rglab/immportr

R wrapper around the ImmPort API and its download tool

ImmPortR

ImmPortR is an R wrapper around the ImmPort API to query datasets from ImmPort Shared Data and upload data to ImmPort Private Data, and it also utilizes the Aspera CLI to download files from ImmPort Shared Data.

What is ImmPort?

ImmPort is funded by the NIH, NIAID and DAIT in support of the NIH mission to share data with the public. Data shared through ImmPort has been provided by NIH-funded programs, other research organizations and individual scientists ensuring these discoveries will be the foundation of future research.

Installation

ImmPortR

# install.packages("remotes")
remotes::install_github("RGLab/ImmPortR")

The Aspera CLI

The IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.

• Download
• Documentation

Take a look at this for guidance on installing the Aspera CLI.

Register and set ImmPort credentials

• Register
• Read the User Agreement for ImmPort
• Set environment variables with your ImmPort credentials, on your R console:

Sys.setenv(ImmPortUsername = "yourImmPortUsername")
Sys.setenv(ImmPortPassword = "yourImmPortPassword")

• Or in .Renviron file in your home directory:

ImmPortUsername=yourImmPortUsername
ImmPortPassword=yourImmPortPassword

Usage

Query datasets

library(ImmPortR)

elisa <- query_dataset("SDY269", "elisa")
elispot <- query_dataset("SDY269", "elispot")
fcsAnalyzed <- query_dataset("SDY269", "fcsAnalyzed")
hai <- query_dataset("SDY269", "hai")
hlaTyping <- query_dataset("SDY269", "hlaTyping")
kirTyping <- query_dataset("SDY269", "kirTyping")
mbaa <- query_dataset("SDY269", "mbaa")
neutAbTiter <- query_dataset("SDY269", "neutAbTiter")
pcr <- query_dataset("SDY269", "pcr")

Download files

download_immport("/SDY1/StudyFiles/Casale_Study_Summary_Report.doc")

Validate data

validate_zip("yourStudyData.zip", workspace_id = 99999, upload_notes = "for SDY9999")

immportr's Issues

ImmPort Access Token Content Has Changed

The ImmPort team has recently changed the way an Access Token is returned. Details can be found at this link: https://docs.immport.org/home/software_release_notes/June_2022_Software_Release/

Basically the token name was changed from "token" to "access_token". This may cause an issue with the ImmPortR code. Thank you for writing and maintaining this code, we try to promote ImmPortR to R users trying to download data from ImmPort

schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326)

Upload related functions produce curl errors in Windows (AppVeyor):

schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed). More detail may be available in the Windows System event log.