| Age | Commit message (Expand) | Author |
|---|
| 2021-11-04 | Implement `compute_partial_correlations_fast`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `compute_partial_correlations_fast` that is a partial migration of
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in
GN1.
This function will probably be reworked once the dependencies are fully
migrated.
It also needs tests to be added.
| Frederick Muriuki Muriithi |
| 2021-10-29 | Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes | Alexander Kabui |
| 2021-10-19 | Fix some linting issues | Frederick Muriuki Muriithi |
| 2021-10-19 | Allow CORS_ORIGINS to be configurable via the environment...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* gn3/app.py: setup CORS after all the configuration sources are loaded.
* gn3/settings.py: Parse CORS_ORIGINS from the environment variables.
Enable the CORS_ORIGINS configuration to be set in the environment variables
to give the application some flexibility when launching.
| Frederick Muriuki Muriithi |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-20 | Enable Cross-Origin Resource Sharing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Fix bugs in data parsing
* gn3/app.py: enable CORS
* gn3/settings.py: add flask-cors configurations
* guix.scm: Add flask-cors dependency
For easier testing of the heatmaps generation feature, this commit activates
the cross-origin resource sharing for all "localhost" origins.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Add WGCNA_SCRIT env to settings | Alexander Kabui |
| 2021-08-31 | Provide utilities for genotype files...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: New module
* gn3/settings.py: Add new configuration variable
* qtlfilesexport.py: Test out new code
Add a module containing functions dealing with the genotype files.
Add a configuration variable to point to the location of the genotype files.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Implement module for interfacing with rust-qtlreaper...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: move `generate_traits_file` function to new
module
* gn3/computations/qtlreaper.py: new module to interface with the
`rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
use functions in new module.
Provide a module with functions to be used to interface with
`rust-qtlreaper`. This module essentially contains all the functions that
are needed to build the files needed for, and to run the qtlreaper utility.
| Muriithi Frederick Muriuki |
| 2021-06-23 | minor fixes for biweight script | Alexander Kabui |
| 2021-06-20 | merge main | Alexander Kabui |
| 2021-06-20 | make requested changes to biweight | Alexander Kabui |
| 2021-05-17 | Added RQTL_WRAPPER_CMD (which is fetched from environment) in settings.py | zsloan |
| 2021-05-13 | Add end-point for running an rQTL program...* gn3/api/general.py (run_r_qtl): New function.
* gn3/settings.py: New variable.
| BonfaceKilz |
| 2021-05-03 | modify default SQL_URI | Alexander Kabui |
| 2021-04-12 | fix merge conflict | Alexander Kabui |
| 2021-04-12 | Integrate correlation API...- add new api for gn2-gn3 sample r integration
- delete map for sample list to values
- add db util file
- add python msql-client dependency
- add db for fetching lit correlation results
- add unittests for db utils
- add tests for db_utils
- modify api for fetching lit correlation results
- refactor Mock Database Connector and unittests
- add sql url parser
- add SQL URI env variable
- refactor code for db utils
- modify return data for lit correlation
- refactor tissue correlation endpoint
- replace db_instance with conn | Alexander Kabui |
| 2021-03-31 | add mysqlclient in guix...add env variable for GN2_URL
| Alexander Kabui |
| 2021-03-23 | Use ipfs to get genotype files | BonfaceKilz |
| 2021-03-15 | Delete redundant gn3/config.py...All default confs should go to one place: gn3/setting.py
* gn3/app.py: Delete get_config. Apply pep-8 formatting.
* gn3/config.py: Delete it. Move conf options to...
* gn3/settings.py: ... here.
| BonfaceKilz |
| 2021-03-08 | Replace APP_DEFAULTS dict with actual conf params | BonfaceKilz |
| 2021-03-08 | Make the name of the redis job queue configurable | BonfaceKilz |
| 2021-02-24 | Add GENODIR extra param | BonfaceKilz |
| 2021-02-16 | Add extra default config for bcrypt | BonfaceKilz |
| 2021-02-15 | Add default redis config | BonfaceKilz |
| 2021-02-12 | Add configuration file for the project | BonfaceKilz |
