| Age | Commit message (Expand) | Author |
|---|---|---|
| 2022-09-20 | Revert "Use member variable `self.conn` to avoid test failure"...This reverts commit 4fafdfd8487ddf61105b2a5ca92534c8014c1db4. While using `self.conn.cursor()` works in the tests, it will not work in the application since the point of initialisation could be very different from the point where the 'property' is called. | Frederick Muriuki Muriithi |
| 2022-09-20 | Use member variable `self.conn` to avoid test failure...Use the `self.conn` variable to prevent test from failing. | Frederick Muriuki Muriithi |
| 2022-09-20 | integrate use of text files | Alexander_Kabui |
| 2022-09-20 | store text files in TMPDIR | Alexander_Kabui |
| 2022-09-20 | write probeset datasets to text files | Alexander_Kabui |
| 2022-09-20 | Decompose file into separate modules...To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently. refactor-data_set_py-20220920 | Frederick Muriuki Muriithi |
| 2022-09-19 | Remove commented-out html | zsloan |
| 2022-09-19 | Provide fixtures for test. Fix error to pass test....Provide the following (empty) files to be used for the test * wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt * wqflask/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt Rework the paths in `wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py` such that they point to the files added above for testing. Do not require that the phenotype file exists in `wqflask/wqflask/marker_regression/gemma_mapping.py` before attempting the mapping. | Frederick Muriuki Muriithi |
| 2022-09-19 | Remove "wrong" assertions...The assertions was checking that the function was implemented a certain way, rather than whether the function was doing the correct thing. | Frederick Muriuki Muriithi |
| 2022-09-19 | Check paths before running gemma command...* Check that the required file paths exist * Check the bimbam directory path only once | Frederick Muriuki Muriithi |
| 2022-09-19 | Improve error reporting for no mapping results...* wqflask/wqflask/marker_regression/exceptions.py: new NoMappingResultsError exception * wqflask/wqflask/templates/mapping_error.html: reword display of the errors * wqflask/wqflask/views.py: Raise the NoMappingResultsError exception in the case where there are no results for the mapping. | Frederick Muriuki Muriithi |
| 2022-09-19 | Check for file size before attempting parsing...Empty files lead to json encoding errors; this commit checks whether the file is empty before attempting to parse the file. | Frederick Muriuki Muriithi |
| 2022-09-19 | Display correct error for missing file/directory...Provide the user with the missing file/directory in the error message to make debugging easier. | Frederick Muriuki Muriithi |
| 2022-09-19 | Refactor: raise appropriate error...If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`. | Frederick Muriuki Muriithi |
| 2022-09-16 | Add example code to docstring of MonadicDictCursor....* wqflask/utility/monads.py (MonadicDictCursor): Add example code to docstring. | Arun Isaac |
| 2022-09-16 | Add example code to docstring of MonadicDict....* wqflask/utility/monads.py (MonadicDict): Add example code to docstring. | Arun Isaac |
| 2022-09-16 | Initialize empty MonadicDict by default....* wqflask/utility/monads.py (MonadicDict)[__init__]: Set default dictionary argument to the empty dictionary. | Arun Isaac |
| 2022-09-14 | Add monadic utilities MonadicDict and MonadicDictCursor....* wqflask/utility/monads.py: New file. | Arun Isaac |
| 2022-09-12 | Add glyphicon for trait page Download table | zsloan |
| 2022-09-12 | Add glyphicons for sample table Export/Reset buttons | zsloan |
| 2022-09-12 | Add glyphicon for GEMMA compute button | zsloan |
| 2022-09-12 | Add glyphicons to Export/Reset buttons in Transform and Filter form | zsloan |
| 2022-09-12 | Move global search button and add glyphicon | zsloan |
| 2022-09-12 | Add search glyphicons + index_page.css for the Info button styling | zsloan |
| 2022-09-12 | Set Species drop-down to same width as Group/Type dropdowns | zsloan |
| 2022-09-13 | Increase table marker limit to 25000 | zsloan |
| 2022-09-13 | Fix bug where passing LOCO into the mapping API endpoint didn't work | zsloan |
| 2022-09-12 | Fix query: Add comma to separate columns. | Frederick Muriuki Muriithi |
| 2022-09-12 | Check for species before calling `lower()` | Frederick Muriuki Muriithi |
| 2022-09-12 | Check there is target data before running correlations | Frederick Muriuki Muriithi |
| 2022-09-12 | Fix query: Remove extraneous bracket | Frederick Muriuki Muriithi |
| 2022-09-12 | Check for traits before computing | Frederick Muriuki Muriithi |
| 2022-09-12 | Fix query: remove wrongly-placed comma | Frederick Muriuki Muriithi |
| 2022-09-12 | Check db resultset before indexing into it...The assumption that the resultset will never be empty was leading to a lot of errors. | Frederick Muriuki Muriithi |
| 2022-09-12 | Check data is truthy before indexing into it. | Frederick Muriuki Muriithi |
| 2022-09-09 | Fix bug in display_mapping_results chromosome query...A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome | zsloan |
| 2022-09-09 | Fix bug in retrieve_other_names...After a recent change, it always tries to unpack 6 values from the query, but it should only be unpacking 4 values if not type ProbeSet (so it was throwing an error for anything not ProbeSet) | zsloan |
| 2022-09-09 | handle cases where tissue dataset vals are empty list | Alexander_Kabui |
| 2022-09-09 | tissue:fetch for query formatting | Alexander_Kabui |
| 2022-09-09 | Fix query: remove string interpolation. | Frederick Muriuki Muriithi |
| 2022-09-09 | Retain only a single import of the same module | Frederick Muriuki Muriithi |
| 2022-09-09 | Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlations...Bug/fix broken correlations | Muriithi Frederick Muriuki |
| 2022-09-09 | Fetch sample values correctly...* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation. | Munyoki Kilyungi |
| 2022-09-09 | Add missing import...* wqflask/base/trait.py: Import utility.hmac | Munyoki Kilyungi |
| 2022-09-09 | Import missing module. | Frederick Muriuki Muriithi |
| 2022-09-09 | Check whether trait_list and sample_data exist before operations | Frederick Muriuki Muriithi |
| 2022-09-09 | Remove `None` values from dataset | Frederick Muriuki Muriithi |
| 2022-09-09 | Filter out Samples without values | Frederick Muriuki Muriithi |
| 2022-09-09 | Refactor: Add tests and handle edge case...Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence. | Frederick Muriuki Muriithi |
| 2022-09-09 | Use `database_connection()`...Call the `database_connection()` function to get a connection to the database. | Frederick Muriuki Muriithi |
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| GeneNetwork (2nd generation) |
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