build: use standard lib urlparse (#181)

Author: jsstevenson

cool_seq_tool/app.py

@@ -13,7 +13,7 @@
     SEQREPO_ROOT_DIR, TRANSCRIPT_MAPPINGS_PATH
 from cool_seq_tool.schemas import Assembly, GenomicData, TranscriptExonData, \
     ResidueMode, GenomicDataResponse, ServiceMeta, TranscriptExonDataResponse
-from cool_seq_tool.data_sources import MANETranscript, MANETranscriptMappings,\
+from cool_seq_tool.data_sources import MANETranscript, MANETranscriptMappings, \
     SeqRepoAccess, TranscriptMappings, UTADatabase, GeneNormalizer
 from cool_seq_tool.version import __version__
 

cool_seq_tool/data_sources/uta_database.py

@@ -4,9 +4,8 @@
 import logging
 from typing import Dict, List, Optional, Tuple, Any, TypeVar, Type, Union
 from os import environ
-from urllib.parse import quote, unquote
+from urllib.parse import quote, unquote, urlparse, ParseResult as UrlLibParseResult
 
-from six.moves.urllib import parse as urlparse
 import pandas as pd
 import asyncpg
 import boto3
@@ -94,7 +93,7 @@ def _get_conn_args(self) -> Dict:
             return dict(host=host, port=int(port), database=database, user=username,
                         password=password)
         else:
-            url = ParseResult(urlparse.urlparse(self.db_url))
+            url = ParseResult(urlparse(self.db_url))
             self.schema = url.schema
             password = unquote(url.password) if url.password else ""
             return dict(host=url.hostname, port=url.port,
@@ -1129,7 +1128,7 @@ def get_secret() -> str:
                 return decoded_binary_secret
 
 
-class ParseResult(urlparse.ParseResult):
+class ParseResult(UrlLibParseResult):
     """Subclass of url.ParseResult that adds database and schema methods,
     and provides stringification.
     Source: https://github.com/biocommons/hgvs

tests/unit/test_mane_transcript.py

@@ -5,7 +5,7 @@
 from mock import patch
 import pandas as pd
 
-from cool_seq_tool.data_sources import MANETranscript, MANETranscriptMappings,\
+from cool_seq_tool.data_sources import MANETranscript, MANETranscriptMappings, \
     SeqRepoAccess, TranscriptMappings, UTADatabase, GeneNormalizer
 from cool_seq_tool.data_sources.mane_transcript import MANETranscriptError
 from cool_seq_tool.schemas import AnnotationLayer, Assembly, ResidueMode