| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-06-18 | Updating READMEs | Pjotr Prins |
| 2023-06-18 | Remove unused locust file | Pjotr Prins |
| 2023-06-18 | Disable document editing - should move to markdown instead. | Pjotr Prins |
| 2023-06-18 | Cleaning up READMEs - moving stuff to gemtext | Pjotr Prins |
| 2023-06-15 | Add genotype page...* wqflask/wqflask/templates/genotype.html: New template.
* wqflask/wqflask/views.py (get_phenotype): New endpoint.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-14 | Fix broken get_trait_units test | zsloan |
| 2023-06-14 | (Hopefully)fix bug where the mapping form submission is sometimes wrongly tre......as a GET, causing the code to check for a hash_of_inputs input that
doesn't exist.
This is hard to troubleshoot because I could never reproduce the issue
(only Rob has mentioned it), but the error Rob showed me seems to
directly imply this was issue, so hopefully this change (which directly
checks if hash_of_inputs is set) will prevent it
from happening. It's possible it will still throw a different error,
though (if it's actually treating it as a GET, it presumably won't have
any of the other inputs it expects). This issue is a bit confusing,
because I'm not sure how/why mapping run from the trait page would ever
be treated as a GET request (since the show_trait page form is POST).
| zsloan |
| 2023-06-14 | Fix main search bug causing AND searches to no longer work...The cause of this bug is that, when the autocomplete feature was
implemented, it checks the OR search field (in order to save its
contents) and only submits the form if
it isn't empty. This means that, if the user fills out the AND field and
submits the form, nothing happens.
I changed it to check both the AND and OR fields (and save both of their
contents). While not perfect (since only one field is ever actually
used), I figured it's best to just store everything (and there isn't
really any way to know which search is intended when both fields are
filled).
| zsloan |
| 2023-06-14 | Increase number of distinct values for showing the 'Block samples by group' a... | zsloan |
| 2023-06-14 | Remove unused color-by-attribute option + put violin plot div in a section-fo... | zsloan |
| 2023-06-14 | Change mapping descriptions | zsloan |
| 2023-06-14 | Remove unused class | zsloan |
| 2023-06-14 | Make basic stats Plotly figures more consistent | zsloan |
| 2023-06-14 | Change plotly layout options for probability plot | zsloan |
| 2023-06-14 | Change CSS for mapping options/description for better fit | zsloan |
| 2023-06-14 | Make default unit_type value with lower-case v | zsloan |
| 2023-06-14 | Remove extra space | zsloan |
| 2023-06-13 | Deactivate correlation correctness tests temporarily. | Frederick Muriuki Muriithi |
| 2023-06-13 | Namespace session variable....Namespace the session variable name to avoid conflicts with other
systems served on the same domain.
| Frederick Muriuki Muriithi |
| 2023-06-12 | Add phenotype page...* wqflask/wqflask/templates/phenotype.html: New template.
* wqflask/wqflask/views.py (get_phenotype): New endpoint.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-08 | bug: Fix URI to prevent unnecessary redirect. | Frederick Muriuki Muriithi |
| 2023-06-08 | Remove authorization restriction on viewing sample data | zsloan |
