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Remove vcf annotator healthcheck #569

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Remove vcf annotator healthcheck #569

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db13804
Remove vcf annotator healthcheck
theferrit32 Jul 23, 2025
cb4f975
Add __init__ check to SeqRepoRESTDataProxy
theferrit32 Jul 23, 2025
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3 changes: 3 additions & 0 deletions src/ga4gh/vrs/dataproxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -254,6 +254,9 @@ def __init__(self, base_url: str):
"""
super().__init__()
self.base_url = f"{base_url}/{self.rest_version}/"
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
Expand Down
9 changes: 0 additions & 9 deletions src/ga4gh/vrs/extras/annotator/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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..."
Expand Down
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