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2022-08-09Integrate rust correlations. Deduplicate similar code.Frederick Muriuki Muriithi
- Use rust correlations rather than the slower python one - Remove code duplicated in the `wqflask/wqflask/correlation/rust_correlation.py` module within the `compute_correlation_rust` function.
2022-08-09Display the probeset name in the editing formMunyoki Kilyungi
* wqflask/wqflask/templates/edit_probeset.html: Add probeset.name to the h1 tag.
2022-08-09Make edit_probeset.html similar to corresponding phenotype pageMunyoki Kilyungi
* wqflask/wqflask/templates/edit_probeset.html: Remove "reset" button. Make button green. Move form element into the "container" div. Add "container" class to form. Left justify labels, and the button. Remove ":" from labels.
2022-08-09Delete "diff" sectionMunyoki Kilyungi
For both the edit phenotype and probeset pages, the diffs can be viewed from history.html. * wqflask/wqflask/templates/edit_phenotype.html: Delete "diffs" section. * wqflask/wqflask/templates/edit_probeset.html: Ditto.
2022-08-09Remove "diff" logic from edit_probesetMunyoki Kilyungi
* wqflask/wqflask/metadata_edits.py (edit_probeset): Delete logic for fetching diff. Move that... (show_history): ... here * wqflask/wqflask/templates/edit_probeset.html: Update template to show diffs in a history.html. Reposition and rename the h1 tag of this page.
2022-08-09Update h1 title of history pageMunyoki Kilyungi
ATM, we don't show the name of the phenotype whose history we are changing. That may be updated in a future commit. * wqflask/wqflask/templates/edit_history.html: Reword h1 and remove "{{}}" which results in a jinja error.
2022-08-09Fix circular import issueFrederick Muriuki Muriithi
2022-08-09Integrate rust correlation for "sample" correlation selectionFrederick Muriuki Muriithi
Integrate the use of the rust code to compute the correlations for the "sample" correlation selection.
2022-08-09Pass trait values (X) as list not stringFrederick Muriuki Muriithi
The trait values (X values) are converted to JSON within the `run_correlation` call. Since JSON has the ability to represent lists of objects, there is no point for the added conversion to and from strings.
2022-08-08remove unnessary append to listAlexander_Kabui
2022-08-08remove test;test is redundantAlexander_Kabui
2022-08-08tests refactoringAlexander_Kabui
2022-08-05Include partial_correlations.js in the search page templatezsloan
2022-08-01Remove console logs from scatterplot.jszsloan
2022-08-01Change Make Default button to Save Settingszsloan
2022-08-01Add date/time to trait page exportzsloan
2022-08-01Add header/description to partial correlation pagezsloan
2022-08-01Add index column and phenotype group code to trait exportzsloan
2022-07-28Use external process to compute sample correlationsFrederick Muriuki Muriithi
2022-07-27Disable PCA when fewer than 3 traitszsloan
2022-07-27Change some text/formatting on Correlation Matrix pagezsloan
2022-07-27Change capitalization on index pagezsloan
2022-07-27Change some text/formatting for the Scree Plotzsloan
2022-07-27Change search result text/formattingzsloan
2022-07-27Change formatting for search term + add line break in description textzsloan
2022-07-25new file module for preprocessing inputAlexander_Kabui
2022-07-25add test routeAlexander_Kabui
2022-07-25enable test routeAlexander_Kabui
2022-07-25Fix BNW linkzsloan
2022-07-25Remove Comparison Bar Chart buttonzsloan
2022-07-25Change Interval Analyst genome browser link to use mm10 instead of mm9zsloan
2022-07-25Return config in app.config or NoneFrederick Muriuki Muriithi
Update the code to return the setting already set up in the app.config dictionary if it exists or None if it does not exist.
2022-07-14Remove column toggle JS from show_trait.html since it's in ↵zsloan
initialize_show_trait_tables.js
2022-07-14Call DataTable() on the table id instead of referring to the_table; notzsloan
sure why this is necessary, but the search doesn't work otherwise
2022-07-12Include genotypes for F1s/reference/non-reference strains when fetchingzsloan
sample data for genotype traits
2022-07-11Increase min-width for div containing tool buttons on search pagezsloan
2022-07-08Add python for exporting case attributeszsloan
2022-07-08Add JS for exporting case attributes (sample metadata)zsloan
2022-07-04wqflask: Remove DebugToolbarExtensionBonfaceKilz
This functionality, at least how we use it, is already provided natively in python's pdb. Should someone need this, they can add it manually. * wqflask/runserver.py (app_config): Remove "flask_debugtoolbar" import and instantiation. * wqflask/utility/startup_config.py (app_config): Ditto.
2022-07-04wqflask: use the raw user string if value is non-existent in redisBonfaceKilz
* wqflask/wqflask/metadata_edits.py (_get_diffs): If a user---whose value is extracted from Redis and encoded in the file name---doesn't exist in Redis, use the raw string extracted from the file.
2022-07-04wqflask: Use a map over a tuple when fetching case-attributesBonfaceKilz
* wqflask/wqflask/metadata_edits.py (update_phenotype): Replace old "get_case_attributes" function call which returned a dict with the new updated version that returns a tuple.
2022-06-21wqflask: views: Delete noisy logging and dead codeBonfaceKilz
- Remove commented out code-blocks - Remove calls with this pattern: logger.info("Sending ...") logger.info(request.url) Should you want to inspect the local context of an environment when troubleshooting, set a breakpoint() and inspect the environment. To view everything in the local context, use "pp locals()"; and to view everything in the global context, use "pp globals()".
2022-06-20Simplify partial correlation method choicesFrederick Muriuki Muriithi
- Have only `Pearson's r` and `Spearman's rho` as the available choices for the partial correlations.
2022-06-15templates: base: Update GN2 footerBonfaceKilz
* wqflask/wqflask/templates/base: Remove links to non-functioning mailing list. Remove link to "#genenetwork" channel that isn't currently owned/moderated. Co-authored-by: Ethan Willis <elwillis1@gmail.com>
2022-06-13Check chromosome for 'Un' in search results and print N/A in such caseszsloan
2022-06-13Check for chromosome of 'Un' and print location as 'Not available' in such caseszsloan
2022-06-13Increase width threshold for using scroller, to prevent issue with blue ↵zsloan
lines at bottom of table
2022-06-13Limit search result descriptions to 500 characterszsloan
2022-06-13Add |safe to ensure HTML entites are correctly escaped for trait descriptionszsloan
2022-06-10Skip failing integration testBonfaceKilz
ATM, it's hard to by-pass the authentication decorators, and as such, skip this test for. This may be deleted later.