NickAkhmetov/CAT-1111, CAT-965, CAT-1148 Organ Page Fixes

CHANGELOG-organ-page-fixes.md

@@ -0,0 +1,4 @@
+- Ensure ovary and fallopian tube organ pages are properly populated with left/right laterality datasets.
+- Ensure urinary bladder organ page includes Bladder datasets.
+- Ensure bladder organ icon displays appropriately.
+- Ensure cell population plot controls drawer does not overlap the app bar.

context/app/organ/fallopian-tube.yaml

@@ -8,4 +8,6 @@ description: Initial section of the oviduct through which the ova pass from the
   to the uterus.
 icon: https://cdn.jsdelivr.net/gh/cns-iu/md-icons@main/other-icons/organs/ico-organs-fallopian-tube-left.svg
 has_iu_component: true
-search: []
+search:
+  - Fallopian Tube (Left)
+  - Fallopian Tube (Right)

context/app/organ/ovary.yaml

@@ -7,4 +7,6 @@ asctb: ovary-v1.2
 description: The gonad of a female organism which contains germ cells.
 icon: https://cdn.jsdelivr.net/gh/cns-iu/md-icons@main/other-icons/organs/ico-organs-ovaries.svg
 has_iu_component: true
-search: []
+search:
+  - Ovary (Left)
+  - Ovary (Right)

context/app/organ/urinary-bladder.yaml

@@ -8,4 +8,5 @@ description: Distensible musculomembranous organ situated in the anterior part o
   the pelvic cavity in which urine collects before excretion[MP].
 icon: https://cdn.jsdelivr.net/gh/cns-iu/md-icons@main/other-icons/organs/ico-organs-bladder.svg
 has_iu_component: true
-search: []
+search:
+  - Bladder

context/app/routes_file_based.py

@@ -7,7 +7,7 @@
 
 import frontmatter
 
-from .utils import get_default_flask_data, make_blueprint, get_organs
+from .utils import get_default_flask_data, get_organ_name_mapping, make_blueprint, get_organs
 
 
 blueprint = make_blueprint(__name__)
@@ -80,13 +80,15 @@ def organ_details_view(name):
 @blueprint.route('/organ/<name>.json')
 def get_organ_details(name):
     organs = get_organs()
+    organ_names = get_organ_name_mapping()
     # Remove all spaces, underscores, and any text in parentheses
     normalized_name = name.lower().strip()
     normalized_name = normalized_name.split('(')[0].strip().replace(
         ' ', '-').replace('_', '-')
-    if normalized_name not in organs:
+    safe_organ_name = organ_names.get(normalized_name)
+    if safe_organ_name not in organs:
         return {}
-    filename = Path(dirname(__file__)) / 'organ' / f'{secure_filename(normalized_name)}.yaml'
+    filename = Path(dirname(__file__)) / 'organ' / f'{secure_filename(safe_organ_name)}.yaml'
     organ = safe_load(filename.read_text())
     return organ
 

context/app/utils.py

@@ -66,6 +66,19 @@ def get_organs():
     return organs
 
 
+def get_organ_name_mapping():
+    organs = get_organs()
+    organ_file_names = {k: k for k, _ in organs.items()}
+    # Add search field for each organ as additional keys
+    for k, v in organs.items():
+        search = v['search']
+        if len(search) > 0:
+            for s in search:
+                organ_file_names[s.lower()] = k
+    print(organ_file_names)
+    return organ_file_names
+
+
 # Redirect to primary dataset if this entity is
 # - non-existent
 # - a support entity (e.g. an image pyramid)

context/package.json

@@ -33,7 +33,7 @@
     "@visx/text": "^3.3.0",
     "@visx/tooltip": "^3.3.0",
     "@xyflow/react": "^12.0.3",
-    "cellpop": "^0.0.12",
+    "cellpop": "^0.0.13",
     "chart.js": "^4.4.2",
     "d3": "^7.9.0",
     "d3-array": "^3.2.4",