| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-03-08 | remove global variables;pep8 formatting | Alexander Kabui | |
| 2022-03-08 | make fixes;variable names and kwargs | Alexander Kabui | |
| 2022-02-27 | code refactoring | Alexander Kabui | |
| 2022-02-25 | integrating generating temp dataset for pca | Alexander Kabui | |
| 2022-02-24 | remove redundant functions and code | Alexander Kabui | |
| 2022-02-24 | init replace rpy2 for pca | Alexander Kabui | |
| 2022-02-21 | Fix incorrect dataset trait data caching | zsloan | |
| 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. | |||
| 2022-02-18 | wqflask: 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. | |||
| 2022-02-14 | Add search text for cis/transLRS/LOD searches | zsloan | |
| There wasn't any search text for cis/trans searches including both chromosome and exclusion zone, so I added somee | |||
| 2022-02-14 | Fix CisTrans search bug | zsloan | |
| ', 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) | |||
| 2022-02-09 | variable naming and docstrings fix | Alexander Kabui | |
| 2022-02-09 | handle exceptions | Alexander Kabui | |
| 2022-02-09 | autopep8 formatting | Alexander Kabui | |
| 2022-02-09 | delete unused js packages | Alexander Kabui | |
| 2022-02-09 | autopep8 formatting | Alexander Kabui | |
| 2022-02-09 | fix for performing parametric analysis | Alexander Kabui | |
| 2022-02-09 | minor template fixes | Alexander Kabui | |
| 2022-02-09 | add trait lists and links to ctl plot | Alexander Kabui | |
| 2022-02-09 | disabble autoslide | Alexander Kabui | |
| 2022-02-09 | fix for ctl ui page | Alexander Kabui | |
| 2022-02-09 | endpoint to download network files | Alexander Kabui | |
| 2022-02-09 | btn download for network sif and node file | Alexander Kabui | |
| 2022-02-09 | modify ctl endpoint | Alexander Kabui | |
| 2022-02-09 | minor fixes for images | Alexander Kabui | |
| 2022-02-09 | fix for dcor and LOD rounding | Alexander Kabui | |
| 2022-02-09 | styling for carousel | Alexander Kabui | |
| 2022-02-09 | add carousel for plots | Alexander Kabui | |
| 2022-02-09 | ui form modifications | Alexander Kabui | |
| 2022-02-09 | minor refactoring to destruct objects | Alexander Kabui | |
| 2022-02-09 | template file cleanup | Alexander Kabui | |
| 2022-02-09 | rename template file | Alexander Kabui | |
| 2022-02-09 | minor bug fixes | Alexander Kabui | |
| 2022-02-09 | process significant table results | Alexander Kabui | |
| 2022-02-09 | delete class initiliazation object | Alexander Kabui | |
| 2022-02-09 | minor refactoring | Alexander Kabui | |
| 2022-02-09 | pep8 formatting | Alexander Kabui | |
| 2022-02-09 | fetch pheno input data | Alexander Kabui | |
| 2022-02-09 | parse geno input data | Alexander Kabui | |
| 2022-02-09 | parse input data | Alexander Kabui | |
| 2022-02-09 | init py file:call gn3 ctl api | Alexander Kabui | |
| 2022-02-09 | add ui template for ctl | Alexander Kabui | |
| 2022-02-07 | Add 'api' to root of partial correlations URL | Frederick Muriuki Muriithi | |
| Add api to the root of the partial correlations URL, making it: /api/correlations/partial rather than: /correlations/partial | |||
| 2022-02-05 | Update live jupyter notebooks | jgart | |
| 2022-02-02 | Add covarstruct for rqtl mapping | zsloan | |
| 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 | |||
| 2022-01-31 | wqflask: Use a more semantic name when downloading samples | BonfaceKilz | |
| * 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" | |||
| 2022-01-29 | Fix bug: rho/r not set appropriately | Frederick 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. | |||
| 2022-01-29 | Include the "Locus" in the display | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi | |||
| 2022-01-29 | Provide missing argument | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi | |||
| 2022-01-29 | Fix check for non-existent values | Frederick Muriuki Muriithi | |
| 2022-01-29 | Hide template row instead of deleting it | Frederick Muriuki Muriithi | |
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