README.md

In Sage-Bionetworks/challengerutils: Synapse Challenge Utility Functions

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.

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.

• 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()

Sage-Bionetworks/challengerutils documentation built on June 24, 2020, 4:59 a.m.