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Fix undefined names #679

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merged 3 commits into from
Sep 11, 2023
Merged

Fix undefined names #679

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5a9002a
Fix undefined names
ecalifornica Aug 26, 2023
d0943b8
Remove SQLite scheme from data provider
ecalifornica Sep 10, 2023
b8fbc96
Fix undefined name errors in tests
ecalifornica Sep 11, 2023
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4 changes: 1 addition & 3 deletions src/hgvs/dataproviders/uta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,9 +103,7 @@ def connect(db_url=None, pooling=hgvs.global_config.uta.pooling, application_nam
_logger.warning(f"You are executing tests using remote data ({db_url})")

url = _parse_url(db_url)
if url.scheme == "sqlite":
conn = UTA_sqlite(url, mode, cache)
elif url.scheme == "postgresql":
if url.scheme == "postgresql":
conn = UTA_postgresql(url=url, pooling=pooling, application_name=application_name, mode=mode, cache=cache)
else:
# fell through connection scheme cases
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2 changes: 2 additions & 0 deletions src/hgvs/normalizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,11 @@
import hgvs
import hgvs.validator
import hgvs.variantmapper
from hgvs.dataproviders.ncbi import connect
from hgvs.exceptions import (HGVSDataNotAvailableError,
HGVSInvalidVariantError,
HGVSUnsupportedOperationError)
from hgvs.parser import Parser
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This introduced a circular dependency from Parser <-> normalizer

from hgvs.utils.norm import normalize_alleles

_logger = logging.getLogger(__name__)
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12 changes: 6 additions & 6 deletions tests/test_hgvs_alignmentmapper.py
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Added these changes since last reviewed, had neglected to run ruff on the tests/ path.

Original file line number Diff line number Diff line change
Expand Up @@ -53,14 +53,14 @@ def x_test_alignmentmapper_AlignmentMapper_LCE3C_uncertain(self):
alt_ac = "NC_000001.10"
test_cases = [
{
"g": parser.parse_g_interval("(?_152573139)"),
"n": parser.parse_n_interval("(?_2)"),
"c": parser.parse_c_interval("(?_-69)"),
"g": self.parser.parse_g_interval("(?_152573139)"),
"n": self.parser.parse_n_interval("(?_2)"),
"c": self.parser.parse_c_interval("(?_-69)"),
},
{
"g": parser.parse_g_interval("(152573138_?)"),
"n": parser.parse_n_interval("(1_?)"),
"c": parser.parse_c_interval("(-70_?)"),
"g": self.parser.parse_g_interval("(152573138_?)"),
"n": self.parser.parse_n_interval("(1_?)"),
"c": self.parser.parse_c_interval("(-70_?)"),
},
]
self.run_cases(tx_ac, alt_ac, test_cases)
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