Modify the Gene Ontology related validators and tests

src/mavedb/lib/validation/constants/general.py

@@ -44,6 +44,7 @@
 variant_count_data = "count_data"
 required_score_column = "score"
 
+multi_value_keys = ["molecular mechanism assessed"]
 valid_dataset_columns = [score_columns, count_columns]
 valid_variant_columns = [variant_score_data, variant_count_data]
 

src/mavedb/lib/validation/keywords.py

@@ -1,13 +1,14 @@
 from typing import Optional
 
+from mavedb.lib.validation.constants.general import multi_value_keys
 from mavedb.lib.validation.exceptions import ValidationError
 from mavedb.lib.validation.utilities import is_null
 
 
 def validate_code(key: str, label: str, code: Optional[str]):
     # TODO(#511) Re-enable the Gene Ontology code requirement.
     pass
-    # if key.lower() == "phenotypic assay mechanism" and label.lower() != "other":
+    # if key.lower() == "molecular mechanism assessed" and label.lower() != "other":
     #     # The Gene Ontology accession is a unique seven digit identifier prefixed by GO:.
     #     # e.g. GO:0005739, GO:1904659, or GO:0016597.
     #     if code is None or not re.match(r"^GO:\d{7}$", code):
@@ -26,9 +27,12 @@ def validate_duplicates(keywords: list):
     keys = []
     labels = []
     for k in keywords:
-        keys.append(k.keyword.key.lower())  # k: ExperimentControlledKeywordCreate object
-        if k.keyword.label.lower() != "other":
-            labels.append(k.keyword.label.lower())
+        key = k.keyword.key.lower()
+        label = k.keyword.label.lower()
+        if key not in multi_value_keys:
+            keys.append(key)
+        if label != "other":
+            labels.append(label)
 
     keys_set = set(keys)
     labels_set = set(labels)

src/mavedb/routers/experiments.py

@@ -459,6 +459,7 @@ async def update_experiment(
     item.raw_read_identifiers = raw_read_identifiers
 
     if item_update.keywords:
+        keywords: list[ExperimentControlledKeywordAssociation] = []
         all_labels_none = all(k.keyword.label is None for k in item_update.keywords)
         if all_labels_none is False:
             # Users may choose part of keywords from dropdown menu. Remove not chosen keywords from the list.
@@ -467,10 +468,18 @@ async def update_experiment(
                 validate_keyword_list(filtered_keywords)
             except ValidationError as e:
                 raise HTTPException(status_code=422, detail=str(e))
-            try:
-                await item.set_keywords(db, filtered_keywords)
-            except Exception as e:
-                raise HTTPException(status_code=500, detail=f"Invalid keywords: {str(e)}")
+            for upload_keyword in filtered_keywords:
+                try:
+                    description = upload_keyword.description
+                    controlled_keyword = search_keyword(db, upload_keyword.keyword.key, upload_keyword.keyword.label)
+                    experiment_controlled_keyword = ExperimentControlledKeywordAssociation(
+                        controlled_keyword=controlled_keyword,
+                        description=description,
+                    )
+                    keywords.append(experiment_controlled_keyword)
+                except ValueError as e:
+                    raise HTTPException(status_code=422, detail=str(e))
+        item.keyword_objs = keywords
 
     item.modified_by = user_data.user
 

tests/helpers/constants.py

@@ -427,21 +427,35 @@
         "special": False,
         "description": "Description",
     },
-    {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+    {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
     {
-        "key": "Phenotypic Assay Mechanism",
+        "key": "Molecular Mechanism Assessed",
         "label": "Other",
         "code": None,
         "special": False,
         "description": "Description",
     },
     {
-        "key": "Phenotypic Assay Mechanism",
-        "label": "Label",
+        "key": "Molecular Mechanism Assessed",
+        "label": "Sodium channel activity",
         "code": "GO:1234567",
         "special": False,
         "description": "Description",
     },
+    {
+        "key": "Molecular Mechanism Assessed",
+        "label": "Calcium-mediated signaling",
+        "code": "GO:1134567",
+        "special": False,
+        "description": "Description",
+    },
+    {
+        "key": "Phenotypic Assay Profiling Strategy",
+        "label": "Shotgun sequencing",
+        "code": None,
+        "special": False,
+        "description": "Description",
+    },
 ]
 
 TEST_KEYWORDS = [
@@ -470,7 +484,7 @@
         },
     },
     {
-        "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+        "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
         "description": "Details of delivery method",
     },
 ]
@@ -492,7 +506,7 @@
     "methodText": "Methods",
     "keywords": [
         {
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Details of delivery method",
         },
     ],
@@ -572,7 +586,7 @@
     "keywords": [
         {
             "recordType": "ExperimentControlledKeyword",
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Details of delivery method",
         },
     ],
@@ -587,6 +601,51 @@
     "numScoreSets": 0,  # NOTE: This is context-dependent and may need overriding per test
 }
 
+TEST_EXPERIMENT_WITH_UPDATE_KEYWORD_RESPONSE = {
+    "recordType": "Experiment",
+    "title": "Test Experiment Title",
+    "shortDescription": "Test experiment",
+    "abstractText": "Abstract",
+    "methodText": "Methods",
+    "createdBy": {
+        "recordType": "User",
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "modifiedBy": {
+        "recordType": "User",
+        "firstName": TEST_USER["first_name"],
+        "lastName": TEST_USER["last_name"],
+        "orcidId": TEST_USER["username"],
+    },
+    "creationDate": date.today().isoformat(),
+    "modificationDate": date.today().isoformat(),
+    "scoreSetUrns": [],
+    "contributors": [],
+    "keywords": [
+        {
+            "recordType": "ExperimentControlledKeyword",
+            "keyword": {
+                "key": "Phenotypic Assay Profiling Strategy",
+                "label": "Shotgun sequencing",
+                "special": False,
+                "description": "Description"
+            },
+            "description": "Details of phenotypic assay profiling strategy",
+        },
+    ],
+    "doiIdentifiers": [],
+    "primaryPublicationIdentifiers": [],
+    "secondaryPublicationIdentifiers": [],
+    "rawReadIdentifiers": [],
+    # keys to be set after receiving response
+    "urn": None,
+    "experimentSetUrn": None,
+    "officialCollections": [],
+    "numScoreSets": 0,  # NOTE: This is context-dependent and may need overriding per test
+}
+
 TEST_EXPERIMENT_WITH_KEYWORD_HAS_DUPLICATE_OTHERS_RESPONSE = {
     "recordType": "Experiment",
     "title": "Test Experiment Title",
@@ -622,7 +681,7 @@
         },
         {
             "recordType": "ExperimentControlledKeyword",
-            "keyword": {"key": "Delivery method", "label": "Other", "special": False, "description": "Description"},
+            "keyword": {"key": "Delivery Method", "label": "Other", "special": False, "description": "Description"},
             "description": "Description",
         },
     ],