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2020-08-17Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-18Fix positioning for many instances of text in the mapping figurezsloan
* 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.
2020-08-17Placed X/Y trait info before the table on the correlation scatterplotzsloan
page * wqflask/wqflask/templates/corr_scatterplot.html - reordered table and X/Y trait info divs
2020-08-10Add fonts for pillowPjotr Prins
* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle method with PIL.ImageFont * wqflask/wqflask/static/fonts: Add fonts in path
2020-08-08Add a basic test for test_display_marking_results.pyBonfaceKilz
* 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.
2020-08-08Change Y Coodinate systemMuriithi Frederick Muriuki
* 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.
2020-08-08Fix placement for axes labelsMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the placement for the axes labels.
2020-08-08Use TEXT_Y_DISPLACEMENT instead of magic numbersMuriithi Frederick Muriuki
* 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.
2020-08-08Give rectangles black outlinesMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the rectangles black outlines to correspond to earlier drawings.
2020-08-08Use new `draw_open_polygon()` utilityMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new `draw_open_polygon()` utility to draw open polygons.
2020-08-08Add draw_open_polygon() utilityMuriithi Frederick Muriuki
* wqflask/utility/pillow_utils.py: New method.
2020-08-08Replace "color" with "fill" keyword argumentMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: (DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
2020-08-08Use draw_rotated_text()Muriithi Frederick Muriuki
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().
2020-08-08Create new utility module for drawingMuriithi Frederick Muriuki
* 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.
2020-08-08Fix font pathsMuriithi Frederick Muriuki
* wqflask/utility/Plot.py: Update font paths. * wqflask/fonts/ttf: Update font files.
2020-08-08Update SNP Browser to PillowMuriithi Frederick Muriuki
* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in place of obsoleted Piddle library.
2020-08-08Add missing font filesMuriithi Frederick Muriuki
* wqflask/fonts/ttf: Add ttf font files.
2020-08-08Migrate code from Piddle to PillowMuriithi Frederick Muriuki
* 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.
2020-08-08Update the colours to use Pillow's ImageColorMuriithi Frederick Muriuki
* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours.
2020-08-07Move wqflask/tests/api to wqflask/tests/wqflaskBonfaceKilz
* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir should mirror the actual module structure
2020-08-06Added endpoint for changing some user detailszsloan
* wqflask/wqflask/user_session.py - Added endpoint for /manage/user that lets the user change their full_name or organization. Still need to add something that lets them change their e-mail, since that will require a confirmation
2020-08-06Made a change that should fix the issue with the Y axis ticks extendingzsloan
too high in mapping results * wqflask/wqflask/marker_regression/display_mapping_results.py - When in ful genome view, I changed it to subject the yTopOffset when drawing the Y axis; single chromosome view seems to work okay so it's conditional on that
2020-08-05Set maximum width for trait page details in order to avoid longzsloan
summaries looking strange * wqflask/wqflask/templates/show_trait_details.html - Set min-width of table containing details to 1400px
2020-08-04Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-04Simplified logic in the @before_request that checks user permissionszsloan
* 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"
2020-08-04Reduced table cell margin a bit to make cell contents better align withzsloan
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
2020-08-04Merge pull request #415 from BonfaceKilz/tests/add-tests-for-gen-menuPjotr Prins
Tests/add tests for gen menu
2020-08-03Fixed table width issue when there's an N columnzsloan
* wqflask/wqflask/show_trait/show_trait.py - Just added more pixels in the function which determines the overall table width
2020-08-03Fixed issue where DataTables was initialized twice when selectingzsloan
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
2020-08-03Remove "+" when concatenating stringsBonfaceKilz
* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+' when joining strings inside brackets
2020-08-03Fix some errors generated by running pylintBonfaceKilz
* wqflask/wqflask/api/gen_menu.py: Apply pylint. * wqflask/tests/api/test_gen_menu.py: Apply pylint.
2020-08-03Add extra test for "build_datasets"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add test.
2020-08-03Move variable to setUpBonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Move variable
2020-08-03Add test for "gen_dropdown_json"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new test
2020-08-03Add tests for "get_datasets"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new tests
2020-08-03Update how boolean is returnedBonfaceKilz
* 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
2020-08-03Remove unreached "else" branchBonfaceKilz
* wqflask/wqflask/api/gen_menu.py(get_types): - Remove unnecessary comment. - Remove unreachable "else" branch.
2020-08-03Add tests for "get_types"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new tests
2020-08-03Add test for "build_types"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: New test
2020-08-03Clean up "if ... else" conditionalBonfaceKilz
* wqflask/wqflask/api/gen_menu.py (build_datasets): Make conditionals more Pythonic
2020-08-03Reformat sql queries to be one lineBonfaceKilz
* wqflask/wqflask/api/gen_menu.py (build_datasets, build_types): Strip white spaces and newlines from query and make the sql query one line.
2020-07-30Add tests for "build_datasets"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new tests for "build_datasets" function
2020-07-29Fixed error that occured for new resources in check_adminzsloan
* 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)
2020-07-29Update how boolean is returnedBonfaceKilz
* wqflask/wqflask/api/gen_menu.py (phenotypes_exist, genotypes_exist): Convert sql result to boolean instead of only checking for "None".
2020-07-29Reformat sql queries to be one lineBonfaceKilz
* 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.
2020-07-29Add tests for "phenotypes_exist" and "genotypes_exist"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: Add new tests
2020-07-29Add test for "get_groups"BonfaceKilz
* wqflask/tests/api/test_gen_menu.py: test that "get_groups" uses the correct sql query and returns the correct group data structure.
2020-07-29Add initial gen_menu testBonfaceKilz
* wqflask/tests/api/__init__.py: Add it * wqflask/tests/api/test_gen_menu.py: Add test for get_species
2020-07-28Fixes issue where zooming in on mapping results in some browsers causedzsloan
the original tab's contents to be removed * wqflask/wqflask/templates/mapping_results.html: minor change to add spaces for readability * wqflask/wqflask/marker_regression/display_mapping_results.py: Removed "return" from chrView and rangeView since it appears to remove original tab's contents in some browers when submitting form
2020-07-27Clean up webqtlCaseData classBonfaceKilz
* 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
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