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2022-09-06Merge pull request #713 from zsloan/feature/generalize_tableszsloan
Feature/generalize tables
2022-09-06Merge branch 'testing' into feature/generalize_tableszsloan
2022-09-06Update link to continuous deployment.Arun Isaac
* README.md (Development): Update link to continuous deployment.
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"].
2022-09-02Add database container.Arun Isaac
* containers/db-container.scm, containers/db-container.sh: New files.
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
2022-08-31Fix failing api/test_mapping.py testzsloan
2022-08-31Re-add read_from_pyfileMunyoki Kilyungi
* wqflask/wqflask/database.py (read_from_pyfile): Re-add it. This is used in the sql_uri() function.
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 onceMunyoki Kilyungi
* wqflask/wqflask/database.py (database_connection): Close connection only once; otherwise an error is raised.
2022-08-25Merge branch 'Alexanderlacuna-chores/gn2-queries-optimization' into testingFrederick Muriuki Muriithi
2022-08-25Merge branch 'chores/gn2-queries-optimization' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/gn2-queries-optimization
2022-08-24Fix issue where literature correlations were always run against their own ↵zsloan
dataset, instead of the target dataset
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.Munyoki Kilyungi
* wqflask/wqflask/database.py: Import contextlib. (database_connection): Refactor to support roll-backs.
2022-08-23Delete unused function and imports.Munyoki Kilyungi
* wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it.
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 testsFrederick Muriuki Muriithi
Sometimes the tests might be run before the service has began running. This commit delays the running of the tests for a while.
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 ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/rust-enhancements
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
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