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Is OhdsiSharing still the mechanism for sharing study results?

Developers
#1

Hi All,

I’m trying to set up a mechanism for collaborators to upload analysis results. Seems that OhdsiSharing is the way to go, but I couldn’t find an explanation (or example showing) how to set it up.

I did manage to use the package to generate private and public keys, encrypt and decrypt files. But when I tried to use the key to sftpConnect (to then create a new study directory), I get the following error + warning:

Error in sftpConnect(privateKeyFileName, userName) :
Private key file does not contain RSA private key
In addition: Warning message:
In readChar(privateKeyFileName, file.info(privateKeyFileName)$size) :
truncating string with embedded nuls

What do I miss?

Thanks, happy new year!

#2

We don’t use encryption anymore, because we found data sites need to inspect whatever they’re sharing, which is not possible when its encrypted with a public key. Instead, the current way to share results is via the SFTP functions implemented in OhdsiSharing.

@lee_evans : could you provide information on the current practice? (It might be good to capture this in a short vignette?)

#3

Thanks for the response, @schuemie, I’d appreciate any information on the current practice or, even better, a short vignette.

#4

I will add this info to the vignette @cyanover @schuemie

#5

@cyanover Here is some information regarding the HADES OhdsiSharing R package. At some point this info should be incorporated into the OhdsiSharing R package vignette.

The OhdsiSharing R package provides the sftpUploadFile() function to upload a zipped results file (generated from an OHDSI network study executed at a local data site) to the OHDSI sftp server.

The OHDSI network study coordinator will provide the below information to all data sites participating in the study.

  • OHDSI sftp server name
  • Study data site sftp userid
  • Study data site private key file

Here is some example R code.

    # one time R package install
    # install_github("ohdsi/OhdsiSharing")

    library("OhdsiSharing")

    # upload local file '/tmp/test_results.zip' to sftp server 

    privateKeyFileName <- "/tmp/study-data-site-studyname"
    userName <- "study-data-site-studyname"
    theFileName <- "/tmp/test_results.zip"
    sftpUploadFile(privateKeyFileName, userName, fileName = theFlleName)
#6

Thanks @admin. I am currently also interested in the study coordinator viewpoint; so:

  • OHDSI sftp server name: is it org.ohdsi.sharing.Sftp? And, as I wrote above, I can’t get sftpConnect to work :point_down: (privateKeyFileName generated using generateKeyPair); what do I miss?
  • Study data site sftp userid: how is it generated?
  • Study data site private key file: I am confused, @schuemie wrote above:

so is provate key still required?

Thanks!

#7

The OHDSI sftp server name is sftp.ohdsi.org

@schuemie noted that the results data zip file is not encrypted, so it can be inspected at the local site before uploading.

A private key file is required to authenticate the secure connection to the OHDSI sftp server.

A new OHDSI study coordinator will need to request the setup of OHDSI sftp space for the study. The private keys for the study coordinator and the data sites will be provided via email to the study coordinator (along with the other information you are requesting here).

Are you working with @schuemie or @krfeeney to setup a new OHDSI study protocol? That would probably be the first step.

#8

Thanks again, @admin.

@schuemie, @krfeeney: study code and protocol are available at https://github.com/ohdsi-studies/IbdCharacterization ; please let me know if anything else is needed. I’d appreciate your help setting up OHDSI sftp space for the study results.

Thanks.

t