Merge pull request #679 from ecalifornica/fix-linter-error-F821

Fix undefined names

src/hgvs/dataproviders/uta.py

@@ -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

src/hgvs/normalizer.py

@@ -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
 from hgvs.utils.norm import normalize_alleles
 
 _logger = logging.getLogger(__name__)

tests/test_hgvs_alignmentmapper.py

@@ -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)