| Age | Commit message (Expand) | Author |
|---|
| 2022-09-08 | Use db_connection and rework "if ... else" clauses...* wqflask/wqflask/snp_browser/snp_browser.py
(SnpBrowser.get_browser_results): Replace "g.db" with
database_connection. Rework "if ... else" logic.
| Munyoki Kilyungi |
| 2022-09-08 | Delete dead comment | Munyoki Kilyungi |
| 2022-09-08 | Refactor if clause to check for string in list...* wqflask/wqflask/docs.py (update_text): Check for the e-mail in a
list.
| Munyoki Kilyungi |
| 2022-09-08 | Refactor "if ... else" block to check the truthy case first...* wqflask/wqflask/docs.py (Docs.__init__): Check the truthy case first
after fetching the results.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Delete unused news module...* wqflask/wqflask/news.py: Delete it.
| Munyoki Kilyungi |
| 2022-09-08 | Merge pull request #727 from Alexanderlacuna/feature/use-textfiles...use text files for Probeset | Alexander Kabui |
| 2022-09-08 | fixup query formatting | Alexander_Kabui |
| 2022-09-08 | gitignore: Add containers/mariadb-state....* .gitignore: Add containers/mariadb-state.
| Arun Isaac |
| 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 pull request #713 from zsloan/feature/generalize_tables...Feature/generalize tables | zsloan |
| 2022-09-06 | Merge branch 'testing' into feature/generalize_tables | zsloan |
| 2022-09-06 | Update link to continuous deployment....* README.md (Development): Update link to continuous deployment.
| Arun Isaac |
| 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 |
| 2022-09-02 | Add database container....* containers/db-container.scm, containers/db-container.sh: New files.
| Arun Isaac |
| 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 |
