feat: removed data modality #4444 (#4447)

* feat: removed data modality #4444

* feat: removed data modality from dataset detail #4444

* fix: updated anvil tests #4444

Author: MillenniumFalconMechanic

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

@@ -105,10 +105,6 @@ export function getDatasetDetails(
     stringifyValues(getAggregatedOrganismTypes(response))
   );
   details.set("Diagnosis", stringifyValues(getAggregatedDiagnoses(response)));
-  details.set(
-    "Data modality",
-    stringifyValues(getAggregatedActivityDataModalities(response))
-  );
   details.set(
     "Phenotypic sex",
     stringifyValues(getAggregatedPhenotypicSexes(response))

e2e/anvil/anvil-filters.spec.ts

@@ -15,14 +15,12 @@ import {
   BIOSAMPLE_TYPE_INDEX,
   CONSENT_GROUP_INDEX,
   DATASET_INDEX,
-  DATA_MODALITY_INDEX,
   DIAGNOSIS_INDEX,
   FILE_FORMAT_INDEX,
   REPORTED_ETHNICITY_INDEX,
 } from "./anvil-tabs";
 
 const FILTER_INDEX_LIST = [
-  DATA_MODALITY_INDEX,
   DATASET_INDEX,
   DIAGNOSIS_INDEX,
   REPORTED_ETHNICITY_INDEX,

e2e/anvil/anvil-tabs.ts

@@ -23,7 +23,6 @@ export const ANVIL_FILTER_NAMES: string[] = [
   "Anatomical Site",
   "BioSample Type",
   "Consent Group",
-  "Data Modality",
   "Dataset",
   "Diagnosis",
   "File Format",
@@ -35,14 +34,13 @@ export const ANVIL_FILTER_NAMES: string[] = [
 export const ANATOMICAL_SITE_INDEX = 0;
 export const BIOSAMPLE_TYPE_INDEX = 1;
 export const CONSENT_GROUP_INDEX = 2;
-export const DATA_MODALITY_INDEX = 3;
-export const DATASET_INDEX = 4;
-export const DIAGNOSIS_INDEX = 5;
-export const FILE_FORMAT_INDEX = 6;
-export const IDENTIFIER_INDEX = 7;
-export const ORGANISM_TYPE_INDEX = 8;
-export const PHENOTYPIC_SEX_INDEX = 9;
-export const REPORTED_ETHNICITY_INDEX = 10;
+export const DATASET_INDEX = 3;
+export const DIAGNOSIS_INDEX = 4;
+export const FILE_FORMAT_INDEX = 5;
+export const IDENTIFIER_INDEX = 6;
+export const ORGANISM_TYPE_INDEX = 7;
+export const PHENOTYPIC_SEX_INDEX = 8;
+export const REPORTED_ETHNICITY_INDEX = 9;
 
 const ANVIL_CMG_SEARCH_FILTERS_PLACEHOLDER_TEXT = "Search all filters...";
 
@@ -125,13 +123,6 @@ export const ANVIL_TABS: AnvilCMGTabCollection = {
           ],
         name: ANVIL_DATASETS_BACKPAGE_HEADER_NAMES.DIAGNOSIS,
       },
-      {
-        correspondingColumn:
-          ANVIL_DATASETS_PRESELECTED_COLUMNS_BY_NAME[
-            ANVIL_COLUMN_NAMES.DATA_MODALITY
-          ],
-        name: ANVIL_DATASETS_BACKPAGE_HEADER_NAMES.DATA_MODALITY,
-      },
       {
         correspondingColumn:
           ANVIL_DATASETS_SELECTABLE_COLUMNS_BY_NAME[

e2e/anvil/constants.ts

@@ -3,7 +3,6 @@ import { ColumnDescription } from "e2e/testInterfaces";
 export const ANVIL_DATASETS_BACKPAGE_HEADER_NAMES = {
   CONSENT_GROUP: "Consent group",
   DATASET_ID: "Dataset Id",
-  DATA_MODALITY: "Data modality",
   DIAGNOSIS: "Diagnosis",
   ORGANISM_TYPE: "Organism type",
   PHENOTYPIC_SEX: "Phenotypic sex",
@@ -18,7 +17,6 @@ export const ANVIL_COLUMN_NAMES = {
   BIOSAMPLE_TYPE: "BioSample Type",
   CONSENT_GROUP: "Consent Group",
   DATASET: "Dataset",
-  DATA_MODALITY: "Data Modality",
   DIAGNOSIS: "Diagnosis",
   DOCUMENT_ID: "Document Id",
   DONOR_ID: "Donor Id",
@@ -34,7 +32,6 @@ export const ANVIL_COLUMN_NAMES = {
 
 export const PLURALIZED_METADATA_LABEL = {
   [ANVIL_COLUMN_NAMES.DIAGNOSIS]: "diagnoses",
-  [ANVIL_COLUMN_NAMES.DATA_MODALITY]: "data modalities",
   [ANVIL_COLUMN_NAMES.DATASET]: "dataset names",
   [ANVIL_COLUMN_NAMES.CONSENT_GROUP]: "consent codes",
   [ANVIL_COLUMN_NAMES.ORGANISM_TYPE]: "organism types",
@@ -52,12 +49,6 @@ export const ANVIL_DATASETS_PRESELECTED_COLUMNS_BY_NAME = {
     pluralizedLabel: PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.DIAGNOSIS],
     sortable: true,
   },
-  [ANVIL_COLUMN_NAMES.DATA_MODALITY]: {
-    name: ANVIL_COLUMN_NAMES.DATA_MODALITY,
-    pluralizedLabel:
-      PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.DATA_MODALITY],
-    sortable: true,
-  },
   [ANVIL_COLUMN_NAMES.DATASET]: {
     name: ANVIL_COLUMN_NAMES.DATASET,
     pluralizedLabel: PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.DATASET],
@@ -113,12 +104,6 @@ export const ANVIL_ACTIVITIES_PRESELECTED_COLUMNS_BY_NAME = {
       PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.ACTIVITY_TYPE],
     sortable: true,
   },
-  [ANVIL_COLUMN_NAMES.DATA_MODALITY]: {
-    name: ANVIL_COLUMN_NAMES.DATA_MODALITY,
-    pluralizedLabel:
-      PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.DATA_MODALITY],
-    sortable: true,
-  },
   [ANVIL_COLUMN_NAMES.BIOSAMPLE_TYPE]: {
     name: ANVIL_COLUMN_NAMES.BIOSAMPLE_TYPE,
     pluralizedLabel:
@@ -263,12 +248,6 @@ export const ANVIL_FILES_PRESELECTED_COLUMNS_BY_NAME = {
     name: ANVIL_COLUMN_NAMES.DRS_URI,
     sortable: false,
   },
-  [ANVIL_COLUMN_NAMES.DATA_MODALITY]: {
-    name: ANVIL_COLUMN_NAMES.DATA_MODALITY,
-    pluralizedLabel:
-      PLURALIZED_METADATA_LABEL[ANVIL_COLUMN_NAMES.DATA_MODALITY],
-    sortable: true,
-  },
   [ANVIL_COLUMN_NAMES.ORGANISM_TYPE]: {
     name: ANVIL_COLUMN_NAMES.ORGANISM_TYPE,
     pluralizedLabel:

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

@@ -54,10 +54,6 @@ export function makeConfig(
               key: ANVIL_CMG_CATEGORY_KEY.DATASET_REGISTERED_ID,
               label: ANVIL_CMG_CATEGORY_LABEL.DATASET_REGISTERED_ID,
             },
-            {
-              key: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_DATA_MODALITY,
-              label: ANVIL_CMG_CATEGORY_LABEL.ACTIVITY_DATA_MODALITY,
-            },
             {
               key: ANVIL_CMG_CATEGORY_KEY.DATASET_CONSENT_GROUP,
               label: ANVIL_CMG_CATEGORY_LABEL.DATASET_CONSENT_GROUP,

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

@@ -49,15 +49,6 @@ export const activitiesEntityConfig: EntityConfig<ActivitiesResponse> = {
         id: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_ACTIVITY_TYPE,
         width: { max: "1fr", min: "200px" },
       },
-      {
-        componentConfig: {
-          component: C.NTagCell,
-          viewBuilder: V.buildDataModality,
-        } as ComponentConfig<typeof C.NTagCell>,
-        header: ANVIL_CMG_CATEGORY_LABEL.ACTIVITY_DATA_MODALITY,
-        id: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_DATA_MODALITY,
-        width: { max: "1fr", min: "200px" },
-      },
       {
         componentConfig: {
           component: C.BasicCell,

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

@@ -121,15 +121,6 @@ export const datasetsEntityConfig: EntityConfig<DatasetsResponse> = {
         id: ANVIL_CMG_CATEGORY_KEY.DIAGNOSE_DISEASE,
         width: { max: "1fr", min: "200px" },
       },
-      {
-        componentConfig: {
-          component: C.NTagCell,
-          viewBuilder: V.buildDataModality,
-        } as ComponentConfig<typeof C.NTagCell>,
-        header: ANVIL_CMG_CATEGORY_LABEL.ACTIVITY_DATA_MODALITY,
-        id: ANVIL_CMG_CATEGORY_KEY.ACTIVITY_DATA_MODALITY,
-        width: { max: "1fr", min: "148px" },
-      },
     ],
     tableOptions: {
       initialState: {

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

@@ -83,15 +83,6 @@ export const filesEntityConfig: EntityConfig<FilesResponse> = {
         id: ANVIL_CMG_CATEGORY_KEY.DRS_URI,
         width: { max: "1fr", min: "120px" },
       },
-      {
-        componentConfig: {
-          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,
-        width: { max: "1fr", min: "140px" },
-      },
       {
         componentConfig: {
           component: C.NTagCell,