| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2021-04-30 | autopep8: Fix E501 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz |
| 2020-10-27 | Get the "first_attr_start_pos" from a samplelist instead of from each individ......* wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos
* wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed
| zsloan |
| 2020-09-18 | Made a bunch of changes to move trait page DataTables initialization to...a separate file (initialize_show_trait_tables.js). The biggest
complication was getting the order of attributes in the rows to sync
with the order of atribute namees in the column headers. Previously this
logic was all in the template.
* wqflask/base/webqtlCaseData.py - added attribute first_attr_col as a
very awkward solution to passing the column position into the column
render function in situations where there are case attribute columns
(which can be variable in number)
* wqflask/wqflask/show_trait/show_trait.py - Replace "attribute_names"
in js_data with "attributes" (which allows the JS access to more
information) and also pass new se_exists and
has_num_cases variables with js_data, so the javascript has access to
whether or not those columns exist in the table
* wqflask/wqflask/static/new/javascript/show_trait.js - Change case
attribute-related logic to use js_data.attributes instead of
js_data.attribute_names
* wqflask/wqflask/templates/show_trait.html - Removed table
initialization from template
* wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
- new file that initializes tables and reproduces what the template
logic used to do with JS logic
| zsloan |
| 2020-07-27 | Clean up webqtlCaseData class...* wqflask/base/webqtlCaseData.py (webqtlCaseData):
- Remove obsolete 'Object' from Class inheritance
- Replace 'str' with 'case_data_string' variable- it collides with python in-builts
- Use pythonic 'is Not None' form
- Remove redundancy in 'if' forms
- Update copyright header
| BonfaceKilz |
| 2019-02-15 | Fixed error caused by change to N values in database (now takes strings inste......Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
| zsloan |
| 2019-02-12 | Added GeneWeaver linkout...Fixed some issues with sorting in various tables
Changed header appearance for some pages
Fixed bug where basic stats table would sometimes be duplicated or show up with empty fields
| zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
| zsloan |
| 2017-06-12 | Fixed issue where 0.0 values would be converted into X's on the trait page | zsloan |
| 2016-12-12 | Moved a bunch of functions out of the GeneralTrait class that didn't need to ......Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static)
Removed some unused code from show_trait.py
changed appearance of table headers some, though needs a little more work
Updated dataset_menu_structure.json
| zsloan |
| 2016-11-15 | Fixed issue where sample values of 0 would sometimes be displayed as 'x', whi......Fixed issue where the mean would sometimes be displayed into of the additive effect
| zsloan |
| 2016-10-03 | Debug: sanitize some output | Pjotr Prins |
| 2016-08-05 | Fixed issue that caused some interval mapping results to be wrong; the cause ......Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days
Updated genofiles
| zsloan |
| 2016-06-18 | Logging settings | Pjotr Prins |
| 2016-06-18 | Logger | Pjotr Prins |
| 2016-06-18 | Changed file permssions to non-executable | Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-05-23 | Reaper mapping results are now correct and account for samples with two names......R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
| zsloan |
| 2015-05-23 | new probability plot (using NVD3 library)...* z scores are computed on the client side (using jStat library)
* added Shapiro-Wilk test results
| Artem Tarasov |
| 2014-07-21 | Fixed issue where sample values were ordered on the trait page | Zachary Sloan |
| 2014-07-18 | Added outlier highlighting...Changed order of tabs in statistics panel on trait page
Started working on heatmap
| Zachary Sloan |
| 2012-10-23 | Finished coffeescript that handles the home page dataset selection dropdowns | Zachary Sloan |
| 2012-09-28 | Finished getting extra attributes to display correctly in the trait data table | Zachary Sloan |
| 2012-09-25 | Got trait data page running for human dataset, changed list of sample objects... | Zachary Sloan |
| 2012-08-29 | Fixed so that outliers are now correctly highlighted | Zachary Sloan |
| 2012-08-28 | Various changes related to the webqtlCaseData object and the way values/varia... | Zachary Sloan |
| 2012-06-05 | Ran reindent.py recursively on wqflask directory | Sam Ockman |
| 2012-05-24 | Trying to get stuff working under new structure | Sam Ockman |
