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2022-08-23Add support for database rollbacks if the db engine supports it.Munyoki Kilyungi
* wqflask/wqflask/database.py: Import contextlib. (database_connection): Refactor to support roll-backs.
2022-08-23Delete unused function and imports.Munyoki Kilyungi
* wqflask/wqflask/database.py: Remove unused sqlalchemy imports. (read_from_pyfile): Delete it.
2022-08-20Divide GEMMA additive effect by 2zsloan
2022-08-20Fix JS for opening new tabs (or not) for collection page tools/optionszsloan
2022-08-17Use context managers for database cursorsFrederick Muriuki Muriithi
2022-08-17Merge branch 'chores/rust-enhancements' of ↵Frederick Muriuki Muriithi
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/rust-enhancements
2022-08-16Merge dicts into single resultFrederick Muriuki Muriithi
2022-08-16Convert list items to single dictFrederick Muriuki Muriithi
2022-08-16rename boolean variablesAlexander_Kabui
2022-08-16linter fixesAlexander_Kabui
2022-08-16enable compute all for testAlexander_Kabui
2022-08-16index error fixAlexander_Kabui
2022-08-16remove flask g objectAlexander_Kabui
2022-08-16minor fixes for computing all correlationsAlexander_Kabui
2022-08-15add default values for num overlap,corr_coeffAlexander_Kabui
2022-08-14init:perform top n sample for probesAlexander_Kabui
2022-08-12Revert "Check for keys before using them."Frederick Muriuki Muriithi
This reverts commit a1cbc12f843bbdc1759d5acac5ae3630fb5d4b81.
2022-08-12Add a profiling scriptFrederick Muriuki Muriithi
Add a script to enable profiling the code.
2022-08-12Fix some issues with the tests. Add notes in code for improvements.Frederick Muriuki Muriithi
2022-08-12Refactor: separate the three correlation typesFrederick Muriuki Muriithi
Refactor the code such that each correlation type (sample, tissue, literature) is computed in its own function. This makes the code clearer, and helps reduce repetition.
2022-08-12Check for keys before using them.Frederick Muriuki Muriithi
2022-08-12Update format to prevent tissue correlation from failingFrederick Muriuki Muriithi
Update the data format of returned values so that it conforms with expectatitions.
2022-08-12Fix formatting for legibilityFrederick Muriuki Muriithi
2022-08-12code to merge results;minor fixesAlexander_Kabui
2022-08-12compute top n tissue resultsAlexander_Kabui
2022-08-12add code to compute top n tissue resultsAlexander_Kabui
2022-08-12Fix minor bug.Frederick Muriuki Muriithi
2022-08-12Integrate 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.
2022-08-11Add data-trait-info attribute to checkboxes on search results pagezsloan
Currently there's a separate trait_info_str function in search_results.py, because search_results.py doesn't build the trait objects (so it can't use the one in collect.py unless I change that to accept traits as either a GeneralTrait class or dict - which might be better, I'm not sure)
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
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