| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2023-07-26 | Fetch `metadata_audit` trails with direct queries | Frederick Muriuki Muriithi | |
| Fetch the `metadata_audit` trails for phenotypes and probesets using direct queries rather than the ORM-dependent functions. | |||
| 2023-07-26 | Create 'metadata_audit' trail: remove ORM-dependent function | Frederick Muriuki Muriithi | |
| Create a 'metadata_audit' record with a direct query rather than using the ORM-dependent function to create it. | |||
| 2023-07-26 | Avoid conflating `dataset_id` with `trait_name`. | Frederick Muriuki Muriithi | |
| 2023-07-26 | Commit changes on success, rollback on failure. | Frederick Muriuki Muriithi | |
| Ensure that changes the database are committed if the query is successful, or rolled back if not. | |||
| 2023-07-24 | Check user is logged in before checking privileges | Frederick Muriuki Muriithi | |
| For editing, ensure the user is logged in before even attempting to check the authorisation privileges. | |||
| 2023-07-24 | Display "Edit" button for all users | Frederick Muriuki Muriithi | |
| Display the "Edit" button for all the users to ensure that they are aware of the feature. | |||
| 2023-07-24 | Protect the "approve" and "reject" endpoints | Frederick Muriuki Muriithi | |
| Protect the actual "approve" or "reject" steps, rather than just the UI elements. | |||
| 2023-07-24 | Fix bugs | Frederick Muriuki Muriithi | |
| * Add missing `.now()` * Provide defaults (not `None`) for required fields | |||
| 2023-07-21 | Fetch and update publication with non-ORM functions | Frederick Muriuki Muriithi | |
| Replace the ORM functions for fetching and updating the publication with non-ORM equivalents. | |||
| 2023-07-19 | Replace ORM code with direct queries for ProbeSets | Frederick Muriuki Muriithi | |
| 2023-07-18 | Remove unused import | zsloan | |
| 2023-07-18 | Fix issue where the full samplelist wasn't used in the values column for the ↵ | zsloan | |
| traits export | |||
| 2023-07-18 | Replace ORM calls with direct queries | Frederick Muriuki Muriithi | |
| Avoid the use of the ORM code for fetching data from the database, and instead use direct queries that indicate easily what is being fetched from the database. | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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