https://github.com/Sage-Bionetworks/challengerutils
Synapse R challenge utility functions. (wraps challengeutils)
https://github.com/Sage-Bionetworks/challengerutils
Last synced: 19 days ago
JSON representation
Synapse R challenge utility functions. (wraps challengeutils)
- Host: GitHub
- URL: https://github.com/Sage-Bionetworks/challengerutils
- Owner: Sage-Bionetworks
- License: apache-2.0
- Created: 2020-05-14T03:28:45.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-06-24T03:41:54.000Z (almost 5 years ago)
- Last Synced: 2024-04-11T01:25:00.179Z (about 1 year ago)
- Language: R
- Homepage: https://github.com/Sage-Bionetworks/challengeutils
- Size: 51.8 KB
- Stars: 4
- Watchers: 8
- Forks: 2
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-synapse - challengerutils - The R version of `challengeutils` (R)
README
# challengerutils
This package uses `reticulate` to wrap `challengeutils` to create the Synapse R challenge utility functions.
## Installation
This package requires the installation of Python > 3.6 and `challengeutils`. *NOTE*: This package will not work with `synapser`. Do not load `library(synapser)` into an R environment that has loaded `library(challengerutils)`
In command line, we recommend you using anaconda. Instructions to install anaconda can be found [here](https://docs.anaconda.com/anaconda/install/).
```
conda create -n challenge python=3.7
pip install challengeutils
```
In R:
```
remotes::install_github("Sage-Bionetworks/challengerutils")
```
## Usage
The functions will mimic the Python implementation of `challengeutils`. Please see the [documentation here](https://sage-bionetworks.github.io/challengeutils/).
* Load `challengerutils` package
```
library(challengerutils)
reticulate::use_condaenv('challenge')
# Must run syn_login() to use any of the functions below
challengerutils::syn_login()
```
* Query Evaluation Queue
```
leaderboard_results <- challengerutils::evaluation_queue_query('select * from evaluation_9614194')
```
* Change submission status
```
status <- challengerutils::change_submission_status("9698553", status="RECEIVED")
```
## synapseclient
As noted above, `library(reticulate)`-based packages like `challengerutils` are not compatible with `synapser`. To use core Synapse client functions in the same R environment as the `challengerutils` package, import the Python `synapseclient` using `reticulate`:
```
synapseclient <- reticulate::import('synapseclient')
syn <- synapseclient$Synapse()
syn$login()
``