chore: staging deploy; 06/12/24

client/src/common/types/entities.ts

@@ -2,7 +2,7 @@
 
 /**
  * Complete list of standard cellxgene column names.
- * https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md#obs-cell-metadata
+ * https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.1.0/schema.md#obs-cell-metadata
  */
 export const STANDARD_CATEGORY_NAMES = [
   "assay",
@@ -13,17 +13,18 @@ export const STANDARD_CATEGORY_NAMES = [
   "development_stage_ontology_term_id",
   "disease",
   "disease_ontology_term_id",
-  "self_reported_ethnicity",
-  "self_reported_ethnicity_ontology_term_id",
+  "donor_id",
+  "in_tissue",
   "is_primary_data",
   "organism",
   "organism_ontology_term_id",
-  "sex_ontology_term_id",
+  "self_reported_ethnicity",
+  "self_reported_ethnicity_ontology_term_id",
   "sex",
-  "tissue_ontology_term_id",
-  "tissue",
+  "sex_ontology_term_id",
   "suspension_type",
-  "donor_id",
+  "tissue",
+  "tissue_ontology_term_id",
 ];
 
 export const EXCLUDED_CATEGORY_NAMES = ["observation_joinid"];

client/src/components/categorical/index.tsx

@@ -70,10 +70,10 @@ class Categories extends React.Component<{}, State> {
   /**
    * Determine if category name is an ontology key.
    * @param catName - Name of category.
-   * @returns True if category name includes ontology key.
+   * @returns True if category exists in ontology term id list.
    */
   isCategoryNameOntologyKey = (catName: string): boolean =>
-    catName.includes(globals.ONTOLOGY_KEY);
+    globals.ONTOLOGY_TERM_ID_KEYS.some((key: string) => catName.includes(key));
 
   /**
    * Categories are included for display if category has more than one category value or categories are not defined

client/src/components/graph/util.ts

@@ -164,12 +164,10 @@ function getSpatialUrl(s3URI: string) {
   if (hostname.includes("staging")) {
     return `https://cellxgene.staging.single-cell.czi.technology/spatial-deep-zoom/${datasetVersionId}/`;
   }
-
-  if (hostname.includes("prod")) {
-    return `https://cellxgene.cziscience.com/spatial-deep-zoom/${datasetVersionId}/`;
+  if (hostname.includes("dev") || hostname.includes("localhost")) {
+    return `https://cellxgene.dev.single-cell.czi.technology/spatial-deep-zoom/${datasetVersionId}/`;
   }
-
-  return `https://cellxgene.dev.single-cell.czi.technology/spatial-deep-zoom/${datasetVersionId}/`;
+  return `https://cellxgene.cziscience.com/spatial-deep-zoom/${datasetVersionId}/`;
 }
 
 function getDatasetVersionId(s3URI: string) {

client/src/components/infoDrawer/infoFormat.tsx

@@ -332,7 +332,11 @@ const buildDatasetMetadataViews = (
 ): MetadataView[] =>
   Array.from(singleValueCategories.entries())
     .filter(([key, value]) => {
-      if (key.indexOf(globals.ONTOLOGY_KEY) >= 0) {
+      if (
+        globals.ONTOLOGY_TERM_ID_KEYS.some((ontologyKey) =>
+          key.includes(ontologyKey)
+        )
+      ) {
         // skip ontology terms
         return false;
       }

client/src/globals.ts

@@ -15,8 +15,17 @@ export const unassignedCategoryLabel = "unassigned";
 /** Maximum number of cells a dataset can have in order to be included for display. */
 export const DATASET_MAX_CELL_COUNT = 2_000_000;
 
-/* Category name suffix used to determine if category name is ontology term id. */
-export const ONTOLOGY_KEY = "ontology_term_id";
+/* Explicit ontology term ids. */
+export const ONTOLOGY_TERM_ID_KEYS = [
+  "assay_ontology_term_id",
+  "cell_type_ontology_term_id",
+  "development_stage_ontology_term_id",
+  "disease_ontology_term_id",
+  "organism_ontology_term_id",
+  "self_reported_ethnicity_ontology_term_id",
+  "sex_ontology_term_id",
+  "tissue_ontology_term_id",
+];
 
 /* Unified navigation bar header height. */
 export const HEADER_HEIGHT_PX = 56;

server/dataset/dataset.py

@@ -346,7 +346,7 @@ def normalize_embedding(embedding, ename, spatial=None):
         Embedding is an ndarray, shape (n_obs, n)., where n is normally 2
         """
 
-        if spatial is not None and ename in "spatial":
+        if spatial and ename in "spatial":
 
             library_id = list(spatial.keys())[0]
             image_properties = spatial[library_id]["image_properties"]