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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
2022-01-29Hide template row instead of deleting itFrederick Muriuki Muriithi
2022-01-29Add more items to trait stringFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2022-01-29Update styling: Display traits in a tabular-like formFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Display the trait details in a tabular-life form without using a table.
2022-01-29Include template to get rid of repetitive template codeFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The generation of input elements that relate to the traits is very similar, therefore this commit pulls it out into a separate template that can be included where needed.
2022-01-29Display results for Geno and ProbeSet tablesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add function to display the results for the **Geno** and **ProbeSet** tables.
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