| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-09-22 | Fix bug in GeneUtil.py query where extra quotes caused an error | zsloan | |
| 2022-09-22 | Use passed in cursor instead of initialising a new cursor. | Frederick Muriuki Muriithi | |
| 2022-09-22 | Provide database cursor as argument for TheSpecies and Chromosomes | Frederick Muriuki Muriithi | |
| 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. | |||
| 2022-09-22 | Update tests: pass in missing arguments. | Frederick Muriuki Muriithi | |
| 2022-09-21 | Added Markers/HumanMarkers import to datasetgroup.py and removed it from | zsloan | |
| __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 | |||
| 2022-09-21 | Refactor: pass redis and db connections as argument | Frederick Muriuki Muriithi | |
| 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. | |||
| 2022-09-20 | Make -logP columns uniform | zsloan | |
| 2022-09-20 | Make -logP columns uniform | zsloan | |
| 2022-09-20 | Re-add collect import to views.py | zsloan | |
| Not sure why this was removed...I guess it looked like an unused import? | |||
| 2022-09-20 | Make Search and Global Search Max -logP columns uniform | zsloan | |
| 2022-09-20 | Fix gsearch ProbeSet query | zsloan | |
| 2022-09-20 | Remove global `Dataset_Getter` variable | Frederick Muriuki Muriithi | |
| 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. | |||
| 2022-09-20 | Revert "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. | |||
| 2022-09-20 | Use member variable `self.conn` to avoid test failure | Frederick Muriuki Muriithi | |
| Use the `self.conn` variable to prevent test from failing. | |||
| 2022-09-20 | Merge branch 'Alexanderlacuna-feature/generate-text-files' into testing | 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 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 | Fix broken test | zsloan | |
| 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. | |||
| 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 | Fix asserts: Use variable for assert | Frederick Muriuki Muriithi | |
| 2022-09-12 | Check there is target data before running correlations | Frederick Muriuki Muriithi | |
| 2022-09-12 | Display cause(s) of test failure. | 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. | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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