| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-11-03 | Fixed a sort used when doing the haplotype analysis to be compatible with ↵ | zsloan | |
| Python 3 * wqflask/wqflask/marker_regression/display_mapping_results.py - The arguments for sort are different in Python 3, so it was changed to be compatible | |||
| 2020-11-03 | Fix false-positive tests | BonfaceKilz | |
| * 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. | |||
| 2020-11-03 | Merge pull request #478 from zsloan/loading_page_n_fix | zsloan | |
| Joined sample names in primary_samples and all_samples with commas be… | |||
| 2020-11-03 | Joined sample names in primary_samples and all_samples with commas because ↵ | zsloan | |
| this list was being split to get the N of samples; not sure why this was working before * wqflask/wqflask/show_trait/show_trait.py primary_samples and all_samples passed as hidden form inputs now have names split by commas so they can be counted correctly when displaying the N on the mapping loading screen | |||
| 2020-11-03 | Delete file | BonfaceKilz | |
| * wqflask/tests/integration/test_glossary.py: Delete it. Earlier renamed to test_markdown_routes. | |||
| 2020-11-03 | Add basic tests for rendering_markdown | BonfaceKilz | |
| * wqflask/tests/unit/wqflask/test_markdown_routes.py: New tests. | |||
| 2020-11-03 | Add basic structure for "/glossary" routes test | BonfaceKilz | |
| 2020-11-03 | Move logic for fetching md files to it's own function | BonfaceKilz | |
| * wqflask/wqflask/markdown_routes.py (render_markdown): New function. (glossary): use render_markdown function. | |||
| 2020-11-03 | Add simple md content in glossary.md | BonfaceKilz | |
| 2020-11-03 | Update glossary template with markdown content | BonfaceKilz | |
| 2020-11-03 | Rename glossary.py to markdown_routes.py | BonfaceKilz | |
| 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. | |||
| 2020-11-03 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | Alexanderlacuna | |
| test-showtrait | |||
| 2020-11-03 | remove unnecessary comments | Alexanderlacuna | |
| 2020-11-03 | add pep8 formatting | Alexanderlacuna | |
| 2020-11-03 | add tests for the get_categorical_variables function | Alexanderlacuna | |
| 2020-11-03 | Remove encoding header for file | BonfaceKilz | |
| In python3 the default encoding is utf-8 so this is redundant. | |||
| 2020-11-03 | Separate unittests from integration tests | BonfaceKilz | |
| 2020-11-03 | Add test for "/glossary" route | BonfaceKilz | |
| 2020-11-03 | Add glossary template and use it | BonfaceKilz | |
| 2020-11-03 | Add and register glossary blueprint | BonfaceKilz | |
| 2020-11-03 | Apply PEP-8 to file | BonfaceKilz | |
| * wqflask/wqflask/__init__.py: Remove unused import and variables. Also add module docstring and pylint errors to ignore. (before_request): Use correct spacing. | |||
| 2020-11-03 | switch from assertFalse to assertIs | Alexanderlacuna | |
| 2020-11-03 | switch from assertTrue/False to assertIs to make the tests tighter | Alexanderlacuna | |
| 2020-11-03 | use assertTrue and assertFalse in while testing boolean | Alexanderlacuna | |
| 2020-11-02 | Merge pull request #476 from zsloan/correlation_errors_fix | zsloan | |
| Correlation errors fix | |||
| 2020-11-02 | Created function for encoding the column value as bytes when fetching from ↵ | zsloan | |
| the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * 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 | |||
| 2020-11-02 | Changed correlation page logic to skip over traits that share fewer than 6 ↵ | zsloan | |
| samples + traits that user doesn't have permission to access * 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 | |||
| 2020-11-02 | add better formatting | Alexanderlacuna | |
| 2020-11-02 | add function docstring | Alexanderlacuna | |
| 2020-11-02 | add tests for show trait module | Alexanderlacuna | |
| 2020-10-31 | Removed a line adding the ceiling of the Max LRS to the Y axis, since it has ↵ | zsloan | |
| the potential to cause an axis tick to appear above the figure * wqflask/wqflask/marker_regression/display_mapping_results.py - Removed a line adding the ceiling of the max LRS/LOD value to the Y axis | |||
| 2020-10-31 | remove redundant classes | Alexanderlacuna | |
| 2020-10-31 | use descriptive variable names | Alexanderlacuna | |
| 2020-10-31 | Use more descriptive variable and class names | Alexanderlacuna | |
| 2020-10-30 | add test for get_export_metadata | Alexanderlacuna | |
| 2020-10-30 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | Alexanderlacuna | |
| test-branch | |||
| 2020-10-29 | Fixed issue with single-chromosome mapping after the bootstrap fix and fixed ↵ | zsloan | |
| error that occurred if either bootstrap or permutations were set to 0 * 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 | |||
| 2020-10-29 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵ | zsloan | |
| reaper_bootstrap_fix | |||
| 2020-10-29 | add test for show_trait | Alexanderlacuna | |
| 2020-10-29 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | Alexanderlacuna | |
| test-branch | |||
| 2020-10-29 | Merge pull request #469 from BonfaceKilz/bug/fix-cookies-verification | BonfaceKilz | |
| Bug/Fix cookie verification bug | |||
| 2020-10-29 | resolve merge conflict | Alexanderlacuna | |
| 2020-10-29 | format file | Alexanderlacuna | |
| 2020-10-29 | remove print statement in for loop | Alexanderlacuna | |
| 2020-10-29 | add test for show_trait/export_trait_data | Alexanderlacuna | |
| 2020-10-29 | Merge pull request #471 from BonfaceKilz/bug/replace-map-on-strip-method | BonfaceKilz | |
| Bug/Replace map on strip with a list comprehension that calls strip() | |||
| 2020-10-28 | Merge pull request #470 from zsloan/mapping_chr_view_fix | zsloan | |
| Fixed error when zooming into a chromosome when mapping | |||
| 2020-10-28 | A non-string being used as a paramter in HT.Link caused an error after the ↵ | zsloan | |
| Python3 switchover, so I converted it to a string * wqflask/wqflask/marker_regression/display_mapping_results.py - cast theGO["snpCount"] as a string | |||
| 2020-10-29 | Replace map on strip with a list comprehension that calls strip() | BonfaceKilz | |
| * 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. | |||
| 2020-10-28 | Use latin-1 encoding when converting hmac secret to bytes | BonfaceKilz | |
| * 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. | |||
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