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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 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
2023-09-11Replace 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
2023-08-31Don'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
2023-08-17Change phenotype CSV endpoint to specify the type of traitzsloan
2023-08-11Revert "Auto-approve Publication Metadata Edit for phenotypes."...This reverts commit ce3568ce8e33a7ad1e722d42261913b5649df27f. It turns out we only ever save the approved commits in the database, so there is no point in adding the extra data to indicate that. This has been documented[^1] for the future. 1: https://github.com/genenetwork/gn-gemtext-threads/commit/4e016e43fd05202287730915d129daaed1a02efc Frederick Muriuki Muriithi
2023-08-11Auto-approve Publication Metadata Edit for phenotypes....Mark all Publication metadata edits as automatically approved. Frederick Muriuki Muriithi
2023-08-10Set up defaults and check for mandatory settings...Use etc/default_settings.py to setup defaults for the application. Check for mandatory settings and notify users if any of the mandatory settings are not defined. Frederick Muriuki Muriithi
2023-08-10Bug: Avoid repetition of data. Simplify UI.Frederick Muriuki Muriithi
2023-08-10Clean up data before attempting to persist.Frederick Muriuki Muriithi
2023-08-07Remove Twitter newsfeedzsloan
2023-08-04Remove use of deprecated, ORM-dependent `update` function.Frederick Muriuki Muriithi
2023-08-03Fix Submit Trait bugzsloan
2023-08-02Remove import of deleted `insert` function.Frederick Muriuki Muriithi
2023-08-02Remove import of deleted functions.Frederick Muriuki Muriithi
2023-08-02Fix Bug: Unchanged Values Were Being Deleted...The original code (using the homebrew ORM system) would simply ignore values that were `None` when doing updates - the new code using direct queries was not. My (fredmanglis) initial fix to provide a default for values in DB that did not accept NULL was incorrect; instead, I needed to remove any key-value pairs from the incoming data that were set to `None` to fix the bug. The fix still feels incorrect: maybe we should do direct comparisons for all old-new value pairs, and set the data to be updated based on the differences, rather than relying on `None`s. Frederick Muriuki Muriithi
2023-07-31Fix searches so they work with chromosomes X/Y and both including and not inc......As far as I can tell, the regex from before wasn't necessary; it seems like a simple matter of extracting the 'chr' substring from the chromosome search term zsloan
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