Merge branch 'main' into bento007/processing_logs

backend/portal/api/curation/curation-api.yml

@@ -582,7 +582,9 @@ components:
       description: Collection metadata
       properties:
         collection_url:
-          description: The CELLxGENE Discover URL for the Collection.
+          description: |
+            The CELLxGENE Discover URL for the Collection. This points to the canonical link unless it's a revision, 
+            in which case it points to the unpublished revision version.
           type: string
         contact_email:
           $ref: "#/components/schemas/contact_email"

backend/portal/api/curation/v1/curation/collections/common.py

@@ -69,6 +69,7 @@ def reshape_for_curation_api(
     if is_published:
         # Published
         collection_id = collection_version.collection_id
+        collection_url = f"{get_collections_base_url()}/collections/{collection_id.id}"
         revision_of = None
         if not user_info.is_user_owner_or_allowed(collection_version.owner):
             _revising_in = None
@@ -78,9 +79,21 @@ def reshape_for_curation_api(
             )
         revising_in = _revising_in.version_id.id if _revising_in else None
     else:
-        # Unpublished
-        collection_id = collection_version.version_id
-        revision_of = collection_version.collection_id.id
+        # Unpublished - need to determine if it's a revision or first time collection
+        # For that, we look at whether the canonical collection is published
+        is_revision = collection_version.canonical_collection.originally_published_at is not None
+        if is_revision:
+            # If it's a revision, both collection_id and collection_url need to point to the version_id
+            collection_id = collection_version.version_id
+            collection_url = f"{get_collections_base_url()}/collections/{collection_id.id}"
+            revision_of = collection_version.collection_id.id
+        else:
+            # If it's an unpublished, unrevised collection, then collection_url will point to the permalink
+            # (aka the link to the canonical_id) and the collection_id will point to version_id.
+            # Also, revision_of should be None
+            collection_id = collection_version.version_id
+            collection_url = f"{get_collections_base_url()}/collections/{collection_version.collection_id}"
+            revision_of = None
         revising_in = None
 
     # get collection dataset attributes
@@ -94,7 +107,7 @@ def reshape_for_curation_api(
     else:
         revised_at = None
     response = dict(
-        collection_url=f"{get_collections_base_url()}/collections/{collection_id.id}",
+        collection_url=collection_url,
         contact_email=collection_version.metadata.contact_email,
         contact_name=collection_version.metadata.contact_name,
         created_at=collection_version.created_at,

frontend/src/common/analytics/events.ts

@@ -30,6 +30,11 @@ export enum EVENTS {
   WMG_CLICKED = "WMG_CLICKED",
   WMG_DOWNLOAD_CLICKED = "WMG_DOWNLOAD_CLICKED",
   WMG_DOWNLOAD_COMPLETE = "WMG_DOWNLOAD_COMPLETE",
+  WMG_FMG_INFO_CLICKED = "WMG_FMG_INFO_CLICKED",
+  WMG_FMG_COPY_GENES_CLICKED = "WMG_FMG_COPY_GENES_CLICKED",
+  WMG_FMG_ADD_GENES_CLICKED = "WMG_FMG_ADD_GENES_CLICKED",
+  WMG_FMG_QUESTION_BUTTON_HOVER = "WMG_FMG_QUESTION_BUTTON_HOVER",
+  WMG_FMG_DOCUMENTATION_CLICKED = "WMG_FMG_DOCUMENTATION_CLICKED",
   BROWSE_COLLECTIONS_CLICKED = "BROWSE_COLLECTIONS_CLICKED",
   DATASET_EXPLORE_CLICKED = "DATASET_EXPLORE_CLICKED",
   BROWSE_TUTORIALS_CLICKED = "BROWSE_TUTORIALS_CLICKED",

frontend/src/common/queries/wheresMyGene.ts

@@ -768,7 +768,7 @@ export async function fetchMarkerGenes({
   cellTypeID,
   organismID,
   tissueID,
-  test = "binomtest",
+  test = "ttest",
 }: FetchMarkerGeneParams): Promise<MarkerGeneResponse> {
   const url = API_URL + API.WMG_MARKER_GENES;
   const body = generateMarkerGeneBody(cellTypeID, tissueID, organismID, test);

frontend/src/views/WheresMyGene/components/CellInfoSideBar/index.tsx

@@ -8,7 +8,9 @@ import {
   TableRow,
   Tooltip,
 } from "czifui";
-import React, { useCallback, useContext } from "react";
+import React, { useCallback, useContext, useState } from "react";
+import { track } from "src/common/analytics";
+import { EVENTS } from "src/common/analytics/events";
 import { ROUTES } from "src/common/constants/routes";
 import { useMarkerGenes } from "src/common/queries/wheresMyGene";
 import { BetaChip } from "src/components/Header/style";
@@ -30,15 +32,16 @@ export interface CellInfoBarProps {
   cellInfoCellType: Exclude<State["cellInfoCellType"], null>;
   tissueName: string;
 }
+
 function CellInfoSideBar({
   cellInfoCellType,
   tissueName,
 }: CellInfoBarProps): JSX.Element | null {
   const urlParams = new URLSearchParams(window.location.search);
-  let testType: "ttest" | undefined = undefined;
+  let testType: "binomtest" | undefined = undefined;
 
-  if (urlParams.get("test") === "ttest") {
-    testType = "ttest";
+  if (urlParams.get("test") === "binomtest") {
+    testType = "binomtest";
   }
   const { isLoading, data } = useMarkerGenes({
     cellTypeID: cellInfoCellType.cellType.id,
@@ -53,14 +56,24 @@ function CellInfoSideBar({
     if (!data) return;
     const genes = Object.keys(data.marker_genes);
     navigator.clipboard.writeText(genes.join(", "));
+    track(EVENTS.WMG_FMG_COPY_GENES_CLICKED);
   }, [data]);
 
   const handleDisplayGenes = useCallback(() => {
     if (!data || !dispatch) return;
     const genes = Object.keys(data.marker_genes);
     dispatch(addSelectedGenes(genes));
+    track(EVENTS.WMG_FMG_ADD_GENES_CLICKED);
   }, [data, dispatch]);
 
+  const [hoverStartTime, setHoverStartTime] = useState(0);
+
+  const handleHoverEnd = useCallback(() => {
+    if (Date.now() - hoverStartTime > 2 * 1000) {
+      track(EVENTS.WMG_FMG_QUESTION_BUTTON_HOVER);
+    }
+  }, [hoverStartTime]);
+
   if (isLoading || !data) return null;
 
   if (!cellInfoCellType) return null;
@@ -78,13 +91,20 @@ function CellInfoSideBar({
             arrow={true}
             title={
               <StyledTooltip>
-                <div>Marker genes are highly and uniquely expressed in the cell type relative to all other cell types.</div>
-                <br/>
                 <div>
-                  <a 
-                    href={ROUTES.FMG_DOCS} 
-                    rel="noopener" 
-                    target="_blank" 
+                  Marker genes are highly and uniquely expressed in the cell
+                  type relative to all other cell types.
+                </div>
+                <br />
+                <div>
+                  <a
+                    href={ROUTES.FMG_DOCS}
+                    rel="noopener"
+                    target="_blank"
+                    onClick={() => {
+                      handleHoverEnd();
+                      track(EVENTS.WMG_FMG_DOCUMENTATION_CLICKED);
+                    }}
                   >
                     Click to read more about the identification method.
                   </a>
@@ -97,6 +117,8 @@ function CellInfoSideBar({
               sdsType="secondary"
               isAllCaps={false}
               style={{ fontWeight: "500" }}
+              onMouseEnter={() => setHoverStartTime(Date.now())}
+              onMouseLeave={handleHoverEnd}
             >
               <StyledIconImage src={questionMarkIcon} />
             </TooltipButton>

frontend/src/views/WheresMyGene/components/HeatMap/components/YAxisChart/index.tsx

@@ -31,6 +31,8 @@ import {
   InfoButtonWrapper,
 } from "./style";
 import { SELECTED_STYLE } from "../../style";
+import { track } from "src/common/analytics";
+import { EVENTS } from "src/common/analytics/events";
 
 const MAX_DEPTH = 2;
 
@@ -192,6 +194,9 @@ const CellTypeButton = ({
               if (isMarkerGenes) {
                 const cellType = deserializeCellTypeMetadata(metadata);
                 generateMarkerGenes(cellType, tissueID);
+                track(EVENTS.WMG_FMG_INFO_CLICKED, {
+                  combination: `${cellType.name}, ${tissue}}`,
+                });
               }
             }}
           >

tests/unit/backend/layers/api/test_curation_api.py

@@ -349,11 +349,11 @@ def test__get_collections_with_auth__OK_5(self):
 
     def test__get_collections_with_auth__OK_6(self):
         "revision_of contains None if the collection is unpublished"
-        unpublished_collection_id = self.generate_unpublished_collection()
+        self.generate_unpublished_collection()
         resp = self._test_response(visibility="PRIVATE", auth=True)
         self.assertEqual(1, len(resp))
         resp_collection = resp[0]
-        self.assertEqual(unpublished_collection_id.collection_id.id, resp_collection["revision_of"])
+        self.assertIsNone(resp_collection["revision_of"])
 
     def test__get_collections_no_auth_visibility_private__403(self):
         self._test_response(visibility="PRIVATE", status_code=403)