| Age | Commit message (Expand) | Author |
|---|
| 2022-02-23 | Add top margin to Partial Correlations button...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)
| zsloan |
| 2022-02-21 | Fix incorrect dataset trait data caching...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.
| zsloan |
| 2022-02-18 | wqflask: Remove python pre-2.2 checks....These checks are only relevant for python pre-2.2.
* wqflask/utility/svg.py: Remove python pre-2.2 checks.
| Arun Isaac |
| 2022-02-18 | README: Replace GitHub actions badge with Laminar CI badge....* README.md: Replace GitHub actions badge with Laminar CI badge.
| Arun Isaac |
| 2022-02-17 | bin: Allow for not starting redis....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.
| Arun Isaac |
| 2022-02-17 | etc: Close VERSION file after opening....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.
| Arun Isaac |
| 2022-02-14 | Add search text for cis/transLRS/LOD searches...There wasn't any search text for cis/trans searches including both
chromosome and exclusion zone, so I added somee
| zsloan |
| 2022-02-14 | Fix CisTrans search bug...', 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)
| zsloan |
| 2022-02-09 | doc: Document how to fetch case-attribute data from a sample-list | BonfaceKilz |
| 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 | Double quote shell variables to prevent globbing and word splitting | Frederick Muriuki Muriithi |
| 2022-02-07 | Add 'api' to root of partial correlations URL...Add api to the root of the partial correlations URL, making it:
/api/correlations/partial
rather than:
/correlations/partial
| Frederick Muriuki Muriithi |
| 2022-02-05 | Update live jupyter notebooks | jgart |
| 2022-02-02 | Add covarstruct for rqtl mapping...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
| zsloan |
| 2022-01-31 | wqflask: Use a more semantic name when downloading samples...* 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"
| BonfaceKilz |
| 2022-01-29 | Fix bug: rho/r not set appropriately...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.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Include the "Locus" in the display...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-29 | Provide missing argument...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 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 |
