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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.
2022-09-08Use "%s" instead of "%2.6f" or "%d" in query.Munyoki Kilyungi
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Use "%s".
2022-09-08Fix sql queriesMunyoki Kilyungi
"%s" should only be used outside table names and column names otherwise a string literal will be inserted thereby leading to errors in the sql statements. * wqflask/base/data_set.py (geno_mrna_confidentiality): Use f-strings for table/columns/clause. * wqflask/base/trait.py (retrieve_trait_info): Ditto. * wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto. * wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Ditto. * wqflask/wqflask/snp_browser/snp_browser.py (SnpBrowser.get_browser_results): Ditto.
2022-09-08Deleting utility.loggerMunyoki Kilyungi
* wqflask/utility/logger.py: Delete.
2022-09-08Add missing "," in cursor.execute()Munyoki Kilyungi
* wqflask/base/data_set.py (DatasetGroup.get_mapping_methods): Fix failing query by adding a missing ",".
2022-09-08Delete unused importsMunyoki Kilyungi
* wqflask/wqflask/search_results.py: Remove unused imports.
2022-09-08Remove intermediate variables that are only used onceMunyoki Kilyungi
* wqflask/base/data_set.py (DatasetGroup.__init__): Remove "query" variable. (DataSet.chunk_dataset): Fix indentation. * wqflask/wqflask/search_results.py (get_GO_symbols): Remove "this_term" variable. * wqflask/wqflask/views.py (search_page): Remove "the_search" variable.
2022-09-08Force pytest to use "importlib" import-mode to be able to runMunyoki Kilyungi
Having "--import-mode=importlib" enables pytest to find the imports in our tests; otherwise we get import errors. * pyproject.toml: New pytest conf file.
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.
2022-09-08Adjust expected table widthMunyoki Kilyungi
* 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.
2022-09-08Condense test-cases for "get_ncbi_summary_request" into one testMunyoki Kilyungi
* 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.
2022-09-08Parametrize test cases for "check_if_attr_exists"Munyoki Kilyungi
* 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".
2022-09-08Add extra distinct_values and id attributes to test TraitObjectMunyoki Kilyungi
* wqflask/tests/wqflask/show_trait/test_show_trait.py (TraitObject): Add self.id and self.distinct_values.
2022-09-08Remove app initialisation in testMunyoki Kilyungi
* wqflask/tests/wqflask/show_trait/test_show_trait.py: Delete "wqflask.app" import. (TestTraits.setUp): Delete it. (TestTraits.tearDown): Ditto.
2022-09-08Recommend pytests in READMEMunyoki Kilyungi
* README.md (Testing): Using pytests instead of unittests.
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.
2022-09-08Replace "g.db" with "database_connection" in documentationMunyoki Kilyungi
2022-09-08Remove "g.db" init from every sessionMunyoki Kilyungi
"g.db" is now replaced with "database_connections". * wqflask/wqflask/views.py: Remove "sqlalchemy" and "SQL_URI" imports. (connect_db): Delete it. (shutdown_session): Ditto.
2022-09-08Remove sql_alchemy initialisation when profiling correlationsMunyoki Kilyungi
* wqflask/scripts/profile_corrs.py: Remove sqlalchemy, connect_db and shutdown_session. (__main__): Remove "g.db".
2022-09-08Delete dead importsMunyoki Kilyungi
* 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.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* wqflask/base/data_set.py (DatasetType.set_dataset_key): Replace g.db with "database_connection()". (DatasetGroup.get_mapping_methods): Ditto. (DataSet.get_accession_id): Ditto. (DataSet.retrieve_other_names): Rework "if ... else" logic to get rid of "query" and "_vars" variables. Also, nest "try ... except" block within "database_connection". (DataSet.chunk_dataset): Replace g.db with "database_connection()". (DataSet.get_probeset_data): Ditto. (DataSet.get_trait_data): Ditto. (PhenotypeDataSet.get_trait_info): Ditto. (PhenotypeDataSet.retrieve_sample_data): Ditto. (GenotypeDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.get_trait_info): Ditto. (MrnaAssayDataSet.retrieve_sample_data): Ditto. (MrnaAssayDataSet.retrieve_genes): Ditto. (TempDataSet): Ditto. (geno_mrna_confidentiality): Ditto. (query_table_timestamp): Ditto. * wqflask/wqflask/api/router.py: Replace "flask.g" with database_connection import. (get_species_list): Replace g.db with "database_connection()". (get_species_info): Ditto. (get_groups_list): Ditto. (get_group_info): Ditto. (get_datasets_for_group): Ditto. (get_dataset_info): Ditto. (fetch_traits): Ditto. (all_sample_data): Ditto. (trait_sample_data): Ditto. (get_trait_info): Ditto. (get_dataset_trait_ids): Ditto. (get_samplelist): Ditto. (get_group_id_from_dataset): Ditto. (get_group_id): Ditto.
2022-09-08Delete logger importMunyoki Kilyungi
* wqflask/base/trait.py: Remove utility.logger
2022-09-08Replace assertion with Value Error for non-existent datasetMunyoki Kilyungi
* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in ValueError.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection. (MrnaAssayTissueData.__init__): Use database_connection. (MrnaAssayTissueData.get_symbol_values_pairs): Ditto. * wqflask/base/species.py: Replace "Flask.g" imports with "database_connection". (Chromosomes.chromosomes): Use database_connection. * wqflask/base/trait.py: Import database_connection. (retrieve_trait_info): Use database_connection. * wqflask/utility/authentication_tools.py: Replace "flask.g" with database_connection. (get_group_code): Use database_connection. * wqflask/utility/helper_functions.py: Replace "flask.g" with "database_connection". (get_species_groups): Use database_connection. * wqflask/wqflask/db_info.py: Replace "Flask" and "g" with "database_connection". (InfoPage.get_info): Use database_connection. * wqflask/wqflask/do_search.py (DoSearch.execute): Use database_connection(). * wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace "Flask" and "g" import with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace "Flask, g" imports with database_connection. (test_chip): Use database_connection. * wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with database_connection. (GSearch.__init__): Use database_connection. * wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Use database_connection(). * wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import" with database_connection. (SampleList.get_attributes): Use database_connection. (SampleList.get_extra_attribute_values): Ditto. * wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g" import with database_connection. (ShowTrait.__init__): Use database_connection. (ShowTrait.get_external_links): Ditto. (get_nearest_marker): Ditto.
2022-09-08Delete insert query that's not runMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete insert query
2022-09-08Remove "if" block that does nothingMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Remove if block that constructs a "final" query that does nothing.
2022-09-08Restructure "if ... else" to first check for a ValueErrorMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): First check for a ValueError Exception.
2022-09-08Raise a ValueError instead of generic exceptionMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Wrap error message in ValueError Exception.
2022-09-08Replace format-strings with f-stringsMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Use f-strings.
2022-09-08Remove '+' when concatenating strings inside bracketsMunyoki Kilyungi
* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete "+".
2022-09-08Use db_connection and rework "if ... else" clausesMunyoki Kilyungi
* wqflask/wqflask/snp_browser/snp_browser.py (SnpBrowser.get_browser_results): Replace "g.db" with database_connection. Rework "if ... else" logic.
2022-09-08Delete dead commentMunyoki Kilyungi
2022-09-08Refactor if clause to check for string in listMunyoki Kilyungi
* wqflask/wqflask/docs.py (update_text): Check for the e-mail in a list.
2022-09-08Refactor "if ... else" block to check the truthy case firstMunyoki Kilyungi
* wqflask/wqflask/docs.py (Docs.__init__): Check the truthy case first after fetching the results.
2022-09-08Replace g.db with database_connection() context managerMunyoki Kilyungi
* wqflask/wqflask/update_search_results.py: Replace "Flask" and "g" import with "database_connection". (GSearch.__init__): Reformat SQL. Rename "re" to "results" since "re" is part of the stdlib. * wqflask/wqflask/marker_regression/rqtl_mapping.py: Replace flask.g with database_connection. (write_covarstruct_file): Replace g.db with database_connection(). * wqflask/wqflask/search_results.py: Replace "Flask" and "g" imports with "database_connection" import. (trait_info_str): Replace g.db with database_connection. * wqflask/wqflask/docs.py (Docs): Use dababase_connection() context manager. (update_text): Ditto. * wqflask/wqflask/marker_regression/display_mapping_results.py: Replace "Flask" and "g" import with "database_connection". (DisplayMappingResults.__init__): Use database_connection. (DisplayMappingResults.drawSNPTrackNew): Ditto.
2022-09-08Delete unused news moduleMunyoki Kilyungi
* wqflask/wqflask/news.py: Delete it.
2022-09-08Merge pull request #727 from Alexanderlacuna/feature/use-textfilesAlexander Kabui
use text files for Probeset
2022-09-08fixup query formattingAlexander_Kabui
2022-09-08gitignore: Add containers/mariadb-state.Arun Isaac
* .gitignore: Add containers/mariadb-state.
2022-09-07catch general errors this will recreate the fileAlexander_Kabui
2022-09-07use csv to parse filesAlexander_Kabui
2022-09-07filter list vals with indexAlexander_Kabui
2022-09-06Change collections/view forms' default action from /delete to /loading ↵zsloan
(because it was weird for it to be /delete)
2022-09-06Add data-trait-info to collections/view columnDefszsloan
2022-09-06Include trait_info_str in trait JSON, so it can be included in collection ↵zsloan
table for partial corr
2022-09-06Fix mistake from generalize_tables mergezsloan
2022-09-06Fix error with dataset menu query in data_set.pyzsloan
I'm only using g.db.execute here because using cursor is throwing an error and I don't want to change the way this query is currently written since I didn't write it (I believe it was initially written using g.db.execute and whoever wrote it just forgot to put the g.db.execute, since previously it just called "fetchall")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 08:43:37 +0000