Chapter 5 Connecting the DataSHIELD client

The federation is built. Now we switch hats from server administrator to analyst: we log the DataSHIELD client into all three sites and attach the OMOP resource on each. This single connection stays open for the rest of the book — every chapter in Part II runs against the conns and omop handles created here.

5.1 Installing the client packages

The client needs four R packages. Step 5’s installer pins them (in particular dsOMOPClient to its 2.0.0 tag):

Rscript 5_client/install_client.R     # or: bash 5_client/setup_client.sh

5_client/install_client.R pulls DSI and DSOpal from CRAN, dsBaseClient from the DataSHIELD repository, and dsOMOPClient 2.0.0 from GitHub:

Package	Role
DSI	The DataSHIELD interface — login, assign, aggregate.
DSOpal	The Opal driver for DSI.
dsBaseClient	The base DataSHIELD analysis functions (ds.*).
dsOMOPClient	The client side of dsOMOP — ds.omop.*.

5.2 Logging in

We describe the three sites with a login builder — one append() per site — and log in. The connection details are the fixed values from the previous chapters: URLs 4808{0,1,2}, administrator / password, the resource omop_demo.gibleed, and the Rock profile omop (the one carrying dsOMOP):

library(DSI); library(DSOpal); library(dsBaseClient); library(dsOMOPClient)

sites <- list(
  aphrc   = "http://localhost:48080",
  dgh     = "http://localhost:48081",
  iressef = "http://localhost:48082"
)

builder <- DSI::newDSLoginBuilder()
for (site in names(sites))
  builder$append(server = site, url = sites[[site]],
                 user = "administrator", password = "password",
                 resource = "omop_demo.gibleed",
                 driver = "OpalDriver", profile = "omop")

conns <- DSI::datashield.login(logins = builder$build())

If you changed a port or the password back in Chapter 2, change the matching value here too.

5.3 Attaching the OMOP resource

datashield.login opened the sessions; now ds.omop.connect attaches the OMOP CDM resource on every server and initialises dsOMOP, binding a live handle to the symbol omop:

ds.omop.connect(resource = "omop_demo.gibleed", symbol = "omop", conns = conns)

The client is now connected to all three sites, each with a live dsOMOP handle:

names(conns)
#> [1] "aphrc"   "dgh"     "iressef"

That is the whole federation, live. Part II uses it to explore the catalogue, extract a fused person-level table, describe it, and fit a federated model.