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2022-09-23Check docstring style using pylint....* .pylintrc: New file. Arun Isaac
2022-09-22Fix bug in GeneUtil.py query where extra quotes caused an errorzsloan
2022-09-22Use passed in cursor instead of initialising a new cursor.Frederick Muriuki Muriithi
2022-09-22Provide database cursor as argument for TheSpecies and Chromosomes...Provide the database cursor as an argument to the methods of the two classes: * wqflask.base.species.TheSpecies * wqflask.base.species.Chromosomes Also update dependent code to initialise and pass the cursor where these classes are used. Frederick Muriuki Muriithi
2022-09-22Update tests: pass in missing arguments.Frederick Muriuki Muriithi
2022-09-21Added Markers/HumanMarkers import to datasetgroup.py and removed it from...__init__.py Previously it threw an error when it tried to use Markers/HumanMarkers in datasetgroup.py; since Markers/HumanMarkers doesn't seem to be used anywhere else, I think it's okay for the import to only be in datasetgroup.py zsloan
2022-09-21Refactor: pass redis and db connections as argument...Pass the redis and database connection/cursors as arguments to the class methods, and do not retain a copy of the connections/cursors. This allows us to do the connection management in the context managers elsewhere - ideally, at the top-level. For now the context manager is within the `create_dataset` function, but this should be moved out to a higher level once the lower levels are verified to be working as expected. Frederick Muriuki Muriithi
2022-09-20Make -logP columns uniformzsloan
2022-09-20Make -logP columns uniformzsloan
2022-09-20Re-add collect import to views.py...Not sure why this was removed...I guess it looked like an unused import? zsloan
2022-09-20Make Search and Global Search Max -logP columns uniformzsloan
2022-09-20Fix gsearch ProbeSet queryzsloan
2022-09-20Remove global `Dataset_Getter` variable...Since the `__post_init__` method in the 'DatasetType' class checks whether data is in redis before hitting the database, it does not matter whether there is a global object of the type, as long as we make sure to call the object correctly. This commit makes that happen. Frederick Muriuki Muriithi
2022-09-20Revert "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
2022-09-20Use member variable `self.conn` to avoid test failure...Use the `self.conn` variable to prevent test from failing. Frederick Muriuki Muriithi
2022-09-20Merge branch 'Alexanderlacuna-feature/generate-text-files' into testingFrederick Muriuki Muriithi
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 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-20220920Frederick Muriuki Muriithi
2022-09-19Fix broken test...Because the input element was changed to a button element there was no longer a "value" attribute. I'm not sure what this assert is for, though; I changed it to just check for "Search" in the inner text, which makes it pass. zsloan
2022-09-19Remove commented-out htmlzsloan
2022-09-19Provide 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
2022-09-19Remove "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
2022-09-19Check paths before running gemma command...* Check that the required file paths exist * Check the bimbam directory path only once Frederick Muriuki Muriithi
2022-09-19Improve 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
2022-09-19Check 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
2022-09-19Display 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
2022-09-19Refactor: raise appropriate error...If a file/directory does not exist, raise the builtin `FileNotFoundError` rather than the generic `Exception`. Frederick Muriuki Muriithi
2022-09-16Add example code to docstring of MonadicDictCursor....* wqflask/utility/monads.py (MonadicDictCursor): Add example code to docstring. Arun Isaac
2022-09-16Add example code to docstring of MonadicDict....* wqflask/utility/monads.py (MonadicDict): Add example code to docstring. Arun Isaac
2022-09-16Initialize empty MonadicDict by default....* wqflask/utility/monads.py (MonadicDict)[__init__]: Set default dictionary argument to the empty dictionary. Arun Isaac
2022-09-14Add monadic utilities MonadicDict and MonadicDictCursor....* wqflask/utility/monads.py: New file. Arun Isaac
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
2022-09-12Fix asserts: Use variable for assertFrederick Muriuki Muriithi
2022-09-12Check there is target data before running correlationsFrederick Muriuki Muriithi
2022-09-12Display cause(s) of test failure.Frederick 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