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2020-08-25Fixed issue in DatasetType that caused an error when trying to load newzsloan
datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error
2020-08-25This should fix an issue where the new qtlreaper wouldn't work properltyzsloan
with genotypes that only have cM positions * wqflask/wqflask/marker_regression/qtlreaper_mapping.py - parse_reaper_output is changed to check if cM and Mb exist in output when creating marker obs * wqflask/wqflask/marker_regression/run_mapping.py - Changed export_mapping_results to properly deal with all combinations of cM and Mb positions (both and either/or)
2020-08-25Merge pull request #425 from ↵zsloan
BonfaceKilz/refactor/extract-htmlgen-methods-to-wrapper-class Refactor/extract htmlgen methods to wrapper class
2020-08-24Use natural.js dataTables extension plugin from guixBonfaceKilz
2020-08-24Remove non-keyword argsBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py (HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function parameters.
2020-08-24Replace "HtmlGen" method calls with those from "HtmlGenWrapper"BonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Replace direct calls to HtmlGen with methods from the constructed wrapper class "HtmlGenWrapper".
2020-08-24Add new wrapper class for HtmlGen methodBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
2020-08-24Add tests for the HtmlGenWrapper classBonfaceKilz
* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add new tests
2020-08-24Fix some pylint errorsBonfaceKilz
* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused imports and add fix some pylint errors
2020-08-24Remove unused importsBonfaceKilz
* 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.
2020-08-24Rename fileBonfaceKilz
* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Rename test_display_marking_results.py to test_display_mapping_results.py
2020-08-24Fix failing testBonfaceKilz
* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data introduced in 092212df Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2020-08-24Fixed issue where im_drawer wasn't being set in drawHaplotypeBandzsloan
* wqflask/wqflask/marker_regression/display_mapping_results.py - defined im_drawer in drawHaplotypeBand to fix errror and removed an unused import
2020-08-24The function draw_rotated_text_ was writing an image to /tmp, which GN2zsloan
user apparently doesn't have access to, so I replaced it with a link to the dynamically set TEMPDIR * wqflask/utility/pillow_utils.py - Replaced "/tmp/" in image location with TEMPDIR
2020-08-22Set min-width for search result table, since the description columnzsloan
often looks weird if it gets below a certain width * wqflask/wqflask/templates/search_result_page.html - Set min-width of table container div to 1500px since that seems to be a reasonable width that prevents the description column from getting too narrow
2020-08-20Changed Molecular Trait Datasets to Molecular Traits in the Typezsloan
drop-down on the home page * wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait Datasets was hardcoded to Molecular Traits
2020-08-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-20Use dataTables.colResize.js and naturalSort from guixBonfaceKilz
2020-08-20Use buttons.colVis.min.js from guixBonfaceKilz
2020-08-20Use buttons.bootstrap.css from guixBonfaceKilz
2020-08-20Use scroller.dataTables.min.css from guixBonfaceKilz
2020-08-20Use dataTables.colReorder.js from guixBonfaceKilz
2020-08-20Use jquery.dataTables.js from guixBonfaceKilz
2020-08-20Use dataTables.buttons.min.js from guixBonfaceKilz
2020-08-20Use buttons.dataTables.min.css from guixBonfaceKilz
2020-08-19Added Invert button to collection pagezsloan
* wqflask/wqflask/templates/collections/view.html - Added the Invert button back to the collection page; it was removed in the past but Rob decided it should be re-added
2020-08-19Tools used from the collection page now use all traits if no rows arezsloan
checked and there are fewer than 100 traits in the table * wqflask/wqflask/static/new/javascript/search_results.js - Created get_traits_from_table function to get the list of traits and check if none are selected, and also renamed the previous function also called get_traits_from_table to submit_traits_to_export_or_bnw since that better describes what the function does
2020-08-19Show short labels by default in Correlation Matrixzsloan
* wqflask/wqflask/templates/correlation_matrix.html - remove display: none for short label div
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
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