graphql/getRunById.server.ts

@@ -92,12 +92,11 @@ const GET_RUN_BY_ID_QUERY = gql(`
           primary_author_status
         }
 
-        authors_with_affiliation: authors(where: { affiliation_name: { _is_null: false } }) {
-          name
-          affiliation_name
-        }
-
-        funding_sources {
+        funding_sources(
+          order_by: {
+            funding_agency_name: asc
+          }
+        ) {
           funding_agency_name
           grant_id
         }

frontend/packages/data-portal/app/graphql/getRunByIdDiffer.ts

@@ -0,0 +1,122 @@
+import { diff } from 'deep-object-diff'
+
+import { GetRunByIdQuery } from 'app/__generated__/graphql'
+import {
+  GetRunByIdV2Query,
+  Sample_Type_Enum,
+  Tiltseries_Microscope_Manufacturer_Enum,
+} from 'app/__generated_v2__/graphql'
+
+/* eslint-disable no-console */
+export function logIfHasDiff(
+  url: string,
+  v1: GetRunByIdQuery,
+  v2: GetRunByIdV2Query,
+): void {
+  console.log('Checking for run query diffs')
+
+  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,
+            cameraManufacturer: runTiltseries.camera_manufacturer,
+            cameraModel: runTiltseries.camera_model,
+            dataAcquisitionSoftware: runTiltseries.data_acquisition_software,
+            id: runTiltseries.id,
+            isAligned: runTiltseries.is_aligned,
+            microscopeAdditionalInfo: runTiltseries.microscope_additional_info,
+            microscopeEnergyFilter: runTiltseries.microscope_energy_filter,
+            microscopeImageCorrector: runTiltseries.microscope_image_corrector,
+            microscopeManufacturer:
+              runTiltseries.microscope_manufacturer as Tiltseries_Microscope_Manufacturer_Enum,
+            microscopeModel: runTiltseries.microscope_model,
+            microscopePhasePlate: runTiltseries.microscope_phase_plate,
+            pixelSpacing: runTiltseries.pixel_spacing!,
+            relatedEmpiarEntry: runTiltseries.related_empiar_entry,
+            sphericalAberrationConstant:
+              runTiltseries.spherical_aberration_constant,
+            tiltAxis: runTiltseries.tilt_axis,
+            tiltMax: runTiltseries.tilt_max,
+            tiltMin: runTiltseries.tilt_min,
+            tiltRange: runTiltseries.tilt_range,
+            tiltSeriesQuality: runTiltseries.tilt_series_quality,
+            tiltStep: runTiltseries.tilt_step,
+            tiltingScheme: runTiltseries.tilting_scheme,
+            totalFlux: runTiltseries.total_flux,
+          },
+        })),
+      },
+      dataset: {
+        __typename: 'Dataset',
+        cellComponentName: run.dataset.cell_component_name,
+        cellComponentId: run.dataset.cell_component_id,
+        cellName: run.dataset.cell_name,
+        cellStrainName: run.dataset.cell_strain_name,
+        cellStrainId: run.dataset.cell_strain_id,
+        cellTypeId: run.dataset.cell_type_id,
+        depositionDate: `${run.dataset.deposition_date}T00:00:00+00:00`,
+        description: run.dataset.description,
+        gridPreparation: run.dataset.grid_preparation,
+        id: run.dataset.id,
+        lastModifiedDate: `${run.dataset.last_modified_date}T00:00:00+00:00`,
+        organismName: run.dataset.organism_name!,
+        organismTaxid: Number(run.dataset.organism_taxid),
+        otherSetup: run.dataset.other_setup,
+        publications: run.dataset.dataset_publications,
+        relatedDatabaseEntries: run.dataset.related_database_entries,
+        releaseDate: `${run.dataset.release_date}T00:00:00+00:00`,
+        s3Prefix: run.dataset.s3_prefix,
+        samplePreparation: run.dataset.sample_preparation,
+        sampleType: run.dataset.sample_type as Sample_Type_Enum,
+        tissueName: run.dataset.tissue_name,
+        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,
+              orcid: author.orcid,
+              primaryAuthorStatus: author.primary_author_status,
+            },
+          })),
+        },
+      },
+    })),
+  }
+
+  const diffObject = diff(v1Transformed, v2)
+
+  if (Object.keys(diffObject).length > 0) {
+    console.log(
+      `DIFF AT ${url}: ${JSON.stringify(diffObject)} | ${JSON.stringify(
+        diff(v2, v1Transformed),
+      )}`,
+    )
+  }
+}

frontend/packages/data-portal/app/graphql/getRunByIdV2.server.ts

@@ -8,17 +8,112 @@ import { gql } from 'app/__generated_v2__'
 import { GetRunByIdV2Query } from 'app/__generated_v2__/graphql'
 
 const GET_RUN_BY_ID_QUERY_V2 = gql(`
-    query GetRunByIdV2 {
-        __typename
+    query GetRunByIdV2(
+      $id: Int
+    ) {
+      runs(where: { id: { _eq: $id } }) {
+        id
+        name
+
+        tiltseries(first: 1) {
+          edges {
+            node {
+              accelerationVoltage
+              alignedTiltseriesBinning
+              binningFromFrames
+              cameraManufacturer
+              cameraModel
+              dataAcquisitionSoftware
+              id
+              isAligned
+              microscopeAdditionalInfo
+              microscopeEnergyFilter
+              microscopeImageCorrector
+              microscopeManufacturer
+              microscopeModel
+              microscopePhasePlate
+              pixelSpacing
+              relatedEmpiarEntry
+              sphericalAberrationConstant
+              tiltAxis
+              tiltMax
+              tiltMin
+              tiltRange
+              tiltSeriesQuality
+              tiltStep
+              tiltingScheme
+              totalFlux
+            }
+          }
+        }
+
+        dataset {
+          cellComponentName
+          cellComponentId
+          cellName
+          cellStrainName
+          cellStrainId
+          cellTypeId
+          depositionDate
+          description
+          gridPreparation
+          id
+          lastModifiedDate
+          organismName
+          organismTaxid
+          otherSetup
+          publications
+          relatedDatabaseEntries
+          relatedDatabaseEntries
+          releaseDate
+          s3Prefix
+          samplePreparation
+          sampleType
+          tissueName
+          tissueId
+          title
+
+          fundingSources(
+            orderBy: {
+              fundingAgencyName: asc
+            }
+          ) {
+            edges {
+              node {
+                fundingAgencyName
+                grantId
+              }
+            }
+          }
+
+          authors(
+            orderBy: {
+              authorListOrder: asc,
+            },
+          ) {
+            edges {
+              node {
+                correspondingAuthorStatus
+                email
+                name
+                orcid
+                primaryAuthorStatus
+              }
+            }
+          }
+        }
+      }
     }
 `)
 
-export async function getRunById({
-  client,
-}: {
-  client: ApolloClient<NormalizedCacheObject>
-}): Promise<ApolloQueryResult<GetRunByIdV2Query>> {
+export async function getRunByIdV2(
+  client: ApolloClient<NormalizedCacheObject>,
+  id: number,
+): Promise<ApolloQueryResult<GetRunByIdV2Query>> {
   return client.query({
     query: GET_RUN_BY_ID_QUERY_V2,
+    variables: {
+      id,
+    },
   })
 }

frontend/packages/data-portal/app/hooks/useRunById.ts

@@ -1,49 +1,55 @@
 import { useTypedLoaderData } from 'remix-typedjson'
 
 import { GetRunByIdQuery } from 'app/__generated__/graphql'
+import { GetRunByIdV2Query } from 'app/__generated_v2__/graphql'
 import { isNotNullish } from 'app/utils/nullish'
 
 export function useRunById() {
-  const data = useTypedLoaderData<GetRunByIdQuery>()
+  const { v1 } = useTypedLoaderData<{
+    v1: GetRunByIdQuery
+    v2: GetRunByIdV2Query
+  }>()
 
-  const run = data.runs[0]
+  const run = v1.runs[0]
 
-  const annotationFiles = data.annotation_files
+  const annotationFiles = v1.annotation_files
 
-  const { tomograms } = data
+  const { tomograms } = v1
 
-  const tomogramsForDownload = data.tomograms_for_download
+  const tomogramsForDownload = v1.tomograms_for_download
 
-  const processingMethods = data.tomograms_for_distinct_processing_methods.map(
+  const processingMethods = v1.tomograms_for_distinct_processing_methods.map(
     (tomogram) => tomogram.processing,
   )
 
-  const objectNames = data.annotations_for_object_names.map(
+  const objectNames = v1.annotations_for_object_names.map(
     (annotation) => annotation.object_name,
   )
 
-  const objectShapeTypes = data.annotation_files_for_shape_types.map(
+  const objectShapeTypes = v1.annotation_files_for_shape_types.map(
     (file) => file.shape_type,
   )
 
-  const annotationSoftwares = data.annotations_for_softwares
+  const annotationSoftwares = v1.annotations_for_softwares
     .map((annotation) => annotation.annotation_software)
     .filter(isNotNullish)
 
-  const resolutions = data.tomograms_for_resolutions.map(
+  const resolutions = v1.tomograms_for_resolutions.map(
     (tomogram) => tomogram.voxel_spacing,
   )
 
   const annotationFilesAggregates = {
-    totalCount: data.annotation_files_aggregate_for_total.aggregate?.count ?? 0,
+    totalCount: v1.annotation_files_aggregate_for_total.aggregate?.count ?? 0,
     filteredCount:
-      data.annotation_files_aggregate_for_filtered.aggregate?.count ?? 0,
+      v1.annotation_files_aggregate_for_filtered.aggregate?.count ?? 0,
     groundTruthCount:
-      data.annotation_files_aggregate_for_ground_truth.aggregate?.count ?? 0,
-    otherCount: data.annotation_files_aggregate_for_other.aggregate?.count ?? 0,
+      v1.annotation_files_aggregate_for_ground_truth.aggregate?.count ?? 0,
+    otherCount: v1.annotation_files_aggregate_for_other.aggregate?.count ?? 0,
   }
 
-  const tomogramsCount = data.tomograms_aggregate.aggregate?.count ?? 0
+  const tomogramsCount = v1.tomograms_aggregate.aggregate?.count ?? 0
+
+  const { deposition } = v1
 
   return {
     run,
@@ -57,6 +63,6 @@ export function useRunById() {
     resolutions,
     annotationFilesAggregates,
     tomogramsCount,
-    deposition: data.deposition,
+    deposition,
   }
 }