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2020-08-27Remove python2 string processing to utf-8•••* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods. * wqflask/wqflask/search_results.py: Remove utf-8 decode method on string. BonfaceKilz
2020-08-27Remove relative imports•••* wqflask/runserver.py: Relative imports leads to import errors. BonfaceKilz
2020-08-27Replace dict.iteritems() with dict.items()•••"iteritems()" got omitted in python3.X BonfaceKilz
2020-08-27Convert sibling imports to relative imports•••See: <https://docs.python.org/2/library/2to3.html#2to3fixer-import> BonfaceKilz
2020-08-27Import "reduce" without a try block•••* wqflask/wqflask/correlation_matrix/show_corr_matrix.py: Import 'reduce' BonfaceKilz
2020-08-27Replace string arguments to "hmac.new" with bytearray•••See: <https://stackoverflow.com/questions/31848293/python3-and-hmac-how-to-handle-string-not-being-binary> BonfaceKilz
2020-08-27Fix failing testsBonfaceKilz
2020-08-27Apply pep-8 formattingBonfaceKilz
2020-08-27Remove comment blockBonfaceKilz
2020-08-27Replace mysqldb's "escape" with the one from utils.db_tools•••Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra step of converting the binary string to a string. BonfaceKilz
2020-08-27Remove redundant methods which are defined elsewhere•••* wqflask/base/data_set.py: Delete "create_in_clause", and "mescape" which are defined in "utility.db_tools" BonfaceKilz
2020-08-27Add global method to convert binary string to plain string•••* wqflask/utility/db_tools.py: escape_string returns a binary string which introduces a bug when composing sql query string. The escaped strings have to be converted to plain text. BonfaceKilz
2020-08-27Remove unused importsBonfaceKilz
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
2020-08-26Replace tabs with spaces•••* scripts/maintenance/readProbeSetMean_v7.py: Run python-autopep8 on this file. BonfaceKilz
2020-08-26Remove debug statement•••* wqflask/wqflask/views.py(search_page): "debugf" raises an error since the first arg is expected to be an int BonfaceKilz
2020-08-26Remove "from __future__ import new_feature" statements•••See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future> BonfaceKilz
2020-08-26Replace "__cmp__" with "__eq__" magic method•••* wqflask/base/GeneralObject.py: "__cmp__" is no longer used in python3. See: <https://stackoverflow.com/questions/8276983/why-cant-i-use-the-method-cmp-in-python-3-as-for-python-2> BonfaceKilz
2020-08-26Rename "unicode" to "str"•••See: <https://docs.python.org/2/library/2to3.html#2to3fixer-unicode> BonfaceKilz
2020-08-26Replace calls to "basestring with "str""•••See: <https://docs.python.org/2/library/2to3.html#2to3fixer-basestring> BonfaceKilz
2020-08-26Fix failing tests that use python2-htmlgen•••* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Fix tests. BonfaceKilz
2020-08-26Replace python2-htmlgen with python-htmlgen•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Use python-htmlgen BonfaceKilz
2020-08-26Update corestats import•••* wqflask/utility/Plot.py: import corestats from the utility module. BonfaceKilz
2020-08-26Remove unused importsBonfaceKilz
2020-08-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-08-25Merge pull request #427 from BonfaceKilz/Build/add-scientific-js-datatables-p...•••Build/add scientific js datatables pluginzsloan
2020-08-26Add check for "scientific.js" dataTables extension plugin•••* test/requests/link_checker.py (check_packaged_file): Add it. BonfaceKilz
2020-08-25Merge pull request #425 from BonfaceKilz/refactor/extract-htmlgen-methods-to-...•••Refactor/extract htmlgen methods to wrapper classzsloan
2020-08-25Use scientific.js dataTables extension plugin from guixBonfaceKilz
2020-08-25Merge pull request #426 from BonfaceKilz/Build/use-naturaljs-datatables-exten...•••Build/use naturaljs datatables extensionszsloan
2020-08-24Add check for "natural.js" in Mechanical Rob•••* test/requests/link_checker.py (check_packaged_file): Add it. BonfaceKilz
2020-08-24Use natural.js dataTables extension plugin from guixBonfaceKilz
2020-08-24Remove non-keyword args•••* wqflask/wqflask/marker_regression/display_mapping_results.py (HtmlGenWrapper)[create_image_tag]: Remove "src" and "alt" as function parameters. BonfaceKilz
2020-08-24Replace "HtmlGen" method calls with those from "HtmlGenWrapper"•••* wqflask/wqflask/marker_regression/display_mapping_results.py (DisplayMappingResults): Replace direct calls to HtmlGen with methods from the constructed wrapper class "HtmlGenWrapper". BonfaceKilz
2020-08-24Add new wrapper class for HtmlGen method•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Add new class BonfaceKilz
2020-08-24Add tests for the HtmlGenWrapper class•••* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Add new tests BonfaceKilz
2020-08-24Fix some pylint errors•••* wqflask/wqflask/marker_regression/display_mapping_results.py: Remove unused imports and add fix some pylint errors BonfaceKilz
2020-08-24Remove unused imports•••* 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. BonfaceKilz
2020-08-24Rename file•••* wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py: Rename test_display_marking_results.py to test_display_mapping_results.py BonfaceKilz
2020-08-24Fix failing test•••* wqflask/tests/wqflask/api/test_gen_menu.py: Update assertion. Result data introduced in 092212df Signed-off-by: BonfaceKilz <bonfacemunyoki@gmail.com> BonfaceKilz
2020-08-24Fixed issue where im_drawer wasn't being set in drawHaplotypeBand•••* wqflask/wqflask/marker_regression/display_mapping_results.py - defined im_drawer in drawHaplotypeBand to fix errror and removed an unused import zsloan
2020-08-24The function draw_rotated_text_ was writing an image to /tmp, which GN2•••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 zsloan
2020-08-23Use Python3 string methods•••* wqflask/utility/webqtlUtil.py (genRandStr): Replace "string.letters" with "string.ascii_letters". BonfaceKilz
2020-08-23Remove unused importsBonfaceKilz
2020-08-22Set min-width for search result table, since the description column•••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 zsloan
2020-08-20Changed Molecular Trait Datasets to Molecular Traits in the Type•••drop-down on the home page * wqflask/wqflask/api_gen_menu.py - Changed where Molecular Trait Datasets was hardcoded to Molecular Traits zsloan
2020-08-20Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-08-20Merge pull request #423 from BonfaceKilz/build/use-datatable-extensions-from-...•••Build/use datatable extensions from guixzsloan
2020-08-20Handle module renames in the standard library•••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> BonfaceKilz
2020-08-20Replace all references to python2.7 with python3.8•••Run: ``` find . -type f -print0 | xargs -0 sed -i \ "s|lib/python2.7/site-packages|lib/python3.8/site-packages|g" ``` BonfaceKilz
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