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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 posit...zsloan
2022-03-22Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s...zsloan
2022-03-22Added genofile name to inputs for processing R/qtl pair-scan results, since i...zsloan
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 D...zsloan
2022-03-22Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ...zsloan
2022-03-22Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ...zsloan
2022-03-22Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i...zsloan
2022-03-22Added line priting pair-scan results to CSV and changed the default step-size...zsloan
2022-03-22- Added scan_func function that determines whether scanone or scantwo...(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints zsloan
2022-03-22Added option for running pairscan to rqtl_wrapper.Rzsloan
2022-03-18README: Update CI badge subdomain....The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org. * README.md: Update CI badge subdomain. Arun Isaac
2022-03-18Clean all csv fields before diffing...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. BonfaceKilz
2022-03-18Create new function for cleaning individual fields in csv text...* 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. BonfaceKilz
2022-03-15Feature/refactored pca (#79)...* 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_pcaAlexander Kabui
2022-03-14Dummy White Space commit to fix laminarBonfaceKilz
2022-03-14Sort import linesBonfaceKilz
2022-03-14Only loop through the diff's modifications if it existsBonfaceKilz
2022-03-14Given a csv text and permissible headers, extract invalid headers...* gn3/csvcmp.py (extract_invalid_csv_headers): New function. * tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers". (test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the above. BonfaceKilz
2022-03-14Get all permissible column data...* gn3/csvcmp.py: Import "Any" and "List". (get_allowable_sampledata_headers): New function. * tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers". (test_get_allowable_csv_headers): Test case for the above. BonfaceKilz
2022-03-12Fix pylint errors in unit_testsBonfaceKilz
2022-03-12Remove unused importsBonfaceKilz
2022-03-12Fix mypy issuesBonfaceKilz
2022-03-12Fix pylint issuesBonfaceKilz
2022-03-12README: Replace "unit-test" instructions with "pytest"BonfaceKilz
2022-03-12Compose csv-diff command within single quotes...* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92 that broke this. BonfaceKilz
2022-03-12Delete noisy "print" statementBonfaceKilz
2022-03-12Store the first element as strain_idBonfaceKilz
2022-03-12Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that the strain name is part of the returned string when extracting "actions". * tests/unit/db/test_sample_data.py: Add test cases for the above. BonfaceKilz
2022-03-12Apply auto-pep8 to sample_data.py and it's test fileBonfaceKilz
2022-03-12Add missing return type-annotations...* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return type for type annotations. (insert_sample_data): Ditto. BonfaceKilz
2022-03-12Update how data is updated by re-using existing functions...* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and "insert_sample_data" when updating data; and also add logic for updating modified data. * tests/unit/db/test_sample_data.py: Add tests for the above. BonfaceKilz
2022-03-12Create action dict that's created when updating data...* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can contain: inserts, deletes and updates. This functions extracts these actions during an update. * tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for the above. BonfaceKilz
2022-03-12Add test cases for inserting and deleting data...* tests/unit/db/test_sample_data.py (test_insert_sample_data): Test inserting data. (test_delete_sample_data): Test deleting data. BonfaceKilz
2022-03-12Remove check for inserted data when inserting individual data...* gn3/db/sample_data.py (insert_sample_data)[__insert_data]: Move check to the main body. With this check here, you have 3 redundant checks. For a successful insert, it will insert the first value to the `PublishData` table and ignore the rest of the inserts. BonfaceKilz
2022-03-12Make `_map` a constant...* gn3/db/sample_data.py: Now constant, `_MAP`. (delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`. (insert_sample_data)[__insert_data]: Ditto. BonfaceKilz
2022-03-12Fix faulty SQL query string when deleting case-attributesBonfaceKilz
2022-03-12Explicitly get CaseAttributeId and fix broken sql query...* gn3/db/sample_data.py (insert_sample_data): Use correct query string. Also, use CaseAttributeId to determine whether case-attributes were inserted. If so, do not attempt an insert. BonfaceKilz
2022-03-12Remove duplicate params...* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove extra parameters. BonfaceKilz
2022-03-12Remove dead codeBonfaceKilz
2022-03-12Check whether publish data already exists before inserting...* gn3/db/sample_data.py (insert_sample_data): If data already exists in the table, do not attempt an insert; otherwise, an error will be generated. BonfaceKilz
2022-03-12Fill in empty values in csv text with: "x"...* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be filled with the default value(set in the args). * tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above. BonfaceKilz
2022-03-12Remove test cases related to sample data...Most of this functions were moved to their own module. BonfaceKilz
2022-03-12Fetch id's separately for the insertion edge-case...* gn3/db/sample_data (get_sample_data_ids): Add an extra condition that caters for inserts: during inserts, joins won't work when fetching the strain_id, publishdata_id, and strain_name. In this case, just create 2 separate queries to do that work. BonfaceKilz
2022-03-12Extract a strain name given a csv string and it's header...* gn3/csvcmp.py (extract_strain_name): New function. * gn3/db/sample_data (delete_sample_data): Use the aforementioned function. (insert_sample_data): Ditto. * tests/unit/test_csvcmp: Test cases for above. BonfaceKilz
2022-03-12Allow deleting case-attribute data during deletion...* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow deleting case-attribute values. BonfaceKilz
2022-03-12Allow inserting case-attribute data during inserts...* gn3/db/sample_data.py (insert_sample_data): Modify this function to allow inserting case-attribute values. BonfaceKilz