Age | Commit message (Collapse) | Author |
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datasets
* wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is
what was causing the error
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BonfaceKilz/Build/add-scientific-js-datatables-plugin
Build/add scientific js datatables plugin
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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)
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BonfaceKilz/refactor/extract-htmlgen-methods-to-wrapper-class
Refactor/extract htmlgen methods to wrapper class
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* wqflask/wqflask/marker_regression/display_mapping_results.py
(HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function
parameters.
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* wqflask/wqflask/marker_regression/display_mapping_results.py
(DisplayMappingResults): Replace direct calls to HtmlGen with methods from
the constructed wrapper class "HtmlGenWrapper".
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class
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* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add
new tests
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* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused
imports and add fix some pylint errors
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* 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.
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* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py:
Rename test_display_marking_results.py to test_display_mapping_results.py
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* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data
introduced in 092212df
Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com>
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* wqflask/wqflask/marker_regression/display_mapping_results.py - defined
im_drawer in drawHaplotypeBand to fix errror and removed an unused
import
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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
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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
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drop-down on the home page
* wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait
Datasets was hardcoded to Molecular Traits
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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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* 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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