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2020-10-20Add pbkdf2 tests...* wqflask/tests/wqflask/test_pbkdf2.py: New tests. BonfaceKilz
2020-10-19Update snpString link...* wqflask/wqflask/marker_regression/display_mapping_results.py: Replace "%" strings with f-strings. Also, replace old "Href" with new htmlgen "Link" method. BonfaceKilz
2020-10-19Delete stale commentBonfaceKilz
2020-10-12Wrap args of print statements correctly using braces...* wqflask/wqflask/wgcna/wgcna_analysis.py: Update print statements by wrapping then in "()". Run: "2to3-3.8 -w wqflask/wqflask/wgcna/wgcna_analysis.py" BonfaceKilz
2020-10-12Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-10-09Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collections...Tests/add extra tests for collectionsBonfaceKilz
2020-10-09Apply PEP 8 to buffer...* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto BonfaceKilz
2020-10-09Add test for process_traits from collections.py...* wqflask/tests/wqflask/test_collect.py: Add it. BonfaceKilz
2020-10-09Fix export function on traits and analysis page...* wqflask/wqflask/views.py (export_trait_excel): Write data as bytes instead of strings. See: https://stackoverflow.com/questions/32075135/python-3-in-memory-zipfile-error-string-argument-expected-got-bytes * wqflask/wqflask/show_trait/export_trait_data.py: Convert cmp function into a key function. BonfaceKilz
2020-10-09Update base64 conversionBonfaceKilz
2020-10-09Replace string concat("+") with python3's f-stringBonfaceKilz
2020-10-09Replace "ncores" with "nthreads" param to r_CTLscanBonfaceKilz
2020-10-09Use built-in array as a named import...* wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use named import method. This is a workaround for using explicitly using "array" which conflicts with something else in the namespace. BonfaceKilz
2020-10-09Update base64 conversion...* wqflask/wqflask/wgcna/wgcna_analysis.py (WGCNA.render_image): Use Python3's base64 library from the stdlib to perform conversion. * wqflask/wqflask/ctl/ctl_analysis.py (CTL.loadImage): Ditto. BonfaceKilz
2020-10-09Convert cmp function into a key function...* wqflask/wqflask/correlation_matrix/show_corr_matrix.py (sortEigenVectors): Convert the comparison function into a key function. See: https://docs.python.org/3/howto/sorting.html#the-old-way-using-the-cmp-parameter BonfaceKilz
2020-10-09Apply PEP-8 formattingBonfaceKilz
2020-10-08Merge pull request #457 from zsloan/bxd_longevity_search_error_fix...Fixed issue where new phenotype groups wouldn't be saved to the self.…zsloan
2020-10-08Fixed remaining issue that applies to all dataset types...* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results zsloan
2020-10-08Fixed issue where new phenotype groups wouldn't be saved to the self.datasets......* wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets zsloan
2020-10-08Merge pull request #452 from zsloan/authentication_bug_fix...Checked if owner_id is "none" to avoid an error when trying to access…zsloan
2020-10-08Merge pull request #455 from zsloan/temp_trait_scatterplot_fix...Temp Trait Scatterplot Error Fixzsloan
2020-10-08When generating links to correlation scatterplots (in corr results and corr m......* wqflask/wqflask/correlation/corr_scatter_plot.py - Create the dataset object using the group name included with Temp dataset names (which take the form "Temp_(group_name)") * wqflask/wqflask/templates/correlation_matrix.html - Change scatterplot links to include the group name if the dataset name is "Temp" * wqflask/wqflask/templates/correlation_page.html - Change scatterplot links to include the group name if the dataset name is "Temp" + a couple minor style changes zsloan
2020-10-06Merge pull request #454 from zsloan/update_docs_fix...Made change that should fix error when trying to change page text usi…zsloan
2020-10-06Made change that should fix error when trying to change page text using ckeditor...* wqflask/wqflask/docs.py - Changed query to include casting as binary to deal with certain unicode characters in ckeditor pages * wqflask/wqflask/views.py - Imported update_text from Docs since it previously wasn't updated, causing an error when attempting to update text zsloan
2020-10-06Merge pull request #453 from zsloan/index_page_textarea_fix...Index page dropdown/textarea fixzsloan
2020-10-06Fixed issue where drop-down arrows and textarea corners couldn't be clicked w......* wqflask/wqflask/templates/index_page_orig.html - Changed the left/right div's padding to prevent them from overlapping and changed the textareas' styles to make them only expandable vertically zsloan
2020-10-02Checked if owner_id is "none" to avoid an error when trying to access the res......* wqflask/wqflask/resource_manager.py - Only get owner user info conditional on owner_id not being "none" (which it will be by default for newly added datasets). Previously it would throw an error due to "owner_info" being None zsloan
2020-10-02Merge pull request #450 from zsloan/corr_matrix_error_fix...Corr matrix error fixzsloan
2020-10-02Ignore utf-8 encoding errors...* wqflask/base/trait.py (retrieve_trait_info): Add extra param to ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position 0: invalid start byte" thrown in Python3. BonfaceKilz
2020-10-02Split author's list into it's own variable...* wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents jinja from throwing an error due to compaing a list type with an int. BonfaceKilz
2020-10-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into build/pyth...BonfaceKilz
2020-10-02Apply PEP 8 formattingBonfaceKilz
2020-10-02Cast variable properly to avoid type exceptions...* wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c. BonfaceKilz
2020-10-02Replace is_integer with isinstance when checking for an int valueBonfaceKilz
2020-10-02Update natural_sort function...* wqflask/wqflask/show_trait/SampleList.py (natural_sort): Add new function. (SampleList.get_attributes): Use new sort function to do natural_sort. BonfaceKilz
2020-10-02Remove unnecessary commented out blocks...* wqflask/wqflask/show_trait/SampleList.py: See above. BonfaceKilz
2020-10-02Cast "previous_chr" to an int...* wqflask/wqflask/marker_regression/gemma_mapping.py (parse_loco_output): Cast "previous_chr" to an int which prevents the error "Python typeerror: ‘>’ not supported between instances of ‘str’ and ‘int’" from being thrown. The error is **only** thrown in Python3. BonfaceKilz
2020-10-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into corr_matri...zsloan
2020-10-01Convert trait attributes to utf-8 strings if they were bytesBonfaceKilz
2020-10-01Make object JSON serializable...* wqflask/wqflask/search_results.py (SearchResultPage.gen_search_result): Some of the items is self.trait_list are in bytes, and *json.loads* can't serialize bytes into JSON. BonfaceKilz
2020-09-30Merge pull request #449 from zsloan/table_sort_fix...Table sort error fixzsloan
2020-09-30Changed the logic for adding 0 to the PCA results to do so when the...shared samples are < 2 instead of 0; this fixed the error when running the correlation matrix, but results in the PCA traits having no values * wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed "if num_overlap == 0" to "if num_overlap < 2" because correlations can't be run if there are fewer than 2 shared samples (and previously would throw an error if there was exactly 1 shared sample) zsloan
2020-09-30Added "natural-minus-na" sorting for relevant columns in the correlation...page * wqflask/wqflask/templates/correlation_page.html - Added natural-minus-na type to columns that can contain N/A values, since I apparently forgot to add it to this table before zsloan
2020-09-30Fixed issue where columns sorted by inner text (text inside link tags)...didn't sort all rows when a table is paginated and has more than one page * wqflask/wqflask/static/new/javascript/search_results.js - Added "extract_inner_text" function for getting the inner text from a string containing HTML in order to avoid using DataTables' orderDataType (which can only fetch values directly from the DOM, which is why sorting wasn't working with multiple pages), and also included this function in the "natural-minus-na" data type (so columns can be sorted that contain both HTML/links and N/A values) * wqflask/wqflask/templates/collections/view.html - Changed record column to use "natural-minus-na" sort method in order to fix the inner-text sorting issue + added sorting to the checkbox column (in the same way as it already works in the search result page) * wqflask/wqflask/templates/search_results_page.html - Replaced the columns that used orderDataType with using the updated "natural-minus-na" data type * wqflask/wqflask/templates/correlation_page.html - Fixed issue where N/As in the Year column (for phenotype correlations) were still displayed as links zsloan
2020-09-30Removed unused code from TempDataSet class...* wqflask/base/data_set.py - TempDataSet class contained some code referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore zsloan
2020-09-30Add missing import...* wqflask/wqflask/correlation/show_corr_results.py: Add it. BonfaceKilz
2020-09-30Apply pep 8 formatting...* wqflask/wqflask/correlation/show_corr_results.py [imports]: Apply pep8 and remove unused imports. BonfaceKilz
2020-09-30Fix StopIteration error thrown in view collections page...* wqflask/wqflask/user_session.py (user_id): Use byte-string when fetching user_id. See: https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458 BonfaceKilz
2020-09-30Fix import in testsBonfaceKilz
2020-09-29Merge pull request #448 from zsloan/misc_rob_changes...Misc rob changeszsloan
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