| 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 |
| 2021-08-23 | Account for situations where the minimum permutation value is also above webq... | zsloan |
| 2021-04-30 | autopep8: Run autopep8 100 times with target rules...Rules used are:
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242,
E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,
E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121,
E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
| BonfaceKilz |
| 2021-04-30 | autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E101, E11 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E70 and E701 | BonfaceKilz |
| 2021-04-30 | autopep8: Fix E501 | 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 |
| 2020-08-26 | Remove "from __future__ import new_feature" statements...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
| BonfaceKilz |
| 2020-08-26 | Update corestats import...* wqflask/utility/Plot.py: import corestats from the utility module.
| BonfaceKilz |
| 2020-08-26 | Merge branch 'testing' into build/python3-migration | BonfaceKilz |
| 2020-08-24 | Remove unused imports...* wqflask/utility/Plot.py: Remove unused imports like "numarray". "numarray" is
does not have py3 support so it's important to remove references to it.
| 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 | Rename xrange() to range() and wrap existing range() calls with list...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
| BonfaceKilz |
| 2020-08-18 | Fix malformed docstring...* wqflask/utility/Plot.py: Update docstring.
| BonfaceKilz |
| 2020-08-08 | Use draw_rotated_text()...Use the new draw_rotated_text() function to draw the text rotated as was
formerly done.
* wqflask/utility/Plot.py (plotBar): Use draw_rotated_text().
* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults) Use draw_rotated_text().
| Muriithi Frederick Muriuki |
| 2020-08-08 | Fix font paths...* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Migrate code from Piddle to Pillow...* wqflask/wqflask/marker_regression/display_mapping_results.py: Add font files
(DisplayMappingResults): Update the code from the Piddle way of things to the
Pillow way of things, for example, replace:
- pid.drawRect(...) with im_drawer.rectangle(...)
- pid.drawString(...) with im_drawer.text(...)
- pid.drawPolygon(...) with im_drawer.polygon(...) etc.
* wqflask/utility/Plot.py: Migrate code from the older, unsupported Piddle to
the newer Pillow library.
| Muriithi Frederick Muriuki |
| 2020-07-08 | Removed remaining unused references to the old qtlreaper | zsloan |
| 2019-02-22 | Fixed some appearance issues with several tables...Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
| zsloan |
| 2018-04-09 | Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty......Also removed some other unused code from the files listed
| zsloan |
| 2018-04-09 | Fixed issue that caused and error for certain types of mapping due to variabl......Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them.
Also removed unused file AJAX_table.py and other unused code from several other files
| zsloan |
| 2018-04-09 | Removed the basicStatistics directory/contents because nothing there was bein......Removed box plot code from Plot.py since we no longer use it either
| zsloan |
| 2016-06-21 | log: replace print statements | Pjotr Prins |
| 2016-06-18 | Logging: behaviours | Pjotr Prins |
| 2016-06-18 | Disable setting sys.paths | Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-04-07 | SNP Track option should now work for GN1 mapping figure...Fixed typo in show_trait html that caused the p-value slider to not work for correlations
| zsloan |
| 2016-04-06 | Permutations (suggestive/significant lines, legend, and histogram) should now......Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome)
Added text below figure when Allele Effects selected/relevant
| zsloan |
| 2012-08-29 | Fixed so that outliers are now correctly highlighted | Zachary Sloan |
| 2012-06-22 | Working my way through getting the review and edit data dynamically generated... | Sam Ockman |
| 2012-06-05 | Ran reindent.py recursively on wqflask directory | Sam Ockman |
| 2012-06-02 | Coming along in trying to get trait page working | Sam Ockman |
| 2012-05-24 | Trying to get stuff working under new structure | Sam Ockman |
