Potential Code Quality Issues

[chgl]

Running flake8 over the repo reveals some potential for improvement:

$ flake8 .

.\src\run.py:33:80: E501 line too long (93 > 79 characters)
.\src\run.py:44:80: E501 line too long (119 > 79 characters)
.\src\run.py:45:80: E501 line too long (106 > 79 characters)
.\src\run.py:49:80: E501 line too long (113 > 79 characters)
.\src\run.py:57:80: E501 line too long (88 > 79 characters) 
.\src\run.py:72:1: E302 expected 2 blank lines, found 1
.\src\run.py:73:5: F841 local variable 'logger' is assigned to but never used
.\src\run.py:73:28: W291 trailing whitespace
.\src\run.py:78:1: E302 expected 2 blank lines, found 1
.\src\run.py:85:5: F841 local variable 'logger' is assigned to but never used
.\src\run.py:140:80: E501 line too long (91 > 79 characters)
.\src\run.py:145:80: E501 line too long (85 > 79 characters)
.\src\run.py:146:80: E501 line too long (89 > 79 characters)
.\src\run.py:147:80: E501 line too long (100 > 79 characters)
.\src\run.py:149:80: E501 line too long (109 > 79 characters)
.\src\run.py:150:80: E501 line too long (117 > 79 characters)
.\src\run.py:156:80: E501 line too long (120 > 79 characters)
.\src\run.py:163:13: W292 no newline at end of file
.\src\run_server.py:18:80: E501 line too long (106 > 79 characters)
.\src\run_server.py:58:80: E501 line too long (81 > 79 characters)
.\src\run_server.py:89:80: E501 line too long (81 > 79 characters)
.\src\run_server.py:101:80: E501 line too long (89 > 79 characters)
.\src\run_server.py:102:80: E501 line too long (98 > 79 characters)
.\src\run_server.py:117:1: E302 expected 2 blank lines, found 1
.\src\run_server.py:120:35: W291 trailing whitespace
.\src\run_server.py:135:80: E501 line too long (88 > 79 characters)
.\src\run_server.py:136:80: E501 line too long (98 > 79 characters)
.\src\run_server.py:142:1: E302 expected 2 blank lines, found 1
.\src\run_server.py:147:80: E501 line too long (81 > 79 characters)
.\src\run_server.py:160:80: E501 line too long (88 > 79 characters)
.\src\run_server.py:161:80: E501 line too long (98 > 79 characters)
.\src\run_server.py:167:1: E302 expected 2 blank lines, found 1
.\src\run_server.py:185:4: W291 trailing whitespace
.\src\run_server.py:232:20: W291 trailing whitespace
.\src\run_server.py:260:80: E501 line too long (89 > 79 characters)
.\src\run_server.py:265:80: E501 line too long (98 > 79 characters)
.\src\run_server.py:293:80: E501 line too long (102 > 79 characters)
.\src\run_server.py:304:80: E501 line too long (93 > 79 characters)
.\src\run_server.py:316:80: E501 line too long (92 > 79 characters)
.\src\run_server.py:326:80: E501 line too long (111 > 79 characters)
.\src\run_server.py:327:80: E501 line too long (114 > 79 characters)
.\src\run_server.py:328:80: E501 line too long (100 > 79 characters)
.\src\run_server.py:329:80: E501 line too long (95 > 79 characters)
.\src\run_server.py:330:80: E501 line too long (92 > 79 characters)
.\src\algorithm\algorithm_step.py:9:80: E501 line too long (86 > 79 characters)
.\src\algorithm\__init__.py:1:1: F401 'algorithm.algorithm_step.AlgorithmStep' imported but unused
.\src\algorithm\steps\build_internal_response.py:7:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\build_internal_response.py:14:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\build_internal_response.py:16:80: E501 line too long (98 > 79 characters)
.\src\algorithm\steps\build_xml_response.py:8:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\build_xml_response.py:21:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\build_xml_response.py:50:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\build_xml_response.py:52:80: E501 line too long (98 > 79 characters)
.\src\algorithm\steps\execute_fhir_queries.py:1:1: F401 'time' imported but unused
.\src\algorithm\steps\execute_fhir_queries.py:5:1: F401 'worker.communication.ProcessingEvent' imported but unused
.\src\algorithm\steps\execute_fhir_queries.py:7:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\execute_fhir_queries.py:14:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\execute_fhir_queries.py:19:80: E501 line too long (97 > 79 characters)
.\src\algorithm\steps\execute_fhir_queries.py:32:80: E501 line too long (105 > 79 characters)
.\src\algorithm\steps\extract_fhir_ids.py:5:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\extract_fhir_ids.py:12:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\generate_fhir_cnf.py:1:1: F401 'typing.List' imported but unused
.\src\algorithm\steps\generate_fhir_cnf.py:7:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\generate_fhir_cnf.py:14:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\generate_fhir_cnf.py:19:1: W391 blank line at end of file
.\src\algorithm\steps\parse.py:7:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\parse.py:14:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\parse.py:16:80: E501 line too long (91 > 79 characters)
.\src\algorithm\steps\resolve_cnf.py:5:80: E501 line too long (81 > 79 characters)
.\src\algorithm\steps\resolve_cnf.py:12:80: E501 line too long (103 > 79 characters)
.\src\algorithm\steps\__init__.py:1:1: F401 'algorithm.steps.parse.ParseStep' imported but unused
.\src\algorithm\steps\__init__.py:2:1: F401 'algorithm.steps.build_internal_response.BuildInternalResponseStep' imported but unused
.\src\algorithm\steps\__init__.py:3:1: F401 'algorithm.steps.build_xml_response.BuildXmlResponseStep' imported but unused
.\src\algorithm\steps\__init__.py:4:1: F401 'algorithm.steps.execute_fhir_queries.ExecuteFhirQueriesStep' imported but unused
.\src\algorithm\steps\__init__.py:5:1: F401 'algorithm.steps.generate_fhir_cnf.GenerateFhirCNFStep' imported but unused
.\src\algorithm\steps\__init__.py:6:1: F401 'algorithm.steps.resolve_cnf.ResolveCNFStep' imported but unused
.\src\algorithm\steps\__init__.py:7:1: F401 'algorithm.steps.extract_fhir_ids.ExtractFhirIdsStep' imported but unused
.\src\algorithm\steps\__init__.py:8:1: W391 blank line at end of file
.\src\configuration\parser_configuration.py:9:80: E501 line too long (81 > 79 characters)
.\src\configuration\process_configuration.py:3:1: F401 'algorithm.steps.ParseStep' imported but unused
.\src\configuration\process_configuration.py:3:80: E501 line too long (113 > 79 characters)
.\src\configuration\process_configuration.py:10:80: E501 line too long (81 > 79 characters)
.\src\configuration\process_configuration.py:16:80: E501 line too long (95 > 79 characters)
.\src\configuration\process_configuration.py:17:80: E501 line too long (112 > 79 characters)
.\src\configuration\process_configuration.py:18:80: E501 line too long (101 > 79 characters)
.\src\configuration\process_configuration.py:21:80: E501 line too long (109 > 79 characters)
.\src\fhir\fhir_executor.py:15:1: F811 redefinition of unused 'urlparse' from line 8
.\src\fhir\fhir_executor.py:18:80: E501 line too long (81 > 79 characters)
.\src\fhir\fhir_executor.py:22:80: E501 line too long (89 > 79 characters)
.\src\fhir\fhir_executor.py:34:1: W293 blank line contains whitespace
.\src\fhir\fhir_executor.py:36:5: E303 too many blank lines (3)
.\src\fhir\fhir_executor.py:45:80: E501 line too long (87 > 79 characters)
.\src\fhir\fhir_executor.py:47:80: E501 line too long (81 > 79 characters)
.\src\fhir\fhir_executor.py:51:80: E501 line too long (98 > 79 characters)
.\src\fhir\fhir_executor.py:60:80: E501 line too long (93 > 79 characters)
.\src\fhir\fhir_executor.py:70:80: E501 line too long (85 > 79 characters)
.\src\fhir\fhir_executor.py:73:80: E501 line too long (85 > 79 characters)
.\src\fhir\fhir_executor.py:109:80: E501 line too long (80 > 79 characters)
.\src\fhir\fhir_executor.py:114:80: E501 line too long (108 > 79 characters)
.\src\fhir\fhir_parser.py:11:80: E501 line too long (108 > 79 characters)
.\src\fhir\fhir_parser.py:49:1: E302 expected 2 blank lines, found 1
.\src\fhir\fhir_parser.py:77:80: E501 line too long (84 > 79 characters)
.\src\fhir\fhir_parser.py:78:71: W291 trailing whitespace
.\src\fhir\fhir_parser.py:84:5: F841 local variable 'x_type' is assigned to but never used
.\src\fhir\fhir_parser.py:96:1: E302 expected 2 blank lines, found 1
.\src\fhir\fhir_parser.py:103:5: F841 local variable 'x_type' is assigned to but never used
.\src\fhir\fhir_parser.py:115:1: E302 expected 2 blank lines, found 1
.\src\fhir\fhir_parser.py:122:5: F841 local variable 'x_type' is assigned to but never used
.\src\fhir\fhir_parser.py:134:1: E302 expected 2 blank lines, found 1
.\src\fhir\fhir_parser.py:171:80: E501 line too long (101 > 79 characters)
.\src\fhir\fhir_parser.py:173:80: E501 line too long (87 > 79 characters)
.\src\fhir\fhir_parser.py:176:80: E501 line too long (117 > 79 characters)
.\src\fhir\fhir_parser.py:186:80: E501 line too long (115 > 79 characters)
.\src\fhir\fhir_query_gen.py:1:1: F401 'os' imported but unused
.\src\fhir\fhir_query_gen.py:39:80: E501 line too long (82 > 79 characters)
.\src\fhir\fhir_query_gen.py:58:80: E501 line too long (87 > 79 characters)
.\src\fhir\fhir_query_gen.py:59:80: E501 line too long (97 > 79 characters)
.\src\fhir\__init__.py:1:1: F401 'fhir.fhir_executor.execute_fhir_query' imported but unused
.\src\fhir\__init__.py:2:1: F401 'fhir.fhir_parser.build_result_set_from_query_results' imported but unused
.\src\fhir\__init__.py:2:1: F401 'fhir.fhir_parser.get_patient_ids_from_bundle' imported but unused
.\src\fhir\__init__.py:2:80: E501 line too long (93 > 79 characters)
.\src\fhir\__init__.py:3:1: F401 'fhir.fhir_query_gen.generate_fhir_cnf' imported but unused
.\src\query_parser\__init__.py:1:1: W391 blank line at end of file
.\src\query_parser\codex\codex_parser.py:1:1: F401 'typing.Optional' imported but unused
.\src\query_parser\codex\codex_parser.py:42:80: E501 line too long (103 > 79 characters)
.\src\query_parser\codex\codex_parser.py:80:1: E302 expected 2 blank lines, found 1
.\src\query_parser\codex\codex_parser.py:92:1: W293 blank line contains whitespace
.\src\query_parser\codex\codex_parser.py:95:1: W293 blank line contains whitespace
.\src\query_parser\codex\codex_parser.py:134:80: E501 line too long (82 > 79 characters)
.\src\query_parser\codex\codex_parser.py:139:80: E501 line too long (83 > 79 characters)
.\src\query_parser\codex\codex_parser.py:149:80: E501 line too long (120 > 79 characters)
.\src\query_parser\codex\codex_parser.py:153:80: E501 line too long (99 > 79 characters)
.\src\query_parser\codex\codex_parser.py:155:80: E501 line too long (99 > 79 characters)
.\src\query_parser\codex\codex_parser.py:184:80: E501 line too long (80 > 79 characters)
.\src\query_parser\codex\codex_parser.py:196:80: E501 line too long (153 > 79 characters)
.\src\query_parser\codex\codex_parser.py:198:80: E501 line too long (86 > 79 characters)
.\src\query_parser\codex\codex_parser.py:201:80: E501 line too long (85 > 79 characters)
.\src\query_parser\codex\codex_parser.py:204:80: E501 line too long (110 > 79 characters)
.\src\query_parser\codex\codex_parser.py:211:1: E302 expected 2 blank lines, found 1
.\src\query_parser\codex\codex_parser.py:216:80: E501 line too long (112 > 79 characters)
.\src\query_parser\codex\codex_parser.py:220:80: E501 line too long (112 > 79 characters)
.\src\query_parser\codex\codex_parser.py:229:80: E501 line too long (89 > 79 characters)
.\src\query_parser\codex\codex_parser.py:237:80: E501 line too long (81 > 79 characters)
.\src\query_parser\codex\codex_parser.py:239:80: E501 line too long (103 > 79 characters)
.\src\query_parser\codex\codex_parser.py:245:80: E501 line too long (82 > 79 characters)
.\src\query_parser\i2b2\i2b2_parser.py:16:80: E501 line too long (117 > 79 characters)
.\src\query_parser\i2b2\i2b2_parser.py:26:80: E501 line too long (109 > 79 characters)
.\src\query_parser\i2b2\i2b2_parser.py:67:80: E501 line too long (80 > 79 characters)
.\src\query_parser\i2b2\i2b2_parser.py:77:80: E501 line too long (82 > 79 characters)
.\src\query_parser\i2b2\mapping\mapping.py:7:80: E501 line too long (85 > 79 characters)
.\src\test\test_codex_parser.py:1:1: E265 block comment should start with '# '
.\src\test\test_codex_parser.py:2:1: F401 'os.close' imported but unused
.\src\test\test_codex_parser.py:6:1: F401 'query_parser.codex.codex_parser.parse_codex_query_string' imported but unused
.\src\test\test_codex_parser.py:16:9: E265 block comment should start with '# '
.\src\test\test_codex_parser.py:21:1: W293 blank line contains whitespace
.\src\test\test_codex_parser.py:23:9: E265 block comment should start with '# '
.\src\test\test_codex_parser.py:24:21: E225 missing whitespace around operator
.\src\test\test_codex_parser.py:25:80: E501 line too long (86 > 79 characters)
.\src\test\test_codex_parser.py:38:1: E305 expected 2 blank lines after class or function definition, found 1
.\src\test\test_codex_parser.py:53:4: W292 no newline at end of file
.\src\test\test_query_sync.py:3:1: F401 'json' imported but unused
.\src\test\test_query_sync.py:9:1: F401 'flask.wrappers.Response' imported but unused
.\src\test\test_query_sync.py:18:44: W291 trailing whitespace
.\src\test\test_query_sync.py:21:5: E303 too many blank lines (2)
.\src\test\test_query_sync.py:37:21: E265 block comment should start with '# '
.\src\test\test_query_sync.py:37:80: E501 line too long (80 > 79 characters)
.\src\test\test_query_sync.py:39:21: E265 block comment should start with '# '
.\src\test\test_query_sync.py:43:21: E303 too many blank lines (2)
.\src\test\test_query_sync.py:46:80: E501 line too long (97 > 79 characters)
.\src\test\test_query_sync.py:47:44: E128 continuation line under-indented for visual indent
.\src\test\test_query_sync.py:47:80: E501 line too long (98 > 79 characters)
.\src\test\test_query_sync.py:51:24: E111 indentation is not a multiple of four
.\src\test\test_query_sync.py:52:1: W293 blank line contains whitespace
.\src\test\test_query_sync.py:57:1: W293 blank line contains whitespace
.\src\test\test_query_sync.py:58:1: W293 blank line contains whitespace
.\src\test\test_query_sync.py:61:9: E303 too many blank lines (4)
.\src\test\test_query_sync.py:61:9: E265 block comment should start with '# '
.\src\test\test_query_sync.py:62:9: E265 block comment should start with '# '
.\src\test\test_query_sync.py:67:5: E303 too many blank lines (2)
.\src\test\test_query_sync.py:67:38: W292 no newline at end of file
.\src\test\__init__.py:1:1: W391 blank line at end of file
.\src\worker\queue_distributor.py:8:80: E501 line too long (111 > 79 characters)
.\src\worker\threadedworker.py:11:80: E501 line too long (80 > 79 characters)
.\src\worker\threadedworker.py:19:80: E501 line too long (103 > 79 characters)
.\src\worker\threadedworker.py:22:80: E501 line too long (135 > 79 characters)
.\src\worker\threadedworker.py:23:80: E501 line too long (110 > 79 characters)
.\src\worker\threadedworker.py:44:80: E501 line too long (87 > 79 characters)
.\src\worker\threadedworker.py:45:80: E501 line too long (87 > 79 characters)
.\src\worker\threadedworker.py:93:80: E501 line too long (87 > 79 characters)
.\src\worker\communication\instruction.py:10:80: E501 line too long (115 > 79 characters)
.\src\worker\communication\instruction.py:11:80: E501 line too long (82 > 79 characters)
.\src\worker\communication\instruction.py:19:80: E501 line too long (115 > 79 characters)
.\src\worker\communication\instruction.py:20:80: E501 line too long (114 > 79 characters)
.\src\worker\communication\instruction.py:22:80: E501 line too long (103 > 79 characters)
.\src\worker\communication\instruction.py:27:80: E501 line too long (83 > 79 characters)
.\src\worker\communication\instruction.py:93:80: E501 line too long (80 > 79 characters)
.\src\worker\communication\instruction.py:111:80: E501 line too long (94 > 79 characters)
.\src\worker\communication\instruction.py:112:80: E501 line too long (101 > 79 characters)
.\src\worker\communication\instruction.py:113:80: E501 line too long (93 > 79 characters)
.\src\worker\communication\instruction.py:115:80: E501 line too long (118 > 79 characters)
.\src\worker\communication\instruction.py:116:80: E501 line too long (97 > 79 characters)
.\src\worker\communication\instruction.py:123:80: E501 line too long (91 > 79 characters)
.\src\worker\communication\instruction.py:138:80: E501 line too long (109 > 79 characters)
.\src\worker\communication\logging_callback.py:12:80: E501 line too long (84 > 79 characters)
.\src\worker\communication\logging_callback.py:16:80: E501 line too long (81 > 79 characters)
.\src\worker\communication\logging_callback.py:18:9: F841 local variable 'event' is assigned to but never used
.\src\worker\communication\logging_callback.py:21:80: E501 line too long (82 > 79 characters)
.\src\worker\communication\__init__.py:1:1: F401 'worker.communication.instruction.Instruction' imported but unused
.\src\worker\communication\__init__.py:2:1: F401 'worker.communication.processing_event.ProcessingEvent' imported but unused

Something like black (https://github.com/psf/black) could be useful.