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2020-11-04Update test_markdown_routes...* wqflask/tests/unit/wqflask/test_markdown_routes.py (test_render_markdown_when_fetching_locally): Fix failing test. BonfaceKilz
2020-11-04Add an edit link button to glossary pageBonfaceKilz
2020-11-04Wrap rendered content in div containerBonfaceKilz
2020-11-04Update glossary markdown fileBonfaceKilz
2020-11-04Use python3-genenetwork2 docker image on commit 0bf4ee6BonfaceKilz
2020-11-03Fix false-positive tests...* wqflask/tests/unit/wqflask/test_markdown_routes.py: (MockRequests404): Pass self in all properties. (MockRequests200): Ditto. (test_render_markdown): Rename to test_render_markdown_when_fetching_locally. (test_render_markdown_when_fetching_remotely): New test. BonfaceKilz
2020-11-03Delete file...* wqflask/tests/integration/test_glossary.py: Delete it. Earlier renamed to test_markdown_routes. BonfaceKilz
2020-11-03Add basic tests for rendering_markdown...* wqflask/tests/unit/wqflask/test_markdown_routes.py: New tests. BonfaceKilz
2020-11-03Add basic structure for "/glossary" routes testBonfaceKilz
2020-11-03Move logic for fetching md files to it's own function...* wqflask/wqflask/markdown_routes.py (render_markdown): New function. (glossary): use render_markdown function. BonfaceKilz
2020-11-03Use python3-genenetwork2 on commit bdce85d in container...* .github/workflows/main.yml: Update gn2 container. BonfaceKilz
2020-11-03Add simple md content in glossary.mdBonfaceKilz
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
2020-11-03Remove stale file...* jquery.qtip.css: Delete it. 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
2020-11-01Merge pull request #472 from Alexanderlacuna/test-branch...Adding more Test for show_trait moduleBonfaceKilz
2020-10-31Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te...Alexanderlacuna
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
2020-10-30Merge pull request #474 from zsloan/mapping_y_axis_fix...Mapping Y Axis Fixzsloan
2020-10-30Removed 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
2020-10-30add test for get_export_metadataAlexanderlacuna
2020-10-30Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te...Alexanderlacuna
2020-10-29Merge pull request #473 from zsloan/reaper_bootstrap_fix...Reaper bootstrap fixzsloan
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
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