| Age | Commit message (Expand) | Author |
|---|
| 2023-03-20 | Disable editing case-attributes...ATM, editing case-attributes is very buggy.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Delete.
* wqflask/wqflask/decorators.py: Remove:
gn3.authentication.get_groups_by_user_uid import.
(case_attributes_edit_access): Delete.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Remove
wqflask.decorators.case_attributes_edit_access,
gn3.db.case_attributes.get_case_attributes,
gn3.db.case_attributes.get_unreviewed_diffs,
gn3.db.case_attributes.insert_case_attribute_audit,
gn3.db.case_attributes.reject_case_attribute and
gn3.db.case_attributes.approve_case_attribute.
(display_phenotype_metadata): Remove headers arg when rendering
template.
(update_phenotype): Remove case attribute headers list when updating a
phenotype.
(show_case_attribute_columns, update_case_attributes): Delete.
(reject_case_attribute_data, approve_case_attribute_data): Ditto.
* wqflask/wqflask/templates/edit_phenotype.html: Remove link that
shows all the listed case-attributes.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2022-12-01 | Reproduce ValueError when query_sql returns None...* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId):
New test cases.
| Munyoki Kilyungi |
| 2022-12-01 | Delete complicated unmaintainable test-cases marked for skipping...* wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes)
[test_set_dataset_key_mrna, test_set_dataset_key_pheno,
test_set_dataset_geno]: Delete.
| Munyoki Kilyungi |
| 2022-10-28 | Refactor: Pass user id to `check_resource_availability`...* Pass the user_id for the current user to the
`check_resource_availability` function as an argument, rather than
using the global `g.user_session.user_id` value.
| Frederick Muriuki Muriithi |
| 2022-10-23 | Inlcude redis_conn in MockGroup for get_samplelist | zsloan |
| 2022-10-20 | Clean Up: Remove unused function...* The function `generate_corr_json` was not used anywhere in the code.
| Frederick Muriuki Muriithi |
| 2022-10-14 | Update mock: Return correct test data. | Frederick Muriuki Muriithi |
| 2022-09-27 | Unit Test: Fix unit test for Chromosome functions. | Frederick Muriuki Muriithi |
| 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 | Adjust expected table width...* wqflask/tests/wqflask/show_trait/test_show_trait.py
(TestTraits.test_get_table_widths): Use new values for the table width
to make the tests pass.
| Munyoki Kilyungi |
| 2022-09-08 | Condense test-cases for "get_ncbi_summary_request" into one test...* wqflask/tests/wqflask/show_trait/test_show_trait.py:
(TestTraits.test_get_ncbi_summary_request_success): Condense this ...
(TestTraits.test_get_ncbi_summary_request): ... and this ...
(test_get_ncbi_summary_request): ... here.
| Munyoki Kilyungi |
| 2022-09-08 | Parametrize test cases for "check_if_attr_exists"...* wqflask/tests/wqflask/show_trait/test_show_trait.py: Import pytest.
(TestTraits.test_check_if_attr_exists_truthy): Delete it.
(TestTraits.test_check_if_attr_exists_empty_attr): Ditto.
(TestTraits.test_check_if_attr_exists_falsey): Ditto.
(TestTraits.test_check_if_attr_exists_falsey): Ditto.
test_check_if_attr_exists: Add new parametrized test case to test
"check_if_attr_exists".
| Munyoki Kilyungi |
| 2022-09-08 | Add extra distinct_values and id attributes to test TraitObject...* wqflask/tests/wqflask/show_trait/test_show_trait.py (TraitObject):
Add self.id and self.distinct_values.
| Munyoki Kilyungi |
| 2022-09-08 | Remove app initialisation in test...* wqflask/tests/wqflask/show_trait/test_show_trait.py: Delete
"wqflask.app" import.
(TestTraits.setUp): Delete it.
(TestTraits.tearDown): 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 |
| 2022-09-08 | Delete dead imports...* wqflask/base/data_set.py: Remove un-used imports.
* wqflask/base/trait.py: Ditto.
wqflask/tests/wqflask/show_trait/test_show_trait.py: Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Ditto.
* wqflask/wqflask/views: Ditto.
| 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 | Skip failing integration test...ATM, it's hard to by-pass the authentication
decorators, and as such, skip this test for. This
may be deleted later.
| BonfaceKilz |
| 2022-06-10 | Reverse polarity for gemma additive effects in tests...Fixes broken test. See: #89a7868.
| BonfaceKilz |
| 2022-04-14 | wqflask: Mock db connection when fetching case attributes...* wqflask/tests/integration/wqflask/test_metadata_edits.py
(test_show_case_attributes): Mock
"database_connection". Fixes this failing test:
<https://ci.genenetwork.org/jobs/genenetwork2/223>
| BonfaceKilz |
| 2022-04-07 | Create a new page to display case-attributes and their descriptions...* wqflask/wqflask/metadata_edits.py: Import
"gn3.db.sample_data.get_case_attributes".
(show_case_attribute_columns): New function/ end-point to show
case-attributes.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: New
integration tests for the above.
* wqflask/tests/integration/wqflask/__init__.py: New file.
* wqflask/wqflask/templates/case_attributes.html: New template file to
display the above.
| 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 |
