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2023-10-09collections: make POST requests...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. Frederick Muriuki Muriithi
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 us...zsloan
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 bein...zsloan
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""...This reverts commit 89abbdd63840b1a1ea27f7dc8c5146563193b23a. Frederick Muriuki Muriithi
2023-09-20Revert "Remove SECRET_KEY from mandatory start up check"...This reverts commit 093cad933bfd241e993afbbd431d64efdd354e1d. Frederick Muriuki Muriithi
2023-09-19Add links to GN-hosted portalszsloan
2023-09-13Remove unnecessary sections....* .github/PULL_REQUEST_TEMPLATE.md: Delete unnecessary sections. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-13Remove GN2 generif link....* wqflask/wqflask/templates/show_trait_details.html: Delete GN2 generif link. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-13add mastadon feed to homepageAlexander_Kabui
2023-09-13Patch MySQLdb.escape_string to use use a connection....* wqflask/utility/db_tools.py: Delete MySQLdb.escape_. Import get_setting, database_connection. (escape_): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-12Replace escape with function that uses conn.escape_stringzsloan
2023-09-12Remove SECRET_KEY from mandatory start up check...* wqflask/wqflask/startup.py <startup_errors>: Remove SECRET_KEY which was introduced in d193cec7a8985. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-11Trigger CI build....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-11Replace string concat with os.path.join....* wqflask/utility/tools.py (assert_writable_dir): Use "os.path.join" to concatenate paths. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-11Add missing key in actual results....* 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> Munyoki Kilyungi
2023-09-08Replace escape with conn.escape_string...* wqflask/wqflask/do_search.py (DoSearch.mescape): Replace escape with conn.escape_string. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-08Remove unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
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 correlation...zsloan
2023-09-05Skip unittest...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Replace assertRegexpMatches with assertRegex...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Replace scipy.isnan with numpy.isnan...* 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> Munyoki Kilyungi
2023-09-05Re-add hard-coded PYTHONPATH...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove PYTHONPATH check...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Trigger CI build...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-09-05Remove PYTHONPATH injection...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-08-31Don't show decimal places when all values are integerszsloan
2023-08-31Update URL on tutorials pagezsloan
2023-08-31Use error-display utility...Use the error-display utility to get rid of an unnecessary error-handling function. Frederick Muriuki Muriithi
2023-08-31Check for token expiry...Check whether a token has expired before attempting to use it. Clear the session if the token has expired. Frederick Muriuki Muriithi
2023-08-24Make download icon on search result page the same as other pageszsloan
2023-08-24Change order of options in mapping page + fix sort for 5th column of tablezsloan
2023-08-24Change inputs for pheno sample data CSV function + only fetch sample data for...zsloan
2023-08-24Change URL for phenotype CSV download + only show sample table if fewer than ...zsloan
2023-08-17Combine pheno/mrna update functions + add dataset_name parameter for fetching...zsloan
2023-08-17Implement ProbeSet sample data editingzsloan
2023-08-17Increase the size of the field for editing phenotype sample data (so it can f...zsloan
2023-08-17Increase the size of the field for editing probe set sample data (so it can f...zsloan
2023-08-17Implement probeset sample data editing up until the approval stepzsloan
2023-08-17Fix probeset editing template to detect changes to sample valueszsloan
2023-08-17Fix probeset editing html to be the same as pheno editingzsloan
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