| Age | Commit message (Expand) | Author |
|---|
| 2020-08-18 | Fix 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 |
| 2020-08-10 | Add 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 |
| 2020-08-08 | Add 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 |
| 2020-08-08 | Change 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 |
| 2020-08-08 | Fix placement for axes labels...* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the
placement for the axes labels.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use 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 |
| 2020-08-08 | Give rectangles black outlines...* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the
rectangles black outlines to correspond to earlier drawings.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Use 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 |
| 2020-08-08 | Add draw_open_polygon() utility...* wqflask/utility/pillow_utils.py: New method.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Replace "color" with "fill" keyword argument...* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
| Muriithi Frederick Muriuki |
| 2020-08-08 | 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 | Create 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 |
| 2020-08-08 | Fix font paths...* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
| Muriithi Frederick Muriuki |
| 2020-08-08 | Update 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 |
| 2020-08-08 | Add missing font files...* wqflask/fonts/ttf: Add ttf 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 |
| 2020-08-08 | Update 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 |
| 2020-08-07 | Move 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 |
| 2020-08-05 | Set 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 |
| 2020-08-04 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2020-08-04 | Simplified 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 |
| 2020-08-04 | Reduced 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 |
| 2020-08-04 | Merge pull request #415 from BonfaceKilz/tests/add-tests-for-gen-menu...Tests/add tests for gen menu | Pjotr Prins |
| 2020-08-03 | Fixed 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 |
| 2020-08-03 | Fixed 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 |
| 2020-08-03 | Remove "+" when concatenating strings...* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+'
when joining strings inside brackets
| BonfaceKilz |
| 2020-08-03 | Fix some errors generated by running pylint...* wqflask/wqflask/api/gen_menu.py: Apply pylint.
* wqflask/tests/api/test_gen_menu.py: Apply pylint.
| BonfaceKilz |
| 2020-08-03 | Add extra test for "build_datasets"...* wqflask/tests/api/test_gen_menu.py: Add test.
| BonfaceKilz |
| 2020-08-03 | Move variable to setUp...* wqflask/tests/api/test_gen_menu.py: Move variable
| BonfaceKilz |
| 2020-08-03 | Add test for "gen_dropdown_json"...* wqflask/tests/api/test_gen_menu.py: Add new test
| BonfaceKilz |
| 2020-08-03 | Add tests for "get_datasets"...* wqflask/tests/api/test_gen_menu.py: Add new tests
| BonfaceKilz |
| 2020-08-03 | Update 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 |
| 2020-08-03 | Remove unreached "else" branch...* wqflask/wqflask/api/gen_menu.py(get_types):
- Remove unnecessary comment.
- Remove unreachable "else" branch.
| BonfaceKilz |
| 2020-08-03 | Add tests for "get_types"...* wqflask/tests/api/test_gen_menu.py: Add new tests
| BonfaceKilz |
| 2020-08-03 | Add test for "build_types"...* wqflask/tests/api/test_gen_menu.py: New test
| BonfaceKilz |
| 2020-08-03 | Clean up "if ... else" conditional...* wqflask/wqflask/api/gen_menu.py (build_datasets): Make conditionals more
Pythonic
| BonfaceKilz |
| 2020-08-03 | Reformat 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 |
| 2020-07-30 | Add tests for "build_datasets"...* wqflask/tests/api/test_gen_menu.py: Add new tests for "build_datasets"
function
| BonfaceKilz |
| 2020-07-29 | Fixed 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 |
| 2020-07-29 | Update 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 |
| 2020-07-29 | Reformat 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 |
| 2020-07-29 | Add tests for "phenotypes_exist" and "genotypes_exist"...* wqflask/tests/api/test_gen_menu.py: Add new tests
| BonfaceKilz |
| 2020-07-29 | Add test for "get_groups"...* wqflask/tests/api/test_gen_menu.py: test that "get_groups" uses the correct
sql query and returns the correct group data structure.
| BonfaceKilz |
| 2020-07-29 | Add initial gen_menu test...* wqflask/tests/api/__init__.py: Add it
* wqflask/tests/api/test_gen_menu.py: Add test for get_species
| BonfaceKilz |
| 2020-07-28 | Fixes issue where zooming in on mapping results in some browsers caused...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
| 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 |
| 2020-07-27 | Add unittests for WebqtlCaseData...* wqflask/tests/base/test_webqtl_case_data.py: Add it
| BonfaceKilz |
| 2020-07-27 | Abstract away redundant code into set_dataset_key method...* wqflask/base/data_set.py (Dataset):
- Add set_dataset_key
- Remove __call__ method
| BonfaceKilz |
| 2020-07-27 | Test that non-existent keys in Dataset are set correctly...* wqflask/tests/base/test_data_set.py: Add more tests.
| BonfaceKilz |
| 2020-07-27 | Use the correct redis instance inside object...* wqflask/base/data_set.py (DatasetType): Use object's redis instance
| BonfaceKilz |
