DataSHIELD Development with DSLite

Source: vignettes/developing-with-dslite.Rmd

Introduction

DSLite is a serverless DataSHIELD Interface (DSI) implementation which purpose is to mimic the behavior of a distant (virtualized or barebone) data repository server (see DSOpal for instance). The datasets that are being analyzed must be fully accessible in the local environment and then the non-disclosive constraint of the analysis is not relevant for DSLite: some DSLite functionalities allows to inspect what is under the hood of the DataSHIELD computation nodes, making it a perfect tool for DataSHIELD analysis package developers.

Development Environment Setup

DataSHIELD Packages

Both client and server side packages must be installed in your local R session. The entry point is still the client side package and DSLite will automatically load the corresponding server side package on DataSHIELD aggregate and assignment functions call, based on the DataSHIELD configuration.

Test Datasets

DSLite comes with a set of datasets that can be easily loaded. You can also provide your own to illustrate a specific data analysis function.

R Package Development Tools

We recommend using the following tools to facilitate R package development:

  • devtools, the collection of package development tools,
  • usethis, automate package and project setup tasks that are otherwise performed manually,
  • testthat, for unit testing,
  • roxygen2, for writing documentation in-line with code,
  • Rstudio, the R editor that integrates the tools mentioned above and more.

DataSHIELD Development Flow

The typical development flow, using DSLite, is:

  1. Build and install your client and/or server side DataSHIELD packages.
  2. Create a new DSLiteServer object instance, refering test datasets. Use or alter the default DataSHIELD configuration.
  3. Test your DataSHIELD client/server functions.
  4. Debug DataSHIELD server nodes using DSLiteServer methods.

DSLiteServer

After your client and/or server side DataSHIELD packages have been built and installed, a new DSLiteServer object instance must be created.

Some DSLiteServer methods can be used to verify or modify the DSLiteServer behaviour:

  • DSLiteServer$strict()
  • DSLiteServer$home()

See the R documentation of the DSLiteServer class for details.

As an example:

library(DSLite)

# prepare test data in a light DS server
data("CNSIM1")
data("CNSIM2")
data("CNSIM3")
dslite.server <- newDSLiteServer(tables=list(CNSIM1=CNSIM1, CNSIM2=CNSIM2, CNSIM3=CNSIM3))
# load corresponding DataSHIELD login data
data("logindata.dslite.cnsim")

The previous example can be simplified using the set-up functions based on the provided test datasets:

library(DSLite)

# load CNSIM test data
logindata.dslite.cnsim <- setupCNSIMTest()

DataSHIELD Configuration

The DataSHIELD configuration (aggregate and assign functions, R options) is automatically discovered by inspecting the R packages installed and having some DataSHIELD settings defined, either in their DESCRIPTION file or in a DATASHIELD file.

This default configuration extracting function is:

The list of the DataSHIELD R packages to be inspected (or excluded) when building the default configuration can be specified as parameters of defaultDSConfiguration().

The DataSHIELD configuration can be specified at DSLiteServer creation time or afterwards with some DSLiteServer methods that can be used to verify or modify the DSLiteServer configuration:

  • DSLiteServer$config()
  • DSLiteServer$aggregateMethods()
  • DSLiteServer$aggregateMethod()
  • DSLiteServer$assignMethods()
  • DSLiteServer$assignMethod()
  • DSLiteServer$options()
  • DSLiteServer$option()

See the R documentation of the DSLiteServer class for details.

As an example:

# verify configuration
dslite.server$config()

DataSHIELD Sessions

The following figure illustrates a setup where a single DSLiteServer holds several data frames and is used by two different DataSHIELD Connection (DSConnection) objects. All these objects live in the same R environment (usually the Global Environment). The “server” is responsible for managing DataSHIELD sessions that are implemented as distinct R environments inside of which R symbols are assigned and R functions are evaluated. Using the R environment paradigm ensures that the different DataSHIELD execution context (client and servers) are contained and exclusive from each other.

DSLite architecture

After performing the login DataSHIELD phase, the DSLiteServer holds the different DataSHIELD server side sessions, i.e. R environments identified by an ID. These IDs are also stored within the DataSHIELD connection objects that are the result of the datashield.login() call. The folllowing example shows how to access these session IDs:

# datashield logins and assignments
conns <- datashield.login(logindata.dslite.cnsim, assign=TRUE)

# get the session ID of "sim1" node connection object
conns$sim1@sid
# the same ID is in the DSLiteServer
dslite.server$hasSession(conns$sim1@sid)

Debugging

Thanks to the DSLiteServer capability to have its configuration modified at any time, it is possible to add some debugging functions without polluting in the DataSHIELD package you are developping.

For instance, this code adds an aggregate function print():

# add a print method to configuration
dslite.server$aggregateMethod("print", function(x){ print(x) })

# and use it to print the D symbol
datashield.aggregate(conns, quote(print(D)))

Another option is to get a symbol value from the server into the client environment. This can be very helpful for complex data structures. The following example illustrates usage of a shortcut function that iterates over all the connection objects and get the corresponding symbol value:

# get data represented by symbol D for each DataSHIELD connection
data <- getDSLiteData(conns, "D")
# get data represented by symbol D from a specific DataSHIELD connection
data1 <- getDSLiteData(conns$sim1, "D")

Limitations

Server Side Environments

For each of the DataSHIELD node, the server side code is evaluated within an environment that has no parent, i.e. detached from the global environment where the client code is executed. Some R functions have a parameter that allows to specify to which environment they apply, for instance assign(), get(), eval(), as.formula(), etc. Their env (or envir) parameter default value is parent.frame() which is the global environment when executed in Opal’s R server, because it is the parent frame of the package’s namespace where the function is defined. In DSLiteServer, the parent frame must be the environment where the server code is evaluated. In order to be consistent between these two execution contexts (Opal R server and DSLiteServer), you must specify the env (or envir) value explicitly to be parent.frame(), which is the parent frame of the block being executed (either the global environment in Opal context, or the environment defined in DSLiteServer).

Example of a valid server side piece of code that assigns a value to a symbol in the DataSHIELD server’s environment (being the Opal R server’s global environment or a DSLiteServer’s environment):

base::assign(x = "D", value = someValue, envir = parent.frame())

See also the Advanced R - Environments documentation to learn more about environments.