| Age | Commit message (Expand) | Author |
|---|
| 2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
| 2022-09-12 | Check db resultset before indexing into it...The assumption that the resultset will never be empty was leading to a
lot of errors.
| Frederick Muriuki Muriithi |
| 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 | 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 |
| 2021-05-26 | db: webqtlDatabaseFunction: Remove comment | BonfaceKilz |
| 2021-05-26 | db: webqtlDatabaseFunction: Remove logger info | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E501 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E401 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz |
| 2021-04-30 | autopep8: 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 |
| 2020-08-20 | Add backward support for urllib...* wqflask/base/trait.py: Remove unused imports
* wqflask/db/call.py (Bench): Add urllib2 fallback for python2
| BonfaceKilz |
| 2020-08-19 | Remove extra whitespace(or add it) from comma separated items...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 2020-08-19 | Handle the rename of urllib and urllib2 to the urllib package...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 2018-04-18 | Removed a little more code in webqtlDatabaseFunction.py and do_search | zsloan |
| 2016-06-26 | gn_server: simplify | Pjotr Prins |
| 2016-06-26 | gn_server: introduced one new query to fetch a dataset record and force fetch... | Pjotr Prins |
| 2016-06-23 | Log: SQL queries | Pjotr Prins |
| 2016-06-23 | Add fetchall iterator | Pjotr Prins |
| 2016-06-23 | Added fetching menu info | Pjotr Prins |
| 2016-06-23 | Fixed missing GN_SERVER_URL | Pjotr Prins |
| 2016-06-23 | Fixed missing GN_SERVER_URL | Pjotr Prins |
| 2016-06-23 | Settings: add GN_SERVER_URL | Pjotr Prins |
| 2016-06-23 | Remove headers | Pjotr Prins |
| 2016-06-23 | Added REST call for species_id | Pjotr Prins |
| 2016-06-23 | Removed unused functions | Pjotr Prins |
| 2016-06-23 | DB: created fetch1 function which can do both SQL and GN_SERVER | Pjotr Prins |
| 2016-06-23 | Backend: moved methods into call module | Pjotr Prins |
| 2016-06-23 | Refactored dir name dbFunction to db | Pjotr Prins |
