feat: update dataset and file lists to use corresponding data modalities (#4258)

Author: hunterckx

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

@@ -45,6 +45,7 @@ export interface BioSampleEntityResponse {
 export interface DatasetEntity {
   accessible: boolean;
   consent_group: (string | null)[];
+  data_modality: (string | null)[];
   dataset_id: string;
   description?: string;
   registered_identifier: (string | null)[];
@@ -88,7 +89,7 @@ export interface DonorSpecies {
  */
 export interface FileEntity {
   accessible: boolean;
-  data_modality: string[];
+  data_modality: (string | null)[];
   date_created: string;
   document_id: string;
   drs_uri: string;

app/apis/azul/anvil-cmg/common/transformers.ts

@@ -22,6 +22,7 @@ import {
 import {
   ActivityEntityResponse,
   BioSampleEntityResponse,
+  DatasetEntityResponse,
   DonorEntityResponse,
   FileEntityResponse,
   LibraryEntityResponse,
@@ -84,6 +85,16 @@ export function getAggregatedBioSampleTypes(
   return processAggregatedOrArrayValue(response.biosamples, "biosample_type");
 }
 
+/**
+ * Maps data modality from index/datasets API response.
+ * @param response - Response model return from index/datasets API.
+ * @returns a list of data modalities.
+ */
+export function getDatasetDataModalities(
+  response: DatasetEntityResponse
+): MetadataValue[] {
+  return processAggregatedOrArrayValue(response.datasets, "data_modality");
+}
 /**
  * Maps dataset-related information, included formatted display text from API response.
  * @param response - Response model return from datasets or dataset API endpoints.

app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders.ts

@@ -58,6 +58,7 @@ import {
 import {
   ActivityEntityResponse,
   BioSampleEntityResponse,
+  DatasetEntityResponse,
   DonorEntityResponse,
   FileEntityResponse,
   FileFormat,
@@ -82,6 +83,7 @@ import {
   getBioSampleId,
   getBioSampleType,
   getConsentGroup,
+  getDatasetDataModalities,
   getDatasetDetails,
   getDatasetEntryId,
   getDocumentId,
@@ -317,6 +319,20 @@ export function buildDatasetAccessibilityBadge(
   return { badgeProps, fadeProps };
 }
 
+/**
+ * Build props for dataset data modality NTagCell component from the given datasets response.
+ * @param response - Response model return from index/datasets API endpoint.
+ * @returns model to be used as props for the NTagCell component.
+ */
+export const buildDatasetDataModality = (
+  response: DatasetEntityResponse
+): React.ComponentProps<typeof C.NTagCell> => {
+  return {
+    label: getPluralizedMetadataLabel(METADATA_KEY.DATA_MODALITY),
+    values: getDatasetDataModalities(response),
+  };
+};
+
 /**
  * Build props for Markdown component from the given entity response.
  * @param datasetsResponse - Response model return from datasets API.

site-config/anvil-cmg/category.ts

@@ -10,6 +10,7 @@ export const ANVIL_CMG_CATEGORY_KEY = {
   BIOSAMPLE_TYPE: "biosample_type",
   DATASET_ACCESSIBLE: "datasets.accessible",
   DATASET_CONSENT_GROUP: "datasets.consent_group",
+  DATASET_DATA_MODALITY: "datasets.data_modality",
   DATASET_ID: "dataset_id",
   DATASET_REGISTERED_ID: "datasets.registered_identifier",
   DATASET_TITLE: "datasets.title",
@@ -19,6 +20,7 @@ export const ANVIL_CMG_CATEGORY_KEY = {
   DONOR_ORGANISM_TYPE: "donors.organism_type",
   DONOR_PHENOTYPIC_SEX: "donors.phenotypic_sex",
   DONOR_REPORTED_ETHNICITY: "donors.reported_ethnicity",
+  FILE_DATA_MODALITY: "files.data_modality",
   FILE_FILE_FORMAT: "files.file_format",
   FILE_FILE_NAME: "files.file_name",
   FILE_FILE_SIZE: "files.file_size",
@@ -27,10 +29,12 @@ export const ANVIL_CMG_CATEGORY_KEY = {
   PREP_MATERIAL_NAME: "prep_material_name",
 };
 
+const DATA_MODALITY_LABEL = "Data Modality";
+
 export const ANVIL_CMG_CATEGORY_LABEL = {
   ACCESSIBLE: "Access",
   ACTIVITY_ACTIVITY_TYPE: "Activity Type",
-  ACTIVITY_DATA_MODALITY: "Data Modality",
+  ACTIVITY_DATA_MODALITY: DATA_MODALITY_LABEL,
   ACTIVITY_DOCUMENT_ID: "Document Id",
   AZUL_FILE_DOWNLOAD: " ",
   BIOSAMPLE_ANATOMICAL_SITE: "Anatomical Site",
@@ -39,6 +43,7 @@ export const ANVIL_CMG_CATEGORY_LABEL = {
   BIOSAMPLE_TYPE: "BioSample Type",
   DATASET_ACCESSIBLE: "Access",
   DATASET_CONSENT_GROUP: "Consent Group",
+  DATASET_DATA_MODALITY: DATA_MODALITY_LABEL,
   DATASET_ID: "Dataset Name",
   DATASET_REGISTERED_ID: "Identifier",
   DATASET_TITLE: "Dataset",
@@ -48,6 +53,7 @@ export const ANVIL_CMG_CATEGORY_LABEL = {
   DONOR_ORGANISM_TYPE: "Organism Type",
   DONOR_PHENOTYPIC_SEX: "Phenotypic Sex",
   DONOR_REPORTED_ETHNICITY: "Reported Ethnicity",
+  FILE_DATA_MODALITY: DATA_MODALITY_LABEL,
   FILE_FILE_FORMAT: "File Format",
   FILE_FILE_NAME: "Name",
   FILE_FILE_SIZE: "Size",

site-config/anvil-cmg/dev/index/datasetsEntityConfig.ts

@@ -134,10 +134,10 @@ export const datasetsEntityConfig: EntityConfig<DatasetsResponse> = {
       {
         componentConfig: {
           component: C.NTagCell,
-          viewBuilder: V.buildDataModality,
+          viewBuilder: V.buildDatasetDataModality,
         } as ComponentConfig<typeof C.NTagCell>,
-        header: ANVIL_CMG_CATEGORY_LABEL.ACTIVITY_DATA_MODALITY,
-        id: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_DATA_MODALITY,
+        header: ANVIL_CMG_CATEGORY_LABEL.DATASET_DATA_MODALITY,
+        id: ANVIL_CMG_CATEGORY_KEY.DATASET_DATA_MODALITY,
         width: { max: "1fr", min: "148px" },
       },
     ],

site-config/anvil-cmg/dev/index/filesEntityConfig.ts

@@ -87,8 +87,8 @@ export const filesEntityConfig: EntityConfig<FilesResponse> = {
           component: C.NTagCell,
           viewBuilder: V.buildFileDataModality,
         } as ComponentConfig<typeof C.NTagCell>,
-        header: ANVIL_CMG_CATEGORY_LABEL.ACTIVITY_DATA_MODALITY,
-        id: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_DATA_MODALITY,
+        header: ANVIL_CMG_CATEGORY_LABEL.FILE_DATA_MODALITY,
+        id: ANVIL_CMG_CATEGORY_KEY.FILE_DATA_MODALITY,
         width: { max: "1fr", min: "140px" },
       },
       {