feat: Migrate annotations table to V2

frontend/packages/data-portal/app/components/Download/ConfigureDownloadContent.tsx

@@ -9,7 +9,10 @@ import { ConfigureTomogramDownloadContent } from './ConfigureTomogramDownloadCon
 
 export function ConfigureDownloadContent() {
   const { t } = useI18n()
-  const { datasetTitle, runName, objectName } = useDownloadModalContext()
+
+  const { annotationToDownload, datasetTitle, runName, objectName } =
+    useDownloadModalContext()
+
   const { annotationName, annotationId, objectShapeType } =
     useDownloadModalQueryParamState()
 
@@ -32,6 +35,12 @@ export function ConfigureDownloadContent() {
       {objectShapeType && (
         <ModalSubtitle label={t('objectShapeType')} value={objectShapeType} />
       )}
+      {annotationToDownload !== undefined && (
+        <ModalSubtitle
+          label={t('alignmentId')}
+          value={`${IdPrefix.Alignment}-${annotationToDownload}`}
+        />
+      )}
 
       <p className="mt-sds-xl text-sds-body-m leading-sds-body-m font-semibold">
         {t('selectDownload')}

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

@@ -2,6 +2,8 @@ import { diff } from 'deep-object-diff'
 
 import { GetRunByIdQuery } from 'app/__generated__/graphql'
 import {
+  Annotation_File_Shape_Type_Enum,
+  Annotation_Method_Type_Enum,
   Fiducial_Alignment_Status_Enum,
   GetRunByIdV2Query,
   Sample_Type_Enum,
@@ -21,6 +23,12 @@ export function logIfHasDiff(
   v2 = structuredClone(v2)
   // There are no alignments in V1.
   delete v2.alignmentsAggregate.aggregate
+  // Sort annotation files for consistency.
+  for (const annotationShape of v2.annotationShapes) {
+    annotationShape.annotationFiles.edges.sort((edge) =>
+      edge.node.format.localeCompare(edge.node.format),
+    )
+  }
   // Tomogram deposition relations in V1 are incomplete.
   for (const tomogram of v2.tomograms) {
     // There are no alignments in V1.
@@ -169,6 +177,63 @@ export function logIfHasDiff(
       },
     })),
     alignmentsAggregate: {},
+    annotationShapes: v1.annotation_files.map((file) => ({
+      shapeType: file.shape_type as Annotation_File_Shape_Type_Enum,
+      annotationFiles: {
+        edges: file.annotation.files
+          .map((nestedFile) => ({
+            node: {
+              format: nestedFile.format,
+              httpsPath: nestedFile.https_path,
+              s3Path: nestedFile.s3_path,
+            },
+          }))
+          .sort((a, b) => a.node.format.localeCompare(b.node.format)),
+      },
+      annotation: {
+        annotationMethod: file.annotation.annotation_method,
+        annotationPublication: file.annotation.annotation_publication,
+        annotationSoftware: file.annotation.annotation_software,
+        confidencePrecision: file.annotation.confidence_precision,
+        confidenceRecall: file.annotation.confidence_recall,
+        depositionDate: file.annotation.deposition_date,
+        groundTruthStatus: file.annotation.ground_truth_status,
+        groundTruthUsed: file.annotation.ground_truth_used,
+        id: file.annotation.id,
+        isCuratorRecommended: file.annotation.is_curator_recommended,
+        lastModifiedDate: file.annotation.last_modified_date!,
+        methodLinks: file.annotation.method_links as string,
+        methodType: file.annotation.method_type as Annotation_Method_Type_Enum,
+        objectCount: file.annotation.object_count,
+        objectDescription: file.annotation.object_description,
+        objectId: file.annotation.object_id,
+        objectName: file.annotation.object_name,
+        objectState: file.annotation.object_state,
+        releaseDate: file.annotation.release_date,
+        authors: {
+          edges: file.annotation.authors.map((author) => ({
+            node: {
+              primaryAuthorStatus: author.primary_author_status,
+              correspondingAuthorStatus: author.corresponding_author_status,
+              name: author.name,
+              email: author.email,
+              orcid: author.orcid,
+            },
+          })),
+        },
+        authorsAggregate: {
+          aggregate: [
+            {
+              count: file.annotation.authors_aggregate.aggregate?.count,
+            },
+          ],
+        },
+        deposition: {
+          id: file.annotation.deposition!.id ?? 0,
+          title: file.annotation.deposition!.title,
+        },
+      },
+    })),
     tomograms: v1.tomograms.map((tomogram) => ({
       ctfCorrected: tomogram.ctf_corrected,
       fiducialAlignmentStatus:

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

@@ -5,11 +5,21 @@ import {
 } from '@apollo/client'
 
 import { gql } from 'app/__generated_v2__'
-import { GetRunByIdV2Query } from 'app/__generated_v2__/graphql'
+import {
+  Annotation_File_Shape_Type_Enum,
+  Annotation_Method_Type_Enum,
+  AnnotationShapeWhereClause,
+  GetRunByIdV2Query,
+} from 'app/__generated_v2__/graphql'
+import { MAX_PER_PAGE } from 'app/constants/pagination'
+import { FilterState, getFilterState } from 'app/hooks/useFilter'
 
 const GET_RUN_BY_ID_QUERY_V2 = gql(`
     query GetRunByIdV2(
       $id: Int
+      $limit: Int
+      $annotationShapesOffset: Int
+      $annotationShapesFilter: AnnotationShapeWhereClause
     ) {
       runs(where: { id: { _eq: $id } }) {
         id
@@ -174,7 +184,82 @@ const GET_RUN_BY_ID_QUERY_V2 = gql(`
       }
 
       # Annotations table
-      # TODO(bchu)
+      annotationShapes(
+        where: $annotationShapesFilter
+        orderBy: [
+          {
+            annotation: {
+              groundTruthStatus: desc
+            }
+          },
+          {
+            annotation: {
+              depositionDate: desc
+            }
+          },
+          {
+            annotation: {
+              id: desc
+            }
+          }
+        ]
+        limitOffset: {
+          limit: $limit
+          offset: $annotationShapesOffset
+        }
+      ) {
+        shapeType
+        annotationFiles {
+          edges {
+            node {
+              format
+              httpsPath
+              s3Path
+            }
+          }
+        }
+        annotation {
+          annotationMethod
+          annotationPublication
+          annotationSoftware
+          confidencePrecision
+          confidenceRecall
+          depositionDate
+          groundTruthStatus
+          groundTruthUsed
+          id
+          isCuratorRecommended
+          lastModifiedDate
+          methodLinks
+          methodType
+          objectCount
+          objectDescription
+          objectId
+          objectName
+          objectState
+          releaseDate
+          authors(orderBy: { authorListOrder: asc }) {
+            edges {
+              node {
+                primaryAuthorStatus
+                correspondingAuthorStatus
+                name
+                email
+                orcid
+              }
+            }
+          }
+          authorsAggregate {
+            aggregate {
+              count
+            }
+          }
+          deposition {
+            id
+            title
+          }
+        }
+      }
 
       # Tomograms table + download selector
       tomograms(where: { run: { id: { _eq: $id } } }) {
@@ -234,14 +319,99 @@ const GET_RUN_BY_ID_QUERY_V2 = gql(`
     }
 `)
 
+function getAnnotationShapesFilter(
+  runId: number,
+  filterState: FilterState,
+): AnnotationShapeWhereClause {
+  const where: AnnotationShapeWhereClause = {
+    annotation: {
+      run: {
+        id: {
+          _eq: runId,
+        },
+      },
+    },
+  }
+
+  // Deposition filter
+  const depositionId = +(filterState.ids.deposition ?? Number.NaN)
+  if (!Number.isNaN(depositionId) && depositionId > 0) {
+    where.annotation!.deposition = {
+      id: {
+        _eq: depositionId,
+      },
+    }
+  }
+
+  // Annotation shape filter
+  const {
+    annotation: { objectShapeTypes },
+  } = filterState
+  if (objectShapeTypes.length > 0) {
+    where.shapeType = {
+      _in: objectShapeTypes as Annotation_File_Shape_Type_Enum[],
+    }
+  }
+
+  // Author filters
+  const { name, orcid } = filterState.author
+  if (name || orcid) {
+    where.annotation!.authors = {}
+  }
+  if (name) {
+    where.annotation!.authors!.name = {
+      _ilike: `%${name}%`,
+    }
+  }
+  if (orcid) {
+    where.annotation!.authors!.orcid = {
+      _ilike: `%${orcid}%`,
+    }
+  }
+
+  // Annotation filters
+  const { objectNames, annotationSoftwares, methodTypes, objectId } =
+    filterState.annotation
+  if (objectNames.length > 0) {
+    where.annotation!.objectName = {
+      _in: objectNames,
+    }
+  }
+  if (objectId) {
+    where.annotation!.objectId = {
+      _ilike: `%${objectId.replace(':', '_')}`,
+    }
+  }
+  if (methodTypes.length > 0) {
+    where.annotation!.methodType = {
+      _in: methodTypes as Annotation_Method_Type_Enum[],
+    }
+  }
+  if (annotationSoftwares.length > 0) {
+    where.annotation!.annotationSoftware = {
+      _in: annotationSoftwares,
+    }
+  }
+
+  return where
+}
+
 export async function getRunByIdV2(
   client: ApolloClient<NormalizedCacheObject>,
   id: number,
+  annotationsPage: number,
+  params: URLSearchParams = new URLSearchParams(),
 ): Promise<ApolloQueryResult<GetRunByIdV2Query>> {
   return client.query({
     query: GET_RUN_BY_ID_QUERY_V2,
     variables: {
       id,
+      limit: MAX_PER_PAGE,
+      annotationShapesOffset: (annotationsPage - 1) * MAX_PER_PAGE,
+      annotationShapesFilter: getAnnotationShapesFilter(
+        id,
+        getFilterState(params),
+      ),
     },
   })
 }

frontend/packages/data-portal/codegen.ts

@@ -6,7 +6,7 @@ const SCHEMA_URL =
 
 const SCHEMA_URL_V2 =
   process.env.API_URL_V2 ||
-  'https://graphql.cryoetdataportal.czscience.com/graphql'
+  'https://graphql.cryoet.staging.si.czi.technology/graphql'
 
 const config: CodegenConfig = {
   generates: {