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2023-11-30Update phenotype retrieval route, incorporate group parameter.Munyoki Kilyungi
* wqflask/wqflask/views.py (get_phenotype): Add "group" parameter. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-29Remove set operator when fetching correlation metadatazsloan
I'm not sure why this was introduced in the first place, but it appears to cause an issue where a semicolon is displayed in the description even when there's no probe target description (and removing it doesn't seem to cause any problems)
2023-11-27Change info file links + make them open in new tabszsloan
2023-11-27Rename metadata/genotype -> metadata/genotypes.Munyoki Kilyungi
* wqflask/wqflask/views.py (get_genotype): Rename genotype -> genotypes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Update genotype UI page.Munyoki Kilyungi
* wqflask/wqflask/templates/genotype.html: Update page. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Update the phenotype page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Rename "/phenotype" -> "phenotypes" endpoint.Munyoki Kilyungi
* wqflask/wqflask/views.py (get_phenotype): Rename "/phenotype" -> "phenotypes". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Revamp UI page for publications.Munyoki Kilyungi
* wqflask/wqflask/templates/publication.html: Update UI. When a particular metadata item does not show up, show "N/A" instead. * wqflask/wqflask/views.py (get_publication): Rename "publication"->"publications". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Remove javascript integrity check for HTMX.Munyoki Kilyungi
Firefox will always give the following error: None of the “sha384” hashes in the integrity attribute match the content of the subresource. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Point htmx to the correct endpoint for dataset search.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Use correct src for htmx.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Improve search-box styling.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Update the lead and place-holder copy for dataset search.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Improve the dataset's styling.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Refactor template to use new json-ld format.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Float the details panel only when metadata exists.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Refactor route and metadata retrieval process for dataset details.Munyoki Kilyungi
* wqflask/wqflask/views.py (get_dataset): Rename "/dataset..." -> "/datasets...". Remove url parsing for metadata keys since we use json-ld now. Remove pull-right check. Only pass the metadata to the template. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Add search bar if a there's a URL miss when displaying data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Make dataset it's own html entity.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Get the last element from url in the key.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Rename metadata to dataset.Munyoki Kilyungi
* wqflask/wqflask/templates/metadata/dataset.html: Rename metadata to dataset. * wqflask/wqflask/views.py (get_dataset): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Use correct fields when fetching a dataset's metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Move dataset template to metadata directory.Munyoki Kilyungi
* wqflask/wqflask/templates/dataset.html: Move this ... * wqflask/wqflask/templates/metadata/dataset.html: here. Also, add htmx library. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-27Delete dead comment.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-25Fix bug caused by NaN p-values in GEMMA mappingzsloan
2023-11-17Log out query errorsFrederick Muriuki Muriithi
Log out failures in querying the database as errors to help with catching issues with and debugging of queries.
2023-11-13Fix bug that caused hitting Enter on regular search after hitting Enter for ↵zsloan
global search to wrongly submit global search instead
2023-11-13Secrets: Enable separate secrets settings fileFrederick Muriuki Muriithi
Enable a separate secrets settings file to be provided where necessary. The secrets settings file will hold security-critical configuration values that should not be exposed in the repository.
2023-11-11DB docsPjotr Prins
2023-11-09Set correlation table width to 90%zsloan
2023-11-09Make adjustments to correlation tablezsloan
- Disable scroller when fewer than 2000 rows. Scroller causes a problem where you can't reach certain rows when manually scroller when rows are too 'tall' (so when descriptions are long and the window is smaller) - Disable width for Abbreviation and increase width for Peak Position so it doesn't get pushed to two lines
2023-11-06Use correct prefix for auth server's url.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-06Revert "Disable SSL check when checking whether user is logged in."Munyoki Kilyungi
This reverts commit b178e8f8944141632032103fb5b06e3a0746d4f3.
2023-11-06Disable SSL check when checking whether user is logged in.Munyoki Kilyungi
* wqflask/wqflask/views.py (index_page): Set "verify=False" in no_token_get. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-06Get full trace of SSL error and reduce number of retries in MR.Munyoki Kilyungi
* test/requests/test-website.py (host_is_online): Reduce tries from 10 to 5. Also, print out the full error---useful for CD debugging. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-06Use latest self-hosted guix-bioinformatics channel.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-06Disable SSL check on Mechanical Rob.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-06Update the default auth url.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-26case-attribute: approve/reject diffFrederick Muriuki Muriithi
Make calls to the API server to approve or reject a diff, depending on the user's actions. Clean up the UI elements to remove debug artifacts.
2023-10-26case-attributes: View the diffs.Frederick Muriuki Muriithi
2023-10-26CaseAttribute: List out the diffsFrederick Muriuki Muriithi
List out the diffs and create placeholders for active elements that do not yet have the back-end code that handles them.
2023-10-26CaseAttributes: Provide UI for diffs list.Frederick Muriuki Muriithi
2023-10-26CaseAttribute: Add link to enable editing case attributes.Frederick Muriuki Muriithi
2023-10-26Rework "success" function.Frederick Muriuki Muriithi
2023-10-26CaseAttributes: Bug: Fix query.Frederick Muriuki Muriithi
2023-10-26Fix URL: Make requests to GN3 not gn-authFrederick Muriuki Muriithi
Provide a "wrapped" requests module that returns an Either monad rather than a request directly. Send requests to GN3 rather than gn-auth
2023-10-26Use auth-server for authenticationFrederick Muriuki Muriithi
Authenticate with the Auth-server (gn-auth) to get the token to use on the API server (GN3).
2023-10-26Call utils to replace unnecessary functions.Frederick Muriuki Muriithi
2023-10-26Process data before sending to APIFrederick Muriuki Muriithi
2023-10-26UI for case-attribute editing.Frederick Muriuki Muriithi
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