chore: deploy staging <- main

client/index.html

@@ -46,7 +46,7 @@
     <script type="text/javascript">
       window.CELLXGENE = {};
       window.CELLXGENE.API = {
-        prefix: `http://localhost:<%= CXG_SERVER_PORT %>${location.pathname}/api/`,
+        prefix: `http://localhost:<%= CXG_SERVER_PORT %>${location.pathname}api/`,
         version: "v0.3/",
       };
     </script>

client/src/common/types/entities.ts

@@ -26,6 +26,8 @@ export const STANDARD_CATEGORY_NAMES = [
   "donor_id",
 ];
 
+export const EXCLUDED_CATEGORY_NAMES = ["observation_joinid"];
+
 /**
  * Author of publication associated with a collection, populated from Crossref as part of collection publication
  * metadata.

client/src/components/categorical/index.tsx

@@ -2,7 +2,10 @@ import React from "react";
 import { connect } from "react-redux";
 import * as globals from "../../globals";
 import Category from "./category";
-import { STANDARD_CATEGORY_NAMES } from "../../common/types/entities";
+import {
+  EXCLUDED_CATEGORY_NAMES,
+  STANDARD_CATEGORY_NAMES,
+} from "../../common/types/entities";
 import {
   CategoricalAnnotationColumnSchema,
   Schema,
@@ -27,19 +30,23 @@ class Categories extends React.Component<{}, State> {
     super(props);
     this.state = {
       createAnnoModeActive: false,
+      // eslint-disable-next-line react/no-unused-state --- FIXME: disabled temporarily
       newCategoryText: "",
+      // eslint-disable-next-line react/no-unused-state --- FIXME: disabled temporarily
       categoryToDuplicate: null,
       expandedCats: new Set(),
     };
   }
 
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
   handleChange = (name: any) => {
+    // eslint-disable-next-line react/no-unused-state --- FIXME: disabled temporarily
     this.setState({ newCategoryText: name });
   };
 
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS.
   handleSelect = (name: any) => {
+    // eslint-disable-next-line react/no-unused-state --- FIXME: disabled temporarily
     this.setState({ newCategoryText: name });
   };
 
@@ -93,6 +100,14 @@ class Categories extends React.Component<{}, State> {
   isCategoryNameStandard = (catName: string): boolean =>
     STANDARD_CATEGORY_NAMES.includes(catName);
 
+  /**
+   * Determine if category is excluded.
+   * @param catName - Name of category.
+   * @returns True if given category name is in the set of standard category names.
+   */
+  isCategoryNameExcluded = (catName: string): boolean =>
+    EXCLUDED_CATEGORY_NAMES.includes(catName);
+
   /**
    * Returns true if category is writable.
    * @param schema - Matrix schema.
@@ -104,10 +119,7 @@ class Categories extends React.Component<{}, State> {
 
   // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS.
   render() {
-    const {
-      createAnnoModeActive,
-      expandedCats,
-    } = this.state;
+    const { createAnnoModeActive, expandedCats } = this.state;
     // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exis... Remove this comment to see the full error message
     const { schema } = this.props;
     /* Names for categorical, string and boolean types, sorted in display order.  Will be rendered in this order */
@@ -121,6 +133,7 @@ class Categories extends React.Component<{}, State> {
     const authorCategoryNames = selectableCategoryNames.filter(
       (catName) =>
         !this.isCategoryNameStandard(catName) &&
+        !this.isCategoryNameExcluded(catName) &&
         (this.isCategoryDisplayable(schema, catName) ||
           this.isCategoryWritable(schema, catName))
     );

client/src/components/geneExpression/quickGene.tsx

@@ -61,6 +61,10 @@ function QuickGene() {
           const df: Dataframe = await annoMatrix.fetch("var", varIndex);
           let dfIds: Dataframe;
           const geneIdCol = "feature_id";
+          const isFilteredCol = "feature_is_filtered";
+          const isFiltered =
+            annoMatrix.getMatrixColumns("var").includes(isFilteredCol) &&
+            (await annoMatrix.fetch("var", isFilteredCol));
 
           // if feature id column is available in var
           if (annoMatrix.getMatrixColumns("var").includes(geneIdCol)) {
@@ -69,7 +73,20 @@ function QuickGene() {
           }
 
           setStatus("success");
-          setGeneNames(df.col(varIndex).asArray() as DataframeValue[]);
+
+          if (isFiltered) {
+            const isFilteredArray = isFiltered.col(isFilteredCol).asArray();
+            setGeneNames(
+              df
+                .col(varIndex)
+                .asArray()
+                .filter(
+                  (_, index) => !isFilteredArray[index] && _
+                ) as DataframeValue[]
+            );
+          } else {
+            setGeneNames(df.col(varIndex).asArray() as DataframeValue[]);
+          }
         } catch (error) {
           setStatus("error");
           throw error;
@@ -159,7 +176,6 @@ function QuickGene() {
       );
     });
   }, [userDefinedGenes, geneNames, geneIds, dispatch]);
-
   return (
     <div style={{ width: "100%", marginBottom: "16px" }}>
       <H4

scripts/explorer-with-portal-rdev.patch

@@ -0,0 +1,30 @@
+diff --git a/.happy/terraform/envs/rdev/main.tf b/.happy/terraform/envs/rdev/main.tf
+index 2977e4d9..9b7a9f8b 100644
+--- a/.happy/terraform/envs/rdev/main.tf
++++ b/.happy/terraform/envs/rdev/main.tf
+@@ -19,2 +19,3 @@ module stack {
+-  data_locator_domain          = "${var.stack_name}-backend.internal.rdev.single-cell.czi.technology"
+-  cxg_bucket_path              = "env-rdev-cellxgene/${var.stack_name}"
++  # data_locator_domain          = "${var.stack_name}-backend.internal.rdev.single-cell.czi.technology" 
++  data_locator_domain          = "internal-happy-rdev-backend-1100870308.us-west-2.elb.amazonaws.com"
++  cxg_bucket_path              = "env-rdev-cellxgene/STACK_NAME"
+diff --git a/hosted/config.yaml b/hosted/config.yaml
+index 86f7ca7e..a2cc5ea2 100644
+--- a/hosted/config.yaml
++++ b/hosted/config.yaml
+@@ -51 +51 @@ server:
+-    api_base: https://${DATA_LOCATOR_DOMAIN}/dp/v1
++    api_base: http://${DATA_LOCATOR_DOMAIN}/dp/v1
+diff --git a/server/dataset/dataset_metadata.py b/server/dataset/dataset_metadata.py
+index 47d0e18c..87514343 100644
+--- a/server/dataset/dataset_metadata.py
++++ b/server/dataset/dataset_metadata.py
+@@ -25 +25 @@ def request_dataset_metadata_from_data_portal(data_portal_api_base: str, explore
+-    headers = {"Content-Type": "application/json", "Accept": "application/json"}
++    headers = {"Content-Type": "application/json", "Accept": "application/json", "Host": "STACK_NAME-backend.rdev.single-cell.czi.technology"}
+@@ -74 +74 @@ def get_dataset_metadata(dataset_root: str, dataset_id: str, app_config: AppConf
+-    explorer_url_path = f"{app_config.server__app__web_base_url}/{dataset_root}/{dataset_id}"
++    explorer_url_path = f"https://STACK_NAME-explorer.rdev.single-cell.czi.technology/{dataset_root}/{dataset_id}"
+@@ -127 +127 @@ def get_dataset_and_collection_metadata(dataset_root: str, dataset_id: str, app_
+-        res = requests.get(f"{data_locator_base_url}/collections/{collection_id}{suffix}")
++        res = requests.get(f"{data_locator_base_url}/collections/{collection_id}{suffix}", headers={"Host": "STACK_NAME-backend.rdev.single-cell.czi.technology"})

scripts/patch-explorer-to-find-portal-rdev-stack.sh

@@ -0,0 +1,8 @@
+# This script applies a (temporary) patch to Explorer so that the RDev
+# stack can find the associated Portal RDev stack and successfully
+# make Portal API calls during manual testing.
+#
+# Usage patch-explorer-to-find-portal-rdev-stack.sh <STACK_NAME>
+
+cd $(git rev-parse --show-toplevel)
+sed -e "s/STACK_NAME/${1}/g" scripts/explorer-with-portal-rdev.patch | patch