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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)*.
2020-09-28Convert 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
2020-09-26Fix 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.
2020-09-26Run 2to3-8 tool through fileBonfaceKilz
* wqflask/wqflask/db_info.py: Run: 2to3-3.8 -w wqflask/wqflask/db_info.py
2020-09-26Fix inconsistent line ending in fileBonfaceKilz
* wqflask/wqflask/db_info.py: Replace ^M with proper unix line endings. See <http://ergoemacs.org/emacs/emacs_line_ending_char.html>
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-23Fix failing buildsBonfaceKilz
* wqflask/wqflask/__init__.py: Move imports from views.py to "__init__.py". Fixes failing build. * wqflask/wqflask/views.py: Ditto.
2020-09-23Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string.
2020-09-22Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-22Fixed a pretty big mistake where user accounts would be saved even whenzsloan
there was some mistake/error during registration * wqflask/wqflask/user_login.py - Previously it would still save a user even if there was some problem like their e-mail already being associated with an account. It would display the error, but still run save_user. I fixed this so that it no longer saves the user if there are any errors
2020-09-22Added something to the mapping result page CSS to change the highlightzsloan
color to match the high color in other tables * wqflask/wqflask/static/new/css/marker_regression.css - changed background color when selecting a row (i.e. "highlight color")
2020-09-22Fixed a couple mistakes in the previous commit and changed the positionzsloan
header on the mapping results page to include the mapping scale * wqflask/wqflask/marker_regression/run_mapping.py - changed how "display_pos" is defined for marker obs * wqflask/wqflask/templates/mapping_results.html - Fixed issues with last commit and changed position header name to include mapping scale
2020-09-22Replaced Chr and Mb/cM columns with a single position column in mappingzsloan
results and also changes the -log(p) to use an endash instead * wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos" to each marker object that is a combination of Chr and Mb/cM * wqflask/wqflask/templates/mapping_results.html - Included "display_pos" in results table and replaced -log(p) with using an endash
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Convert "target_string" to a str typeBonfaceKilz
* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string" to a str, otherwise an exception will be thrown if it's None.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"BonfaceKilz
* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value.
2020-09-17Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
2020-09-17Fix errors in testsBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py test_check_resource_availability_non_default_mask): Mock flask's global 'g' variable properly. * wqflask/tests/base/test_trait.py: Ditto. * wqflask/tests/utility/test_authentication_tools.py: Ditto.
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-17Apply pep8BonfaceKilz
* wqflask/utility/hmac.py: Apply pep8 and fix typo.
2020-09-17Add tests for hmac utilityBonfaceKilz
* wqflask/tests/utility/test_hmac.py: New tests.
2020-09-16Add new tests for "base/trait.py"BonfaceKilz
* wqflask/tests/base/test_trait.py: New tests.
2020-09-16Apply pep8BonfaceKilz
* wqflask/utility/authentication_tools.py: Apply pep8 formatting to file.
2020-09-16Add tests for "add_new_resource" methodBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py: Add them.
2020-09-16Remove unnecessary if branchBonfaceKilz
* wqflask/utility/authentication_tools.py (check_resource_availability): Combine if statements into one boolean check in one if branch.
2020-09-16Add tests for authentication toolsBonfaceKilz
Catches bugs in: - https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8 * wqflask/tests/utility/test_authentication_tools.py: New file. Add tests for "check_resource_availability".
2020-09-15Fix failing testsBonfaceKilz
* wqflask/tests/base/test_data_set.py: Update failing tests introduced by the change in 301bdd2f4.
2020-09-14Merge branch 'scroller_testing' of github.com:zsloan/genenetwork2 into testingzsloan
2020-09-13Added in-progress info-page to views.py as well as in-progresszsloan
authorization/security guide * wqflask/wqflask/views.py - Added endpoint for info page and authorization/security tutorial
2020-09-11Wrote code and template for reproducing GN1's Info Page (page thatzsloan
displays info about a dataset + download links for its data) * wqflask/wqflask/db_info.py - Python that pulls the info out of the DB and parses the download links from the ipfs response * wqflask/wqflask/templates/info_page.html - template for displaying db info; need to make a lot of changes to its format/aesthetics
2020-09-10Modified "natural-minus-na" sort function to treat an array of valueszsloan
as equivalent to "N/A" (since different tables sometimes include other values that imply there's no value) and applied it to some extra columns in the Interval Analyst table * wqflask/wqflask/static/new/javascript/search_results.js - Modified sort_NAs function to take an array of "N/A"-equivalent values instead of just comparing against the string "N/A" * wqflask/wqflask/templates/mapping_results.html - Applied "natural-minus-na" sort method to several columns that include "--" in the Interval Analyst table
2020-09-10Fixed several sorting issues and moved orderDataType definitions intozsloan
search_results.js since all the tables that use them import that file (that file's name needs to be changed, though) * wqflask/wqflask/static/new/javascript/search_results.js - Added the dom-checkbox and dom-inner-text order types into this file; they were previously duplicated across several template files * wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type to relevant columns with hyperlink contents and disabled deferRender since it conflicted with use of both pagination and orderDataType for sorting * wqflask/wqflask/templates/gsearch_pheno.html - Same as above * wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a few columns that have hyperlink values - still need to modify natural-minus-na to also include other "N/A"-equivalent values like "--" * wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox and dom-inner-text order types from this file since they were moved to search_results.js
2020-09-08Changed the Add button color for all the different pages that use itzsloan
* wqflask/wqflask/templates/collections/view.html - changed Add button color * wqflask/wqflask/templates/correlation_matrix.html - changed Add button color * wqflask/wqflask/templates/correlation_page.html - changed Add button color * wqflask/wqflask/templates/mapping_results.html - changed Add button color * wqflask/wqflask/templates/search_result_page.html - changed Add button color
2020-09-08Search code now checks if there are more than 50,000 results beforezsloan
running the code that queries the DB for max LRS locus information (which is what takes the most time to run) and sets a variable that indicates to the template (search_results.html) that it shouldn't show the results * wqflask/wqflask/search_results.py - Check number of results from base query in order to prevent certain searches from running too long
2020-09-08Changed regular and global search results table to use the new sortzsloan
method that always places NAs at bottom, changed the Add to Collection button's color, and added something to the regular search page template to display alternative text if there are more than 50000 results * wqflask/wqflask/templates/gsearch_gene.html - Added natural-minus-na sort to certain columns and changed Add button color * wqflask/wqflask/templates/gsearch_pheno.html - Added natural-minus-na sort to certain columns and changed Add button color * wqflask/wqflask/templates/search_result_page.html - Added natural-minus-na sort to certain columns, changed Add button color, and added template logic that shows alternative text if there are more than 50,000 results
2020-09-08Added a sort function (derived from the natural sort import) that alwayszsloan
places N/As at the bottom regardless of search direction * wqflask/wqflask/static/new/javascript/search_results.js - created "natural-minus-na" sort
2020-09-04Update how static js/ css files are fetchedBonfaceKilz
* wqflask/wqflask/views.p:(css, js) Add "css" router decorator. Also, if "js_alt" is in path, fetch the file from "GUIX_PROFILE/share/javascript" instead of the default directory: "GUIX_PROFILE/share/genenetwork2/javascript" See: <https://github.com/genenetwork/genenetwork2/issues/436>
2020-09-01There was a missing quote in one of the javascript imports added by thezsloan
PR changing them to get fetched from GUIX; I need to check and see if there are other situations like this * wqflask/wqflask/templates/mapping_results.html - Added missing quote
2020-09-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-01Fixed indent issue that could cause error when showing the haplotypezsloan
analyst in the mapping chromosome view * wqflask/wqflask/marker_regression/display_mapping_results.py - Indented a bit of code that was wrongly indented in such a way that the variable "ind" wasn't set if "plotbxd" is 0
2020-09-01Use "md5.min.js" from guixBonfaceKilz
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