feat: add lungmap analysis portals (#4669)

app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/constants.ts

@@ -1,7 +1,11 @@
 import { ANALYSIS_PORTAL, AnalysisPortal, ProjectEdit } from "./entities";
 
+const azimuthIcon = "/images/icons/azimuth.png";
+const bioDataCatalystIcon = "/images/icons/bio-data-catalyst.png";
 const cxgIcon = "/images/icons/cxg.png";
 const genomeBrowserIcon = "/images/icons/ucsc-genome.svg";
+const jbrowseIcon = "/images/icons/jbrowse.png";
+const lcaIcon = "/images/icons/lca.png";
 const lgeaIcon = "/images/icons/lgea.png";
 const lungmapIcon = "/images/icons/lungmap.svg";
 const shinyIcon = "/images/icons/shiny.png";
@@ -10,6 +14,24 @@ const stemCellHubIcon = "/images/icons/stem.svg";
 const toppCellIcon = "/images/icons/toppcell.png";
 const ucscCellBrowserIcon = "/images/icons/ucsc-cell.svg";
 
+/**
+ * Azimuth analysis portal.
+ */
+const AZIMUTH: Omit<AnalysisPortal, "url"> = {
+  icon: azimuthIcon,
+  label: "Azimuth",
+  name: ANALYSIS_PORTAL.AZIMUTH,
+};
+
+/**
+ * BioData Catalyst analysis portal.
+ */
+const BIO_DATA_CATALYST: Omit<AnalysisPortal, "url"> = {
+  icon: bioDataCatalystIcon,
+  label: "BioData Catalyst",
+  name: ANALYSIS_PORTAL.BIO_DATA_CATALYST,
+};
+
 /**
  * CZ CELLxGENE analysis portal.
  */
@@ -28,6 +50,24 @@ const GENOME_BROWSER: Omit<AnalysisPortal, "url"> = {
   name: ANALYSIS_PORTAL.GENOME_BROWSER,
 };
 
+/**
+ * JBrowse analysis portal.
+ */
+const JBROWSE: Omit<AnalysisPortal, "url"> = {
+  icon: jbrowseIcon,
+  label: "JBrowse",
+  name: ANALYSIS_PORTAL.JBROWSE,
+};
+
+/**
+ * LCA analysis portal.
+ */
+const LCA: Omit<AnalysisPortal, "url"> = {
+  icon: lcaIcon,
+  label: "LCA",
+  name: ANALYSIS_PORTAL.LCA,
+};
+
 /**
  * LGEA analysis portal.
  */
@@ -607,6 +647,10 @@ export const baseProjectEdits: ProjectEdit[] = [
   },
   {
     analysisPortals: [
+      {
+        ...BIO_DATA_CATALYST,
+        url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/",
+      },
       {
         ...CZ_CELLXGENE,
         url: "https://cellxgene.cziscience.com/collections/48d354f5-a5ca-4f35-a3bb-fa3687502252",
@@ -649,6 +693,14 @@ export const baseProjectEdits: ProjectEdit[] = [
   },
   {
     analysisPortals: [
+      {
+        ...AZIMUTH,
+        url: "https://app.lungmap.net/app/azimuth-mouse-lung-cellref-seed",
+      },
+      {
+        ...CZ_CELLXGENE,
+        url: "https://app.lungmap.net/app/cellxgene-mouse-cellref",
+      },
       {
         ...LGEA,
         url: "https://research.cchmc.org/pbge/lunggens/SCLAB.html",
@@ -657,6 +709,10 @@ export const baseProjectEdits: ProjectEdit[] = [
         ...LUNGMAP_APPS,
         url: "https://lungmap.net/breath-omics-experiment-page/?experiment_id=LMEX0000001222",
       },
+      {
+        ...SHINY,
+        url: "https://app.lungmap.net/app/shinycell-mouse-lung-cellref",
+      },
     ],
     entryId: "1bdcecde-16be-4208-88f4-78cd2133d11d",
   },
@@ -1671,6 +1727,14 @@ export const baseProjectEdits: ProjectEdit[] = [
   },
   {
     analysisPortals: [
+      {
+        ...BIO_DATA_CATALYST,
+        url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/",
+      },
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004409",
+      },
       {
         ...SINGLE_CELL,
         url: "https://singlecell.broadinstitute.org/single_cell/study/SCP1157/bronchiolitis-obliterans-syndrome-lungmap",
@@ -1685,16 +1749,21 @@ export const baseProjectEdits: ProjectEdit[] = [
   {
     analysisPortals: [
       {
-        ...LUNGMAP_APPS,
-        url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004396",
+        ...CZ_CELLXGENE,
+        url: "https://cellxgene.cziscience.com/collections/f86d6317-7215-409e-bfda-3f4ded3dadaa",
+      },
+      {
+        ...JBROWSE,
+        // eslint-disable-next-line sonarjs/no-hardcoded-passwords -- shared session link, not a secret
+        url: "https://jbrowse.lungmap.net/?session=share-U7sOFrqK09&password=4cHnL",
       },
       {
         ...LGEA,
         url: "https://research.cchmc.org/pbge/lunggens/tools/lung_at_glance.html?tab=reference&species=Human",
       },
       {
-        ...CZ_CELLXGENE,
-        url: "https://cellxgene.cziscience.com/collections/f86d6317-7215-409e-bfda-3f4ded3dadaa",
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004396",
       },
       {
         ...SHINY,
@@ -1709,6 +1778,14 @@ export const baseProjectEdits: ProjectEdit[] = [
   },
   {
     analysisPortals: [
+      {
+        ...BIO_DATA_CATALYST,
+        url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/",
+      },
+      {
+        ...CZ_CELLXGENE,
+        url: "https://cellxgene.cziscience.com/collections/3a5dbf8a-9b3e-4309-b4c5-d8a024f83734",
+      },
       {
         ...LUNGMAP_APPS,
         url: "https://www.lungmap.net/omics/?experiment_id=LMEX0000004400",
@@ -1717,10 +1794,6 @@ export const baseProjectEdits: ProjectEdit[] = [
         ...SHINY,
         url: "https://app.lungmap.net/app/shinycell-bpd",
       },
-      {
-        ...CZ_CELLXGENE,
-        url: "https://cellxgene.cziscience.com/collections/3a5dbf8a-9b3e-4309-b4c5-d8a024f83734",
-      },
     ],
     entryId: "1977dc47-8414-4263-a870-6b0f207d8ab3",
   },
@@ -1826,10 +1899,84 @@ export const baseProjectEdits: ProjectEdit[] = [
   {
     analysisPortals: [
       {
-        ...LGEA,
+        ...LCA,
         url: "https://research.cchmc.org/pbge/lunggens/LCA/LCA.html",
       },
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004412",
+      },
     ],
     entryId: "ccea5717-a848-4c06-8d2d-d1b694e89441",
   },
+  {
+    analysisPortals: [
+      {
+        ...CZ_CELLXGENE,
+        url: "https://lungcells.app.vumc.org/",
+      },
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004401",
+      },
+      {
+        ...SHINY,
+        url: "https://app.lungmap.net/app/shinycell-bpd-vanderbilt",
+      },
+    ],
+    entryId: "9393acbf-e8d8-4b96-9c71-996e245e5f23",
+  },
+  {
+    analysisPortals: [
+      {
+        ...BIO_DATA_CATALYST,
+        url: "https://gen3.biodatacatalyst.nhlbi.nih.gov/",
+      },
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004406",
+      },
+    ],
+    entryId: "834e0d16-71b6-4425-a8ab-022b5000961c",
+  },
+  {
+    analysisPortals: [
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004415",
+      },
+    ],
+    entryId: "e651ac3e-03aa-46fa-9ed3-70c6fda4e440",
+  },
+  {
+    analysisPortals: [
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004407",
+      },
+    ],
+    entryId: "3a02d15f-9c6a-4ef7-852b-4ddec733b70b",
+  },
+  {
+    analysisPortals: [
+      {
+        ...LUNGMAP_APPS,
+        url: "https://www.lungmap.net/dataset/?dataset_id=LMEX0000004414",
+      },
+      {
+        ...SHINY,
+        url: "https://app.lungmap.net/app/shinycell-iaec2",
+      },
+    ],
+    entryId: "1f009151-2206-4294-929a-9c720f19a13f",
+  },
+  {
+    analysisPortals: [
+      {
+        ...LUNGMAP_APPS,
+        url: "https://lungmap-data-submissions.s3.us-east-1.amazonaws.com/tmp/spatial_data_new.html?name=Xenium+Pilot",
+      },
+    ],
+    entryId: "e99faee2-7706-4c1a-9d28-76c68320f549",
+  },
 ];

app/viewModelBuilders/azul/hca-dcp/common/projectMapper/projectEdits/entities.ts

@@ -9,8 +9,12 @@ import {
  * Set of analysis portal names.
  */
 export enum ANALYSIS_PORTAL {
+  AZIMUTH = "AZIMUTH",
+  BIO_DATA_CATALYST = "BIO_DATA_CATALYST",
   CZ_CELLXGENE = "CZ_CELLXGENE",
   GENOME_BROWSER = "GENOME_BROWSER",
+  JBROWSE = "JBROWSE",
+  LCA = "LCA",
   LGEA = "LGEA",
   LUNGMAP_APPS = "LUNGMAP_APPS",
   SHINY = "SHINY",