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2020-11-03Update glossary template with markdown contentBonfaceKilz
2020-11-03Rename glossary.py to markdown_routes.py...Evary page with markdown content will have routes added in markdown_routes.py * markdown_routes.py: New file. * wqflask/wqflask/glossary.py: Delete it. * wqflask/wqflask/__init__.py: Update import. BonfaceKilz
2020-11-03Remove encoding header for file...In python3 the default encoding is utf-8 so this is redundant. BonfaceKilz
2020-11-03Separate unittests from integration testsBonfaceKilz
2020-11-03Add test for "/glossary" routeBonfaceKilz
2020-11-03Add glossary template and use itBonfaceKilz
2020-11-03Add and register glossary blueprintBonfaceKilz
2020-11-03Apply PEP-8 to file...* wqflask/wqflask/__init__.py: Remove unused import and variables. Also add module docstring and pylint errors to ignore. (before_request): Use correct spacing. BonfaceKilz
2020-11-02Merge pull request #476 from zsloan/correlation_errors_fix...Correlation errors fixzsloan
2020-11-02Created function for encoding the column value as bytes when fetching from th......* wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis zsloan
2020-11-02Changed correlation page logic to skip over traits that share fewer than 6 sa......* wqflask/wqflask/correlation/show_corr_results.py - Moved the num_overlap check so that it never attempts to calculate the correlation if it's too low + checked if trait_object is None in the main loop (since it would be returned as None if the user doesn't have permissions zsloan
2020-10-31Removed a line adding the ceiling of the Max LRS to the Y axis, since it has ......* wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis zsloan
2020-10-31remove redundant classesAlexanderlacuna
2020-10-31use descriptive variable namesAlexanderlacuna
2020-10-31Use more descriptive variable and class namesAlexanderlacuna
2020-10-30add test for get_export_metadataAlexanderlacuna
2020-10-30Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te...Alexanderlacuna
2020-10-29Fixed issue with single-chromosome mapping after the bootstrap fix and fixed ......* wqflask/wqflask/marker_regression/display_mapping_results.py - Cast self.qtlresults 'chr' as a string since the comparison between it and the chromosome names was faililng due to numeric chromosomes being int type + used a list comprehension that converts None to an empty string when creating a comma-joined string from the list of mapping output files zsloan
2020-10-29Merge branch 'testing' of github.com:genenetwork/genenetwork2 into reaper_boo...zsloan
2020-10-29add test for show_traitAlexanderlacuna
2020-10-29Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te...Alexanderlacuna
2020-10-29Merge pull request #469 from BonfaceKilz/bug/fix-cookies-verification...Bug/Fix cookie verification bugBonfaceKilz
2020-10-29resolve merge conflictAlexanderlacuna
2020-10-29format fileAlexanderlacuna
2020-10-29remove print statement in for loopAlexanderlacuna
2020-10-29add test for show_trait/export_trait_dataAlexanderlacuna
2020-10-29Merge pull request #471 from BonfaceKilz/bug/replace-map-on-strip-method...Bug/Replace map on strip with a list comprehension that calls strip()BonfaceKilz
2020-10-28Merge pull request #470 from zsloan/mapping_chr_view_fix...Fixed error when zooming into a chromosome when mappingzsloan
2020-10-28A non-string being used as a paramter in HT.Link caused an error after the Py......* wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string zsloan
2020-10-29Replace map on strip with a list comprehension that calls strip()...* scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map string.strip on a list of strings. Instead use a list comprehension and apply strip() on each element of the list. * wqflask/wqflask/marker_regression/plink_mapping.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto. BonfaceKilz
2020-10-28Use latin-1 encoding when converting hmac secret to bytes...* wqflask/utility/hmac.py (hmac_creation): Use latin-1 when serializing the hmac secret. This ensures that the behaviour of *verify_cookie* remains the same as in the python2 tip. BonfaceKilz
2020-10-28Add new test for hmac_creation with latin-1 secret...* wqflask/tests/utility/test_hmac.py (test_hmac_creation_with_cookie): New test. For this test, use a secret that behaves differently when encoded to either utf-8 or latin-1. BonfaceKilz
2020-10-28Add tests for cookie verificationBonfaceKilz
2020-10-28Merge pull request #468 from zsloan/export_fix...Fixed trait page export issue caused by Scrollerzsloan
2020-10-28Fixed trait page export to work with Scroller + added metadata for non-Pheno......* wqflask/wqflask/show_trait/export_trait_data.py - Added metadata for non-Phenotype traits and column headers (which didn't previously exist) * wqflask/wqflask/static/new/javascript/show_trait.js - Changed export_sample_table_data to use DataTables API instead of just selecting from the DOM with JQuery zsloan
2020-10-27Cast ProbeSet description as binary to fix encoding issue on global search page...* wqflask/wqflask/gsearch.py - Cast ProbeSet description as binary zsloan
2020-10-27Merge pull request #466 from zsloan/show_trait_attributes_fix...Fix issue where attribute values were displayed in the wrong columnszsloan
2020-10-27Get the "first_attr_start_pos" from a samplelist instead of from each individ......* wqflask/base/webqtlCaseData.py - Removed code getting first_attr_start_pos * wqflask/wqflask/show_trait/SampleList.py - Added code getting first_attr_start_pos and assigning it to all samples + removing one unnecessary sort * wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js - Fixed issue that was causing the N column to not be displayed zsloan
2020-10-27Cast post and pre-publication descriptions into binary...* wqflask/wqflask/gsearch.py (GSearch): There's an exception thrown when the decode method is called on that description string. If the casting is absent, and the decode statements are removed, the some characters get broken. BonfaceKilz
2020-10-27Merge pull request #465 from Alexanderlacuna/test-branch...add test for trait_dataBonfaceKilz
2020-10-27switch from single quote to double quoteAlexanderlacuna
2020-10-27address failuresAlexanderlacuna
2020-10-27added changes to fileAlexanderlacuna
2020-10-27modified to use pep8 standardsAlexanderlacuna
2020-10-27Merge pull request #422 from BonfaceKilz/build/python3-migration...Build/python3 migrationBonfaceKilz
2020-10-26modified test fileAlexanderlacuna
2020-10-26Add page load metrics to footer...* wqflask/wqflask/__init__.py (before_request): New function. Add method for calculating total request_time to global context. * wqflask/wqflask/templates/base.html: - Display total server load time. - Display total page rendering time, and add js functionality to calculate it. BonfaceKilz
2020-10-23Fixed bootstrap results when using interval mapping for the full genome view;......* wqflask/wqflask/marker_regression/display_mapping_results.py - Fixed bootstrap results by iterating through qtlresults instead of self.genotype (the latter didn't have intervals added, resulting in the bootstrap result positions being wrong) zsloan
2020-10-23Merge pull request #462 from zsloan/fix_export_error...Fixed trait export for situations where there's no authors/title/journalzsloan
2020-10-23Fixed trait export for situations where there's no authors/title/journalzsloan
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