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2022-09-08Deleting utility.logger...* wqflask/utility/logger.py: Delete. Munyoki Kilyungi
2022-09-08Replace g.db with database_connection() context manager...* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection. (MrnaAssayTissueData.__init__): Use database_connection. (MrnaAssayTissueData.get_symbol_values_pairs): Ditto. * wqflask/base/species.py: Replace "Flask.g" imports with "database_connection". (Chromosomes.chromosomes): Use database_connection. * wqflask/base/trait.py: Import database_connection. (retrieve_trait_info): Use database_connection. * wqflask/utility/authentication_tools.py: Replace "flask.g" with database_connection. (get_group_code): Use database_connection. * wqflask/utility/helper_functions.py: Replace "flask.g" with "database_connection". (get_species_groups): Use database_connection. * wqflask/wqflask/db_info.py: Replace "Flask" and "g" with "database_connection". (InfoPage.get_info): Use database_connection. * wqflask/wqflask/do_search.py (DoSearch.execute): Use database_connection(). * wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace "Flask" and "g" import with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace "Flask, g" imports with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with database_connection. (GSearch.__init__): Use database_connection. * wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Use database_connection(). * wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import" with database_connection. (SampleList.get_attributes): Use database_connection. (SampleList.get_extra_attribute_values): Ditto. * wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g" import with database_connection. (ShowTrait.__init__): Use database_connection. (ShowTrait.get_external_links): Ditto. (get_nearest_marker): Ditto. Munyoki Kilyungi
2022-09-08Replace g.db with database_connection() context manager...* wqflask/wqflask/update_search_results.py: Replace "Flask" and "g" import with "database_connection". (GSearch.__init__): Reformat SQL. Rename "re" to "results" since "re" is part of the stdlib. * wqflask/wqflask/marker_regression/rqtl_mapping.py: Replace flask.g with database_connection. (write_covarstruct_file): Replace g.db with database_connection(). * wqflask/wqflask/search_results.py: Replace "Flask" and "g" imports with "database_connection" import. (trait_info_str): Replace g.db with database_connection. * wqflask/wqflask/docs.py (Docs): Use dababase_connection() context manager. (update_text): Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py: Replace "Flask" and "g" import with "database_connection". (DisplayMappingResults.__init__): Use database_connection. (DisplayMappingResults.drawSNPTrackNew): Ditto. Munyoki Kilyungi
2022-08-31Delete benchmark module...* wqflask/utility/benchmark.py: Delete module. Munyoki Kilyungi
2022-08-31Remove usage of "logger" and un-necessary comments wrt the same...Logging is used to introspect variables or notify the commencement of a given operation. Logging should only be used to log errors. Also, most of the logging is either "logger.debug" or "logger.info"; and this won't show up in production/testing since we need a logging level above "WARNING" for them to show up. * wqflask/base/data_set.py (create_datasets_list): Remove logger. (Markers.add_pvalues): Ditto. (DataSet.retrieve_other_names): Ditto. * wqflask/base/mrna_assay_tissue_data.py: Ditto. * wqflask/base/webqtlCaseData.py: Ditto. * wqflask/db/call.py (fetch1): Ditto. (gn_server): Ditto. * wqflask/db/gn_server.py: Ditto. * wqflask/maintenance/set_resource_defaults.py: Ditto. * wqflask/utility/Plot.py (find_outliers): Ditto. * wqflask/utility/gen_geno_ob.py: Ditto. * wqflask/utility/helper_functions.py: Ditto. * wqflask/utility/pillow_utils.py: Ditto. * wqflask/utility/redis_tools.py: Ditto. * wqflask/wqflask/api/gen_menu.py (get_groups): Ditto. * wqflask/wqflask/api/mapping.py: Ditto. * wqflask/wqflask/api/router.py (get_dataset_info): Ditto. * wqflask/wqflask/collect.py (report_change): Ditto. * wqflask/wqflask/correlation/corr_scatter_plot.py: Ditto. * wqflask/wqflask/ctl/ctl_analysis.py (CTL): Ditto. (CTL.__init__): Ditto. (CTL.run_analysis): Ditto. (CTL.process_results): Ditto. * wqflask/wqflask/db_info.py: Ditto. * wqflask/wqflask/do_search.py (DoSearch.execute): Ditto. (DoSearch.mescape): Ditto. (DoSearch.get_search): Ditto. (MrnaAssaySearch.run_combined): Ditto. (MrnaAssaySearch.run): Ditto. (PhenotypeSearch.run_combined): Ditto. (GenotypeSearch.get_where_clause): Ditto. (LrsSearch.get_where_clause): Ditto. (MeanSearch.run): Ditto. (RangeSearch.get_where_clause): Ditto. (PvalueSearch.run): Ditto. * wqflask/wqflask/docs.py: Ditto. * wqflask/wqflask/export_traits.py: Ditto. * wqflask/wqflask/external_tools/send_to_bnw.py: Ditto. * wqflask/wqflask/external_tools/send_to_geneweaver.py: Ditto. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto. * wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto. * wqflask/wqflask/heatmap/heatmap.py: Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Ditto. * wqflask/wqflask/marker_regression/gemma_mapping.py: Ditto. * wqflask/wqflask/marker_regression/plink_mapping.py (run_plink): Ditto. * wqflask/wqflask/marker_regression/qtlreaper_mapping.py (run_reaper): Ditto. * wqflask/wqflask/marker_regression/rqtl_mapping.py: Ditto. * wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto. * wqflask/wqflask/parser.py (parse): Ditto. * wqflask/wqflask/search_results.py (SearchResultPage.__init__): Ditto. * wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto. * wqflask/wqflask/user_login.py (send_email): Ditto. (logout): Ditto. (forgot_password_submit): Ditto. (password_reset): Ditto. (password_reset_step2): Ditto. (register): Ditto. * wqflask/wqflask/user_session.py (create_signed_cookie): Ditto. Munyoki Kilyungi
2022-08-31Remove unused "string" import...* wqflask/utility/logger.py: Delete "import string". Munyoki Kilyungi
2022-07-25Return config in app.config or None...Update the code to return the setting already set up in the app.config dictionary if it exists or None if it does not exist. Frederick Muriuki Muriithi
2022-07-04wqflask: Remove DebugToolbarExtension...This functionality, at least how we use it, is already provided natively in python's pdb. Should someone need this, they can add it manually. * wqflask/runserver.py (app_config): Remove "flask_debugtoolbar" import and instantiation. * wqflask/utility/startup_config.py (app_config): Ditto. BonfaceKilz
2022-04-04Return None in load_json_from_redis when the item doesn't exist...For some reason that isn't clear to me yet, a logged-in user session ID was set even when a user wasn't logged in, causing the user session code to attempt to fetch user information for a non-existent user ID zsloan
2022-02-18wqflask: Remove python pre-2.2 checks....These checks are only relevant for python pre-2.2. * wqflask/utility/svg.py: Remove python pre-2.2 checks. Arun Isaac
2021-11-25Delete noisy loggingBonfaceKilz
2021-11-04Removes unused importjgart
2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-10-28Remove the use of '@deprecated'...This causes noisy logging. BonfaceKilz
2021-10-25utility: redis_tools: Remove dead functionsBonfaceKilz
2021-10-25authentication_tools: Mark `check_owner_or_admin` as deprecated...Use the new auth proxy tools instead. BonfaceKilz
2021-10-25utility.hmac: Label "hmac_creation" as deprecated...This function is coupled to "wqflask.app", therefore requiring it's import at the module level. This may lead circular importation issues when working with blueprints. BonfaceKilz
2021-10-25Mark `get_resource_info` as deprecatedBonfaceKilz
2021-10-22Fix line pulling GN3_LOCAL_URL from settingszsloan
2021-10-22Replace hardcoded GN proxy URLs with one pulled from settingszsloan
2021-10-22Added proxy and local GN3 URLs in tools.py (which should be set in the settin...zsloan
2021-10-04Changed get_user_groups to pull both the ID and details in the for loop from ...zsloan
2021-09-10Removed encoding, since it's apparently not needed since the Python 3 switcho...zsloan
2021-08-23Account for situations where the minimum permutation value is also above webq...zsloan
2021-08-20startup_config.py: Add DebugToobarExtension for wsgi DEBUG mode...* wqflask/utility/startup_config.py (app_config): Add DebugToolbarExtension BonfaceKilz
2021-07-12Encode user_id as bytestring if not already bytestring to account for some us...zsloan
2021-06-17remove print statementsAlexander Kabui
2021-06-15Fix issue where column values were used as str instead of bytes; pretty sure ...zsloan
2021-05-08utility: startup_config: Use python3 f-stringsBonfaceKilz
2021-05-08utility: startup_config: Break up long import statementBonfaceKilz
2021-05-08utility: startup_config: Remove dead commentsBonfaceKilz
2021-05-07Fixed issue that caused /submit_trait page to not load properlyzsloan
2021-04-30autopep8: Run autopep8 100 times with target rules...Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133 BonfaceKilz
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27...Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3 BonfaceKilz
2021-04-29Merge branch 'testing' into Feature/Add-upload-data-formsBonfaceKilz
2021-04-29Run `sed -i 's/(object)//g'`...See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g' BonfaceKilz
2021-04-23Apply PEP-8BonfaceKilz
2021-04-23Move looped sql query into one statement in "get_species_groups"...It's in-efficient to have a sql query executed in a loop. As data grows, the query becomes slower. It's better to let sql handle such queries. BonfaceKilz
2021-04-23Remove stale commentsBonfaceKilz
2021-04-19Specify only getting the first two items after splitting the trait/dataset in...zsloan
2021-03-16Fixed encoding in load_json_from_redis to account for the first that column v...zsloan
2021-03-16Fixed encoding to make get_user_groups work properly, since the user IDs for ...zsloan
2021-03-16Removed unnecessary encoding of user_id from authentication_tools.pyzsloan
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