Age | Commit message (Collapse) | Author |
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* 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
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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
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* wqflask/wqflask/templates/correlation_matrix.html - remove display:
none for short label div
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Resolve merge conflicts from Pil Pillow conversion branch
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* 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.
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page
* wqflask/wqflask/templates/corr_scatterplot.html - reordered table and
X/Y trait info divs
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* wqflask/wqflask/marker_regression/display_mapping_results.py: replace piddle
method with PIL.ImageFont
* wqflask/wqflask/static/fonts: Add fonts in path
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* 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.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Fix the
placement for the axes labels.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Give the
rectangles black outlines to correspond to earlier drawings.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Use the new
`draw_open_polygon()` utility to draw open polygons.
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* wqflask/utility/pillow_utils.py: New method.
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* wqflask/wqflask/marker_regression/display_mapping_results.py:
(DisplayMappingResults): Pillow uses 'fill' in place of 'color'.
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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().
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* 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.
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* wqflask/utility/Plot.py: Update font paths.
* wqflask/fonts/ttf: Update font files.
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* wqflask/wqflask/snp_browser/snp_browser.py: Use newer, and supported Pillow in
place of obsoleted Piddle library.
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* wqflask/fonts/ttf: Add ttf font files.
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* 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.
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Use Pillow's ImageColor module in place of the older Piddle colours.
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* wqflask/tests(api): Move all the files here to tests/wqflask. The test dir
should mirror the actual module structure
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* 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
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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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summaries looking strange
* wqflask/wqflask/templates/show_trait_details.html - Set min-width of
table containing details to 1400px
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* 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"
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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
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Tests/add tests for gen menu
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* wqflask/wqflask/show_trait/show_trait.py - Just added more pixels in
the function which determines the overall table width
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cofactors, leading to an error in non-Chrome browsers
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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
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* wqflask/wqflask/api/gen_menu.py (build_types, build_datasets): Replace '+'
when joining strings inside brackets
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* wqflask/wqflask/api/gen_menu.py: Apply pylint.
* wqflask/tests/api/test_gen_menu.py: Apply pylint.
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* wqflask/tests/api/test_gen_menu.py: Add test.
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* wqflask/tests/api/test_gen_menu.py: Move variable
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* wqflask/tests/api/test_gen_menu.py: Add new test
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* wqflask/tests/api/test_gen_menu.py: Add new tests
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* 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
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* wqflask/wqflask/api/gen_menu.py(get_types):
- Remove unnecessary comment.
- Remove unreachable "else" branch.
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* wqflask/tests/api/test_gen_menu.py: Add new tests
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* wqflask/tests/api/test_gen_menu.py: New test
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* wqflask/wqflask/api/gen_menu.py (build_datasets): Make conditionals more
Pythonic
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* wqflask/wqflask/api/gen_menu.py (build_datasets, build_types): Strip white
spaces and newlines from query and make the sql query one line.
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* wqflask/tests/api/test_gen_menu.py: Add new tests for "build_datasets"
function
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* 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)
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* wqflask/wqflask/api/gen_menu.py (phenotypes_exist, genotypes_exist): Convert
sql result to boolean instead of only checking for "None".
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* 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.
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* wqflask/tests/api/test_gen_menu.py: Add new tests
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