feat: configure file manifest summary (#888) (#3591)

Co-authored-by: Fran McDade <[email protected]>

Author: frano-m

explorer/app/apis/azul/anvil-cmg/common/entities.ts

@@ -15,6 +15,14 @@ export interface ActivityEntityResponse {
   activities: ActivityEntity[];
 }
 
+/**
+ * Model of activity type returned from the /index/summary API endpoint.
+ */
+export interface ActivityType {
+  count: number;
+  type: string;
+}
+
 /**
  * Model of core biosample value returned from the /index/biosamples API endpoint.
  */
@@ -67,6 +75,14 @@ export interface DonorEntityResponse {
   donors: DonorEntity[];
 }
 
+/**
+ * Model of donor species returned from the /index/summary API endpoint.
+ */
+export interface DonorSpecies {
+  count: number;
+  species: null; // TODO - when species type is known (currently returns null value).
+}
+
 /**
  * Model of core file value returned from the /index/files API endpoint.
  */
@@ -98,6 +114,14 @@ export interface LibraryEntity {
   prep_material_name: string;
 }
 
+/**
+ * Model of file format returned from the /index/summary API endpoint.
+ */
+export interface FileFormat {
+  count: number;
+  format: string;
+}
+
 /**
  * Model of singleton array containing core library value returned from the /index/libraries API endpoint.
  */

explorer/app/apis/azul/anvil-cmg/common/responses.ts

@@ -10,10 +10,13 @@ import {
 } from "./aggregatedEntities";
 import {
   ActivityEntityResponse,
+  ActivityType,
   BioSampleEntityResponse,
   DatasetEntityResponse,
   DonorEntityResponse,
+  DonorSpecies,
   FileEntityResponse,
+  FileFormat,
   LibraryEntityResponse,
 } from "./entities";
 
@@ -83,3 +86,19 @@ export type LibrariesResponse = AzulHit &
   AggregatedDatasetResponse &
   AggregatedDonorResponse &
   AggregatedFileResponse;
+
+/**
+ * Model of response returned from /index/summary API endpoint.
+ */
+export type SummaryResponse = {
+  activityCount: number;
+  activityTypes: ActivityType[];
+  biosampleCount: number;
+  datasetCount: number;
+  donorCount: number;
+  donorDiagnosisDiseases: unknown[]; // TODO - when type is known.
+  donorDiagnosisPhenotypes: unknown[]; // TODO - when type is known.
+  donorSpecies: DonorSpecies[];
+  fileCount: number;
+  fileFormats: FileFormat[];
+};

explorer/app/apis/azul/hca-dcp/common/entities.ts

@@ -6,6 +6,15 @@ export interface AccessionResponse {
   namespace: string;
 }
 
+/**
+ * Model of cell count summary from index/summary API endpoints.
+ */
+export interface CellCountSummary {
+  countOfDocsWithOrganType: number;
+  organType: string[];
+  totalCellCountByOrgan: number;
+}
+
 /**
  * Model of contributor value in the response from index/projects API endpoint.
  */
@@ -44,6 +53,16 @@ export interface FileResponse {
   version: string;
 }
 
+/**
+ * Model of file type summary from index/summary API endpoints.
+ */
+export interface FileTypeSummary {
+  count: number;
+  format: string;
+  matrixCellCount: number;
+  totalSize: number;
+}
+
 /**
  * Model of file "leaf" values in matrix tree response from Azul.
  */
@@ -89,6 +108,14 @@ export interface ProjectsEntityResponse {
   projects: ProjectResponse[];
 }
 
+/**
+ * Model of project summary in the response from /index/summary API endpoint.
+ */
+export interface ProjectSummary {
+  cellSuspensions: { totalCells: number };
+  projects: { estimatedCellCount: number };
+}
+
 /**
  * Model of publication value in the response from index/projects API endpoint.
  */

explorer/app/apis/azul/hca-dcp/common/responses.ts

@@ -9,8 +9,11 @@ import {
   AggregatedSpecimensResponse,
 } from "./aggregatedEntities";
 import {
+  CellCountSummary,
   FilesEntityResponse,
+  FileTypeSummary,
   ProjectsEntityResponse,
+  ProjectSummary,
   SamplesEntityResponse,
 } from "./entities";
 
@@ -54,3 +57,20 @@ export type SamplesResponse = AzulHit &
   AggregatedProjectsResponse &
   AggregatedProtocolsResponse &
   AggregatedSpecimensResponse;
+
+/**
+ * Model of response returned from /index/summary API endpoint.
+ */
+export type SummaryResponse = {
+  cellCountSummaries: CellCountSummary[];
+  donorCount: number;
+  fileCount: number;
+  fileTypeSummaries: FileTypeSummary[];
+  labCount: number;
+  organTypes: string[];
+  projectCount: number;
+  projects: ProjectSummary[];
+  speciesCount: number;
+  specimenCount: number;
+  totalFileSize: number | string;
+};

explorer/app/components/Index/common/utils.ts

@@ -1,27 +1,34 @@
 import { AzulSummaryResponse } from "@clevercanary/data-explorer-ui/lib/apis/azul/common/entities";
+import { FileFormat } from "../../../apis/azul/anvil-cmg/common/entities";
+import { ProjectSummary } from "../../../apis/azul/hca-dcp/common/entities";
 
 /**
  * Calculates the summary file format count using count values returned for each file format in the summary response.
+ * TODO review configuration of summary response model and use of this method to calculate file formats.
  * @param summaryResponse - Response model return from summary API.
  * @returns count of file formats.
  */
 export function calculateSummaryFileFormatsCount(
   summaryResponse: AzulSummaryResponse
 ): number {
-  return (summaryResponse.fileFormats ?? []).reduce((accum, { count }) => {
-    return accum + count;
-  }, 0);
+  return ((summaryResponse.fileFormats as FileFormat[]) ?? []).reduce(
+    (accum, { count }) => {
+      return accum + count;
+    },
+    0 as number
+  );
 }
 
 /**
  * Calculates the summary total cell count using the estimatedCellCount and totalCells values fom the summary response.
+ * TODO review configuration of summary response model and use of this method to calculate total cell count.
  * @param summaryResponse - Response model return from summary API.
  * @returns count of total cell count.
  */
 export function calculateSummaryTotalCellCount(
   summaryResponse: AzulSummaryResponse
 ): number {
-  return (summaryResponse.projects ?? []).reduce(
+  return ((summaryResponse.projects as ProjectSummary[]) ?? []).reduce(
     (accum, { cellSuspensions, projects }) => {
       if (
         projects &&

explorer/app/components/Index/components/AccessStatusBadge/accessStatusBadge.styles.ts

@@ -5,7 +5,9 @@ interface AccessStatusBadgeProps {
   accessible: boolean;
 }
 
-export const AccessStatusBadge = styled(Chip)<AccessStatusBadgeProps>`
+export const AccessStatusBadge = styled(Chip, {
+  shouldForwardProp: (prop) => prop !== "accessible",
+})<AccessStatusBadgeProps>`
   background-color: ${({ accessible, theme }) =>
     accessible ? theme.palette.success.light : theme.palette.warning.light};
   color: ${({ accessible, theme }) =>

explorer/app/viewModelBuilders/azul/hca-dcp/common/dataSummaryMapper/dataSummaryMapper.ts

@@ -1,20 +1,11 @@
 import { LABEL } from "@clevercanary/data-explorer-ui/lib/apis/azul/common/entities";
 import { stringifyValues } from "@clevercanary/data-explorer-ui/lib/common/utils";
 import { Value } from "@clevercanary/data-explorer-ui/lib/components/common/KeyValuePairs/keyValuePairs";
-import {
-  displaySummaryTerms,
-  listSelectedTermsOfFacet,
-} from "@clevercanary/data-explorer-ui/lib/components/Export/components/ExportSummary/common/utils";
 import { ANCHOR_TARGET } from "@clevercanary/data-explorer-ui/lib/components/Links/common/entities";
 import { Links } from "@clevercanary/data-explorer-ui/lib/components/Links/links";
 import { getConfig } from "@clevercanary/data-explorer-ui/lib/config/config";
-import { FileManifest } from "@clevercanary/data-explorer-ui/lib/hooks/useFileManifest/common/entities";
 import { formatCountSize } from "@clevercanary/data-explorer-ui/lib/utils/formatCountSize";
-import { formatFileSize } from "@clevercanary/data-explorer-ui/lib/utils/formatFileSize";
-import {
-  HCA_DCP_CATEGORY_KEY,
-  HCA_DCP_CATEGORY_LABEL,
-} from "../../../../../../site-config/hca-dcp/category";
+import { HCA_DCP_CATEGORY_KEY } from "../../../../../../site-config/hca-dcp/category";
 import {
   processAggregatedBooleanOrArrayValue,
   processAggregatedNumberEntityValue,
@@ -226,87 +217,3 @@ export function mapProjectDataSummary(
   details.set(DATA_SUMMARY.DONOR_COUNT, formatCountSize(donorCount)); // Donor Count
   return details;
 }
-
-/**
- * Maps export summary related information, included formatted display text from the given file manifest.
- * @param fileManifest - File manifest.
- * @returns summaries key-value pairs of data summary and corresponding value.
- */
-export function mapExportSummary(
-  fileManifest: FileManifest
-): Map<DATA_SUMMARY | string, string> {
-  const { filesFacets, fileSummary } = fileManifest;
-  // Grab summary values.
-  const donorCount = fileSummary.donorCount;
-  const donorDisease = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.DONOR_DISEASE
-  );
-  const fileCount = fileSummary.fileCount;
-  const genusSpecies = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.GENUS_SPECIES
-  );
-  const libraryConstructionApproach = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.LIBRARY_CONSTRUCTION_METHOD
-  );
-  const organ = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.ORGAN
-  );
-  const organPart = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.ORGAN_PART
-  );
-  const pairedEnd = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.PAIRED_END
-  );
-  const projectCount = fileSummary.projectCount;
-  const specimenCount = fileSummary.specimenCount;
-  const specimenDisease = listSelectedTermsOfFacet(
-    filesFacets,
-    HCA_DCP_CATEGORY_KEY.SPECIMEN_DISEASE
-  );
-  const totalCellCount = fileSummary.totalCellCount;
-  const totalFileSize = fileSummary.totalFileSize;
-
-  // Map summary by summary key or display text.
-  const summaryBySummaryKey = new Map<DATA_SUMMARY | string, string>();
-  summaryBySummaryKey.set("Estimated Cells", formatCountSize(totalCellCount));
-  summaryBySummaryKey.set(
-    HCA_DCP_CATEGORY_LABEL.FILE_SIZE,
-    formatFileSize(totalFileSize)
-  );
-  summaryBySummaryKey.set("Files", formatCountSize(fileCount));
-  summaryBySummaryKey.set("Projects", formatCountSize(projectCount));
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.GENUS_SPECIES,
-    displaySummaryTerms(genusSpecies)
-  );
-  summaryBySummaryKey.set("Donors", formatCountSize(donorCount));
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.DONOR_DISEASE,
-    displaySummaryTerms(donorDisease)
-  ); // Disease Status (Donor)
-  summaryBySummaryKey.set("Specimens", formatCountSize(specimenCount));
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.DISEASE,
-    displaySummaryTerms(specimenDisease)
-  ); // Disease Status (Specimen)
-  summaryBySummaryKey.set(DATA_SUMMARY.ORGAN, displaySummaryTerms(organ)); // Anatomical Entity
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.ORGAN_PART,
-    displaySummaryTerms(organPart)
-  );
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.LIBRARY_CONSTRUCTION_APPROACH,
-    displaySummaryTerms(libraryConstructionApproach)
-  ); // Library Construction Method
-  summaryBySummaryKey.set(
-    DATA_SUMMARY.PAIRED_END,
-    displaySummaryTerms(pairedEnd)
-  ); // Paired End
-  return summaryBySummaryKey;
-}

explorer/app/viewModelBuilders/azul/hca-dcp/common/summaryMapper/constants.ts

@@ -0,0 +1,33 @@
+import { HCA_DCP_CATEGORY_LABEL } from "../../../../../../site-config/hca-dcp/category";
+import { FileSummary, SUMMARY } from "./entities";
+
+export const DEFAULT_SUMMARY: FileSummary = {
+  donorCount: 0,
+  fileCount: 0,
+  fileTypeSummaries: [],
+  organTypes: [],
+  projectCount: 0,
+  specimenCount: 0,
+  totalCellCount: 0,
+  totalFileSize: 0,
+};
+
+/**
+ * Display text for summaries.
+ */
+export const SUMMARY_DISPLAY_TEXT = {
+  [SUMMARY.DONOR_COUNT]: "Donors",
+  [SUMMARY.DONOR_DISEASE]: "Disease Status (Donor)",
+  [SUMMARY.FILE_COUNT]: "Files",
+  [SUMMARY.GENUS_SPECIES]: "Species",
+  [SUMMARY.LIBRARY_CONSTRUCTION_APPROACH]:
+    HCA_DCP_CATEGORY_LABEL.LIBRARY_CONSTRUCTION_METHOD,
+  [SUMMARY.ORGAN]: HCA_DCP_CATEGORY_LABEL.ANATOMICAL_ENTITY, // anatomical entity
+  [SUMMARY.ORGAN_PART]: HCA_DCP_CATEGORY_LABEL.ORGAN_PART,
+  [SUMMARY.PAIRED_END]: HCA_DCP_CATEGORY_LABEL.PAIRED_END,
+  [SUMMARY.PROJECT_COUNT]: "Projects",
+  [SUMMARY.SPECIMEN_COUNT]: "Specimens",
+  [SUMMARY.SPECIMEN_DISEASE]: "Disease Status (Specimen)",
+  [SUMMARY.TOTAL_CELL_COUNT]: "Estimated Cells",
+  [SUMMARY.TOTAL_FILE_SIZE]: HCA_DCP_CATEGORY_LABEL.FILE_SIZE,
+};

explorer/app/viewModelBuilders/azul/hca-dcp/common/summaryMapper/entities.ts

@@ -0,0 +1,42 @@
+/**
+ * Model of file summary.
+ */
+export interface FileSummary {
+  donorCount: number;
+  fileCount: number;
+  fileTypeSummaries: FileTypeSummary[];
+  organTypes: string[];
+  projectCount: number;
+  specimenCount: number;
+  totalCellCount: number;
+  totalFileSize: number;
+}
+
+/**
+ * Model of file type summary.
+ */
+export interface FileTypeSummary {
+  count: number;
+  fileType: string;
+  matrixCellCount: number;
+  totalSize: number;
+}
+
+/**
+ * Possible set of summaries.
+ */
+export const enum SUMMARY {
+  DONOR_COUNT = "DONOR_COUNT",
+  DONOR_DISEASE = "DONOR_DISEASE",
+  FILE_COUNT = "FILE_COUNT",
+  GENUS_SPECIES = "GENUS_SPECIES",
+  LIBRARY_CONSTRUCTION_APPROACH = "LIBRARY_CONSTRUCTION_APPROACH",
+  ORGAN = "ORGAN",
+  ORGAN_PART = "ORGAN_PART",
+  PAIRED_END = "PAIRED_END",
+  PROJECT_COUNT = "PROJECT_COUNT",
+  SPECIMEN_COUNT = "SPECIMEN_COUNT",
+  SPECIMEN_DISEASE = "SPECIMEN_DISEASE",
+  TOTAL_CELL_COUNT = "TOTAL_CELL_COUNT",
+  TOTAL_FILE_SIZE = "TOTAL_FILE_SIZE",
+}