| Age | Commit message (Expand) | Author |
|---|
| 2022-09-08 | Make GN_SERVER_URL the genenetwork3 API endpoint....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.
| Arun Isaac |
| 2022-09-08 | Replace "asserts" with ValueErrors...* wqflask/wqflask/api/correlation.py (do_correlation): Raise a
ValueError if variables are not in the start_vars.
| Munyoki Kilyungi |
| 2022-09-08 | Delete unused imports...* wqflask/wqflask/external_tools/send_to_geneweaver.py: Delete unused
imports.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Simplify how chromosomes are fetched...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Add type-hints to database_connection...* 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.
| Munyoki Kilyungi |
| 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 | Removing object notation after a cursor fetch...* wqflask/wqflask/show_trait/SampleList.py
(SampleList.get_attributes): Remove object notation.
(SampleList.get_extra_attribute_values): Ditto.
| Munyoki Kilyungi |
| 2022-09-08 | Remove redundant cursor.fetchone()...* wqflask/base/data_set.py (DataSet.retrieve_other_names): Call
cursor.fetchone() only once.
| 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 | Use "%s" instead of "%2.6f" or "%d" in query....* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Use "%s".
| Munyoki Kilyungi |
| 2022-09-08 | Fix sql queries..."%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.
| Munyoki Kilyungi |
| 2022-09-08 | Deleting utility.logger...* wqflask/utility/logger.py: Delete.
| Munyoki Kilyungi |
| 2022-09-08 | Add missing "," in cursor.execute()...* wqflask/base/data_set.py (DatasetGroup.get_mapping_methods): Fix
failing query by adding a missing ",".
| Munyoki Kilyungi |
| 2022-09-08 | Delete unused imports...* wqflask/wqflask/search_results.py: Remove unused imports.
| Munyoki Kilyungi |
| 2022-09-08 | Remove intermediate variables that are only used once...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Force pytest to use "importlib" import-mode to be able to run...Having "--import-mode=importlib" enables pytest to find the imports in
our tests; otherwise we get import errors.
* pyproject.toml: New pytest conf file.
| 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 | Recommend pytests in README...* README.md (Testing): Using pytests instead of unittests.
| 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 | Replace "g.db" with "database_connection" in documentation | Munyoki Kilyungi |
| 2022-09-08 | Remove "g.db" init from every session..."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.
| Munyoki Kilyungi |
| 2022-09-08 | Remove sql_alchemy initialisation when profiling correlations...* wqflask/scripts/profile_corrs.py: Remove sqlalchemy, connect_db and
shutdown_session.
(__main__): Remove "g.db".
| 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 |
| 2022-09-08 | Replace g.db with database_connection() context manager...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Delete logger import...* wqflask/base/trait.py: Remove utility.logger
| Munyoki Kilyungi |
| 2022-09-08 | Replace assertion with Value Error for non-existent dataset...* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in
ValueError.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Delete insert query that's not run...* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete insert query
| Munyoki Kilyungi |
| 2022-09-08 | Remove "if" block that does nothing...* wqflask/wqflask/db_info.py (InfoPage.get_info): Remove if block that
constructs a "final" query that does nothing.
| Munyoki Kilyungi |
| 2022-09-08 | Restructure "if ... else" to first check for a ValueError...* wqflask/wqflask/db_info.py (InfoPage.get_info): First check for a
ValueError Exception.
| Munyoki Kilyungi |
| 2022-09-08 | Raise a ValueError instead of generic exception...* wqflask/wqflask/db_info.py (InfoPage.get_info): Wrap error message
in ValueError Exception.
| Munyoki Kilyungi |
| 2022-09-08 | Replace format-strings with f-strings...* wqflask/wqflask/db_info.py (InfoPage.get_info): Use f-strings.
| Munyoki Kilyungi |
| 2022-09-08 | Remove '+' when concatenating strings inside brackets...* wqflask/wqflask/db_info.py (InfoPage.get_info): Delete "+".
| Munyoki Kilyungi |
| 2022-09-08 | Use db_connection and rework "if ... else" clauses...* wqflask/wqflask/snp_browser/snp_browser.py
(SnpBrowser.get_browser_results): Replace "g.db" with
database_connection. Rework "if ... else" logic.
| Munyoki Kilyungi |
| 2022-09-08 | Delete dead comment | Munyoki Kilyungi |
| 2022-09-08 | Refactor if clause to check for string in list...* wqflask/wqflask/docs.py (update_text): Check for the e-mail in a
list.
| Munyoki Kilyungi |
| 2022-09-08 | Refactor "if ... else" block to check the truthy case first...* wqflask/wqflask/docs.py (Docs.__init__): Check the truthy case first
after fetching the results.
| Munyoki Kilyungi |
| 2022-09-08 | Replace g.db with database_connection() context manager...* 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.
| Munyoki Kilyungi |
| 2022-09-08 | Delete unused news module...* wqflask/wqflask/news.py: Delete it.
| Munyoki Kilyungi |
| 2022-09-08 | Merge pull request #727 from Alexanderlacuna/feature/use-textfiles...use text files for Probeset | Alexander Kabui |
| 2022-09-08 | fixup query formatting | Alexander_Kabui |
| 2022-09-08 | gitignore: Add containers/mariadb-state....* .gitignore: Add containers/mariadb-state.
| Arun Isaac |
