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2022-03-26Make creation of database connections more flexibleFrederick Muriuki Muriithi
* Pass the URI string to parse into `gn3.db_utils.parse_db_url` rather than relying on a global variable. * Pass the URI string to use to generate the database connection to the `gn3.db_utils.database_connector` function rather than depending on a global variable. Use the global `SQL_URI` variable as a default value if one is not provided when calling the function. The changes above make the creation of the database connection more flexible, since the database URI passed into the function can be changed at the site where the call is made. The port is also parsed, and used where present, to allow for either a socket connection or one based on a port.
2022-03-24Test Fixture: Create new test database and get connection to itFrederick Muriuki Muriithi
Implement a fixture that: * Creates a new test database * Copies over table structure from existing database * Gets connection to new test database and returns it * Cleans up after itself when the tests have run
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.
2022-03-22Merge pull request #29 from zsloan/feature/add_rqtl_pairscanzsloan
Feature/add rqtl pairscan
2022-03-22Merge branch 'feature/add_rqtl_pairscan' of ↵zsloan
https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan
2022-03-22Change order of if statements for running genoprob commandzsloan
Now it checks for pairscan first, just in case interval ends up being passed (which is an irrelevant parameter for pairscan) Also added a couple more verbose prints
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
2022-03-22Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵zsloan
we need the list of markers/pseudomarkers and their positions)
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
2022-03-22Added line priting pair-scan results to CSV and changed the default ↵zsloan
step-size to 10cM for pair-scan
2022-03-22- Added scan_func function that determines whether scanone or scantwozsloan
(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
2022-03-22Added option for running pairscan to rqtl_wrapper.Rzsloan
2022-03-18README: Update CI badge subdomain.Arun Isaac
The CI has been migrated from penguin2.genenetwork.org to ci.genenetwork.org. * README.md: Update CI badge subdomain.
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
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 headersBonfaceKilz
* 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.
2022-03-14Get all permissible column dataBonfaceKilz
* 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.
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 quotesBonfaceKilz
* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92 that broke this.
2022-03-12Delete noisy "print" statementBonfaceKilz
2022-03-12Store the first element as strain_idBonfaceKilz
2022-03-12Append the strain name when extracting "actions"BonfaceKilz
* 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.
2022-03-12Apply auto-pep8 to sample_data.py and it's test fileBonfaceKilz
2022-03-12Add missing return type-annotationsBonfaceKilz
* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return type for type annotations. (insert_sample_data): Ditto.
2022-03-12Update how data is updated by re-using existing functionsBonfaceKilz
* 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.
2022-03-12Create action dict that's created when updating dataBonfaceKilz
* 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.
2022-03-12Add test cases for inserting and deleting dataBonfaceKilz
* tests/unit/db/test_sample_data.py (test_insert_sample_data): Test inserting data. (test_delete_sample_data): Test deleting data.
2022-03-12Remove check for inserted data when inserting individual dataBonfaceKilz
* 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.
2022-03-12Make `_map` a constantBonfaceKilz
* gn3/db/sample_data.py: Now constant, `_MAP`. (delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`. (insert_sample_data)[__insert_data]: Ditto.
2022-03-12Fix faulty SQL query string when deleting case-attributesBonfaceKilz
2022-03-12Explicitly get CaseAttributeId and fix broken sql queryBonfaceKilz
* 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.
2022-03-12Remove duplicate paramsBonfaceKilz
* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove extra parameters.
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