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2022-02-28Add distinct to fix issue where GeneRIF search returns duplicateszsloan
2022-02-27code refactoringAlexander Kabui
2022-02-26Remove CSS from partial_correlations.csszsloan
This CSS is overwritten by CSS from trait_list.css and show_trait.css
2022-02-26Add container divzsloan
2022-02-26Add checkbox and index columnszsloan
2022-02-26Include DataTables imports and necessary CSSzsloan
2022-02-26Add JS initializing DataTableszsloan
2022-02-25integrating generating temp dataset for pcaAlexander Kabui
2022-02-24Fix ProbeSet query for aliaseszsloan
ProbeSet queries previously weren't dealing with aliases correctly, because it was doing a MATCH/AGAINST against the ProbeSet.alias field, but that field usually contains a list of gene symbols separated by semi-colons (so it wouldn't detect the alias unless there was only a single alias. To fix this, I added some LIKE conditions, searching for the possible variations. This is a little awkward, because I needed to make sure to avoid a situation where, for example, an alias like 'LPD-1' matches a search for 'PD-1'. I don't think the way it currently works is efficient, but I don't know of any good alternative without changing the way we store aliases in the database.
2022-02-24Fix alias queryzsloan
2022-02-24Change parser.py to also detect hyphen in search termszsloan
2022-02-24remove redundant functions and codeAlexander Kabui
2022-02-24init replace rpy2 for pcaAlexander Kabui
2022-02-23Fix Heatmap GN3 URLzsloan
2022-02-23Improve Heatmap options' appearancezsloan
Moved the Heatmap display area above the table selection options (since it didn't make sense to have it below those) Added a button for clearing the Heatmap area and hiding the Heatmap options Added some margins to the Heatmap options
2022-02-23Show heatmap options when heatmap is runzsloan
Heatmap options are now shown after the user clicks the button I also reordered the Heatmap and Partial Correlation buttons, since it's awkward to get the Heatmap options to display well if its button is second. We'll probably completely rework this later, but for now this looks a little less ugly.
2022-02-23Reposition Partial Correlations and Heatmap buttonszsloan
Moved Partial Correlations and Generate Heatmap buttons to be lined up below the other buttons and hide the Heatmap orientation selection (JS will be added to show it after Heatmap is run)
2022-02-23Add top margin to Partial Correlations buttonzsloan
Later this button should just be included with the other function buttons. There's no need for it to be in a separate form, since it should be able to take the same trait list input as all the other collection page functions (with just the action url for the form changing)
2022-02-21Fix incorrect dataset trait data cachingzsloan
Trait data caching wasn't working correctly because it didn't account for the samplelist, causing caching to work incorrect in any situation where the target dataset's samplelist wasn't the same as that of the trait being correlated against. Trait data is stored as a dictionary where the keys are trait IDs and values are *lists* of sample values. This means that the caching needs to account for the exact same set of samples; otherwise you'll end up with samples being mismatched (since "the third sample with a value" for one dataset's trait might not be the same as "the third sample with a value" for another dataset's trait). To fix this, I added the samplelist to the functions that generate and fetch the hash file. This will require more cache files, though, so this should probably be reexamined later to make the code work with only a single cache file for each dataset.
2022-02-18wqflask: Remove python pre-2.2 checks.Arun Isaac
These checks are only relevant for python pre-2.2. * wqflask/utility/svg.py: Remove python pre-2.2 checks.
2022-02-18README: Replace GitHub actions badge with Laminar CI badge.Arun Isaac
* README.md: Replace GitHub actions badge with Laminar CI badge.
2022-02-17bin: Allow for not starting redis.Arun Isaac
redis needs to be started and managed as a separate service. We create a flag NO_REDIS so that it can be so. If NO_REDIS is not defined, the present behavior of starting redis remains. Thus current use cases are not broken. * bin/genenetwork2: Allow for not starting redis with the NO_REDIS flag.
2022-02-17etc: Close VERSION file after opening.Arun Isaac
Use a context manager so that the VERSION file is automatically closed on exiting the block. * etc/default_settings.py: Close VERSION file after opening.
2022-02-14Add search text for cis/transLRS/LOD searcheszsloan
There wasn't any search text for cis/trans searches including both chromosome and exclusion zone, so I added somee
2022-02-14Fix CisTrans search bugzsloan
', Geno' was being added to the FROM clause, which is wrong becausee Geno is included in the query via a JOIN (and caused an error making those searches not work)
2022-02-09doc: Document how to fetch case-attribute data from a sample-listBonfaceKilz
2022-02-09variable naming and docstrings fixAlexander Kabui
2022-02-09handle exceptionsAlexander Kabui
2022-02-09autopep8 formattingAlexander Kabui
2022-02-09delete unused js packagesAlexander Kabui
2022-02-09autopep8 formattingAlexander Kabui
2022-02-09 fix for performing parametric analysisAlexander Kabui
2022-02-09minor template fixesAlexander Kabui
2022-02-09add trait lists and links to ctl plotAlexander Kabui
2022-02-09disabble autoslideAlexander Kabui
2022-02-09fix for ctl ui pageAlexander Kabui
2022-02-09endpoint to download network filesAlexander Kabui
2022-02-09btn download for network sif and node fileAlexander Kabui
2022-02-09modify ctl endpointAlexander Kabui
2022-02-09minor fixes for imagesAlexander Kabui
2022-02-09fix for dcor and LOD roundingAlexander Kabui
2022-02-09styling for carouselAlexander Kabui
2022-02-09add carousel for plotsAlexander Kabui
2022-02-09ui form modificationsAlexander Kabui
2022-02-09minor refactoring to destruct objectsAlexander Kabui
2022-02-09template file cleanupAlexander Kabui
2022-02-09rename template fileAlexander Kabui
2022-02-09minor bug fixesAlexander Kabui
2022-02-09process significant table resultsAlexander Kabui
2022-02-09delete class initiliazation objectAlexander Kabui