Merge branch 'main' into refactor-set-header

src/ga4gh/vrs/dataproxy.py

@@ -353,6 +353,8 @@ def create_dataproxy(uri: str | None = None) -> _DataProxy:
     * seqrepo+http://localhost:5000/seqrepo
     * seqrepo+https://somewhere:5000/seqrepo
 
+    :raise ValueError: if URI doesn't match recognized schemes, e.g. is missing provider
+        prefix (`"seqrepo+"`)
     """
     uri = uri or os.environ.get("GA4GH_VRS_DATAPROXY_URI", None)
 

src/ga4gh/vrs/extras/annotator/vcf.py

@@ -7,14 +7,12 @@
 
 import pysam
 from biocommons.seqrepo import SeqRepo
-from pydantic import ValidationError
 
 from ga4gh.core.identifiers import (
     VrsObjectIdentifierIs,
     use_ga4gh_compute_identifier_when,
 )
 from ga4gh.vrs.dataproxy import (
-    DataProxyValidationError,
     SeqRepoDataProxy,
     SeqRepoRESTDataProxy,
 )
@@ -270,33 +268,16 @@ def _get_vrs_object(
                 assembly_name=assembly,
                 require_validation=require_validation,
             )
-        except (ValidationError, DataProxyValidationError):
-            vrs_obj = None
-            _logger.exception(
-                "ValidationError when translating %s from gnomad", vcf_coords
-            )
-            raise
-        except KeyError:
-            vrs_obj = None
-            _logger.exception("KeyError when translating %s from gnomad", vcf_coords)
-            raise
-        except AssertionError:
-            vrs_obj = None
-            _logger.exception(
-                "AssertionError when translating %s from gnomad", vcf_coords
-            )
-            raise
         except Exception:
             vrs_obj = None
             _logger.exception(
-                "Unhandled Exception when translating %s from gnomad", vcf_coords
+                "Exception encountered during translation of variation: %s", vcf_coords
             )
             raise
-        else:
-            if not vrs_obj:
-                _logger.debug(
-                    "None was returned when translating %s from gnomad", vcf_coords
-                )
+        if vrs_obj is None:
+            _logger.debug(
+                "None was returned when translating %s from gnomad", vcf_coords
+            )
 
         if vrs_data and vrs_obj:
             key = vrs_data_key if vrs_data_key else vcf_coords

tests/test_dataproxy.py

@@ -0,0 +1,67 @@
+import os
+import re
+
+import pytest
+
+from ga4gh.vrs.dataproxy import create_dataproxy
+
+
+@pytest.mark.parametrize("dp", ["rest_dataproxy", "dataproxy"])
+@pytest.mark.vcr
+def test_data_proxies(dp, request):
+    dataproxy = request.getfixturevalue(dp)
+    r = dataproxy.get_metadata("NM_000551.3")
+    assert r["length"] == 4560
+    assert "ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_" in r["aliases"]
+
+    r = dataproxy.get_metadata("NC_000013.11")
+    assert r["length"] == 114364328
+    assert "ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT" in r["aliases"]
+
+    seq = dataproxy.get_sequence("ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_")
+    assert seq.startswith("CCTCGCCTCCGTTACAACGGCCTACGGTGCTGGAGGATCCTTCTGCGCAC")
+
+    seq = dataproxy.get_sequence(
+        "ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_", start=0, end=50
+    )
+    assert seq == "CCTCGCCTCCGTTACAACGGCCTACGGTGCTGGAGGATCCTTCTGCGCAC"
+
+
+def test_data_proxy_configs():
+    with pytest.raises(
+        ValueError,
+        match=re.escape(
+            "create_dataproxy scheme must include provider (e.g., `seqrepo+http:...`)"
+        ),
+    ):
+        create_dataproxy("file:///path/to/seqrepo/root")
+
+    with pytest.raises(
+        ValueError,
+        match=re.escape("SeqRepo URI scheme seqrepo+fake-scheme not implemented"),
+    ):
+        create_dataproxy("seqrepo+fake-scheme://localhost:5000")
+
+    with pytest.raises(
+        ValueError, match="DataProxy provider fake-dataprovider not implemented"
+    ):
+        create_dataproxy("fake-dataprovider+http://localhost:5000")
+
+    with pytest.raises(
+        ValueError,
+        match="No data proxy URI provided or found in GA4GH_VRS_DATAPROXY_URI",
+    ):
+        create_dataproxy(None)
+
+    # check that fallback on env var works
+    os.environ["GA4GH_VRS_DATAPROXY_URI"] = "seqrepo+:tests/data/seqrepo/latest"
+    create_dataproxy(None)
+
+    # check that method arg takes precedence by passing an invalid arg
+    with pytest.raises(
+        ValueError,
+        match=re.escape(
+            "create_dataproxy scheme must include provider (e.g., `seqrepo+http:...`)"
+        ),
+    ):
+        create_dataproxy("file:///path/to/seqrepo/root")