| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-09-20 | write probeset datasets to text files | Alexander_Kabui | |
| 2022-09-20 | Decompose file into separate modulesrefactor-data_set_py-20220920 | Frederick Muriuki Muriithi | |
| To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently. | |||
| 2022-09-19 | Remove commented-out html | zsloan | |
| 2022-09-19 | Provide fixtures for test. Fix error to pass test. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2022-09-19 | Remove "wrong" assertions | Frederick Muriuki Muriithi | |
| The assertions was checking that the function was implemented a certain way, rather than whether the function was doing the correct thing. | |||
| 2022-09-19 | Check paths before running gemma command | Frederick Muriuki Muriithi | |
| * Check that the required file paths exist * Check the bimbam directory path only once | |||
| 2022-09-19 | Improve error reporting for no mapping results | Frederick Muriuki Muriithi | |
| * 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. | |||
| 2022-09-19 | Check for file size before attempting parsing | Frederick Muriuki Muriithi | |
| Empty files lead to json encoding errors; this commit checks whether the file is empty before attempting to parse the file. | |||
| 2022-09-19 | Display correct error for missing file/directory | Frederick Muriuki Muriithi | |
| Provide the user with the missing file/directory in the error message to make debugging easier. | |||
| 2022-09-19 | Refactor: raise appropriate error | Frederick Muriuki Muriithi | |
| If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`. | |||
| 2022-09-16 | Add example code to docstring of MonadicDictCursor. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDictCursor): Add example code to docstring. | |||
| 2022-09-16 | Add example code to docstring of MonadicDict. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDict): Add example code to docstring. | |||
| 2022-09-16 | Initialize empty MonadicDict by default. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDict)[__init__]: Set default dictionary argument to the empty dictionary. | |||
| 2022-09-14 | Add monadic utilities MonadicDict and MonadicDictCursor. | Arun Isaac | |
| * wqflask/utility/monads.py: New file. | |||
| 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 | Frederick Muriuki Muriithi | |
| The assumption that the resultset will never be empty was leading to a lot of errors. | |||
| 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 | zsloan | |
| A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome | |||
| 2022-09-09 | Fix bug in retrieve_other_names | zsloan | |
| 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) | |||
| 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 | Muriithi Frederick Muriuki | |
| Bug/fix broken correlations | |||
| 2022-09-09 | Fetch sample values correctly | Munyoki Kilyungi | |
| * wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation. | |||
| 2022-09-09 | Add missing import | Munyoki Kilyungi | |
| * wqflask/base/trait.py: Import utility.hmac | |||
| 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 | Frederick Muriuki Muriithi | |
| Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence. | |||
| 2022-09-09 | Use `database_connection()` | Frederick Muriuki Muriithi | |
| Call the `database_connection()` function to get a connection to the database. | |||
| 2022-09-09 | Replace `g.db.execute` with `cursor.execute` | Frederick Muriuki Muriithi | |
| 2022-09-09 | Comment out pickling to avoid error | Frederick Muriuki Muriithi | |
| Pickling was failing with "TypeError: cannot pickle 'Connection' object" This commit avoids the error by temporarily commenting out the line to prevent the pickling to actually test the working of the system on the CI/CD server. | |||
| 2022-09-09 | If port is null, use MySQL's default 3306 | Frederick Muriuki Muriithi | |
| 2022-09-09 | Use `urllib.parse.urljoin` for urls | Frederick Muriuki Muriithi | |
| Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity. | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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