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2023-06-26Bug: Pass the dataset name/id for authorisation checksFrederick Muriuki Muriithi
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.
2023-06-22Update calls to `database_connection` functionFrederick Muriuki Muriithi
Pass in the database URI at call time.
2023-06-22Pass in the URI to the databaseFrederick Muriuki Muriithi
Pass in the URI to the database, rather than coupling the `database_connection` function to the application environment and settings.
2023-06-22Create new entry-point module to reduce chances of circular imports.Frederick Muriuki Muriithi
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.
2023-06-20Change getSampleTableData function to include a includeNAs parameterzsloan
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).
2023-06-18Updating READMEsPjotr Prins
2023-06-18Remove unused locust filePjotr Prins
2023-06-18Disable document editing - should move to markdown instead.Pjotr Prins
2023-06-18Cleaning up READMEs - moving stuff to gemtextPjotr Prins
2023-06-15Add genotype pageMunyoki Kilyungi
* wqflask/wqflask/templates/genotype.html: New template. * wqflask/wqflask/views.py (get_phenotype): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-14Fix broken get_trait_units testzsloan
2023-06-14(Hopefully)fix bug where the mapping form submission is sometimes wrongly ↵zsloan
treated 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).
2023-06-14Fix main search bug causing AND searches to no longer workzsloan
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).
2023-06-14Increase number of distinct values for showing the 'Block samples by group' ↵zsloan
attributes from 10 to 500
2023-06-14Remove unused color-by-attribute option + put violin plot div in a ↵zsloan
section-form-div
2023-06-14Change mapping descriptionszsloan
2023-06-14Remove unused classzsloan
2023-06-14Make basic stats Plotly figures more consistentzsloan
2023-06-14Change plotly layout options for probability plotzsloan
2023-06-14Change CSS for mapping options/description for better fitzsloan
2023-06-14Make default unit_type value with lower-case vzsloan
2023-06-14Remove extra spacezsloan
2023-06-13Deactivate correlation correctness tests temporarily.Frederick Muriuki Muriithi
2023-06-13Namespace session variable.Frederick Muriuki Muriithi
Namespace the session variable name to avoid conflicts with other systems served on the same domain.
2023-06-12Add phenotype pageMunyoki Kilyungi
* wqflask/wqflask/templates/phenotype.html: New template. * wqflask/wqflask/views.py (get_phenotype): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-08bug: Fix URI to prevent unnecessary redirect.Frederick Muriuki Muriithi
2023-06-08Remove authorization restriction on viewing sample datazsloan
2023-06-08Fix bug by providing anon_id to collections/addzsloan
2023-06-07Add publication pageMunyoki Kilyungi
* wqflask/wqflask/templates/publication.html: New page. * wqflask/wqflask/views.py (get_dataset): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Add 1 to LRS_LOD_MAX in order to prevent situations where a tick is missing ↵zsloan
for the highest points on the manhattan plot
2023-06-06Align probability plot title to the left ('xanchor: right' does this for ↵zsloan
some reason)
2023-06-06Make geoSeries a linkMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Put metadata name in a new lineMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Fix geoplatform link in datasets pageMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Fix some titles in INFOPAGEMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06If a title doesn't exist, use the metadata name insteadMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-06Update dataset page to match GN1Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Add dataset link that uses RDFMunyoki Kilyungi
* wqflask/wqflask/templates/dataset.html: New page. * wqflask/wqflask/templates/show_trait_details.html: Add link to GN2 datasets page. * wqflask/wqflask/views.py (get_dataset): New endpoint. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-02Delete trait metadata from the show_traits pageMunyoki Kilyungi
* wqflask/wqflask/templates/show_metadata_details.html: Delete. * wqflask/wqflask/templates/show_trait.html: Delete if block that checks includes trait metadata. * wqflask/wqflask/views.py: Remove "metadata". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-31Use utility.tools to get configuration variablesFrederick Muriuki Muriithi
Using flask.current_app.config for configurations does not give the appropriate configurations.
2023-05-31Compute dataset type from name.Frederick Muriuki Muriithi
2023-05-30Fix test: Sort values to avoid equality problems.Frederick Muriuki Muriithi
2023-05-30Fix test: Expect tuple not set.Frederick Muriuki Muriithi
2023-05-30Fix test: Expect tuple not set.Frederick Muriuki Muriithi
2023-05-25auth: Show publicly visible traits.Frederick Muriuki Muriithi
2023-05-25Rework UI. Set resource publicly viewable by default.Frederick Muriuki Muriithi
Reorganise the UI for resource creation. Add a checkbox that sets the resource as publicly viewable by default.
2023-05-24Add link to user-account registration page.Frederick Muriuki Muriithi
2023-05-23oauth2: Enable admins to masquerade as other usersFrederick Muriuki Muriithi
2023-05-22Initialize exonStarts and exonEnds for mouse, since it currently throws an ↵zsloan
error if there's nothing in the GeneList table for the interval selected
2023-05-22Allow for editing values of samples that don't currently have valueszsloan
Deletions aren't working yet. This is dependent on a GN3 chance that allows the sample_list to be passed to get_trait_csv_sample_data
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-30 05:31:38 +0000