fix: removed hca specific config from lungmap (#4287) (#4295)

site-config/lungmap/dev/config.ts

@@ -1,15 +1,15 @@
-import { CategoryGroupConfig } from "@databiosphere/findable-ui/lib/config/entities";
-import hcaConfig, {
+import {
   DATA_URL as HCA_DATA_URL,
   PORTAL_URL as HCA_PORTAL_URL,
 } from "site-config/hca-dcp/ma-dev/config";
 import * as C from "../../../app/components/index";
 import { FLATTEN, GIT_HUB_REPO_URL } from "../../common/constants";
 import { SiteConfig } from "../../common/entities";
-import { filesEntityConfig as hcaFilesEntityConfig } from "../../hca-dcp/dev/index/filesEntityConfig";
-import { samplesEntityConfig as hcaSamplesEntityConfig } from "../../hca-dcp/dev/index/samplesEntityConfig";
 import { exportConfig } from "./export/exportConfig";
+import { CATEGORY_GROUPS } from "./index/common/category";
+import { filesEntityConfig } from "./index/filesEntityConfig";
 import { projectsEntityConfig } from "./index/projectsEntityConfig";
+import { samplesEntityConfig } from "./index/samplesEntityConfig";
 import { summary } from "./index/summary";
 import { socialMedia } from "./socialMedia";
 
@@ -40,7 +40,7 @@ export function makeConfig(
     authentication: undefined,
     browserURL: browserUrl,
     categoryGroupConfig: {
-      ...(hcaConfig.categoryGroupConfig as CategoryGroupConfig),
+      categoryGroups: CATEGORY_GROUPS,
       key: "lungmap",
     },
     contentDir: "lungmap",
@@ -53,11 +53,7 @@ export function makeConfig(
       },
       url: `${dataUrl}/`,
     },
-    entities: [
-      projectsEntityConfig,
-      hcaSamplesEntityConfig,
-      hcaFilesEntityConfig,
-    ],
+    entities: [projectsEntityConfig, samplesEntityConfig, filesEntityConfig],
     explorerTitle: "Explore Data",
     export: exportConfig,
     exportToTerraUrl: EXPORT_TO_TERRA_URL,

site-config/lungmap/dev/detail/project/exportMainColumn.ts

@@ -1,9 +1,10 @@
 import { ALERT_PROPS } from "@databiosphere/findable-ui/lib/components/common/Alert/constants";
 import { ComponentConfig } from "@databiosphere/findable-ui/lib/config/entities";
 import { SIZE } from "@databiosphere/findable-ui/lib/styles/common/constants/size";
+import { ProjectsResponse } from "app/apis/azul/hca-dcp/common/responses";
 import * as C from "../../../../../app/components";
 import * as MDX from "../../../../../app/components/common/MDXContent/lungmap";
-import { mainColumn as hcaExportMainColumn } from "../../../../hca-dcp/dev/detail/project/exportMainColumn";
+import * as V from "../../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders";
 
 export const mainColumn: ComponentConfig[] = [
   {
@@ -14,5 +15,8 @@ export const mainColumn: ComponentConfig[] = [
       size: SIZE.LARGE,
     },
   } as ComponentConfig<typeof MDX.AlertBatchCorrectionWarning>,
-  hcaExportMainColumn[1],
+  {
+    component: C.ExportToTerra,
+    viewBuilder: V.buildExportEntityToTerra,
+  } as ComponentConfig<typeof C.ExportToTerra, ProjectsResponse>,
 ];

site-config/lungmap/dev/detail/project/mainColumn.ts

@@ -2,30 +2,67 @@ import {
   ComponentConfig,
   ComponentsConfig,
 } from "@databiosphere/findable-ui/lib/config/entities";
+import { ProjectsResponse } from "app/apis/azul/hca-dcp/common/responses";
 import * as C from "../../../../../app/components";
 import * as MDX from "../../../../../app/components/common/MDXContent/lungmap";
-import { mainColumn as hcaOverviewMainColumn } from "../../../../hca-dcp/dev/detail/project/overviewMainColumn";
+import * as V from "../../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders";
 
-// Data Release Policy
-const DATA_RELEASE_POLICY: ComponentConfig = {
-  children: [
-    {
-      component: MDX.DataReleasePolicy,
-    } as ComponentConfig<typeof MDX.DataReleasePolicy>,
-  ],
-  component: C.CollapsableSection,
-  props: {
-    collapsable: false,
-    title: "Data Access Policy",
-  },
-};
-
-/**
- * Returns overview main column components.
- * @returns overview main column components.
- */
-export function getOverviewMainColumn(): ComponentsConfig {
-  const mainColumn = [...hcaOverviewMainColumn];
-  mainColumn.pop(); // Remove the last element (HCA Data Release Policy).
-  return [...mainColumn, DATA_RELEASE_POLICY];
-}
+export const mainColumn: ComponentsConfig = [
+  {
+    component: C.Description,
+    viewBuilder: V.buildDescription,
+  } as ComponentConfig<typeof C.Description, ProjectsResponse>,
+  {
+    component: C.Contacts,
+    viewBuilder: V.buildContacts,
+  } as ComponentConfig<typeof C.Contacts, ProjectsResponse>,
+  {
+    component: C.Publications,
+    viewBuilder: V.buildPublications,
+  } as ComponentConfig<typeof C.Publications, ProjectsResponse>,
+  {
+    component: C.Contributors,
+    viewBuilder: V.buildContributors,
+  } as ComponentConfig<typeof C.Contributors, ProjectsResponse>,
+  {
+    component: C.CollaboratingOrganizations,
+    viewBuilder: V.buildCollaboratingOrganizations,
+  } as ComponentConfig<typeof C.CollaboratingOrganizations, ProjectsResponse>,
+  {
+    component: C.DataCurators,
+    viewBuilder: V.buildDataCurators,
+  } as ComponentConfig<typeof C.DataCurators, ProjectsResponse>,
+  {
+    component: C.Citation,
+    viewBuilder: V.buildCitation,
+  } as ComponentConfig<typeof C.Citation, ProjectsResponse>,
+  {
+    component: C.SupplementaryLinks,
+    viewBuilder: V.buildSupplementaryLinks,
+  } as ComponentConfig<typeof C.SupplementaryLinks>,
+  {
+    children: [
+      {
+        component: C.KeyValuePairs,
+        viewBuilder: V.buildAccessions,
+      } as ComponentConfig<typeof C.KeyValuePairs, ProjectsResponse>,
+    ],
+    component: C.CollapsableSection,
+    props: {
+      collapsable: true,
+      title: "Accessions",
+    },
+  } as ComponentConfig<typeof C.CollapsableSection>,
+  {
+    children: [
+      {
+        component: MDX.DataReleasePolicy,
+      } as ComponentConfig<typeof MDX.DataReleasePolicy>,
+    ],
+    component: C.CollapsableSection,
+    props: {
+      collapsable: false,
+      title: "Data Access Policy",
+    },
+  } as ComponentConfig<typeof C.CollapsableSection>,
+];

site-config/lungmap/dev/detail/project/metadataMainColumn.ts

@@ -0,0 +1,11 @@
+import { ComponentConfig } from "@databiosphere/findable-ui/lib/config/entities";
+import { ProjectsResponse } from "../../../../../app/apis/azul/hca-dcp/common/responses";
+import * as C from "../../../../../app/components";
+import * as V from "../../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders";
+
+export const mainColumn: ComponentConfig[] = [
+  {
+    component: C.ManifestDownloadEntity,
+    viewBuilder: V.buildManifestDownloadEntity,
+  } as ComponentConfig<typeof C.ManifestDownloadEntity, ProjectsResponse>,
+];

site-config/lungmap/dev/detail/project/overviewSideColumn.ts

@@ -0,0 +1,47 @@
+import { ComponentConfig } from "@databiosphere/findable-ui/lib/config/entities";
+import { ProjectsResponse } from "../../../../../app/apis/azul/hca-dcp/common/responses";
+import * as C from "../../../../../app/components";
+import * as V from "../../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders";
+
+export const sideColumn: ComponentConfig[] = [
+  {
+    children: [
+      {
+        children: [
+          {
+            component: C.SectionTitle,
+            props: {
+              title: "Analysis Portals",
+            },
+          } as ComponentConfig<typeof C.SectionTitle>,
+          {
+            component: C.KeyValuePairs,
+            viewBuilder: V.buildAnalysisPortals,
+          } as ComponentConfig<typeof C.KeyValuePairs, ProjectsResponse>,
+        ],
+        component: C.Grid,
+        props: {
+          gridSx: { gap: 4 },
+        },
+      } as ComponentConfig<typeof C.Grid>,
+    ],
+    component: C.GridPaperSection,
+  } as ComponentConfig<typeof C.GridPaperSection>,
+  {
+    component: C.Details,
+    viewBuilder: V.buildDetails,
+  } as ComponentConfig<typeof C.Details>,
+  {
+    children: [
+      {
+        component: C.KeyValuePairs,
+        viewBuilder: V.buildFileCounts,
+      } as ComponentConfig<typeof C.KeyValuePairs, ProjectsResponse>,
+    ],
+    component: C.CollapsableSection,
+    props: {
+      collapsable: true,
+      title: "File Counts",
+    },
+  } as ComponentConfig<typeof C.CollapsableSection>,
+];

site-config/lungmap/dev/export/exportConfig.ts

@@ -3,6 +3,8 @@ import {
   ExportConfig,
   ExportMethodConfig,
 } from "@databiosphere/findable-ui/lib/config/entities";
+import * as C from "../../../../app/components";
+import * as HCAViewModelBuilders from "../../../../app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders";
 import * as V from "../../../../app/viewModelBuilders/azul/lungmap/common/viewModelBuilders";
 import {
   ROUTE_BULK_DOWNLOAD,
@@ -17,7 +19,22 @@ export const exportConfig: ExportConfig = {
   ...getExportConfig(hcaExportConfig),
   tabs: [
     {
-      ...hcaExportConfig.tabs[0],
+      label: "Choose Export Method",
+      mainColumn: [
+        {
+          component: C.ExportMethod,
+          viewBuilder: HCAViewModelBuilders.buildExportMethodBulkDownload,
+        } as ComponentConfig<typeof C.ExportMethod>,
+        {
+          component: C.ExportMethod,
+          viewBuilder: HCAViewModelBuilders.buildExportMethodManifestDownload,
+        } as ComponentConfig<typeof C.ExportMethod>,
+        {
+          component: C.ExportMethod,
+          viewBuilder: HCAViewModelBuilders.buildExportMethodTerra,
+        } as ComponentConfig<typeof C.ExportMethod>,
+      ],
+      route: "/export",
       sideColumn: [
         ...getExportCurrentQueryAndDataSummary(),
         ...getExportDataReleasePolicy(),

site-config/lungmap/dev/index/common/category.ts

@@ -0,0 +1,75 @@
+import { CategoryGroup } from "@databiosphere/findable-ui/lib/config/entities";
+import {
+  ANALYSIS_PROTOCOL,
+  ANATOMICAL_ENTITY,
+  BIOLOGICAL_SEX,
+  CONTACT_NAME,
+  CONTENT_DESCRIPTION,
+  DEVELOPMENT_STAGE,
+  DONOR_DISEASE,
+  FILE_FORMAT,
+  FILE_SOURCE,
+  GENUS_SPECIES,
+  INSTITUTION,
+  INSTRUMENT_MANUFACTURER_MODEL,
+  LIBRARY_CONSTRUCTION_METHOD,
+  MODEL_ORGAN,
+  NUCLEIC_ACID_SOURCE,
+  ORGAN_PART,
+  PAIRED_END,
+  PRESERVATION_METHOD,
+  PROJECT_TITLE,
+  SAMPLE_ENTITY_TYPE,
+  SELECTED_CELL_TYPE,
+  SPECIMEN_DISEASE,
+} from "../../../../hca-dcp/dev/index/common/category";
+
+export const CATEGORY_GROUP: Record<string, CategoryGroup> = {
+  DONOR: {
+    categoryConfigs: [
+      BIOLOGICAL_SEX,
+      DEVELOPMENT_STAGE,
+      DONOR_DISEASE,
+      GENUS_SPECIES,
+    ],
+    label: "Donor",
+  },
+  FILE: {
+    categoryConfigs: [CONTENT_DESCRIPTION, FILE_FORMAT, FILE_SOURCE],
+    label: "File",
+  },
+  PROJECT: {
+    categoryConfigs: [PROJECT_TITLE, CONTACT_NAME, INSTITUTION],
+    label: "Project",
+  },
+  PROTOCOL: {
+    categoryConfigs: [
+      ANALYSIS_PROTOCOL, // workflow
+      INSTRUMENT_MANUFACTURER_MODEL,
+      LIBRARY_CONSTRUCTION_METHOD,
+      NUCLEIC_ACID_SOURCE,
+      PAIRED_END,
+    ],
+    label: "Protocol",
+  },
+  SAMPLE: {
+    categoryConfigs: [
+      ANATOMICAL_ENTITY, // specimenOrgan
+      ORGAN_PART,
+      PRESERVATION_METHOD,
+      MODEL_ORGAN,
+      SAMPLE_ENTITY_TYPE,
+      SELECTED_CELL_TYPE,
+      SPECIMEN_DISEASE,
+    ],
+    label: "Sample",
+  },
+};
+
+export const CATEGORY_GROUPS: CategoryGroup[] = [
+  CATEGORY_GROUP.PROJECT,
+  CATEGORY_GROUP.DONOR,
+  CATEGORY_GROUP.SAMPLE,
+  CATEGORY_GROUP.PROTOCOL,
+  CATEGORY_GROUP.FILE,
+];