| Age | Commit message (Expand) | Author |
|---|
| 2022-09-26 | Add indexing script for global search....* wqflask/scripts/index.py: New file.
| Arun Isaac |
| 2022-09-26 | Add xapian database connection utilities....* etc/default_settings.py (XAPIAN_DB_PATH): New variable.
* wqflask/wqflask/database.py: Import xapian.
(xapian_database, xapian_writable_database): New functions.
| Arun Isaac |
| 2022-09-26 | Generalize sql_uri function to get any setting....* wqflask/wqflask/database.py (sql_uri): Generalize to get_setting.
(database_connection): Call get_setting instead of sql_uri.
| Arun Isaac |
| 2022-09-25 | Fix issue where the display name was used in the hmac for phenotype traits | zsloan |
| 2022-09-23 | Remove click handler on global search....check_search_term is not relevant to global search. It checks search
terms in the unrelated #or_search and #and_search fields.
* wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js:
Do not call check_search_term on clicking global search button.
| Arun Isaac |
| 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...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 |
| 2022-09-22 | Update tests: pass in missing arguments. | Frederick Muriuki Muriithi |
| 2022-09-21 | Added 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 |
| 2022-09-21 | Refactor: 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 |
| 2022-09-20 | Make -logP columns uniform | zsloan |
| 2022-09-20 | Make -logP columns uniform | zsloan |
| 2022-09-20 | Re-add collect import to views.py...Not sure why this was removed...I guess it looked like an unused import?
| zsloan |
| 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...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 |
| 2022-09-20 | 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 |
