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2020-10-09Fix export function on traits and analysis pageBonfaceKilz
* 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.
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 importBonfaceKilz
* 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.
2020-10-09Update base64 conversionBonfaceKilz
* 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.
2020-10-09Convert cmp function into a key functionBonfaceKilz
* 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
2020-10-09Apply PEP-8 formattingBonfaceKilz
2020-10-02Ignore utf-8 encoding errorsBonfaceKilz
* 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.
2020-10-02Split author's list into it's own variableBonfaceKilz
* wqflask/wqflask/templates/correlation_page.html: Ditto. Prevents jinja from throwing an error due to compaing a list type with an int.
2020-10-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵BonfaceKilz
build/python3-migration
2020-10-02Apply PEP 8 formattingBonfaceKilz
2020-10-02Cast variable properly to avoid type exceptionsBonfaceKilz
* wqflask/wqflask/marker_regression/run_mapping.py: See 94c36c8c.
2020-10-02Replace is_integer with isinstance when checking for an int valueBonfaceKilz
2020-10-02Update natural_sort functionBonfaceKilz
* wqflask/wqflask/show_trait/SampleList.py (natural_sort): Add new function. (SampleList.get_attributes): Use new sort function to do natural_sort.
2020-10-02Remove unnecessary commented out blocksBonfaceKilz
* wqflask/wqflask/show_trait/SampleList.py: See above.
2020-10-02Cast "previous_chr" to an intBonfaceKilz
* 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.
2020-10-01Convert trait attributes to utf-8 strings if they were bytesBonfaceKilz
2020-10-01Make object JSON serializableBonfaceKilz
* 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.
2020-09-30Merge pull request #449 from zsloan/table_sort_fixzsloan
Table sort error fix
2020-09-30Added "natural-minus-na" sorting for relevant columns in the correlationzsloan
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
2020-09-30Fixed issue where columns sorted by inner text (text inside link tags)zsloan
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
2020-09-30Add missing importBonfaceKilz
* wqflask/wqflask/correlation/show_corr_results.py: Add it.
2020-09-30Apply pep 8 formattingBonfaceKilz
* wqflask/wqflask/correlation/show_corr_results.py [imports]: Apply pep8 and remove unused imports.
2020-09-30Fix StopIteration error thrown in view collections pageBonfaceKilz
* wqflask/wqflask/user_session.py (user_id): Use byte-string when fetching user_id. See: https://github.com/genenetwork/genenetwork2/pull/422#issuecomment-701082458
2020-09-30Fix import in testsBonfaceKilz
2020-09-29Merge pull request #448 from zsloan/misc_rob_changeszsloan
Misc rob changes
2020-09-29Trait page link-out buttons were previously inside <a> tags, but thiszsloan
caused there to be a small line between buttons when hovering over them (because the <a> tags were wider than the button itself); this was changed to instead just be an "onclick" on the button (which is also a bit more concise) * wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags with onclick for trait page link-out buttons
2020-09-29Removed "Color By Trait" button from the Bar Chart, because it was meantzsloan
to work with the figure we used before switching to Plotly. This feature will need to be redone to work with Plotly * wqflask/wqflask/templates/show_trait_statistics.html - commented out Color By Trait button until it's reimplemented
2020-09-29Made a variety of changes to table pageszsloan
* wqflask/wqflask/static/new/css/show_trait.css - Adding position relative and a 2px offset for glyphicons to make them better align with button text * wqflask/wqflask/templates/collections/view.html - Added glyphicon to Download button, changed a couple head names (Peak Location and Effect Size), made Location and Peak Location columns the same width, and made the "?" glossary links a little larger and red * wqflask/wqflask/templates/search_result_page.html - same as above * wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon to Export button
2020-09-29Remove undefined variableBonfaceKilz
2020-09-29Apply pep 8 to bufferBonfaceKilz
* wqflask/wqflask/user_manager.py: Remove some stale comments. (imports): Apply pep-8 and remove unused imports.
2020-09-29Fixed issue where negative additive effect values weren't beingzsloan
displayed in the "view collection" page * wqflask/wqflask/templates/collections/view.html - Apparently the correct way to check if a value can be cast to a float in Jinja2 is to say "value != 0"; it previous said "value > 0" which exlcuded all negative values
2020-09-29Changed Add (to collection) button color to match other Add buttons andzsloan
changed the text for the GN1 link button * wqflask/wqflask/templates/show_trait_details.html - Changed Add button class to btn-success (to make it green like the other Add buttons) and changed text from "View in GN1" to "Go to GN1"
2020-09-29Changed the DataTables column sort arrows to a different color byzsloan
changing the image they're referencing * wqflask/wqflask/templates/base.html - Added CSS changing the table sort arrow image directly into base.html because it requires using url_for to reference the images in the GUIX profile (so it needs to be in the template and can't just be added to a CSS file)
2020-09-29Add check for bytesBonfaceKilz
* wqflask/wqflask/collect.py (process_traits): Check whether the passed "unprocessed_traits" is a byte otherwise an error is generated when bytes(the default) are passed.
2020-09-29Add test for process_traits from collections.pyBonfaceKilz
* wqflask/tests/wqflask/test_collect.py: Add it.
2020-09-28Changed add to collection to open the collection in a new tab/page sozsloan
the results on the initial page aren't lost * wqflask/wqflask/static/new/javascript/search_results.js - Changed the add to collection method name to "add_to_collection" because it was previously "add" which is a terrible method name * wqflask/wqflask/templates/collections/add.html - Added target="_blank" to the add to collection form so it will open in a new tab/window
2020-09-28Fix failing testBonfaceKilz
* wqflask/tests/base/test_trait.py: Add app_context to test class, otherwise an error related to working outside the app_context is generated. Adding the app_context is required when mocking "Flask.g".
2020-09-28Merge branch 'build/python3-migration' of ↵BonfaceKilz
github.com:BonfaceKilz/genenetwork2 into build/python3-migration
2020-09-28Fix casting errorBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*.
2020-09-28Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-28Fix casting errorBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): If the description_string or discription_display value return a None object, evaluate to an empty string. Fixes errors related to *len(None)*.
2020-09-28Merge pull request #446 from BonfaceKilz/Bug/Fix-casting-errorBonfaceKilz
Bug/fix casting error
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-28Update trait testsBonfaceKilz
* wqflask/tests/base/test_trait.py (test_retrieve_trait_info_with_non_empty_lrs): Check trait.LRS_score_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_lrs_field): Check trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_chr_field): Check test_trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.locus is None.
2020-09-26Fix failing tests by replacing mock with unittest.mockBonfaceKilz
* wqflask/tests/base/test_data_set.py (imports): Run: `find . -type f -name "*py" -print0 | xargs -0 sed -i \ "s|import mock|from unittest import mock|g"` * wqflask/tests/base/test_trait.py(imports): Ditto. * wqflask/tests/utility/test_authentication_tools.py(imports): Ditto. * wqflask/tests/utility/test_hmac.py(imports). Ditto. * wqflask/tests/wqflask/api/test_gen_menu.py: Ditto
2020-09-26Use Python3 image to run testsBonfaceKilz
2020-09-26Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: Remove decode function call which is no longer supported in python3.
2020-09-26Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/db_info.py: Run pep8 through buffers. Fixes inconsistent use of tabs and spaces in indentation which trips up unittests.
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