Age | Commit message (Expand) | Author |
---|---|---|
2022-09-07 | catch general errors this will recreate the file | Alexander_Kabui |
2022-09-07 | use csv to parse files | Alexander_Kabui |
2022-09-07 | filter list vals with index | Alexander_Kabui |
2022-09-06 | Change collections/view forms' default action from /delete to /loading (becau... | zsloan |
2022-09-06 | Add data-trait-info to collections/view columnDefs | zsloan |
2022-09-06 | Include trait_info_str in trait JSON, so it can be included in collection tab... | zsloan |
2022-09-06 | Fix mistake from generalize_tables merge | zsloan |
2022-09-06 | Fix error with dataset menu query in data_set.py...I'm only using g.db.execute here because using cursor is throwing an error and I don't want to change the way this query is currently written since I didn't write it (I believe it was initially written using g.db.execute and whoever wrote it just forgot to put the g.db.execute, since previously it just called "fetchall") | zsloan |
2022-09-06 | Fix a few problems with ind_genofile conversion script | zsloan |
2022-09-06 | Merge branch 'testing' into feature/generalize_tables | zsloan |
2022-09-06 | Placeholder: Set trait location to ??? if the Mb is NULL | Frederick Muriuki Muriithi |
2022-09-06 | Refactor: Use joins for queries...Use joins to relate tables when fetching data. | Frederick Muriuki Muriithi |
2022-09-06 | Set up the self.* variables from query results...Set up the appropriate self.* variables from the results of running the appropriate query. | Frederick Muriuki Muriithi |
2022-09-06 | Use dataset name if dataset group name is not set. | Frederick Muriuki Muriithi |
2022-09-05 | Fix failing mapping test by using get to fetch values from a dict...Should a key not exist when running: "my_dict['some_key']", an exception is raised. As such, use "my_dict.get('some_key')" which defaults to "None" if a key is non-existent. * wqflask/wqflask/api/mapping.py (do_mapping_for_api): Replace instances of "my_dict['some_key']" with "my_dict.get('some_key')". | Munyoki Kilyungi |
2022-09-05 | Replace "assert" with ValueError...* wqflask/wqflask/api/mapping.py (do_mapping_for_api): Raise a ValueError if 'db' and 'trait_id' or not present in 'start_vars' instead of doing an "assert". | Munyoki Kilyungi |
2022-09-05 | Update values for "additive" in failing gemma test...* wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py (TestGemmaMapping.test_parse_loco_outputfile_found): Use a halved value in expected_results["additive"]. | Munyoki Kilyungi |
2022-09-01 | Remove unused string import....* wqflask/wqflask/database.py: Do not import Template from string. | Arun Isaac |
2022-09-01 | Allow connecting to SQL database without a password....* wqflask/wqflask/database.py (database_connection): Use empty string as password when there is none. | Arun Isaac |
2022-08-31 | Delete unused modules...* wqflask/base/data_set.py: Delete "menu_main" import. * wqflask/db/call.py: Delete it. * wqflask/db/gn_server.py: Ditto. * wqflask/wqflask/submit_bnw.py: Ditto. | Munyoki Kilyungi |
2022-08-31 | Replace fetchall, fetchone, fetch1 with database_connection...* wqflask/base/data_set.py: Replace "db.call" import with "database_connection". (create_datasets_list): Use "database_connection" to fetch data. (DatasetGroup.__init__): Ditto. (DataSet.retrieve_other_names): Ditto. (PhenotypeDataSet.setup): Remove query escaping in string and format the string. (GenotypeDataSet.setup): Ditto. (MrnaAssayDataSet.setup): Ditto. * wqflask/db/webqtlDatabaseFunction.py: Remove db.call import. (retrieve_species): Use database_connection() to fetch data. (retrieve_species_id): Ditto. | Munyoki Kilyungi |
2022-08-31 | Delete benchmark module...* wqflask/utility/benchmark.py: Delete module. | Munyoki Kilyungi |
2022-08-31 | Remove "with Bench ..." calls..."with Bench" instruments how long a function takes and generates time reports on as INFO logs. This should be done on a developer server. Should the log level be low enough, this bench marks will generate a lot of noise. Instrumentation should be done during development. * wqflask/base/data_set.py (create_datasets_list): Remove "with Bench...". * wqflask/db/call.py (fetchone): Ditto. (fetchall): Ditto. (gn_server): Ditto. * wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults.__init__): Ditto. * wqflask/wqflask/marker_regression/run_mapping.py (RunMapping.__init__): Ditto. * wqflask/wqflask/update_search_results.py (GSearch.__init__): Ditto. * wqflask/wqflask/views.py (search_page): Ditto. (heatmap_page): Ditto. (mapping_results_page): Ditto. | Munyoki Kilyungi |
2022-08-31 | Remove 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 |
2022-08-31 | Remove unused "string" import...* wqflask/utility/logger.py: Delete "import string". | Munyoki Kilyungi |
2022-08-31 | Replace 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 |
2022-08-31 | Add transform parameter to mapping api unit test | zsloan |
2022-08-31 | Change qnorm parameter to transform, so other transforms can be added later | zsloan |
2022-08-31 | Add qnorm option to mapping api | zsloan |
2022-08-31 | Move normf function out of quantile_normalize_vals so it can be imported by m... | zsloan |
2022-08-31 | Fix failing api/test_mapping.py test | zsloan |
2022-08-31 | integrate text files | Alexander_Kabui |
2022-08-31 | add new environment variable:TEXTDIR | Alexander_Kabui |
2022-08-31 | read and parse text files | Alexander_Kabui |
2022-08-31 | Re-add read_from_pyfile...* wqflask/wqflask/database.py (read_from_pyfile): Re-add it. This is used in the sql_uri() function. | Munyoki Kilyungi |
2022-08-31 | add function to fetch probeset text files | Alexander_Kabui |
2022-08-30 | Remove logging and unused imports from api/mapping.py | zsloan |
2022-08-30 | Add genofile parameter to mapping API endpoint | zsloan |
2022-08-30 | Close a database connection only once...* wqflask/wqflask/database.py (database_connection): Close connection only once; otherwise an error is raised. | Munyoki Kilyungi |
2022-08-25 | Merge branch 'chores/gn2-queries-optimization' of github.com:Alexanderlacuna/... | Frederick Muriuki Muriithi |
2022-08-24 | Fix issue where literature correlations were always run against their own dat... | zsloan |
2022-08-24 | Limit literature correlation results to top N as specified in the form | zsloan |
2022-08-23 | Add 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 |
2022-08-23 | Delete unused function and imports....* wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it. | Munyoki Kilyungi |
2022-08-23 | integrate code for fetching traits metadata | Alexander_Kabui |
2022-08-23 | function to fetch metadata | Alexander_Kabui |
2022-08-20 | Divide GEMMA additive effect by 2 | zsloan |
2022-08-20 | Fix JS for opening new tabs (or not) for collection page tools/options | zsloan |
2022-08-18 | bulk fetch n number of traits type probeset | Alexander_Kabui |
2022-08-17 | Use context managers for database cursors | Frederick Muriuki Muriithi |