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2022-09-08Remove sql_alchemy initialisation when profiling correlationsMunyoki Kilyungi
* wqflask/scripts/profile_corrs.py: Remove sqlalchemy, connect_db and shutdown_session. (__main__): Remove "g.db".
2022-09-08Delete dead importsMunyoki Kilyungi
* wqflask/base/data_set.py: Remove un-used imports. * wqflask/base/trait.py: Ditto. wqflask/tests/wqflask/show_trait/test_show_trait.py: Ditto. * wqflask/wqflask/show_trait/show_trait.py: Ditto. * wqflask/wqflask/views: Ditto.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* wqflask/base/data_set.py (DatasetType.set_dataset_key): Replace g.db with "database_connection()". (DatasetGroup.get_mapping_methods): Ditto. (DataSet.get_accession_id): Ditto. (DataSet.retrieve_other_names): Rework "if ... else" logic to get rid of "query" and "_vars" variables. Also, nest "try ... except" block within "database_connection". (DataSet.chunk_dataset): Replace g.db with "database_connection()". (DataSet.get_probeset_data): Ditto. (DataSet.get_trait_data): Ditto. (PhenotypeDataSet.get_trait_info): Ditto. (PhenotypeDataSet.retrieve_sample_data): Ditto. (GenotypeDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.get_trait_info): Ditto. (MrnaAssayDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.retrieve_genes): Ditto. (TempDataSet): Ditto. (geno_mrna_confidentiality): Ditto. (query_table_timestamp): Ditto. * wqflask/wqflask/api/router.py: Replace "flask.g" with database_connection import. (get_species_list): Replace g.db with "database_connection()". (get_species_info): Ditto. (get_groups_list): Ditto. (get_group_info): Ditto. (get_datasets_for_group): Ditto. (get_dataset_info): Ditto. (fetch_traits): Ditto. (all_sample_data): Ditto. (trait_sample_data): Ditto. (get_trait_info): Ditto. (get_dataset_trait_ids): Ditto. (get_samplelist): Ditto. (get_group_id_from_dataset): Ditto. (get_group_id): Ditto.
2022-09-08Delete logger importMunyoki Kilyungi
* wqflask/base/trait.py: Remove utility.logger
2022-09-08Replace assertion with Value Error for non-existent datasetMunyoki Kilyungi
* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in ValueError.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* 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.
2022-09-08Delete insert query that's not runMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete insert query
2022-09-08Remove "if" block that does nothingMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Remove if block that constructs a "final" query that does nothing.
2022-09-08Restructure "if ... else" to first check for a ValueErrorMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): First check for a ValueError Exception.
2022-09-08Raise a ValueError instead of generic exceptionMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Wrap error message in ValueError Exception.
2022-09-08Replace format-strings with f-stringsMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Use f-strings.
2022-09-08Remove '+' when concatenating strings inside bracketsMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete "+".
2022-09-08Use db_connection and rework "if ... else" clausesMunyoki Kilyungi
* wqflask/wqflask/snp_browser/snp_browser.py (SnpBrowser.get_browser_results): Replace "g.db" with database_connection. Rework "if ... else" logic.
2022-09-08Delete dead commentMunyoki Kilyungi
2022-09-08Refactor if clause to check for string in listMunyoki Kilyungi
* wqflask/wqflask/docs.py (update_text): Check for the e-mail in a list.
2022-09-08Refactor "if ... else" block to check the truthy case firstMunyoki Kilyungi
* wqflask/wqflask/docs.py (Docs.__init__): Check the truthy case first after fetching the results.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* 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.
2022-09-08Delete unused news moduleMunyoki Kilyungi
* wqflask/wqflask/news.py: Delete it.
2022-09-08Merge pull request #727 from Alexanderlacuna/feature/use-textfilesAlexander Kabui
use text files for Probeset
2022-09-08fixup query formattingAlexander_Kabui
2022-09-07catch general errors this will recreate the fileAlexander_Kabui
2022-09-07use csv to parse filesAlexander_Kabui
2022-09-07filter list vals with indexAlexander_Kabui
2022-09-06Change collections/view forms' default action from /delete to /loading ↵zsloan
(because it was weird for it to be /delete)
2022-09-06Add data-trait-info to collections/view columnDefszsloan
2022-09-06Include trait_info_str in trait JSON, so it can be included in collection ↵zsloan
table for partial corr
2022-09-06Fix mistake from generalize_tables mergezsloan
2022-09-06Fix error with dataset menu query in data_set.pyzsloan
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")
2022-09-06Fix a few problems with ind_genofile conversion scriptzsloan
2022-09-06Merge branch 'testing' into feature/generalize_tableszsloan
2022-09-06Placeholder: Set trait location to ??? if the Mb is NULLFrederick Muriuki Muriithi
2022-09-06Refactor: Use joins for queriesFrederick Muriuki Muriithi
Use joins to relate tables when fetching data.
2022-09-06Set up the self.* variables from query resultsFrederick Muriuki Muriithi
Set up the appropriate self.* variables from the results of running the appropriate query.
2022-09-06Use dataset name if dataset group name is not set.Frederick Muriuki Muriithi
2022-09-05Fix failing mapping test by using get to fetch values from a dictMunyoki Kilyungi
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')".
2022-09-05Replace "assert" with ValueErrorMunyoki Kilyungi
* 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".
2022-09-05Update values for "additive" in failing gemma testMunyoki Kilyungi
* wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py (TestGemmaMapping.test_parse_loco_outputfile_found): Use a halved value in expected_results["additive"].
2022-09-01Remove unused string import.Arun Isaac
* wqflask/wqflask/database.py: Do not import Template from string.
2022-09-01Allow connecting to SQL database without a password.Arun Isaac
* wqflask/wqflask/database.py (database_connection): Use empty string as password when there is none.
2022-08-31Delete unused modulesMunyoki Kilyungi
* 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.
2022-08-31Replace fetchall, fetchone, fetch1 with database_connectionMunyoki Kilyungi
* 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.
2022-08-31Delete benchmark moduleMunyoki Kilyungi
* wqflask/utility/benchmark.py: Delete module.
2022-08-31Remove "with Bench ..." callsMunyoki Kilyungi
"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.
2022-08-31Remove usage of "logger" and un-necessary comments wrt the sameMunyoki Kilyungi
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.
2022-08-31Remove unused "string" importMunyoki Kilyungi
* wqflask/utility/logger.py: Delete "import string".
2022-08-31Replace debug with error logs in Except block pre/post a sessionMunyoki Kilyungi
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.
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 ↵zsloan
mapping api
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