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2022-05-31Extract utility functions from `fetch_all_database_data`Frederick Muriuki Muriithi
Extract the utility functions to help with understanding the what the `fetch_all_database_data` function is doing. This helps with maintenance.
2022-05-30Pass trait data as args to `fix_strains` and fix some bugsFrederick Muriuki Muriithi
The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function.
2022-05-27Move sql for CRUD operations on case-attrs from gn2 to gn3BonfaceKilz
2022-05-27Move sql for modifying case-attributes from gn2 to gn3BonfaceKilz
2022-05-27Return all the results from CaseAttributes column as isBonfaceKilz
* gn3/db/sample_data.py: Remove "collections" import. Add "Optional" import. (get_case_attributes): Return the results of "fetchall" from the case attributes. * tests/unit/db/test_sample_data.py (test_get_case_attributes): Update failing test.
2022-05-26Add Endpoint to get menu items for use in UIFrederick Muriuki Muriithi
2022-05-24Run partial correlations with external scriptFrederick Muriuki Muriithi
Use new external script to run the partial correlations for both cases, i.e. - against an entire dataset, or - against selected traits
2022-05-24New script to compute partial correlationsFrederick Muriuki Muriithi
* Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order.
2022-05-21Fix linting errorsFrederick Muriuki Muriithi
2022-05-21Use multiprocessing to improve performanceFrederick Muriuki Muriithi
2022-05-21Process primary, target and control traits in a single iterationFrederick Muriuki Muriithi
Rework the code to process the traits in a single iteration to improve performance.
2022-05-21Return generator object rather than tuplesFrederick Muriuki Muriithi
Return generator objects rather than pre-computed tuples to reduce the number of iterations needed to process the data, and thus improve the performance of the system somewhat.
2022-05-16Run computation in one-shot asynchronous processFrederick Muriuki Muriithi
After reworking the worker/runner to have a one-shot mode, add a function that queues up the task and then runs the worker in the one-shot mode to process the computation in the background.
2022-05-06Fix linting and typing errorsFrederick Muriuki Muriithi
2022-05-06Hook up pcorrs with target traits computationsFrederick Muriuki Muriithi
Enable the endpoint to actually compute partial correlations with selected target traits rather than against an entire dataset. Fix some issues caused by recent refactor that broke pcorrs against a dataset
2022-05-05Compute partial correlation with selected traitsFrederick Muriuki Muriithi
Compute partial correlations against a selection of traits rather than against an entire dataset.
2022-05-05Extract common error checking. Rename function.Frederick Muriuki Muriithi
* Extract the common error checking code into a separate function * Rename the function to make its use clearer
2022-05-03Refactor: Remove unnecessary loopFrederick Muriuki Muriithi
Remove an unnecessary looping construct to help with speeding up the partial correlations somewhat.
2022-04-29Replace whole header with the longest one, instead of just thezsloan
non-CaseAttribute headers (before this caused issues if someone was adding case attributes to a file that already contained some case attributes)
2022-04-29Get max string length instead when comparing headerszsloan
Apparently max(string1, string2) in Python gets the strong that is highest alphabetically, but I'm pretty sure this line was intenteded to get the header with the most items (which this commit doesn't fully address; you could still end up with a situation where some case attributes were removed while others were added, though that should be rare)
2022-04-12Delete "get_allowable_sampledata_headers"BonfaceKilz
* gn3/csvcmp.py (get_allowable_sampledata_headers): Delete it. * tests/unit/test_csvcmp.py: Remove "get_allowable_sampledata_headers" import. (test_get_allowable_csv_headers): Delete it.
2022-04-12Strip any newline, tab or carriage-return chars from sample dataBonfaceKilz
* gn3/db/sample_data.py (get_trait_csv_sample_data): Strip out "\n", "\t", or "\r" from the sample data. See: <https://issues.genenetwork.org/issues/csv-error-ITP_10001-longevity-data-set.html>
2022-04-07Fix pylint errorsBonfaceKilz
2022-04-07Fix mypy errorBonfaceKilz
2022-04-07Use case attribute id inside brackets if present during insertionsBonfaceKilz
* gn3/db/sample_data.py (delete_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_delete_sample_data): Update tests to capture the above.
2022-04-07Use case attribute id inside brackets if present during insertionsBonfaceKilz
* gn3/db/sample_data.py (insert_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_insert_sample_data): Update tests to capture the above.
2022-04-07Use case attribute id inside brackets if present during updatesBonfaceKilz
* gn3/db/sample_data.py: Import "parse_csv_column". (update_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to capture the above.
2022-04-07Add method for fetching the case_attributesBonfaceKilz
* gn3/db/sample_data.py (get_case_attributes): New function. * tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for the above.
2022-04-07Run python black on fileBonfaceKilz
* gn3/db/sample_data.py: Run "python black -l 79 ..."
2022-04-07Add method for parsing a csv header from uploaded sample-data fileBonfaceKilz
* gn3/csvcmp.py (parse_csv_column): New function. * tests/unit/test_csvcmp.py: Test case for the above.
2022-04-01Run python-black in fileBonfaceKilz
* gn3/csvcmp.py: Run "black -l 79 ..." * tests/unit/db/test_sample_data.py: Ditto. * tests/unit/test_csvcmp.py: Ditto.
2022-03-30Revert "Run json.loads on request.get_json, since request.get_json was just ↵Frederick Muriuki Muriithi
returning a string" This reverts commit b93b22386056347d8002dd2e403425beeb4657cd. The appropriate fix should have been in GN2. The original statement args = request.get_json() was correct, since `request.get_json()` should return a python object parsed from the JSON string in the request. Unfortunately, GN2 was encoding the request data two times, which led to the call returning a JSON-encoded string instead of the expected object. The issue has been fixed in GN2 and therefore, the "fix" here can be reverted.
2022-03-29Remove unused moduleFrederick Muriuki Muriithi
* Remove a module that is no longer in use
2022-03-28Run json.loads on request.get_json, since request.get_json was just ↵zsloan
returning a string
2022-03-23Run python-black on file and fix other pylint issues.BonfaceKilz
See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126> * gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also, manually fix other pylint issues.
2022-03-22Fixes pylint errorszsloan
2022-03-22Fixed mypy typing errorszsloan
2022-03-22Tried to make the docstrings more consistentzsloan
2022-03-22Add typing to some functionszsloan
2022-03-22Add functions for getting proximal/distal markers for each pseudomarker ↵zsloan
position in pair-scan results + return only the sorted top 500 results
2022-03-22Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't ↵zsloan
selected
2022-03-22Added genofile name to inputs for processing R/qtl pair-scan results, since ↵zsloan
it's needed to store the proximal/distal markers for each position
2022-03-22Removed quotes from beginning and end of chromosome stringzsloan
2022-03-22Fixed a cople function calls to use the updated function nameszsloan
2022-03-22Create pairscan_for_figure and pairscan_for_table functions that return the ↵zsloan
Dict and List respectively used for the pair scan figure and the table showing the results
2022-03-22Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵zsloan
api/rqtl.py
2022-03-22Added pairscan boolean kwarg and process_rqtl_pairscan function for reading ↵zsloan
in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
2022-03-18Clean all csv fields before diffingBonfaceKilz
There was a subtle bug where "csvdiff" generated an error related to "different column headings" caused something akin to diffing: "a, b \n, ..." with "a, b\n, ...". * gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing. * tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to capture aforementioned bug.
2022-03-18Create new function for cleaning individual fields in csv textBonfaceKilz
* gn3/csvcmp.py (clean_csv_text): New function. * tests/unit/test_csvcmp.py: Import "csv_text". (test_clean_csv_text): Test case for the above.
2022-03-15Feature/refactored pca (#79)Alexander Kabui
* compute zscore function * test case for computing zscore * function to compute pca * generate scree plot data * generate new pca trait data from zscores and eigen_vec * remove redundant functions * generate factor loading table data * generate pca temp dataset dict * variable naming and error fixes * unit test for processing factor loadings * minor fixes for generating temp pca dataset * pass datetime as argument to generate_pca temp dataset function * add unittest for caching pca datasets * cache temp datasets * ignore missing imports for sklearn * mypy fixes * pylint fixes * refactor tests for pca * remove ununsed imports * fix for generating pca traits vals * mypy and code refactoring * pep8 formatting and add docstrings * remove comments /pep8 formatting * sort eigen vectors based on eigen values * minor fix for zscores * fix for rounding variance ratios * refactor tests * rename module to pca * rename datasets to traits * fix failing tests * fix caching function * fixes return x and y coordinates for scree plot * expand exception scope * fix for deprecated numpy.matrix function * fix for failing tests * pep8 fixes * remove comments * fix merge conflict * pylint fixes * rename module name to test_pca
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 10:31:14 +0000