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2022-02-24remove redundant functions and codeAlexander Kabui
2022-02-24init replace rpy2 for pcaAlexander Kabui
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
2022-02-09minor refactoringAlexander Kabui
2022-02-09pep8 formattingAlexander Kabui
2022-02-09fetch pheno input dataAlexander Kabui
2022-02-09parse geno input dataAlexander Kabui
2022-02-09parse input dataAlexander Kabui
2022-02-09init py file:call gn3 ctl apiAlexander Kabui
2022-02-09add ui template for ctlAlexander Kabui
2022-02-07Double quote shell variables to prevent globbing and word splittingFrederick Muriuki Muriithi
2022-02-07Add 'api' to root of partial correlations URLFrederick Muriuki Muriithi
Add api to the root of the partial correlations URL, making it: /api/correlations/partial rather than: /correlations/partial
2022-02-05Update live jupyter notebooksjgart
2022-02-02Add covarstruct for rqtl mappingzsloan
Added a function for generating a covarstruct file required for R/qtl mapping This file contains info on whether each covariate is categorical or numerical and is generated by querying the TraitMetadata table in the DB
2022-01-31wqflask: Use a more semantic name when downloading samplesBonfaceKilz
* wqflask/wqflask/metadata_edits.py (get_sample_data_as_csv): Save csv file to be downloaded as "sample-name-<dataset_id>.csv" instead of "myplot.csv"
2022-01-29Fix bug: rho/r not set appropriatelyFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The column heading, and the "data-column-heading" values depend on the correlation method. The initial idea had been to set these values up from the server. With the use of Javascript, however, the system defaults to using `r`, which is a bug when the method is any of the Spearman's methods.
2022-01-29Include the "Locus" in the displayFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Provide missing argumentFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Fix check for non-existent valuesFrederick Muriuki Muriithi
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