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2020-08-25Merge pull request #427 from ↵zsloan
BonfaceKilz/Build/add-scientific-js-datatables-plugin Build/add scientific js datatables plugin
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
2020-08-25Use scientific.js dataTables extension plugin from guixBonfaceKilz
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
2020-08-23Use Python3 string methodsBonfaceKilz
* wqflask/utility/webqtlUtil.py (genRandStr): Replace "string.letters" with "string.ascii_letters".
2020-08-23Remove unused importsBonfaceKilz
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
2020-08-20Handle module renames in the standard libraryBonfaceKilz
Run: ``` 2to3-3.8 -f imports -w . && \ 2to3-3.8 -f imports2 -w . ``` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
2020-08-20Disable python2 QTLReaperBonfaceKilz
* wqflask/base/data_set.py: Remove usage of "reaper" to load datasets
2020-08-20Add backward support for urllibBonfaceKilz
* wqflask/base/trait.py: Remove unused imports * wqflask/db/call.py (Bench): Add urllib2 fallback for python2
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
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Make Python more idiomaticBonfaceKilz
Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19Rename xrange() to range() and wrap existing range() calls with listBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-xrange>
2020-08-19Handle the rename of urllib and urllib2 to the urllib packageBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Replace backtick repr with the repr() functionBonfaceKilz
* wqflask/base/trait.py: See <https://docs.python.org/2/library/2to3.html#2to3fixer-repr>
2020-08-19Handle the move of reduce() to functools.reduce()BonfaceKilz
Run `2to3-3.8 -f reduce -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-reduce>
2020-08-19Wrap `raise` statements in parenthesisBonfaceKilz
Run `2to3-3.8 -f raise -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
2020-08-19Convert the use of iterator’s next() methods to the next() functionBonfaceKilz
Run `2to3-3.8 -f next -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-next>
2020-08-19Convert the old not-equal syntax, <>, to !=BonfaceKilz
Run `2to3-3.8 -f ne -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
2020-08-19Replace `izip` with python's built-in equivalentBonfaceKilz
Run `2to3-3.8 -f itertools -w . && 2to3-3.8 -f itertools_imports -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools_imports> and <https://docs.python.org/2/library/2to3.html#2to3fixer-itertools>
2020-08-19Change `dict.has_key(key)` to `key in dict`BonfaceKilz
Run `2to3-3.8 -f has_key -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-has_key>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-08-19Remove erroneous `if .. else` branchBonfaceKilz
* wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error if either height or width is not defined. Fixes parsing error when running `2to3-3.8 -f apply -w .`
2020-08-19Wrap `map()` in a `list` callBonfaceKilz
Run `2to3-3.8 -f map -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
2020-08-18Apply pep8BonfaceKilz
* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running `2to3-3.8 -w .`: ```` RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403) ````
2020-08-18Replace "<>" with "!="BonfaceKilz
* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
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