Merge branch 'main' into atar-mg-data-file

.github/workflows/push-tests.yml

@@ -83,7 +83,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -142,7 +142,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -201,7 +201,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -260,7 +260,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -316,7 +316,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -372,7 +372,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*
@@ -431,7 +431,7 @@ jobs:
           fetch-depth: 2
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v44.0.0
+        uses: tj-actions/changed-files@v44.3.0
         with:
           files: |
             Dockerfile*

backend/layers/processing/process_validate.py

@@ -117,12 +117,11 @@ def get_spatial_metadata(self, spatial_dict: Dict[str, Any]) -> Optional[Spatial
         """
         is_single = spatial_dict.get("is_single")
         has_fullres = False
-        # schema validation ensures nested 'fullres' key is only included when is_single is True
-        if is_single:
-            # schema validation ensures there can only be one other key in uns["spatial"] if "is_single" is True
-            library_id = [key for key in spatial_dict if key != "is_single"][0]
-            if "fullres" in spatial_dict[library_id]["images"]:
-                has_fullres = True
+        spatial_library_ids = [key for key in spatial_dict if key != "is_single"]
+        # schema validation ensures there can only be at max, one other key in uns["spatial"] if "is_single" is True
+        library_id = spatial_library_ids.pop() if spatial_library_ids else None
+        if library_id and "images" in spatial_dict[library_id] and "fullres" in spatial_dict[library_id]["images"]:
+            has_fullres = True
         return SpatialMetadata(is_single=bool(is_single), has_fullres=has_fullres)
 
     @logit

frontend/.gitignore

@@ -87,18 +87,8 @@ loginState.json
 public/sitemap*
 public/robots.txt
 
-# Cell Guide
-src/views/CellGuide/common/fixtures/allCellTypeDescriptions.json
-src/views/CellGuide/common/fixtures/allCellTypeDescriptionsSEO.json
-src/views/CellGuide/common/fixtures/allCellTypeMarkerGenes.json
-src/views/CellGuide/common/fixtures/allCellTypeOwlDescriptions.json
-src/views/CellGuide/common/fixtures/allCellTypes.json
-src/views/CellGuide/common/fixtures/allEnrichedGenes/
-src/views/CellGuide/common/fixtures/allSourceData.json
-src/views/CellGuide/common/fixtures/allTissueDescriptions.json
-src/views/CellGuide/common/fixtures/allTissues.json
-src/views/CellGuide/common/fixtures/ontologyTree.json
-src/views/CellGuide/common/fixtures/ontologyTreeStatePerCellType.json
-src/views/CellGuide/common/fixtures/ontologyTreeStatePerTissue.json
-
-certificates
+# Filter descendants
+src/components/common/Filter/descendant_mappings/cell_type_descendants.json
+src/components/common/Filter/descendant_mappings/tissue_descendants.json
+
+certificates

frontend/Dockerfile

@@ -18,14 +18,25 @@ RUN apt-get update && apt-get install -y make wget \
     lsb-release xdg-utils nano vim procps moreutils ripgrep \
     && rm -rf /var/lib/apt/lists/*
 
+# Create the directory `make retrieve-descendants` expects before running npm ci, which runs `make retrieve-descendants`
+# as a preinstall script
+RUN mkdir -p src/components/common/Filter/descendant_mappings
+
+COPY Makefile ./
 COPY package*.json ./
 RUN npm ci --verbose --no-optional && npm cache clean --force
+
 ENV PATH /opt/node_app/node_modules/.bin:$PATH
 
 # -- TODO, we should try turning this back on later.
 # ADD --chown=node . /corpora-frontend
 ADD . /corpora-frontend
+
+# Explicitly copy the JSON files from the earlier steps
+RUN cp -r /opt/node_app/src/components/common/Filter/descendant_mappings/* /corpora-frontend/src/components/common/Filter/descendant_mappings/
+
 WORKDIR /corpora-frontend
+
 ADD ./src/configs/build.js src/configs/configs.js
 RUN mkdir -p node_modules
 RUN ln -sf /opt/node_app/node_modules/* /opt/node_app/node_modules/.bin ./node_modules/.

frontend/package.json

@@ -118,8 +118,7 @@
   ],
   "license": "MIT",
   "scripts": {
-    "predev": "make retrieve-descendants",
-    "prebuild": "make retrieve-descendants",
+    "preinstall": "make retrieve-descendants",
     "dev": "next dev --experimental-https",
     "build": "NODE_OPTIONS=\"--max_old_space_size=2048\" next build",
     "start": "next start",

frontend/src/global.d.ts

@@ -20,3 +20,13 @@ namespace HubSpotFormAPI {
 }
 
 declare const hbspt: HubSpotFormAPI.HubSpot;
+
+declare module "src/components/common/Filter/descendant_mappings/cell_type_descendants.json" {
+  const value: { [key: string]: string[] };
+  export default value;
+}
+
+declare module "src/components/common/Filter/descendant_mappings/tissue_descendants.json" {
+  const value: { [key: string]: string[] };
+  export default value;
+}

tests/unit/processing/test_extract_metadata.py

@@ -290,7 +290,7 @@ def test_get_spatial_metadata__is_single_and_fullres_true(self):
         }
         self.assertEqual(self.pdv.get_spatial_metadata(spatial_dict), SpatialMetadata(is_single=True, has_fullres=True))
 
-    def test_get_spatial_metadata__is_single_true_fullres_false(self):
+    def test_get_spatial_metadata__is_single_true_and_fullres_false(self):
         spatial_dict = {
             "is_single": True,
             "dummy_library_id": {"images": {}},
@@ -299,6 +299,12 @@ def test_get_spatial_metadata__is_single_true_fullres_false(self):
             self.pdv.get_spatial_metadata(spatial_dict), SpatialMetadata(is_single=True, has_fullres=False)
         )
 
+    def test_get_spatial_metadata__is_single_true_and_no_library_id(self):
+        spatial_dict = {"is_single": np.bool_(True)}
+        self.assertEqual(
+            self.pdv.get_spatial_metadata(spatial_dict), SpatialMetadata(is_single=True, has_fullres=False)
+        )
+
     def test_get_spatial_metadata__is_single_false(self):
         spatial_dict = {"is_single": np.bool_(False)}
         self.assertEqual(