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2022-06-21test_file_utils: Disable test cases for "cache_ipfs_file"...* tests/unit/test_file_utils.py (test_cache_ipfs_file_cache_hit): Skip it. (test_cache_ipfs_file_cache_miss): Ditto. BonfaceKilz
2022-06-21integration: test_gemma: Skip "GemmaAPITest"BonfaceKilz
2022-05-30Pass trait data as args to `fix_strains` and fix some bugs...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. Frederick Muriuki Muriithi
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 is...* 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. BonfaceKilz
2022-05-26Add Endpoint to get menu items for use in UIFrederick Muriuki Muriithi
2022-05-05Extract common error checking. Rename function....* Extract the common error checking code into a separate function * Rename the function to make its use clearer Frederick Muriuki Muriithi
2022-04-12Delete "get_allowable_sampledata_headers"...* 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. BonfaceKilz
2022-04-12Test that a carriage return is removed when generating csv...* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data". (test_get_trait_csv_sample_data): New test function. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during insertions...* 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. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during insertions...* 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. BonfaceKilz
2022-04-07Use case attribute id inside brackets if present during updates...* 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. BonfaceKilz
2022-04-07Add method for fetching the case_attributes...* 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. BonfaceKilz
2022-04-07Add method for parsing a csv header from uploaded sample-data file...* gn3/csvcmp.py (parse_csv_column): New function. * tests/unit/test_csvcmp.py: Test case for the above. BonfaceKilz
2022-04-01Run python-black in file...* gn3/csvcmp.py: Run "black -l 79 ..." * tests/unit/db/test_sample_data.py: Ditto. * tests/unit/test_csvcmp.py: Ditto. BonfaceKilz
2022-03-24Test Fixture: Create new test database and get connection to it...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 Frederick Muriuki Muriithi
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
2022-03-14Sort import linesBonfaceKilz
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
2022-03-12Append 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
2022-03-12Update 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
2022-03-12Fill 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
2022-03-12Extract 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
2022-03-12Don't add extra key "Column" to dict if there are no changes...gn3/csvcmp.py (csv_diff): If the diff is empty, don't add an extra key "Column" to the dictionary. tests/unit/test_csvcmp (test_csv_diff_only_column_change): Add test-case for the above. BonfaceKilz
2022-03-12Test edges cases for csv files when running csvdiff...* tests/unit/test_csvcmp.py (test_csv_diff): Delete it. (test_csv_diff_same_columns): Test csv_diff against csv texts with the same columns. (test_csv_diff_different_columns): Test csv texts against csv texts with different varying columns. BonfaceKilz
2022-03-12Create new method for filling csv with a default value...* gn3/csvcmp.py (fill_csv): Given a csv text with uneven or incomplete fields whole length are less than width, fill them with a value which defaults to "x". * tests/unit/test_csvcmp.py (test_fill_csv): Test cases for the above. BonfaceKilz
2022-03-12Add methods for working with csv data...gn3/csvcmp.py: New file (create_dirs_if_not_exists): From a list of dirs, create them if they don't exist. (remove_insignificant_edits): Given a dict with a "Modification" key, remove edits with "delta < ε". (csv_diff): Generate a csv_diff using the "csvdiff" tool packaged in guix. tests/unit/test_csvcmp.py: Add some tests for "gn3/csvcmp.py" BonfaceKilz
2022-03-12Append case attributes to csv data if they existBonfaceKilz
2022-03-11Fix some linting issuesFrederick Muriuki Muriithi
2022-03-08Remove unused function and its testsFrederick Muriuki Muriithi
2022-03-08Fix tests, and issues caught by tests...Fix some issues caught by tests due to changes introducing the hand-off of the partial correlations computations to an external process Fix some issues due to the changes that introduce context managers for database connections Update some tests to take the above two changes into consideration Frederick Muriuki Muriithi
2022-02-24gn3: Explicitly specify UTF-8 to be the file encoding....When the encoding is not specified explicitly, the system default encoding is used. This is not recommended. * gn3/computations/ctl.py (call_ctl_script), gn3/computations/gemma.py (generate_pheno_txt_file), gn3/computations/parsers.py (parse_genofile), gn3/computations/partial_correlations.py (partial_correlations_fast), gn3/computations/rqtl.py (process_rqtl_output, process_perm_output), gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script), gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file encoding. * tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file), tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test for call to open with encoding='utf-8' argument. Arun Isaac
2022-02-21Fix minor issues introduced while fixing linting errorsFrederick Muriuki Muriithi
2022-02-21Fix a myriad of linter issues...* Use `with` in place of plain `open` * Use f-strings in place of `str.format()` * Remove string interpolation from queries - provide data as query parameters * other minor fixes Frederick Muriuki Muriithi
2022-02-21Add test to ensure samples are read correctly from .geno files...* tests/unit/db/test_genotypes2.py: New file Frederick Muriuki Muriithi
2022-02-21Test partial corrs API with mix of existing and non-existing control traits...Test that the partial correlations endpoint handles a mix of existing and non-existing control traits gracefully and issues a warning to the user. Summary of changes: * gn3/computations/partial_correlations.py: Issue a warning for all non-existing control traits * gn3/db/partial_correlations.py: update queries - use `INNER JOIN` for tables instead of comma-separated list of tables * tests/integration/conftest.py: Add `db_conn` fixture to provide a database connection to the tests. This will probably be changed in the future to connect to a temporary database for tests. * tests/integration/test_partial_correlations.py: Add test to check for correct behaviour with a mix of existing and non-existing control traits Frederick Muriuki Muriithi
2022-02-19Test partial corrs endpoint with non-existing control traits...Test that if the endpoint is queried and not a single one of the control traits exists in the database, then the endpoint will respond with a 404 (not-found) status code. Summary of changes: * gn3/computations/partial_correlations.py: Check whether any control trait is found. If none is found, return "not-found" message. * gn3/db/partial_correlations.py: Fix bug in Geno query. * tests/integration/test_partial_correlations.py: Add test for non-existing control traits. Rename function to make it clearer what it is testing for. Remove obsoleted comments. Frederick Muriuki Muriithi
2022-02-18Remove erroneous test based on wrong assumptions...Related to commit 75dcfe295af57b16428c586cc11dbaa827a5feba This commit removes the related test that was checking for the wrong thing. Frederick Muriuki Muriithi
2022-02-18Test partial correlations endpoint with non-existent primary traits...Test that the partial correlations endpoint responds with an appropriate "not-found" message and the corresponding 404 status code in the case where a request is made and the primary trait requested for does not exist in the database. Summary of the changes in each file: * gn3/api/correlation.py: generalise the building of the response * gn3/computations/partial_correlations.py: return with a "not-found" if the primary trait does not exist in the database * gn3/db/partial_correlations.py: Fix a number of bugs that led to exceptions in the case that the primary trait did not exist * pytest.ini: register a `slow` pytest marker * tests/integration/test_partial_correlations.py: Add a new test to check for an appropriate 404 response in case of a primary trait that does not exist in the database. Frederick Muriuki Muriithi
2022-02-17Test partial correlations endpoint with missing data in POST request...Add a test for the partial correlations endpoint, with: - no data in the request - missing items in the data Fix the bugs caught by the test Frederick Muriuki Muriithi
2022-02-17Create client fixture for integration tests...Create a client fixture to help with the integration tests Frederick Muriuki Muriithi