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2023-10-26Remove group from resourceFrederick Muriuki Muriithi
A resource is not linked directly to a user group any more.
2023-10-26Update role view: Add link to resource.Frederick Muriuki Muriithi
2023-10-26Fetch system roles from new `/auth/system/roles` endpoint.Frederick Muriuki Muriithi
2023-10-26Use gn-auth as the authorisation server.Frederick Muriuki Muriithi
2023-10-25Always cache mapping results for a month, even if Copy and Share isn't clickedzsloan
2023-10-25Remove expiration time when caching mapping inputszsloan
2023-10-24Add script for converting the HXBBXH genotype file provided by Hao.zsloan
Paths and sample/chromosome lists are hard-coded just because this was probably a one-time thing, but still commiting it since it's good to have it around in case we need to use it again
2023-10-24Add script for creating list of ProbeSet datasets with NAs for Max QTLzsloan
2023-10-24Make DataTables automatically adjust columns are generating the tablezsloan
2023-10-24Prevent search result table from having the scroll bar not be visible at the ↵zsloan
edge of the browser window
2023-10-11Fix placeholder text for correlation page Select Rows featurezsloan
2023-10-11Re-enable filter options for correlations against phenotype traitszsloan
2023-10-09collections: make POST requestsFrederick Muriuki Muriithi
Convert the requests that either create a new collection, or add traits to an existing collection to use the "POST" method, since such requests are not idempotent.
2023-10-06Change WebGestalt URL to use HTTPSzsloan
2023-10-06Provide default `CORRELATION_COMMAND` setting. Remove unused import.Frederick Muriuki Muriithi
2023-10-03Include cached_trait parameter for scatterplot, so it knows which trait to ↵zsloan
use the cached data for
2023-09-25Remove parents/f1s from Other sample groupzsloan
2023-09-25Invert rows/columns for multi-trait exportzsloan
2023-09-25Swap parameters for mapping scatterplot, since the genotype markers were ↵zsloan
being pulled from the dataid instead of the trait sample values
2023-09-25Update function for getting number of collections in scatterplot pagezsloan
2023-09-21Fix the way id_ is accessed from existing_publicationzsloan
2023-09-21Remove check for collections from mapping cofactor selection UIzsloan
2023-09-21Add update_cross_reference to importszsloan
2023-09-20Revert "Revert "Remove SECRET_KEY from mandatory start up check""Frederick Muriuki Muriithi
This reverts commit 89abbdd63840b1a1ea27f7dc8c5146563193b23a.
2023-09-20Revert "Remove SECRET_KEY from mandatory start up check"Frederick Muriuki Muriithi
This reverts commit 093cad933bfd241e993afbbd431d64efdd354e1d.
2023-09-19Add links to GN-hosted portalszsloan
2023-09-13Remove unnecessary sections.Munyoki Kilyungi
* .github/PULL_REQUEST_TEMPLATE.md: Delete unnecessary sections. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-13Remove GN2 generif link.Munyoki Kilyungi
* wqflask/wqflask/templates/show_trait_details.html: Delete GN2 generif link. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-13add mastadon feed to homepageAlexander_Kabui
2023-09-13Patch MySQLdb.escape_string to use use a connection.Munyoki Kilyungi
* wqflask/utility/db_tools.py: Delete MySQLdb.escape_. Import get_setting, database_connection. (escape_): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-12Replace escape with function that uses conn.escape_stringzsloan
2023-09-12Remove SECRET_KEY from mandatory start up checkMunyoki Kilyungi
* wqflask/wqflask/startup.py <startup_errors>: Remove SECRET_KEY which was introduced in d193cec7a8985. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Trigger CI build.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Replace string concat with os.path.join.Munyoki Kilyungi
* wqflask/utility/tools.py (assert_writable_dir): Use "os.path.join" to concatenate paths. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-11Add missing key in actual results.Munyoki Kilyungi
* wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py (TestExportTraits.test_get_export_metadata)<results>: Add "group" as extra key. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-08Replace escape with conn.escape_stringMunyoki Kilyungi
* wqflask/wqflask/do_search.py (DoSearch.mescape): Replace escape with conn.escape_string. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-08Remove unused importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-07Handle 'invalid_token' errorFrederick Muriuki Muriithi
2023-09-05Fix export for temp traitszsloan
2023-09-05Fix issue where X and Y axis were the same when using data ID for ↵zsloan
correlation scatterplot
2023-09-05Skip unittestMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace assertRegexpMatches with assertRegexMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace scipy.isnan with numpy.isnanMunyoki Kilyungi
* wqflask/wqflask/api/correlation.py (get_sample_r_and_p_values): Replace scipy.isnan with numpy.isnan. scipy.isnan is deprecated and will be removed in SciPy 2.0.0 Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Re-add hard-coded PYTHONPATHMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove PYTHONPATH checkMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Trigger CI buildMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove PYTHONPATH injectionMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-31Don't show decimal places when all values are integerszsloan
2023-08-31Update URL on tutorials pagezsloan
2023-08-31Use error-display utilityFrederick Muriuki Muriithi
Use the error-display utility to get rid of an unnecessary error-handling function.
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