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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
2022-08-31Replace debug with error logs in Except block pre/post a session...Put error logs in an Except block for easier parsing and re-word the error messages in them. * wqflask/wqflask/views.py: Delete "utility.logger" and "logger". (connect_db): Delete "g._database". Delete "logger.debug()". Use "app.logger.error" in Except block. (shutdown_session): Delete "logger.debug()". Use "app.logger.error" in Except block. Munyoki Kilyungi
2022-08-31Add transform parameter to mapping api unit testzsloan
2022-08-31Change qnorm parameter to transform, so other transforms can be added laterzsloan
2022-08-31Add qnorm option to mapping apizsloan
2022-08-31Move normf function out of quantile_normalize_vals so it can be imported by m...zsloan
2022-08-31Fix failing api/test_mapping.py testzsloan
2022-08-31integrate text filesAlexander_Kabui
2022-08-31add new environment variable:TEXTDIRAlexander_Kabui
2022-08-31read and parse text filesAlexander_Kabui
2022-08-31Re-add read_from_pyfile...* wqflask/wqflask/database.py (read_from_pyfile): Re-add it. This is used in the sql_uri() function. Munyoki Kilyungi
2022-08-31add function to fetch probeset text filesAlexander_Kabui
2022-08-30Remove logging and unused imports from api/mapping.pyzsloan
2022-08-30Add genofile parameter to mapping API endpointzsloan
2022-08-30Close a database connection only once...* wqflask/wqflask/database.py (database_connection): Close connection only once; otherwise an error is raised. Munyoki Kilyungi
2022-08-25Merge branch 'Alexanderlacuna-chores/gn2-queries-optimization' into testingFrederick Muriuki Muriithi
2022-08-25Merge branch 'chores/gn2-queries-optimization' of github.com:Alexanderlacuna/...Frederick Muriuki Muriithi
2022-08-24Fix issue where literature correlations were always run against their own dat...zsloan
2022-08-24Limit literature correlation results to top N as specified in the formzsloan
2022-08-23Add support for database rollbacks if the db engine supports it....* wqflask/wqflask/database.py: Import contextlib. (database_connection): Refactor to support roll-backs. Munyoki Kilyungi
2022-08-23Delete unused function and imports....* wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it. Munyoki Kilyungi
2022-08-23integrate code for fetching traits metadataAlexander_Kabui
2022-08-23function to fetch metadataAlexander_Kabui
2022-08-20Divide GEMMA additive effect by 2zsloan
2022-08-20Fix JS for opening new tabs (or not) for collection page tools/optionszsloan
2022-08-19Fix message and function keyFrederick Muriuki Muriithi
2022-08-18bulk fetch n number of traits type probesetAlexander_Kabui
2022-08-17Reduce incremental backoff timeFrederick Muriuki Muriithi
2022-08-17Do incremental backoff for mechanical rob tests...Sometimes the tests might be run before the service has began running. This commit delays the running of the tests for a while. Frederick Muriuki Muriithi
2022-08-17Merge branch 'Alexanderlacuna-chores/rust-enhancements' into testingFrederick Muriuki Muriithi
2022-08-17Use context managers for database cursorsFrederick Muriuki Muriithi
2022-08-17Merge branch 'chores/rust-enhancements' of github.com:Alexanderlacuna/genenet...Frederick Muriuki Muriithi
2022-08-16Merge dicts into single resultFrederick Muriuki Muriithi
2022-08-16Convert list items to single dictFrederick Muriuki Muriithi
2022-08-16rename boolean variablesAlexander_Kabui
2022-08-16linter fixesAlexander_Kabui
2022-08-16enable compute all for testAlexander_Kabui
2022-08-16index error fixAlexander_Kabui
2022-08-16remove flask g objectAlexander_Kabui
2022-08-16minor fixes for computing all correlationsAlexander_Kabui
2022-08-16Setup default GN_PROXY settingFrederick Muriuki Muriithi
2022-08-15add default values for num overlap,corr_coeffAlexander_Kabui
2022-08-14init:perform top n sample for probesAlexander_Kabui
2022-08-12Update to newer lxml APIFrederick Muriuki Muriithi
2022-08-12Revert "Check for keys before using them."...This reverts commit a1cbc12f843bbdc1759d5acac5ae3630fb5d4b81. Frederick Muriuki Muriithi
2022-08-12Merge branch 'integrate-rust-correlations' of github.com:genenetwork/genenetw...Frederick Muriuki Muriithi
2022-08-12Add a profiling script...Add a script to enable profiling the code. Frederick Muriuki Muriithi
2022-08-12Fix some issues with the tests. Add notes in code for improvements.Frederick Muriuki Muriithi
2022-08-12Refactor: separate the three correlation types...Refactor the code such that each correlation type (sample, tissue, literature) is computed in its own function. This makes the code clearer, and helps reduce repetition. Frederick Muriuki Muriithi
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