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2022-09-20Revert "Use member variable `self.conn` to avoid test failure"Frederick Muriuki Muriithi
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.
2022-09-20Use member variable `self.conn` to avoid test failureFrederick Muriuki Muriithi
Use the `self.conn` variable to prevent test from failing.
2022-09-20integrate use of text filesAlexander_Kabui
2022-09-20store text files in TMPDIRAlexander_Kabui
2022-09-20write probeset datasets to text filesAlexander_Kabui
2022-09-20Decompose file into separate modulesrefactor-data_set_py-20220920Frederick Muriuki Muriithi
To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently.
2022-09-19Remove commented-out htmlzsloan
2022-09-19Provide 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.
2022-09-19Remove "wrong" assertionsFrederick Muriuki Muriithi
The assertions was checking that the function was implemented a certain way, rather than whether the function was doing the correct thing.
2022-09-19Check paths before running gemma commandFrederick Muriuki Muriithi
* Check that the required file paths exist * Check the bimbam directory path only once
2022-09-19Improve error reporting for no mapping resultsFrederick 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.
2022-09-19Check for file size before attempting parsingFrederick Muriuki Muriithi
Empty files lead to json encoding errors; this commit checks whether the file is empty before attempting to parse the file.
2022-09-19Display correct error for missing file/directoryFrederick Muriuki Muriithi
Provide the user with the missing file/directory in the error message to make debugging easier.
2022-09-19Refactor: raise appropriate errorFrederick Muriuki Muriithi
If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`.
2022-09-16Add example code to docstring of MonadicDictCursor.Arun Isaac
* wqflask/utility/monads.py (MonadicDictCursor): Add example code to docstring.
2022-09-16Add example code to docstring of MonadicDict.Arun Isaac
* wqflask/utility/monads.py (MonadicDict): Add example code to docstring.
2022-09-16Initialize empty MonadicDict by default.Arun Isaac
* wqflask/utility/monads.py (MonadicDict)[__init__]: Set default dictionary argument to the empty dictionary.
2022-09-14Add monadic utilities MonadicDict and MonadicDictCursor.Arun Isaac
* wqflask/utility/monads.py: New file.
2022-09-12Add glyphicon for trait page Download tablezsloan
2022-09-12Add glyphicons for sample table Export/Reset buttonszsloan
2022-09-12Add glyphicon for GEMMA compute buttonzsloan
2022-09-12Add glyphicons to Export/Reset buttons in Transform and Filter formzsloan
2022-09-12Move global search button and add glyphiconzsloan
2022-09-12Add search glyphicons + index_page.css for the Info button stylingzsloan
2022-09-12Set Species drop-down to same width as Group/Type dropdownszsloan
2022-09-13Increase table marker limit to 25000zsloan
2022-09-13Fix bug where passing LOCO into the mapping API endpoint didn't workzsloan
2022-09-12Fix query: Add comma to separate columns.Frederick Muriuki Muriithi
2022-09-12Check for species before calling `lower()`Frederick Muriuki Muriithi
2022-09-12Check there is target data before running correlationsFrederick Muriuki Muriithi
2022-09-12Fix query: Remove extraneous bracketFrederick Muriuki Muriithi
2022-09-12Check for traits before computingFrederick Muriuki Muriithi
2022-09-12Fix query: remove wrongly-placed commaFrederick Muriuki Muriithi
2022-09-12Check db resultset before indexing into itFrederick Muriuki Muriithi
The assumption that the resultset will never be empty was leading to a lot of errors.
2022-09-12Check data is truthy before indexing into it.Frederick Muriuki Muriithi
2022-09-09Fix bug in display_mapping_results chromosome queryzsloan
A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome
2022-09-09Fix bug in retrieve_other_nameszsloan
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)
2022-09-09handle cases where tissue dataset vals are empty listAlexander_Kabui
2022-09-09tissue:fetch for query formattingAlexander_Kabui
2022-09-09Fix query: remove string interpolation.Frederick Muriuki Muriithi
2022-09-09Retain only a single import of the same moduleFrederick Muriuki Muriithi
2022-09-09Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlationsMuriithi Frederick Muriuki
Bug/fix broken correlations
2022-09-09Fetch sample values correctlyMunyoki Kilyungi
* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation.
2022-09-09Add missing importMunyoki Kilyungi
* wqflask/base/trait.py: Import utility.hmac
2022-09-09Import missing module.Frederick Muriuki Muriithi
2022-09-09Check whether trait_list and sample_data exist before operationsFrederick Muriuki Muriithi
2022-09-09Remove `None` values from datasetFrederick Muriuki Muriithi
2022-09-09Filter out Samples without valuesFrederick Muriuki Muriithi
2022-09-09Refactor: Add tests and handle edge caseFrederick Muriuki Muriithi
Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence.
2022-09-09Use `database_connection()`Frederick Muriuki Muriithi
Call the `database_connection()` function to get a connection to the database.