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2022-09-13Fix bug where passing LOCO into the mapping API endpoint didn't workzsloan
2022-09-12Fix query: Add comma to separate columns.Frederick Muriuki Muriithi
2022-09-12Check for species before calling `lower()`Frederick Muriuki Muriithi
2022-09-12Check there is target data before running correlationsFrederick Muriuki Muriithi
2022-09-12Fix query: Remove extraneous bracketFrederick Muriuki Muriithi
2022-09-12Check for traits before computingFrederick Muriuki Muriithi
2022-09-12Fix query: remove wrongly-placed commaFrederick Muriuki Muriithi
2022-09-12Check db resultset before indexing into itFrederick Muriuki Muriithi
The assumption that the resultset will never be empty was leading to a lot of errors.
2022-09-12Check data is truthy before indexing into it.Frederick Muriuki Muriithi
2022-09-09Fix bug in display_mapping_results chromosome queryzsloan
A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome
2022-09-09Fix bug in retrieve_other_nameszsloan
After a recent change, it always tries to unpack 6 values from the query, but it should only be unpacking 4 values if not type ProbeSet (so it was throwing an error for anything not ProbeSet)
2022-09-09handle cases where tissue dataset vals are empty listAlexander_Kabui
2022-09-09tissue:fetch for query formattingAlexander_Kabui
2022-09-09Fix query: remove string interpolation.Frederick Muriuki Muriithi
2022-09-09Retain only a single import of the same moduleFrederick Muriuki Muriithi
2022-09-09Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlationsMuriithi Frederick Muriuki
Bug/fix broken correlations
2022-09-09Fetch sample values correctlyMunyoki Kilyungi
* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation.
2022-09-09Add missing importMunyoki Kilyungi
* wqflask/base/trait.py: Import utility.hmac
2022-09-09Import missing module.Frederick Muriuki Muriithi
2022-09-09Check whether trait_list and sample_data exist before operationsFrederick Muriuki Muriithi
2022-09-09Remove `None` values from datasetFrederick Muriuki Muriithi
2022-09-09Filter out Samples without valuesFrederick Muriuki Muriithi
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.
2022-09-09Use `database_connection()`Frederick Muriuki Muriithi
Call the `database_connection()` function to get a connection to the database.
2022-09-09Replace `g.db.execute` with `cursor.execute`Frederick Muriuki Muriithi
2022-09-09Comment out pickling to avoid errorFrederick Muriuki Muriithi
Pickling was failing with "TypeError: cannot pickle 'Connection' object" This commit avoids the error by temporarily commenting out the line to prevent the pickling to actually test the working of the system on the CI/CD server.
2022-09-09If port is null, use MySQL's default 3306Frederick Muriuki Muriithi
2022-09-09Use `urllib.parse.urljoin` for urlsFrederick Muriuki Muriithi
Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity.
2022-09-08Filter export by checked rows (when any rows are checked)zsloan
2022-09-08Fix getCheckedRows so that it only selects checkbox input elementszsloan
2022-09-08Convert variables to camelCase and remove some unused variableszsloan
2022-09-08Remove commented out codezsloan
2022-09-08Remove console logzsloan
2022-09-08Remove some unused initialized variableszsloan
2022-09-08Make GN_SERVER_URL the genenetwork3 API endpoint.Arun Isaac
From now on, GN_SERVER_URL will be the genenetwork3 API endpoint. For example, GN_SERVER_URL=https://gn3.genenetwork.org/api * wqflask/wqflask/collect.py (view_collection), wqflask/wqflask/partial_correlations_views.py (partial_correlations, poll_partial_correlation_results), wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js (defaultStatusCodeFunctions): Do not append api to GN_SERVER_URL. * etc/default_settings.py (GN_SERVER_URL): Append /api.
2022-09-08Replace "asserts" with ValueErrorsMunyoki Kilyungi
* wqflask/wqflask/api/correlation.py (do_correlation): Raise a ValueError if variables are not in the start_vars.
2022-09-08Delete unused importsMunyoki Kilyungi
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Delete unused imports. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto.
2022-09-08Simplify how chromosomes are fetchedMunyoki Kilyungi
* wqflask/base/species.py: Import "Any" and "Union". (TheSpecies): Add type hints. Get rid of redundant "if ... else" statement. (IndChromosome.mb_length): Add type hints. (Chromosomes): Inject conn and add type hints.
2022-09-08Add type-hints to database_connectionMunyoki Kilyungi
* wqflask/wqflask/database.py: Import Protocol, Any and Iterator. (Connection): New protocol class for type-hints. (read_from_pyfile): Add type-hints. (sql_uri): Ditto. (database_connection): Ditto.
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.
2022-09-08Removing object notation after a cursor fetchMunyoki Kilyungi
* wqflask/wqflask/show_trait/SampleList.py (SampleList.get_attributes): Remove object notation. (SampleList.get_extra_attribute_values): Ditto.
2022-09-08Remove redundant cursor.fetchone()Munyoki Kilyungi
* wqflask/base/data_set.py (DataSet.retrieve_other_names): Call cursor.fetchone() only once.
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 ",".
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