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2022-09-27Unit Test: Fix unit test for Chromosome functions.Frederick Muriuki Muriithi
2022-09-22Provide database cursor as argument for TheSpecies and ChromosomesFrederick Muriuki Muriithi
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.
2022-09-22Update tests: pass in missing arguments.Frederick Muriuki Muriithi
2022-09-20Decompose file into separate modulesrefactor-data_set_py-20220920Frederick Muriuki Muriithi
To ease future refactors on the code, decompose the file into a module with multiple modules that can be refactored semi-independently.
2022-09-19Provide fixtures for test. Fix error to pass test.Frederick Muriuki Muriithi
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.
2022-09-19Remove "wrong" assertionsFrederick Muriuki Muriithi
The assertions was checking that the function was implemented a certain way, rather than whether the function was doing the correct thing.
2022-09-09Refactor: Add tests and handle edge caseFrederick Muriuki Muriithi
Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence.
2022-09-08Test the creation of the_species, indchromosomes and chromosome objsMunyoki Kilyungi
* 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.
2022-09-08Use "%s" in sql queryMunyoki Kilyungi
* 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.
2022-09-08Move test case to mrna_assay_tissue_data test moduleMunyoki Kilyungi
* 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
2022-09-08Inject database connection to mrna_assay_tissue_data classMunyoki Kilyungi
* 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.
2022-09-08Rewrite "test_tissue_corr_computation" as a pytestMunyoki Kilyungi
* wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py (TestCorrelationFunctions): Convert this unittest class to ... (test_tissue_corr_computation): ... a pytest function.
2022-09-08Replace "g.db" mocks with "database_connection" mocksMunyoki Kilyungi
* 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.
2022-09-08Move data.gen_menu_json to test_data_set.pyMunyoki Kilyungi
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.
2022-09-05Update values for "additive" in failing gemma testMunyoki Kilyungi
* wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py (TestGemmaMapping.test_parse_loco_outputfile_found): Use a halved value in expected_results["additive"].
2022-08-31Add transform parameter to mapping api unit testzsloan
2022-08-31Fix failing api/test_mapping.py testzsloan
2022-08-08remove unnessary append to listAlexander_Kabui
2022-08-08remove test;test is redundantAlexander_Kabui
2022-08-08tests refactoringAlexander_Kabui
2022-06-10Reverse polarity for gemma additive effects in testsBonfaceKilz
Fixes broken test. See: #89a7868.
2022-03-22Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscanzsloan
2022-03-17Lint some test filesBonfaceKilz
2022-03-17Fix failing testBonfaceKilz
2022-03-17Skip unittestsBonfaceKilz
These tests touch on core data-structures in gn2; and there's a chance that refactoring said data-structures may break many things.
2022-03-17Replace "g.db" object with a proper database connectionBonfaceKilz
* 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.
2022-01-14Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
feature/add_rqtl_pairscan
2021-11-04use gn3 importsBonfaceKilz
2021-10-25Update failing tests when testing `get_user_access_roles`BonfaceKilz
2021-10-25Replace "resource_id" with "resource_info" dictBonfaceKilz
This avoids calling Redis twice when fetching metadata about the resource.
2021-10-25Get a users access maskBonfaceKilz
If a user has several access roles, select the highest role.
2021-10-25Add test-cases for `get_user_membership`BonfaceKilz
2021-10-25Move markdown_routes to api/markdownBonfaceKilz
All new API definitions should be migrated to "wqflask/ api"
2021-10-13resolve merge conflictAlexander Kabui
2021-10-12Fixed filename in test_gen_covariates_file; I think that the hash changed ↵zsloan
because I changed the test dataset name from 'dataser_1' to 'dataset_1'
2021-10-12Fix R/qtl mapping testzsloan
2021-10-12Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
feature/add_rqtl_pairscan
2021-10-12Fixed test_gen_covariates_filezsloan
2021-10-12Fixed export_mapping_results test in test_run_mapping.pyzsloan
2021-10-09unittest for processing wgcna outputAlexander Kabui
2021-10-06tests: test_run_mapping: Add missing "name" attribute to testsBonfaceKilz
2021-10-06tests: test_run_mapping: Add missing callsBonfaceKilz
After adding the missing attribute to "self.trait", we need to also need to update some missing calls.
2021-10-06tests: test_run_mapping: Fix failing assert when getting perm strataBonfaceKilz
2021-10-06tests: test_run_mapping: Add missing attribute to "self.trait"BonfaceKilz
2021-10-06tests: test_run_mapping: Add missing positional argument "vals_hash"BonfaceKilz
2021-07-06replace rpy2 for tissue corrAlexander Kabui
2021-05-27Merge pull request #579 from zsloan/feature/rqtl_with_gn3zsloan
Use GN3 API for R/qtl
2021-05-27Fix the way Mock is initializedzsloan
2021-05-27Change test_rqtl_mapping.py to account for full results being returned from ↵zsloan
the GN3 request
2021-05-27Fixed way MockGroup was initializedzsloan
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