Merge pull request #69 from cancervariants/issue-60

Add previous symbols to extensions
cancervariants · Aug 9, 2021 · a935f11 · a935f11
2 parents 33ab615 + efd641a
commit a935f11
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Showing 4 changed files with 46 additions and 4 deletions.
diff --git a/gene/query.py b/gene/query.py
@@ -419,11 +419,14 @@ def add_gene_descriptor(self, response, record, match_type,
         extension_and_record_labels = [
             ("symbol_status", "symbol_status"),
             ("approved_name", "label"),
-            ("chromsome_location", "locations"),
-            ("associated_with", "associated_with")
+            ("chromosome_location", "locations"),
+            ("associated_with", "associated_with"),
+            ("previous_symbols", "previous_symbols")
         ]
         for ext_label, record_label in extension_and_record_labels:
             if record_label in record and record[record_label]:
+                if ext_label == 'chromosome_location':
+                    record[record_label] = record[record_label][0]
                 extensions.append(Extension(
                     name=ext_label,
                     value=record[record_label]

diff --git a/gene/schemas.py b/gene/schemas.py
@@ -236,7 +236,7 @@ class Extension(BaseModel):
 
     type = "Extension"
     name: StrictStr
-    value: Union[StrictStr, List[Dict], List[StrictStr]]
+    value: Union[StrictStr, List[Dict], List[StrictStr], Dict]
 
     class Config:
         """Configure model example"""

diff --git a/gene/version.py b/gene/version.py
@@ -1 +1 @@
-__version__ = "0.1.14"
+__version__ = "0.1.15"
diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -47,6 +47,14 @@ def normalized_ache():
             "ACEE"
         ],
         "extensions": [
+            {
+                "name": "previous_symbols",
+                "value": [
+                    "ACEE",
+                    "YT"
+                ],
+                "type": "Extension"
+            },
             {
                 "name": "approved_name",
                 "value": "acetylcholinesterase (Cartwright blood group)",
@@ -193,6 +201,15 @@ def normalized_abl1():
             "ABL"
         ],
         "extensions": [
+            {
+                "name": "previous_symbols",
+                "value": [
+                    "LOC116063",
+                    "LOC112779",
+                    "ABL"
+                ],
+                "type": "Extension"
+            },
             {
                 "name": "approved_name",
                 "value": "ABL proto-oncogene 1, non-receptor tyrosine kinase",
@@ -368,6 +385,7 @@ def compare_gene_descriptor(test, actual):
     if extensions_present:
         assert len(actual["extensions"]) == len(test["extensions"]), \
             "len of extensions"
+        n_ext_correct = 0
         for test_ext in test["extensions"]:
             for actual_ext in actual["extensions"]:
                 if actual_ext["name"] == test_ext["name"]:
@@ -379,6 +397,9 @@ def compare_gene_descriptor(test, actual):
                     else:
                         assert actual_ext["value"] == test_ext["value"]
                     assert actual_ext["type"] == test_ext["type"]
+                    n_ext_correct += 1
+        assert n_ext_correct == len(test['extensions']), \
+            "number of correct extensions"
 
 
 def test_search_query(query_handler, num_sources):
@@ -504,6 +525,12 @@ def test_ache_query(query_handler, num_sources, normalized_ache):
     compare_normalize_resp(resp, q, MatchType.PREV_SYMBOL, cpy_normalized_ache,
                            expected_source_meta=expected_source_meta)
 
+    q = "ACEE"
+    resp = query_handler.normalize(q)
+    cpy_normalized_ache["id"] = "normalize.gene:ACEE"
+    compare_normalize_resp(resp, q, MatchType.PREV_SYMBOL, cpy_normalized_ache,
+                           expected_source_meta=expected_source_meta)
+
     q = "omim:100740"
     resp = query_handler.normalize(q)
     cpy_normalized_ache["id"] = "normalize.gene:omim%3A100740"
@@ -574,6 +601,12 @@ def test_braf_query(query_handler, num_sources, normalized_braf):
     compare_normalize_resp(resp, q, MatchType.ALIAS, cpy_normalized_braf,
                            expected_source_meta=expected_source_meta)
 
+    q = "b-raf"
+    resp = query_handler.normalize(q)
+    cpy_normalized_braf["id"] = "normalize.gene:b-raf"
+    compare_normalize_resp(resp, q, MatchType.ALIAS, cpy_normalized_braf,
+                           expected_source_meta=expected_source_meta)
+
     q = "omim:164757"
     resp = query_handler.normalize(q)
     cpy_normalized_braf["id"] = "normalize.gene:omim%3A164757"
@@ -650,6 +683,12 @@ def test_abl1_query(query_handler, num_sources, normalized_abl1):
     compare_normalize_resp(resp, q, MatchType.PREV_SYMBOL, cpy_normalized_abl1,
                            expected_source_meta=expected_source_meta)
 
+    q = "LOC112779"
+    resp = query_handler.normalize(q)
+    cpy_normalized_abl1["id"] = "normalize.gene:LOC112779"
+    compare_normalize_resp(resp, q, MatchType.PREV_SYMBOL, cpy_normalized_abl1,
+                           expected_source_meta=expected_source_meta)
+
     q = "ABL"
     resp = query_handler.normalize(q)
     cpy_normalized_abl1["id"] = "normalize.gene:ABL"