| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-07-21 | Fetch and update publication with non-ORM functions...Replace the ORM functions for fetching and updating the publication
with non-ORM equivalents.
| Frederick Muriuki Muriithi |
| 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 |
| 2023-07-18 | Replace ORM calls with direct queries...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.
| Frederick Muriuki Muriithi |
| 2023-07-18 | BugFix: Use reworked `retrieve_phenotype_group_name` function...Use the reworked `retrieve_phenotype_group_name` to fetch the group
name for phenotype datasets.
== Bug Description ==
There was a subtle bug in the original calls to `retrieve_group_name`
function where the `dataset_id` was passed in as an argument, rather
than the group id.
For some Datasets, the `group_id` and `dataset_id` share the same
value, and would end up querying the correct values, but that was a
fluke where doing the wrong thing ended up with the expected values.
This commit fixes that by using the reworked function, which does the
correct indirection from `dataset_id` to the appropriate `group_id`.
See
https://github.com/genenetwork/genenetwork3/commit/088b6181457ef4e528b7dcbf04b7aca29b274d1f
for the reworked function.
| Frederick Muriuki Muriithi |
| 2023-07-17 | Enable deletion of sample values. | Frederick Muriuki Muriithi |
| 2023-07-17 | Serialize to JSON with custom encoder...Serialize values to JSON using the custom encoder that is aware of
data types the default encoder might not be aware of.
| Frederick Muriuki Muriithi |
| 2023-07-17 | UI: Change input elements...Change the input elements from all "<textarea ...>" to more closely
adhere to the data that each element is concerned with.
| Frederick Muriuki Muriithi |
| 2023-07-14 | Bug: Assign group within the db context manager...Assign the value to group within the db connection's context
manager. Initialise the group to an empty tuple at the very begining.
Fixes the error noted in
https://github.com/genenetwork/gn-docs/blob/master/api/questions-to-ask-GN.md
and should now allow the curl invocation:
curl -s https://genenetwork.org/api/v_pre1/group/BXD
to work as expected.
| Frederick Muriuki Muriithi |
| 2023-07-12 | Bug: Provide missing argument. | Frederick Muriuki Muriithi |
| 2023-07-12 | Fix check for numeric values...The `str.isnumeric()` function returns false for numbers such as
'9.99', '88.8' etc. This commit provides a slightly more robust check
for strings that are numbers. It will fail for numbers with exponents
though.
| Frederick Muriuki Muriithi |
| 2023-07-12 | Use new session to get user (author) information...* wqflask/utility/json/__init__.py: Custom JSON for serialising UUIDs
into a JSON representantion
* wqflask/utility/json/encoders.py: Custom JSON for serialising UUIDs
into a JSON representation
* wqflask/wqflask/metadata_edits.py: Use new sessions for author
information
| Frederick Muriuki Muriithi |
| 2023-07-12 | Provide message when there are no diffs. | Frederick Muriuki Muriithi |
| 2023-07-12 | Check whether user is authorised to act on diff | Frederick Muriuki Muriithi |
| 2023-07-12 | Update `login_required` decorator...Change how the check for user login works.
| Frederick Muriuki Muriithi |
| 2023-07-11 | Fix bug with add a trait to a collection from the trait page...Apparently collections/add needs the input to be passed as POST
| zsloan |
| 2023-07-11 | BugFix: Fix the sorting key functions...Update the sort-key functions to use the correct dictionary keys to
retrieve the comparison value for the sort.
| Frederick Muriuki Muriithi |
| 2023-07-11 | BugFix: UX: Display the success notification correctly | Frederick Muriuki Muriithi |
| 2023-07-11 | BugFix: Display diff file only once...The code filtering the diffs to ensure that only the diffs for the
traits that the user has access to are visible was leading to the
diffs that relate to the same trait showing up more than once. This
commit fixes that, ensuring that each diff shows up once.
| Frederick Muriuki Muriithi |
| 2023-07-11 | Handle HTTP status codes 4** in a special way. | Frederick Muriuki Muriithi |
| 2023-07-11 | Use new auth to determine access to diffs...* wqflask/wqflask/metadata_edits.py: Filter out diffs that the user
has access to before sending them to the template.
* wqflask/wqflask/templates/display_files.html: Remove access control
code in the UI template.
| Frederick Muriuki Muriithi |
| 2023-07-10 | Fix issue where correlation matrix tables had two IDs, causing things to not ... | zsloan |
| 2023-07-10 | Fix bug when adding PCA traits to a collection...The bug was caused by PCA traits not having description_display
| zsloan |
