README.md

In thomasyu888/puresynapser: R client for Sage Bionetworks' Synapse API

puresynapser

This is a proof of concept Synapse R client. There are other iterations of the client that can be found:

• synapser - Official Synapse R package currently.
• rSynapseClient - old pure R client. This package has been deprecated
• synapserprototype - This is a prototype of the client using reticulate + synapse python client.
• synr-sdk-client - This is an openAPI auto generated R client using the manually created synapse openapi

Usage

This is how you can install the package:

# Assuming you have the repository cloned locally
install.packages("./")
# install from github
remotes::install_github("thomasyu888/puresynapser")

This package currently only works with the Synapse Personal Access token. You will have to set it as an environmental variable, or you can add this to your .Renviron file.

Sys.setenv(SYNAPSE_AUTH_TOKEN="tokenhere")

Currently you may pass in any of the GET, PUT, DELETE, POST, rest calls covered under this endpoint: https://repo-prod.prod.sagebase.org/repo/v1. You can see more details of the rest calls in our rest docs. Here is an example below that utilizes all the rest calls on the /entity endpoint.

library(stringi)
library(puresynapser)
# Create a project
# Use SYNAPSE_AUTH_TOKEN env var
puresynapser::login()
# or specify PAT here.
# puresynapser::login(authtoken="...")
project_name = paste0("test-project-", stringi::stri_rand_strings(1, 30))
project_resp = puresynapser::rest_POST("entity",
                                       body=list(name = project_name,
                                                 concreteType="org.sagebionetworks.repo.model.Project"))
# Get the project
project = rest_GET(paste0("entity/", project_resp$content$id))

# Create a folder in the project
folder = puresynapser::rest_POST("entity",
                                 body=list(name = "test-me-now",
                                           parentId=project$content$id,
                                           concreteType="org.sagebionetworks.repo.model.Folder"))

# Update the folder name
changed_entity = list(
  name = "change-my-name",
  parentId = folder$content$parentId,
  id = folder$content$id,
  etag = folder$content$etag,
  concreteType = folder$content$concreteType
)
changed_ent = puresynapser::rest_PUT(paste0("entity/", folder$content$id),
                                     body=changed_entity)
# Delete the project
puresynapser::rest_DELETE(paste0("entity/", project_resp$content$id))

Contributing

Want to contribute? Please read our contributing guide

thomasyu888/puresynapser documentation built on Jan. 30, 2022, 12:14 p.m.