Modify the Gene Ontology related validators and tests.

Author: EstelleDa

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)

tests/helpers/constants.py

@@ -429,19 +429,26 @@
     },
     {"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",

tests/routers/test_experiments.py

@@ -528,8 +528,8 @@ def test_create_experiment_that_keyword_gene_ontology_has_valid_code(client, set
         "keywords": [
             {
                 "keyword": {
-                    "key": "Phenotypic Assay Mechanism",
-                    "label": "Label",
+                    "key": "Molecular Mechanism Assessed",
+                    "label": "Sodium channel activity",
                     "code": "GO:1234567",
                     "special": False,
                     "description": "Description",
@@ -541,8 +541,8 @@ def test_create_experiment_that_keyword_gene_ontology_has_valid_code(client, set
     response = client.post("/api/v1/experiments/", json=experiment)
     assert response.status_code == 200
     response_data = response.json()
-    assert response_data["keywords"][0]["keyword"]["key"] == "Phenotypic Assay Mechanism"
-    assert response_data["keywords"][0]["keyword"]["label"] == "Label"
+    assert response_data["keywords"][0]["keyword"]["key"] == "Molecular Mechanism Assessed"
+    assert response_data["keywords"][0]["keyword"]["label"] == "Sodium channel activity"
     assert response_data["keywords"][0]["keyword"]["code"] == "GO:1234567"
 
 
@@ -551,7 +551,7 @@ def test_create_experiment_that_keyword_gene_ontology_is_other_without_code(clie
         "keywords": [
             {
                 "keyword": {
-                    "key": "Phenotypic Assay Mechanism",
+                    "key": "Molecular Mechanism Assessed",
                     "label": "Other",
                     "code": None,
                     "description": "Description",
@@ -564,17 +564,60 @@ def test_create_experiment_that_keyword_gene_ontology_is_other_without_code(clie
     response = client.post("/api/v1/experiments/", json=experiment)
     assert response.status_code == 200
     response_data = response.json()
-    assert response_data["keywords"][0]["keyword"]["key"] == "Phenotypic Assay Mechanism"
+    assert response_data["keywords"][0]["keyword"]["key"] == "Molecular Mechanism Assessed"
     assert response_data["keywords"][0]["keyword"]["label"] == "Other"
 
 
+def test_create_experiment_that_keywords_has_multiple_molecular_mechanism_assessed_labels(client, setup_router_db):
+    valid_keywords = {
+        "keywords": [
+            {
+                "keyword": {
+                    "key": "Molecular Mechanism Assessed",
+                    "label": "Sodium channel activity",
+                    "code": "GO:1234567",
+                    "special": False,
+                    "description": "Description",
+                },
+            },
+            {
+                "keyword": {
+                    "key": "Molecular Mechanism Assessed",
+                    "label": "Calcium-mediated signaling",
+                    "code": "GO:1134567",
+                    "special": False,
+                    "description": "Description",
+                },
+            }
+        ],
+    }
+    experiment = {**TEST_MINIMAL_EXPERIMENT, **valid_keywords}
+    response = client.post("/api/v1/experiments/", json=experiment)
+    assert response.status_code == 200
+    response_data = response.json()
+    assert len(response_data["keywords"]) == 2
+    labels = {kw["keyword"]["label"] for kw in response_data["keywords"]}
+    codes = {kw["keyword"]["code"] for kw in response_data["keywords"]}
+    keys = {kw["keyword"]["key"] for kw in response_data["keywords"]}
+
+    assert keys == {"Molecular Mechanism Assessed"}
+    assert labels == {
+        "Sodium channel activity",
+        "Calcium-mediated signaling",
+    }
+    assert codes == {
+        "GO:1234567",
+        "GO:1134567",
+    }
+
+
 # TODO(#511) Re-enable the Gene Ontology code requirement.
 # def test_cannot_create_experiment_that_keyword_has_an_invalid_code(client, setup_router_db):
 #     invalid_keyword = {
 #         "keywords": [
 #             {
 #                 "keyword": {
-#                     "key": "Phenotypic Assay Mechanism",
+#                     "key": "Molecular Mechanism Assessed",
 #                     "label": "Label",
 #                     "code": "invalid",
 #                     "description": "Description",