| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-09-21 | Remove check for collections from mapping cofactor selection UI | zsloan | |
| 2023-09-21 | Add update_cross_reference to imports | zsloan | |
| 2023-09-20 | Revert "Revert "Remove SECRET_KEY from mandatory start up check"" | Frederick Muriuki Muriithi | |
| This reverts commit 89abbdd63840b1a1ea27f7dc8c5146563193b23a. | |||
| 2023-09-20 | Revert "Remove SECRET_KEY from mandatory start up check" | Frederick Muriuki Muriithi | |
| This reverts commit 093cad933bfd241e993afbbd431d64efdd354e1d. | |||
| 2023-09-19 | Add links to GN-hosted portals | zsloan | |
| 2023-09-13 | Remove GN2 generif link. | Munyoki Kilyungi | |
| * wqflask/wqflask/templates/show_trait_details.html: Delete GN2 generif link. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-13 | add mastadon feed to homepage | Alexander_Kabui | |
| 2023-09-13 | Patch MySQLdb.escape_string to use use a connection. | Munyoki Kilyungi | |
| * wqflask/utility/db_tools.py: Delete MySQLdb.escape_. Import get_setting, database_connection. (escape_): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-12 | Replace escape with function that uses conn.escape_string | zsloan | |
| 2023-09-12 | Remove SECRET_KEY from mandatory start up check | Munyoki Kilyungi | |
| * wqflask/wqflask/startup.py <startup_errors>: Remove SECRET_KEY which was introduced in d193cec7a8985. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-11 | Replace string concat with os.path.join. | Munyoki Kilyungi | |
| * wqflask/utility/tools.py (assert_writable_dir): Use "os.path.join" to concatenate paths. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-11 | Add missing key in actual results. | Munyoki Kilyungi | |
| * wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py (TestExportTraits.test_get_export_metadata)<results>: Add "group" as extra key. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-08 | Replace escape with conn.escape_string | Munyoki Kilyungi | |
| * wqflask/wqflask/do_search.py (DoSearch.mescape): Replace escape with conn.escape_string. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-08 | Remove unused import | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-07 | Handle 'invalid_token' error | Frederick Muriuki Muriithi | |
| 2023-09-05 | Fix export for temp traits | zsloan | |
| 2023-09-05 | Fix issue where X and Y axis were the same when using data ID for ↵ | zsloan | |
| correlation scatterplot | |||
| 2023-09-05 | Skip unittest | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Replace assertRegexpMatches with assertRegex | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-09-05 | Replace scipy.isnan with numpy.isnan | Munyoki Kilyungi | |
| * wqflask/wqflask/api/correlation.py (get_sample_r_and_p_values): Replace scipy.isnan with numpy.isnan. scipy.isnan is deprecated and will be removed in SciPy 2.0.0 Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-08-31 | Don't show decimal places when all values are integers | zsloan | |
| 2023-08-31 | Update URL on tutorials page | zsloan | |
| 2023-08-31 | Use error-display utility | Frederick Muriuki Muriithi | |
| Use the error-display utility to get rid of an unnecessary error-handling function. | |||
| 2023-08-31 | Check for token expiry | Frederick Muriuki Muriithi | |
| Check whether a token has expired before attempting to use it. Clear the session if the token has expired. | |||
| 2023-08-24 | Make download icon on search result page the same as other pages | zsloan | |
| 2023-08-24 | Change order of options in mapping page + fix sort for 5th column of table | zsloan | |
| 2023-08-24 | Change inputs for pheno sample data CSV function + only fetch sample data ↵ | zsloan | |
| for table when fewer than 2000 samples | |||
| 2023-08-24 | Change URL for phenotype CSV download + only show sample table if fewer than ↵ | zsloan | |
| 2000 samples | |||
| 2023-08-17 | Combine pheno/mrna update functions + add dataset_name parameter for ↵ | zsloan | |
| fetching group name | |||
| 2023-08-17 | Implement ProbeSet sample data editing | zsloan | |
| 2023-08-17 | Increase the size of the field for editing phenotype sample data (so it can ↵ | zsloan | |
| fit up to 6 digits) | |||
| 2023-08-17 | Increase the size of the field for editing probe set sample data (so it can ↵ | zsloan | |
| fit up to 6 digits) | |||
| 2023-08-17 | Implement probeset sample data editing up until the approval step | zsloan | |
| 2023-08-17 | Fix probeset editing template to detect changes to sample values | zsloan | |
| 2023-08-17 | Fix probeset editing html to be the same as pheno editing | zsloan | |
| 2023-08-17 | Change phenotype CSV endpoint to specify the type of trait | zsloan | |
| 2023-08-11 | Revert "Auto-approve Publication Metadata Edit for phenotypes." | Frederick Muriuki Muriithi | |
| This reverts commit ce3568ce8e33a7ad1e722d42261913b5649df27f. It turns out we only ever save the approved commits in the database, so there is no point in adding the extra data to indicate that. This has been documented[^1] for the future. 1: https://github.com/genenetwork/gn-gemtext-threads/commit/4e016e43fd05202287730915d129daaed1a02efc | |||
| 2023-08-11 | Auto-approve Publication Metadata Edit for phenotypes. | Frederick Muriuki Muriithi | |
| Mark all Publication metadata edits as automatically approved. | |||
| 2023-08-10 | Set up defaults and check for mandatory settings | Frederick Muriuki Muriithi | |
| Use etc/default_settings.py to setup defaults for the application. Check for mandatory settings and notify users if any of the mandatory settings are not defined. | |||
| 2023-08-10 | Bug: Avoid repetition of data. Simplify UI. | Frederick Muriuki Muriithi | |
| 2023-08-10 | Clean up data before attempting to persist. | Frederick Muriuki Muriithi | |
| 2023-08-07 | Remove Twitter newsfeed | zsloan | |
| 2023-08-04 | Remove use of deprecated, ORM-dependent `update` function. | Frederick Muriuki Muriithi | |
| 2023-08-03 | Fix Submit Trait bug | zsloan | |
| 2023-08-02 | Remove import of deleted `insert` function. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Remove import of deleted functions. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Fix Bug: Unchanged Values Were Being Deleted | Frederick Muriuki Muriithi | |
| The original code (using the homebrew ORM system) would simply ignore values that were `None` when doing updates - the new code using direct queries was not. My (fredmanglis) initial fix to provide a default for values in DB that did not accept NULL was incorrect; instead, I needed to remove any key-value pairs from the incoming data that were set to `None` to fix the bug. The fix still feels incorrect: maybe we should do direct comparisons for all old-new value pairs, and set the data to be updated based on the differences, rather than relying on `None`s. | |||
| 2023-07-31 | Fix searches so they work with chromosomes X/Y and both including and not ↵ | zsloan | |
| including 'chr' As far as I can tell, the regex from before wasn't necessary; it seems like a simple matter of extracting the 'chr' substring from the chromosome search term | |||
| 2023-07-31 | Paginate resource data items | Frederick Muriuki Muriithi | |
| Provide a means to paginate the data items in the resources page. | |||
| 2023-07-26 | bug: Fix bug where diffs were not computing correctly. | Frederick Muriuki Muriithi | |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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