feat: Convert deposition page query to V2

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

@@ -1,5 +1,15 @@
 import { Depositions_Bool_Exp } from 'app/__generated__/graphql'
-import { Tomogram_Reconstruction_Method_Enum } from 'app/__generated_v2__/graphql'
+import {
+  Annotation_File_Shape_Type_Enum,
+  DatasetWhereClause,
+  Fiducial_Alignment_Status_Enum,
+  Tomogram_Reconstruction_Method_Enum,
+} from 'app/__generated_v2__/graphql'
+import {
+  DEFAULT_TILT_RANGE_MAX,
+  DEFAULT_TILT_RANGE_MIN,
+} from 'app/constants/tiltSeries'
+import { FilterState } from 'app/hooks/useFilter'
 
 export const depositionWithAnnotationFilter: Depositions_Bool_Exp = {
   annotations_aggregate: {
@@ -28,3 +38,249 @@ export function convertReconstructionMethodToV2(
       return Tomogram_Reconstruction_Method_Enum.Unknown
   }
 }
+
+export interface GetDatasetsFilterParams {
+  filterState: FilterState
+  depositionId?: number
+  searchText?: string
+}
+
+export function getDatasetsFilter({
+  filterState,
+  depositionId,
+  searchText,
+}: GetDatasetsFilterParams): DatasetWhereClause {
+  const where: DatasetWhereClause = {}
+
+  // Search by Dataset Name
+  if (searchText) {
+    where.title = {
+      _ilike: `%${searchText}%`,
+    }
+  }
+
+  // INCLUDED CONTENTS SECTION
+  // Ground Truth Annotation
+  if (filterState.includedContents.isGroundTruthEnabled) {
+    where.runs ??= { annotations: {} }
+    where.runs.annotations ??= {}
+    where.runs.annotations.groundTruthStatus = {
+      _eq: true,
+    }
+  }
+  // Available Files
+  // TODO(bchu): Implement when available in API.
+  // filterState.includedContents.availableFiles.forEach((file) =>
+  //   match(file)
+  //     .with('raw-frames', () =>
+  //       where.push({
+  //         runs: {
+  //           tiltseries: {
+  //             frames_count: {
+  //               _gt: 0,
+  //             },
+  //           },
+  //         },
+  //       }),
+  //     )
+  //     .with('tilt-series', () =>
+  //       where.push({
+  //         runs: {
+  //           tiltseries_aggregate: {
+  //             count: {
+  //               predicate: {
+  //                 _gt: 0,
+  //               },
+  //             },
+  //           },
+  //         },
+  //       }),
+  //     )
+  //     .with('tilt-series-alignment', () =>
+  //       where.push({
+  //         runs: {
+  //           tiltseries: {
+  //             https_alignment_file: {
+  //               _is_null: false,
+  //             },
+  //           },
+  //         },
+  //       }),
+  //     )
+  //     .with('tomogram', () =>
+  //       where.push({
+  //         runs: {
+  //           tomogram_voxel_spacings: {
+  //             tomograms_aggregate: {
+  //               count: {
+  //                 predicate: {
+  //                   _gt: 0,
+  //                 },
+  //               },
+  //             },
+  //           },
+  //         },
+  //       }),
+  //     )
+  //     .exhaustive(),
+  // )
+  // Number of Runs
+  // TODO: Implement when available in API.
+  // if (filterState.includedContents.numberOfRuns) {
+  //   const runCount = +filterState.includedContents.numberOfRuns.slice(1)
+  //   where.push({
+  //     runs_aggregate: {
+  //       count: {
+  //         predicate: { _gte: runCount },
+  //       },
+  //     },
+  //   })
+  // }
+
+  // NAME/ID SECTION
+  // Dataset IDs
+  const datasetId =
+    filterState.ids.dataset !== null
+      ? parseInt(filterState.ids.dataset)
+      : undefined
+  if (Number.isInteger(datasetId)) {
+    where.id = {
+      _eq: datasetId,
+    }
+  }
+  const empiarId = filterState.ids.empiar
+  const emdbId = filterState.ids.emdb
+  if (empiarId && emdbId) {
+    where.relatedDatabaseEntries = {
+      _regex: `(EMPIAR-${empiarId}.*EMD-${emdbId})|(EMD-${emdbId}.*EMPIAR-${empiarId})`, // Ignores order
+    }
+  } else if (empiarId) {
+    where.relatedDatabaseEntries = {
+      _regex: `EMPIAR-${empiarId}`,
+    }
+  } else if (emdbId) {
+    where.relatedDatabaseEntries = {
+      _regex: `EMD-${emdbId}`,
+    }
+  }
+  // Dataset Author
+  if (filterState.author.name) {
+    where.authors ??= {}
+    where.authors.name = {
+      _ilike: `%${filterState.author.name}%`,
+    }
+  }
+  if (filterState.author.orcid) {
+    where.authors ??= {}
+    where.authors.orcid = {
+      _ilike: `%${filterState.author.orcid}%`,
+    }
+  }
+  // Deposition ID
+  const filterDepositionId =
+    filterState.ids.deposition !== null
+      ? parseInt(filterState.ids.deposition)
+      : undefined
+  if (depositionId !== undefined || Number.isInteger(filterDepositionId)) {
+    where.runs ??= { annotations: {} }
+    where.runs.annotations ??= {}
+    where.runs.annotations.depositionId = {
+      _eq: depositionId ?? filterDepositionId,
+    }
+  }
+
+  // SAMPLE AND EXPERIMENT CONDITIONS SECTION
+  const { organismNames } = filterState.sampleAndExperimentConditions
+  if (organismNames.length > 0) {
+    where.organismName = {
+      _in: organismNames,
+    }
+  }
+
+  // ANNOTATION METADATA SECTION
+  const { objectNames, objectId, objectShapeTypes } = filterState.annotation
+  // Object Name
+  if (objectNames.length > 0) {
+    where.runs ??= { annotations: {} }
+    where.runs.annotations ??= {}
+    where.runs.annotations.objectName = {
+      _in: objectNames,
+    }
+  }
+  // Object ID
+  if (objectId) {
+    where.runs ??= { annotations: {} }
+    where.runs.annotations ??= {}
+    where.runs.annotations.objectId = {
+      _eq: objectId,
+    }
+  }
+  // Object Shape Type
+  if (objectShapeTypes.length > 0) {
+    where.runs ??= { annotations: {} }
+    where.runs.annotations ??= {}
+    where.runs.annotations.annotationShapes = {
+      shapeType: {
+        _in: objectShapeTypes as Annotation_File_Shape_Type_Enum[], // TODO(bchu): Remove typecast.
+      },
+    }
+  }
+
+  // HARDWARE SECTION
+  if (filterState.hardware.cameraManufacturer) {
+    where.runs ??= { tiltseries: {} }
+    where.runs.tiltseries ??= {}
+    where.runs.tiltseries.cameraManufacturer = {
+      _eq: filterState.hardware.cameraManufacturer,
+    }
+  }
+
+  // TILT SERIES METADATA SECTION
+  const tiltRangeMin = parseFloat(filterState.tiltSeries.min)
+  const tiltRangeMax = parseFloat(filterState.tiltSeries.max)
+  if (Number.isFinite(tiltRangeMin) || Number.isFinite(tiltRangeMax)) {
+    where.runs ??= { tiltseries: {} }
+    where.runs.tiltseries ??= {}
+    where.runs.tiltseries.tiltRange = {
+      _gte: Number.isFinite(tiltRangeMin)
+        ? tiltRangeMin
+        : DEFAULT_TILT_RANGE_MIN,
+      _lte: Number.isFinite(tiltRangeMax)
+        ? tiltRangeMax
+        : DEFAULT_TILT_RANGE_MAX,
+    }
+  }
+
+  // TOMOGRAM METADATA SECTION
+  // Fiducial Alignment Status
+  if (filterState.tomogram.fiducialAlignmentStatus) {
+    where.runs ??= { tomograms: {} }
+    where.runs.tomograms ??= {}
+    where.runs.tomograms.fiducialAlignmentStatus = {
+      _eq:
+        filterState.tomogram.fiducialAlignmentStatus === 'true'
+          ? Fiducial_Alignment_Status_Enum.Fiducial
+          : Fiducial_Alignment_Status_Enum.NonFiducial,
+    }
+  }
+  // Reconstruction Method
+  if (filterState.tomogram.reconstructionMethod) {
+    where.runs ??= { tomograms: {} }
+    where.runs.tomograms ??= {}
+    where.runs.tomograms.reconstructionMethod = {
+      _eq: convertReconstructionMethodToV2(
+        filterState.tomogram.reconstructionMethod,
+      ),
+    }
+  }
+  // Reconstruction Software
+  if (filterState.tomogram.reconstructionSoftware) {
+    where.runs ??= { tomograms: {} }
+    where.runs.tomograms ??= {}
+    where.runs.tomograms.reconstructionSoftware = {
+      _eq: filterState.tomogram.reconstructionSoftware,
+    }
+  }
+
+  return where
+}

frontend/packages/data-portal/app/graphql/fragments/getDatasetsFilterValuesV2.server.ts → frontend/packages/data-portal/app/graphql/fragments/getDatasetsAggregatesV2.server.ts

@@ -4,12 +4,12 @@ import { gql } from 'app/__generated_v2__'
  * Shares aggregate queries between datasets and deposition pages (the 2 pages are very similar).
  *
  * Parent query must define the following variables:
- * - $datasetsFilter
- * - $datasetsByDepositionFilter
- * - $tiltseriesByDepositionFilter
- * - $tomogramsByDepositionFilter
- * - $annotationsByDepositionFilter
- * - $annotationShapesByDepositionFilter
+ * - $datasetsFilter: DatasetWhereClause
+ * - $datasetsByDepositionFilter: DatasetWhereClause
+ * - $tiltseriesByDepositionFilter: TiltseriesWhereClause
+ * - $tomogramsByDepositionFilter: TomogramWhereClause
+ * - $annotationsByDepositionFilter: AnnotationWhereClause
+ * - $annotationShapesByDepositionFilter: AnnotationShapeWhereClause
  */
 export const GET_DATASETS_AGGREGATES_FRAGMENT = gql(`
   fragment DatasetsAggregates on Query {