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2020-08-19Wrap `map()` in a `list` call...Run `2to3-3.8 -f map -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map> BonfaceKilz
2020-08-18Apply pep8...* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running `2to3-3.8 -w .`: ```` RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403) ```` BonfaceKilz
2020-08-18Replace "raw_input" with "input"...* scripts/maintenance/readProbeSetMean_v7.py: Use "input". See https://docs.python.org/3/whatsnew/3.0.html#builtins BonfaceKilz
2020-08-18Replace "<>" with "!="...* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3 BonfaceKilz
2020-08-18Wrap print statements in parenthesesBonfaceKilz
2020-08-18Fix malformed docstring...* wqflask/utility/Plot.py: Update docstring. BonfaceKilz
2020-08-18Replace DOS style line endings with UNIX style ones...* scripts/maintenance/readProbeSetSE_v7.py: Run *dos2unix* against file BonfaceKilz
2020-08-18Apply pep8...* scripts/maintenance/readProbeSetSE_v7.py: Apply pep8 to file to replace tabs with spaces and use correct indentation. BonfaceKilz
2020-08-17Merge pull request #417 from BonfaceKilz/feature/pil-pillow-conversion...Resolve merge conflicts from Pil Pillow conversion branchzsloan
2020-08-18Fix positioning for many instances of text in the mapping figure...* wqflask/wqflask/marker_regression/display_mapping_results.py: Many text instances had their positions changed by the switch from piddle to PIL. Change various Y offsets and in some cases changing the logic of the way text is positioned related to its length and font size. * wqflask/wqflask/static/fonts/verdanab.ttf: Add bold Verdana, since there needs to be a separate font file for bold text. zsloan
2020-08-10Add fonts for pillow...* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle method with PIL.ImageFont * wqflask/wqflask/static/fonts: Add fonts in path Pjotr Prins
2020-08-08Add a basic test for test_display_marking_results.py...* wqflask/tests/wqflask/marker_regression/__init__.py: Add it * wqflask/tests/wqflask/marker_regression/test_display_marking_results.py: Check that PIL colors are being used instead of the deprecated Piddle colors. BonfaceKilz
2020-08-08Change Y Coodinate system...* wqflask/wqflask/marker_regression/display_mapping_results.py: Piddle seemed to centre text about the given Y coordinate, while Pillow requires specification to top-left corner of the text. This slight change means text all over the image is displaced somewhat, and this fixes the coordinate system for some of the text. Muriithi Frederick Muriuki
2020-08-08Fix placement for axes labels...* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the placement for the axes labels. Muriithi Frederick Muriuki
2020-08-08Use TEXT_Y_DISPLACEMENT instead of magic numbers...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use TEXT_Y_DISPLACEMENT instead of magic numbers to help with making it clear that the drawn text is displaced somewhat. Muriithi Frederick Muriuki
2020-08-08Give rectangles black outlines...* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the rectangles black outlines to correspond to earlier drawings. Muriithi Frederick Muriuki
2020-08-08Use new `draw_open_polygon()` utility...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new `draw_open_polygon()` utility to draw open polygons. Muriithi Frederick Muriuki
2020-08-08Add draw_open_polygon() utility...* wqflask/utility/pillow_utils.py: New method. Muriithi Frederick Muriuki
2020-08-08Replace "color" with "fill" keyword argument...* wqflask/wqflask/marker_regression/display_mapping_results.py: (DisplayMappingResults): Pillow uses 'fill' in place of 'color'. Muriithi Frederick Muriuki
2020-08-08Use 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
2020-08-08Create new utility module for drawing...* wqflask/utility/pillow_utils.py: Create a module to hold some utility functions for drawing with Pillow. Initialise the module with a function to draw rotated text. Muriithi Frederick Muriuki
2020-08-08Fix font paths...* wqflask/utility/Plot.py: Update font paths. * wqflask/fonts/ttf: Update font files. Muriithi Frederick Muriuki
2020-08-08Update SNP Browser to Pillow...* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in place of obsoleted Piddle library. Muriithi Frederick Muriuki
2020-08-08Add missing font files...* wqflask/fonts/ttf: Add ttf font files. Muriithi Frederick Muriuki
2020-08-08Migrate 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
2020-08-08Update the colours to use Pillow's ImageColor...* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours. Muriithi Frederick Muriuki
2020-08-07Move wqflask/tests/api to wqflask/tests/wqflask...* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir should mirror the actual module structure BonfaceKilz
2020-08-05Set maximum width for trait page details in order to avoid long...summaries looking strange * wqflask/wqflask/templates/show_trait_details.html - Set min-width of table containing details to 1400px zsloan
2020-08-04Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-04Simplified logic in the @before_request that checks user permissions...* wqflask/wqflask/views.py - Removed an if statement that was unnecessary, because it already checks if dataset is either the string "Temp" or of type "Temp" zsloan
2020-08-04Reduced table cell margin a bit to make cell contents better align with...header * wqflask/wqflask/static/new/css/show_trait.css - Changed right margin from 20px to 15px to better account for the width of the sort arrows in the header cell zsloan
2020-08-04Merge pull request #415 from BonfaceKilz/tests/add-tests-for-gen-menu...Tests/add tests for gen menuPjotr Prins
2020-08-03Fixed table width issue when there's an N column...* wqflask/wqflask/show_trait/show_trait.py - Just added more pixels in the function which determines the overall table width zsloan
2020-08-03Fixed issue where DataTables was initialized twice when selecting...cofactors, leading to an error in non-Chrome browsers * wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js - Added a line that checks if the table already exists before initializing it; this issue is caused by a circular import issue, but I'm not sure how to get around it yet zsloan
2020-08-03Remove "+" when concatenating strings...* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+' when joining strings inside brackets BonfaceKilz
2020-08-03Fix some errors generated by running pylint...* wqflask/wqflask/api/gen_menu.py: Apply pylint. * wqflask/tests/api/test_gen_menu.py: Apply pylint. BonfaceKilz
2020-08-03Add extra test for "build_datasets"...* wqflask/tests/api/test_gen_menu.py: Add test. BonfaceKilz
2020-08-03Move variable to setUp...* wqflask/tests/api/test_gen_menu.py: Move variable BonfaceKilz
2020-08-03Add test for "gen_dropdown_json"...* wqflask/tests/api/test_gen_menu.py: Add new test BonfaceKilz
2020-08-03Add tests for "get_datasets"...* wqflask/tests/api/test_gen_menu.py: Add new tests BonfaceKilz
2020-08-03Update how boolean is returned...* wqflask/wqflask/api/gen_menu.py (get_datasets): convert return value directly using "bool" to be more general and cater for cases wher "None" is returned BonfaceKilz
2020-08-03Remove unreached "else" branch...* wqflask/wqflask/api/gen_menu.py(get_types): - Remove unnecessary comment. - Remove unreachable "else" branch. BonfaceKilz
2020-08-03Add tests for "get_types"...* wqflask/tests/api/test_gen_menu.py: Add new tests BonfaceKilz
2020-08-03Add test for "build_types"...* wqflask/tests/api/test_gen_menu.py: New test BonfaceKilz
2020-08-03Clean up "if ... else" conditional...* wqflask/wqflask/api/gen_menu.py (build_datasets): Make conditionals more Pythonic BonfaceKilz
2020-08-03Reformat sql queries to be one line...* wqflask/wqflask/api/gen_menu.py (build_datasets, build_types): Strip white spaces and newlines from query and make the sql query one line. BonfaceKilz
2020-07-30Add tests for "build_datasets"...* wqflask/tests/api/test_gen_menu.py: Add new tests for "build_datasets" function BonfaceKilz
2020-07-29Fixed error that occured for new resources in check_admin...* wqflask/utility/authentication_tools.py: the code forgot to get resource_info when a resource wasn't in Redis yet, causing an error when it was referenced, so I added a line getting the resource info (and also a couple comments for other lines related to authentication) zsloan
2020-07-29Update how boolean is returned...* wqflask/wqflask/api/gen_menu.py (phenotypes_exist, genotypes_exist): Convert sql result to boolean instead of only checking for "None". BonfaceKilz
2020-07-29Reformat sql queries to be one line...* wqflask/wqflask/api/gen_menu.py (get_species, get_groups, phenotypes_exist) (genotypes_exist)[sql]: Strip white spaces and newlines from query and make the sql query one line. BonfaceKilz