| Age | Commit message (Expand) | 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...The assumption that the resultset will never be empty was leading to a
lot of errors.
| Frederick Muriuki Muriithi |
| 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`...Only add a value to the path if it is actually set
| Frederick Muriuki Muriithi |
| 2022-09-12 | Add tests for correlations...* Add a test to catch a regression
| Frederick Muriuki Muriithi |
| 2022-09-09 | Fix bug in display_mapping_results chromosome query...A tuple of chromosome names was being passed into the query as a single
argument, while it expected a separate argument for each chromosome
| zsloan |
| 2022-09-09 | Fix bug in retrieve_other_names...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)
| zsloan |
| 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...Bug/fix broken correlations | Muriithi Frederick Muriuki |
| 2022-09-09 | Fetch sample values correctly...* wqflask/base/data_set.py (MrnaAssayDataSet.retrieve_sample_data):
Fix indentation.
| Munyoki Kilyungi |
| 2022-09-09 | Add missing import...* wqflask/base/trait.py: Import utility.hmac
| Munyoki Kilyungi |
| 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...Remove mutation of state, and handle the edge case where the
sub-sequence could be an empty sequence.
| Frederick Muriuki Muriithi |
| 2022-09-09 | Use `database_connection()`...Call the `database_connection()` function to get a connection to the
database.
| Frederick Muriuki Muriithi |
| 2022-09-09 | Replace `g.db.execute` with `cursor.execute` | Frederick Muriuki Muriithi |
| 2022-09-09 | Comment out pickling to avoid error...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.
| Frederick Muriuki Muriithi |
| 2022-09-09 | If port is null, use MySQL's default 3306 | Frederick Muriuki Muriithi |
| 2022-09-09 | Use `urllib.parse.urljoin` for urls...Use the `urllib.parse.urljoin` function to join urls rather than
string concatenation for uniformity.
| Frederick Muriuki Muriithi |
| 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....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 |
