| Age | Commit message (Expand) | Author |
|---|---|---|
| 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 |
| 2022-09-20 | 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 | 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 |
| 2022-09-09 | Refactor: Add tests and handle edge case...Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence. | Frederick Muriuki Muriithi |
| 2022-09-08 | Test the creation of the_species, indchromosomes and chromosome objs...* wqflask/tests/unit/base/test_species.py (TestTheSpecies): Delete. (TestIndChromosome): Move to pytest and parametrize. (TestChromosomes): Ditto. (test_species): Ditto. (test_create_ind_chromosome): Ditto. (test_create_chromosomes): Ditto. | Munyoki Kilyungi |
| 2022-09-08 | Use "%s" in sql query...* wqflask/base/mrna_assay_tissue_data.py: Delete db_tools. (MrnaAssayTissueData.get_symbol_values_pairs): Re-format query. * wqflask/tests/unit/base/test_mrna_assay_tissue_data.py: (test_get_trait_symbol_and_tissue_values): Add test for above. | Munyoki Kilyungi |
| 2022-09-08 | Move test case to mrna_assay_tissue_data test module...* wqflask/tests/unit/base/test_mrna_assay_tissue_data.py * wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py (TestCorrelationFunctions.test_tissue_corr_computation): Delete. (TestCorrelationFunctions): Move this ... (test_mrna_assay_tissue_data_initialisation): ... here | Munyoki Kilyungi |
| 2022-09-08 | Inject database connection to mrna_assay_tissue_data class...* wqflask/base/mrna_assay_tissue_data.py: Imports: Delete database_connection, escape, and database_connector. (MrnaAssayTissueData): Inject conn. Re-format queries. Rework 'if ... else' logic. Re-work how results are assigned to 'self.data[symbol]' - remove dot-notation. (MrnaAssayTissueData.get_symbol_values_pairs): Move box-comments to doc-string. Rework how results are assigned to 'symbol_values_dict' - remove dot-notation. * wqflask/tests/unit/base/test_mrna_assay_tissue_data.py (test_mrna_assay_tissue_data_initialisation): New test. * wqflask/wqflask/correlation/correlation_functions.py: Import database_connection. (get_trait_symbol_and_tissue_values): Inject conn object. | Munyoki Kilyungi |
| 2022-09-08 | Rewrite "test_tissue_corr_computation" as a pytest...* wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py (TestCorrelationFunctions): Convert this unittest class to ... (test_tissue_corr_computation): ... a pytest function. | Munyoki Kilyungi |
| 2022-09-08 | Replace "g.db" mocks with "database_connection" mocks...* wqflask/tests/unit/base/test_trait.py: Delete "wqflask.app" import. (TestRetrieveTraitInfo.setUp): Delete it. (TestRetrieveTraitInfo.tearDown): Ditto. (TestRetrieveTraitInfo.test_retrieve_trait_info_with_empty_dataset): Replace "g" mock with "database_connection" mock. (test_retrieve_trait_info_with_empty_trait_info): Ditto. (test_retrieve_trait_info_with_non_empty_trait_info): Ditto. (test_retrieve_trait_info_utf8_parsing): Ditto. * wqflask/tests/wqflask/show_trait/test_show_trait.py (TestTraits): (test_get_nearest_marker): Ditto. (test_get_nearest_marker_empty_db): Ditto. | Munyoki Kilyungi |
| 2022-09-08 | Move data.gen_menu_json to test_data_set.py...This is done to avoid relative imports. wqflask/tests/unit/base/data.py: Delete it. * wqflask/tests/unit/base/test_data_set.py: Add new variable GEN_MENU_JSON. (TestDataSetTypes.test_data_set_type_with_empty_redis): Upper-case "gen_menu_json" variable. | Munyoki Kilyungi |
| 2022-09-05 | Update values for "additive" in failing gemma test...* wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py (TestGemmaMapping.test_parse_loco_outputfile_found): Use a halved value in expected_results["additive"]. | Munyoki Kilyungi |
| 2022-08-31 | Add transform parameter to mapping api unit test | zsloan |
| 2022-08-31 | Fix failing api/test_mapping.py test | zsloan |
| 2022-08-08 | remove unnessary append to list | Alexander_Kabui |
| 2022-08-08 | remove test;test is redundant | Alexander_Kabui |
| 2022-08-08 | tests refactoring | Alexander_Kabui |
| 2022-06-10 | Reverse polarity for gemma additive effects in tests...Fixes broken test. See: #89a7868. | BonfaceKilz |
| 2022-03-22 | Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscan | zsloan |
| 2022-03-17 | Lint some test files | BonfaceKilz |
| 2022-03-17 | Fix failing test | BonfaceKilz |
| 2022-03-17 | Skip unittests...These tests touch on core data-structures in gn2; and there's a chance that refactoring said data-structures may break many things. | BonfaceKilz |
| 2022-03-17 | Replace "g.db" object with a proper database connection...* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper database connection instead of the db connection attached at "g.db". * wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto. * wqflask/wqflask/api/correlation.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto. | BonfaceKilz |
| 2022-01-14 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/ad... | zsloan |
| 2021-11-04 | use gn3 imports | BonfaceKilz |
| 2021-10-25 | Update failing tests when testing `get_user_access_roles` | BonfaceKilz |
| 2021-10-25 | Replace "resource_id" with "resource_info" dict...This avoids calling Redis twice when fetching metadata about the resource. | BonfaceKilz |
| 2021-10-25 | Get a users access mask...If a user has several access roles, select the highest role. | BonfaceKilz |
| 2021-10-25 | Add test-cases for `get_user_membership` | BonfaceKilz |
| 2021-10-25 | Move markdown_routes to api/markdown...All new API definitions should be migrated to "wqflask/ api" | BonfaceKilz |
| 2021-10-13 | resolve merge conflict | Alexander Kabui |
| 2021-10-12 | Fixed filename in test_gen_covariates_file; I think that the hash changed bec... | zsloan |
| 2021-10-12 | Fix R/qtl mapping test | zsloan |
| 2021-10-12 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/ad... | zsloan |
| 2021-10-12 | Fixed test_gen_covariates_file | zsloan |
| 2021-10-12 | Fixed export_mapping_results test in test_run_mapping.py | zsloan |
| 2021-10-09 | unittest for processing wgcna output | Alexander Kabui |
| 2021-10-06 | tests: test_run_mapping: Add missing "name" attribute to tests | BonfaceKilz |
| 2021-10-06 | tests: test_run_mapping: Add missing calls...After adding the missing attribute to "self.trait", we need to also need to update some missing calls. | BonfaceKilz |
| 2021-10-06 | tests: test_run_mapping: Fix failing assert when getting perm strata | BonfaceKilz |
| 2021-10-06 | tests: test_run_mapping: Add missing attribute to "self.trait" | BonfaceKilz |
| 2021-10-06 | tests: test_run_mapping: Add missing positional argument "vals_hash" | BonfaceKilz |
| 2021-07-06 | replace rpy2 for tissue corr | Alexander Kabui |
| 2021-05-27 | Merge pull request #579 from zsloan/feature/rqtl_with_gn3...Use GN3 API for R/qtl | zsloan |
| 2021-05-27 | Fix the way Mock is initialized | zsloan |
| 2021-05-27 | Change test_rqtl_mapping.py to account for full results being returned from t... | zsloan |
| 2021-05-27 | Fixed way MockGroup was initialized | zsloan |
| 2021-05-27 | Forgot to import dataclass | zsloan |
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| GeneNetwork (2nd generation) |
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