| Age | Commit message (Expand) | Author |
|---|
| 2023-09-12 | Replace escape with function that uses conn.escape_string | zsloan |
| 2023-09-12 | Remove SECRET_KEY from mandatory start up check...* wqflask/wqflask/startup.py <startup_errors>: Remove SECRET_KEY which
was introduced in d193cec7a8985.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | Replace string concat with os.path.join....* wqflask/utility/tools.py (assert_writable_dir): Use "os.path.join"
to concatenate paths.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-11 | Add missing key in actual results....* 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>
| Munyoki Kilyungi |
| 2023-09-08 | Replace escape with conn.escape_string...* wqflask/wqflask/do_search.py (DoSearch.mescape): Replace escape with
conn.escape_string.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-08 | Remove unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 correlation... | zsloan |
| 2023-09-05 | Skip unittest...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace assertRegexpMatches with assertRegex...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace scipy.isnan with numpy.isnan...* 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>
| Munyoki Kilyungi |
| 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...Use the error-display utility to get rid of an unnecessary
error-handling function.
| Frederick Muriuki Muriithi |
| 2023-08-31 | Check for token expiry...Check whether a token has expired before attempting to use it. Clear
the session if the token has expired.
| Frederick Muriuki Muriithi |
| 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 for... | zsloan |
| 2023-08-24 | Change URL for phenotype CSV download + only show sample table if fewer than ... | zsloan |
| 2023-08-17 | Combine pheno/mrna update functions + add dataset_name parameter for fetching... | zsloan |
| 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 f... | zsloan |
| 2023-08-17 | Increase the size of the field for editing probe set sample data (so it can f... | zsloan |
| 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."...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
| Frederick Muriuki Muriithi |
| 2023-08-11 | Auto-approve Publication Metadata Edit for phenotypes....Mark all Publication metadata edits as automatically approved.
| Frederick Muriuki Muriithi |
| 2023-08-10 | Set up defaults and check for mandatory settings...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.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 2023-07-31 | Fix searches so they work with chromosomes X/Y and both including and not inc......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
| zsloan |
| 2023-07-31 | Paginate resource data items...Provide a means to paginate the data items in the resources page.
| Frederick Muriuki Muriithi |
| 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...Fetch the `metadata_audit` trails for phenotypes and probesets using
direct queries rather than the ORM-dependent functions.
| Frederick Muriuki Muriithi |
| 2023-07-26 | Create 'metadata_audit' trail: remove ORM-dependent function...Create a 'metadata_audit' record with a direct query rather than using
the ORM-dependent function to create it.
| Frederick Muriuki Muriithi |
| 2023-07-26 | Avoid conflating `dataset_id` with `trait_name`. | Frederick Muriuki Muriithi |
| 2023-07-26 | Commit changes on success, rollback on failure....Ensure that changes the database are committed if the query is
successful, or rolled back if not.
| Frederick Muriuki Muriithi |
| 2023-07-24 | Check user is logged in before checking privileges...For editing, ensure the user is logged in before even attempting to
check the authorisation privileges.
| Frederick Muriuki Muriithi |
| 2023-07-24 | Display "Edit" button for all users...Display the "Edit" button for all the users to ensure that they are
aware of the feature.
| Frederick Muriuki Muriithi |
| 2023-07-24 | Protect the "approve" and "reject" endpoints...Protect the actual "approve" or "reject" steps, rather than just the
UI elements.
| Frederick Muriuki Muriithi |
| 2023-07-24 | Fix bugs...* Add missing `.now()`
* Provide defaults (not `None`) for required fields
| Frederick Muriuki Muriithi |
