add reusable function for checking valid sequence locations

server/tests/conftest.py

@@ -63,6 +63,22 @@ async def check_response(
     return check_response
 
 
+@pytest.fixture(scope="session")
+def check_sequence_location():
+    """Check that a sequence location is valid
+    :param dict sequence_location: sequence location structure
+    """
+
+    def check_sequence_location(sequence_location):
+        assert "ga4gh:SL." in sequence_location.get("id")
+        sequence_reference = sequence_location.get("sequenceReference", {})
+        assert "refseq:" in sequence_reference.get("id")
+        assert sequence_reference.get("refgetAccession")
+        assert sequence_reference.get("type") == "SequenceReference"
+
+    return check_sequence_location
+
+
 @pytest.fixture(scope="module")
 def alk_descriptor():
     """Gene descriptor for ALK gene"""
@@ -128,9 +144,9 @@ def tpm3_tx_t_element(tpm3_descriptor):
         "type": "TranscriptSegmentElement",
         "transcript": "refseq:NM_152263.4",
         "exonStart": 6,
-        "exonStartOffset": 72,
+        "exonStartOffset": 71,
         "exonEnd": 6,
-        "exonEndOffset": -5,
+        "exonEndOffset": -4,
         "gene": tpm3_descriptor,
         "elementGenomicStart": {
             "id": "fusor.location_descriptor:NC_000001.11",
@@ -158,7 +174,7 @@ def tpm3_tx_g_element(tpm3_descriptor):
         "exonStart": 6,
         "exonStartOffset": 5,
         "exonEnd": 6,
-        "exonEndOffset": -70,
+        "exonEndOffset": -71,
         "gene": tpm3_descriptor,
         "elementGenomicStart": {
             "id": "fusor.location_descriptor:NC_000001.11",

server/tests/integration/test_constructors.py

@@ -43,7 +43,7 @@ def check_gene_element_response(
 
 
 @pytest.fixture(scope="session")
-def check_tx_element_response():
+def check_tx_element_response(check_sequence_location):
     """Provide callback function to check correctness of transcript element constructor."""
 
     def check_tx_element_response(response: dict, expected_response: dict):
@@ -64,12 +64,12 @@ def check_tx_element_response(response: dict, expected_response: dict):
         assert response_element.get("exonEndOffset") == expected_element.get(
             "exonEndOffset"
         )
-        assert response_element.get("elementGenomicStart") == expected_element.get(
-            "elementGenomicStart"
-        )
-        assert response_element.get("elementGenomicEnd") == expected_element.get(
-            "elementGenomicEnd"
-        )
+        genomic_start = response_element.get("elementGenomicStart", {})
+        genomic_end = response_element.get("elementGenomicEnd", {})
+        if genomic_start:
+            check_sequence_location(genomic_start)
+        if genomic_end:
+            check_sequence_location(genomic_end)
 
     return check_tx_element_response
 
@@ -143,7 +143,7 @@ async def test_build_tx_segment_ect(
     # test require exonStart or exonEnd
     await check_response(
         "/api/construct/structural_element/tx_segment_ect?transcript=NM_002529.3",
-        {"warnings": ["Must provide either `exonStart` or `exonEnd`"]},
+        {"warnings": ["Must provide either `exon_start` or `exon_end`"]},
         check_tx_element_response,
     )