Remove vcf annotator healthcheck

src/ga4gh/vrs/dataproxy.py

@@ -247,13 +247,17 @@ class SeqRepoRESTDataProxy(_SeqRepoDataProxyBase):
 
     rest_version = "1"
 
-    def __init__(self, base_url: str):
+    def __init__(self, base_url: str, disable_healthcheck: bool = False):
         """Initialize REST-based dataproxy instance.
 
         :param base_url: root URL to server
         """
         super().__init__()
         self.base_url = f"{base_url}/{self.rest_version}/"
+        if not disable_healthcheck:
+            ping_url = self.base_url + "ping"
+            ping_resp = requests.get(ping_url)  # noqa: S113
+            ping_resp.raise_for_status()
 
     def _get_sequence(
         self, identifier: str, start: int | None = None, end: int | None = None

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

@@ -11,7 +11,6 @@
 from timeit import default_timer as timer
 
 import click
-import requests
 
 from ga4gh.vrs.dataproxy import create_dataproxy
 from ga4gh.vrs.extras.annotator.vcf import VcfAnnotator, VcfAnnotatorArgsError
@@ -200,14 +199,6 @@ def _annotate_vcf_cli(
      * seqrepo+:../relative/path/to/seqrepo/root
     """  # noqa: D301
     data_proxy = create_dataproxy(dataproxy_uri)
-    try:
-        data_proxy.get_metadata("GRCh38:1")
-    except requests.exceptions.ConnectionError:
-        msg = f"Connection to SeqRepo dataproxy at {dataproxy_uri} failed. Is the REST service running?"
-        _logger.exception(msg)
-        if not silent:
-            click.echo(msg, err=True)
-        exit(1)
     annotator = VcfAnnotator(data_proxy)
     start = timer()
     msg = f"Annotating {vcf_in} with the VCF Annotator..."

tests/conftest.py

@@ -39,7 +39,8 @@ def dataproxy():
 @pytest.fixture(scope="session")
 def rest_dataproxy():
     return SeqRepoRESTDataProxy(
-        base_url=os.environ.get("SEQREPO_REST_URL", "http://localhost:5000/seqrepo")
+        base_url=os.environ.get("SEQREPO_REST_URL", "http://localhost:5000/seqrepo"),
+        disable_healthcheck=True,
     )
 
 

tests/extras/cassettes/test_annotate_vcf_grch37_attrs.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_grch38_attrs.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_grch38_attrs_altsonly.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_grch38_noattrs.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_input_validation.yaml

@@ -0,0 +1,18 @@
+interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
+version: 1

tests/extras/cassettes/test_annotate_vcf_pickle_only.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_rle.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_annotate_vcf_vcf_only.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/cassettes/test_get_vrs_object_invalid_input.yaml

@@ -1,4 +1,20 @@
 interactions:
+- request:
+    body: null
+    headers: {}
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/ping
+  response:
+    body:
+      string: "{\n  \"dependencies\": {\n    \"bioutils\": {\n      \"url\": \"https://github.com/biocommons/bioutils/\",\n
+        \     \"version\": \"0.5.8.post1\"\n    },\n    \"seqrepo\": {\n      \"root\":
+        \"/usr/local/share/seqrepo/2024-12-20\",\n      \"url\": \"https://github.com/biocommons/biocommons.seqrepo/\",\n
+        \     \"version\": \"0.6.6\"\n    }\n  },\n  \"url\": \"https://github.com/biocommons/seqrepo-rest-service/\",\n
+        \ \"version\": \"0.2.3.dev0+ge4124b9.d20231114\"\n}\n"
+    headers: {}
+    status:
+      code: 200
+      message: OK
 - request:
     body: null
     headers: {}

tests/extras/test_annotate_vcf.py

@@ -182,6 +182,7 @@ def test_annotate_vcf_vcf_only(
     assert not Path(output_vrs_pkl).exists()
 
 
+@pytest.mark.vcr
 def test_annotate_vcf_input_validation(vcf_annotator: VcfAnnotator, input_vcf: Path):
     with pytest.raises(
         VcfAnnotatorError,