| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-09-13 | Increase table marker limit to 25000 | zsloan | |
| 2022-09-13 | Fix bug where passing LOCO into the mapping API endpoint didn't work | zsloan | |
| 2022-09-12 | Fix query: Add comma to separate columns. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Check for species before calling `lower()` | Frederick Muriuki Muriithi | |
| 2022-09-12 | Fix asserts: Use variable for assert | Frederick Muriuki Muriithi | |
| 2022-09-12 | Check there is target data before running correlations | Frederick Muriuki Muriithi | |
| 2022-09-12 | Display cause(s) of test failure. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Fix query: Remove extraneous bracket | Frederick Muriuki Muriithi | |
| 2022-09-12 | Check for traits before computing | Frederick Muriuki Muriithi | |
| 2022-09-12 | Fix query: remove wrongly-placed comma | Frederick Muriuki Muriithi | |
| 2022-09-12 | Check db resultset before indexing into it | Frederick Muriuki Muriithi | |
| The assumption that the resultset will never be empty was leading to a lot of errors. | |||
| 2022-09-12 | Check data is truthy before indexing into it. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Enable running correlation tests alone. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Clean up print out. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Exit with an error condition if tests fail. | Frederick Muriuki Muriithi | |
| 2022-09-12 | Pass in missing argument | Frederick Muriuki Muriithi | |
| 2022-09-12 | Cleanup `PYTHONPATH` | Frederick Muriuki Muriithi | |
| Only add a value to the path if it is actually set | |||
| 2022-09-12 | Add tests for correlations | Frederick Muriuki Muriithi | |
| * Add a test to catch a regression | |||
| 2022-09-09 | Fix bug in display_mapping_results chromosome query | zsloan | |
| A tuple of chromosome names was being passed into the query as a single argument, while it expected a separate argument for each chromosome | |||
| 2022-09-09 | Fix bug in retrieve_other_names | zsloan | |
| 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) | |||
| 2022-09-09 | handle cases where tissue dataset vals are empty list | Alexander_Kabui | |
| 2022-09-09 | tissue:fetch for query formatting | Alexander_Kabui | |
| 2022-09-09 | Fix query: remove string interpolation. | Frederick Muriuki Muriithi | |
| 2022-09-09 | Retain only a single import of the same module | Frederick Muriuki Muriithi | |
| 2022-09-09 | Merge pull request #732 from BonfaceKilz/bug/fix-broken-correlations | Muriithi Frederick Muriuki | |
| Bug/fix broken correlations | |||
| 2022-09-09 | Fetch sample values correctly | Munyoki Kilyungi | |
| * wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data): Fix indentation. | |||
| 2022-09-09 | Add missing import | Munyoki Kilyungi | |
| * wqflask/base/trait.py: Import utility.hmac | |||
| 2022-09-09 | Import missing module. | Frederick Muriuki Muriithi | |
| 2022-09-09 | Check whether trait_list and sample_data exist before operations | Frederick Muriuki Muriithi | |
| 2022-09-09 | Remove `None` values from dataset | Frederick Muriuki Muriithi | |
| 2022-09-09 | Filter out Samples without values | Frederick Muriuki Muriithi | |
| 2022-09-09 | Refactor: Add tests and handle edge case | Frederick Muriuki Muriithi | |
| Remove mutation of state, and handle the edge case where the sub-sequence could be an empty sequence. | |||
| 2022-09-09 | Use `database_connection()` | Frederick Muriuki Muriithi | |
| Call the `database_connection()` function to get a connection to the database. | |||
| 2022-09-09 | Replace `g.db.execute` with `cursor.execute` | Frederick Muriuki Muriithi | |
| 2022-09-09 | Comment out pickling to avoid error | Frederick 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. | |||
| 2022-09-09 | If port is null, use MySQL's default 3306 | Frederick Muriuki Muriithi | |
| 2022-09-09 | Use `urllib.parse.urljoin` for urls | Frederick Muriuki Muriithi | |
| Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity. | |||
| 2022-09-08 | Filter export by checked rows (when any rows are checked) | zsloan | |
| 2022-09-08 | Fix getCheckedRows so that it only selects checkbox input elements | zsloan | |
| 2022-09-08 | Convert variables to camelCase and remove some unused variables | zsloan | |
| 2022-09-08 | Remove commented out code | zsloan | |
| 2022-09-08 | Remove console log | zsloan | |
| 2022-09-08 | Remove some unused initialized variables | zsloan | |
| 2022-09-08 | Make 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. | |||
| 2022-09-08 | Replace "asserts" with ValueErrors | Munyoki Kilyungi | |
| * wqflask/wqflask/api/correlation.py (do_correlation): Raise a ValueError if variables are not in the start_vars. | |||
| 2022-09-08 | Delete unused imports | Munyoki Kilyungi | |
| * wqflask/wqflask/external_tools/send_to_geneweaver.py: Delete unused imports. * wqflask/wqflask/external_tools/send_to_webgestalt.py: Ditto. | |||
| 2022-09-08 | Simplify how chromosomes are fetched | Munyoki 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. | |||
| 2022-09-08 | Add type-hints to database_connection | Munyoki 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. | |||
| 2022-09-08 | Test the creation of the_species, indchromosomes and chromosome objs | Munyoki 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. | |||
| 2022-09-08 | Removing object notation after a cursor fetch | Munyoki Kilyungi | |
| * wqflask/wqflask/show_trait/SampleList.py (SampleList.get_attributes): Remove object notation. (SampleList.get_extra_attribute_values): Ditto. | |||
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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