| Age | Commit message (Expand) | Author |
|---|
| 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 | Also have repository function as a guix channel | Efraim Flashner |
| 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 |
| 2023-07-10 | Remove `OVERRIDES` global variable. | Frederick Muriuki Muriithi |
| 2023-07-05 | Remove broken Time Machine link...Add GN3 Github link
Move News Twitter feed below Links (at least until the Twitter embed
starts working again)
| zsloan |
| 2023-07-05 | Change traits export to include all samples, including parents/f1s | zsloan |
| 2023-07-05 | Fix bug where mapping is sometimes wrongly submitted as a GET request...I think this bug was caused by changing the /run_mapping endpoint to
accept both GET and POST requests, and it only seemed to occur for some
users (only Rob that I'm aware of).
I'm still not sure why it was happening, but I addressed it by returning
/run_mapping to being only POST requests, and instead allowing the
mapping hashes to be linked to with the pattern /run_mapping/<hash>
(instead of the GET request /run_mapping?hash=<hash>). This appears to
have prevented the problem from happening.
| zsloan |
| 2023-07-05 | Compute the GN_VERSION in setup code not shell script | Frederick Muriuki Muriithi |
| 2023-07-05 | Get setting from config files on envvars...The main code should only ever get its configs from the application
configurations, and not directly from the envvars. This helps with
maintenance by ensuring that the application configurations are done
in one place, and can be traced for debugging purposes.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Config: Remove unused `OVERRIDES`...The `OVERRIDES` variable has no actual use in the application,
therefore, this commit removes it and its dependent code.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Remove unused configs...The individual parts of the URI to the database are not used in the
application and thus serve no purpose.
| Frederick Muriuki Muriithi |
| 2023-07-05 | Remove unused import | Frederick Muriuki Muriithi |
| 2023-07-03 | Remove unnecessary (and I think wrong) data-url from mapping submission buttons | zsloan |
| 2023-07-03 | UX: Improve error messages...Make the error messages a little less cryptic in order to improve the
user's experience of the site.
| Frederick Muriuki Muriithi |
| 2023-06-30 | Fixed URL scheme issues | zsloan |
| 2023-06-26 | Bug: Pass dataset name for 'Publish' data...The dataset name is needed for authorisation checks.
| Frederick Muriuki Muriithi |
| 2023-06-26 | Bug: Pass the dataset name/id for authorisation checks...The new authorisation checks need the dataset name/id for checking the
access level the user has on any data. This commit passes the dataset
name/id through the requests.
We also add some exceptions to ensure that this data is passed through
before even attempting to check for the authorisation.
| Frederick Muriuki Muriithi |
| 2023-06-22 | Update calls to `database_connection` function...Pass in the database URI at call time.
| Frederick Muriuki Muriithi |
| 2023-06-22 | Pass in the URI to the database...Pass in the URI to the database, rather than coupling the
`database_connection` function to the application environment and
settings.
| Frederick Muriuki Muriithi |
| 2023-06-22 | Create new entry-point module to reduce chances of circular imports....This commit creates a new entry-point module (wqflask/gn2_main.py) and
imports all the other modules that import the application object with
something like:
`from wqflask import app`
This breaks the subtle circular-import cycle that tends to cause a lot
of inconveniences when developing the application.
| Frederick Muriuki Muriithi |
| 2023-06-20 | Change getSampleTableData function to include a includeNAs parameter...This is so the export function can show all rows, including ones with no
value. Previously it only fetched the rows with values (which is fine
for correlations/mapping, but not export).
| zsloan |
