update fusor version, coolseqtool version, and tests due to those upd…

…ates + pydantic
cancervariants · Jul 10, 2024 · bd2f5e9 · bd2f5e9
1 parent 7838e83
commit bd2f5e9
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Showing 6 changed files with 14 additions and 37 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -25,7 +25,7 @@ decorator==5.1.1
 executing==1.2.0
 fake-useragent==1.1.3
 fastapi==0.100.0
-fusor==0.0.30.dev1
+fusor==0.1.0
 ga4gh.vrs==0.8.4
 ga4gh.vrsatile.pydantic==0.2.0
 gene-normalizer==0.1.40-dev1

diff --git a/server/setup.cfg b/server/setup.cfg
@@ -16,7 +16,7 @@ install_requires =
     fastapi >= 0.72.0
     aiofiles
     asyncpg
-    fusor ~= 0.0.30-dev1
+    fusor ~= 0.1.0
     sqlparse >= 0.4.2
     urllib3 >= 1.26.5
     click

diff --git a/server/tests/conftest.py b/server/tests/conftest.py
@@ -182,9 +182,9 @@ def tpm3_tx_g_element(tpm3_descriptor):
         "type": "TranscriptSegmentElement",
         "transcript": "refseq:NM_152263.4",
         "exon_start": 6,
-        "exon_start_offset": 5,
+        "exon_start_offset": 72,
         "exon_end": 6,
-        "exon_end_offset": -70,
+        "exon_end_offset": -5,
         "gene_descriptor": tpm3_descriptor,
         "element_genomic_start": {
             "id": "fusor.location_descriptor:NC_000001.11",
@@ -195,8 +195,8 @@ def tpm3_tx_g_element(tpm3_descriptor):
                 "sequence_id": "refseq:NC_000001.11",
                 "interval": {
                     "type": "SequenceInterval",
-                    "start": {"type": "Number", "value": 154171483},
-                    "end": {"type": "Number", "value": 154171484},
+                    "start": {"type": "Number", "value": 154171416},
+                    "end": {"type": "Number", "value": 154171417},
                 },
             },
         },
@@ -209,8 +209,8 @@ def tpm3_tx_g_element(tpm3_descriptor):
                 "sequence_id": "refseq:NC_000001.11",
                 "interval": {
                     "type": "SequenceInterval",
-                    "start": {"type": "Number", "value": 154171482},
-                    "end": {"type": "Number", "value": 154171483},
+                    "start": {"type": "Number", "value": 154171417},
+                    "end": {"type": "Number", "value": 154171418},
                 },
             },
         },

diff --git a/server/tests/integration/test_constructors.py b/server/tests/integration/test_constructors.py
@@ -187,25 +187,6 @@ async def test_build_tx_segment_ect(
     )
 
 
-@pytest.mark.asyncio
-async def test_build_segment_gct(
-    check_response, check_tx_element_response, tpm3_tx_t_element
-):
-    """Test correct functioning of transcript segment element construction using
-    genomic coordinates and transcript.
-    """
-    await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",  # noqa: E501
-        {"element": tpm3_tx_t_element},
-        check_tx_element_response,
-    )
-    await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=refseq%3ANM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",  # noqa: E501
-        {"element": tpm3_tx_t_element},
-        check_tx_element_response,
-    )
-
-
 @pytest.mark.asyncio
 async def test_build_segment_gcg(
     check_response, check_tx_element_response, tpm3_tx_g_element
@@ -214,7 +195,7 @@ async def test_build_segment_gcg(
     genomic coordinates and gene name.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_gcg?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",  # noqa: E501
+        "/api/construct/structural_element/tx_segment_gcg?gene=TPM3&chromosome=NC_000001.11&transcript=NM_152263.4&start=154171416&end=154171417&strand=-",  # noqa: E501
         {"element": tpm3_tx_g_element},
         check_tx_element_response,
     )

diff --git a/server/tests/integration/test_lookup.py b/server/tests/integration/test_lookup.py
@@ -45,6 +45,8 @@ async def test_normalize_gene(async_client: AsyncClient):
     response = await async_client.get("/api/lookup/gene?term=sdfliuwer")
     assert response.status_code == 200
     assert response.json() == {
+        "cased": "",
+        "symbol": "",
         "term": "sdfliuwer",
         "warnings": ["Lookup of gene term sdfliuwer failed."],
     }
diff --git a/server/tests/integration/test_nomenclature.py b/server/tests/integration/test_nomenclature.py
@@ -177,9 +177,7 @@ async def test_tx_segment_nomenclature(
         "/api/nomenclature/transcript_segment?first=true&last=false", json=epcam_invalid
     )
     assert response.status_code == 200
-    assert response.json().get("warnings", []) == [
-        "1 validation error for TranscriptSegmentElement\ntranscript\n  field required (type=value_error.missing)"  # noqa: E501
-    ]
+    assert "field required" in response.json().get("warnings", [])[0].lower()
 
 
 @pytest.mark.asyncio
@@ -196,9 +194,7 @@ async def test_gene_element_nomenclature(
         json={"type": "GeneElement", "associated_gene": {"id": "hgnc:427"}},
     )
     assert response.status_code == 200
-    assert response.json().get("warnings", []) == [
-        "2 validation errors for GeneElement\ngene_descriptor\n  field required (type=value_error.missing)\nassociated_gene\n  extra fields not permitted (type=value_error.extra)"  # noqa: E501
-    ]
+    assert "field required" in response.json().get("warnings", [])[0].lower()
 
 
 @pytest.mark.asyncio
@@ -234,9 +230,7 @@ async def test_templated_sequence_nomenclature(
         },
     )
     assert response.status_code == 200
-    assert response.json().get("warnings", []) == [
-        "1 validation error for TemplatedSequenceElement\nstrand\n  field required (type=value_error.missing)"  # noqa: E501
-    ]
+    assert "field required" in response.json().get("warnings", [])[0].lower()
 
 
 @pytest.mark.asyncio