Using workspaces • DSMolgenisArmadillo

To store the assigned data in the Armadillo service, you can use workspaces to make sure a certain state of the data is maintained on the service.

Saving the workspaces can be done during datashield.logout or at runtime.

library(dsBaseClient)
library(DSMolgenisArmadillo)

# specify server url
armadillo_url <- "https://armadillo.dev.molgenis.org"

# get token from central authentication server
token <- armadillo.get_token(armadillo_url)

## [1] "We're opening a browser so you can log in with code QR4XJ9"

# build the login dataframe
builder <- DSI::newDSLoginBuilder()
builder$append(server = "armadillo",
               url = armadillo_url,
               token = token,
               table = "gecko/2_1-core-1_0/nonrep",
               driver = "ArmadilloDriver")

# create loginframe
logindata <- builder$build()

conns <- datashield.login(login = logindata)

## 
## Logging into the collaborating servers

## 
  Logged in all servers [================================================================] 100% / 0s

datashield.assign.table(conns = conns,
                        table = "gecko/2_1-core-1_0/nonrep",
                        symbol = "J",
                        variables = c("recruit_age", "child_id"))

## 
  Assigned all table (J <- ...) [========================================================] 100% / 0s

datashield.logout(conns, save = "my-workspace")

conns <- datashield.login(logins = logindata,
                          assign = FALSE,
                          restore = "my-workspace")

## 
## Logging into the collaborating servers

datashield.symbols(conns)

## $armadillo
## [1] "J"

datashield.workspace_save(conns, "my-workspace-version-2")

You can overwrite workspaces using the same name again when saving the workspace.

datashield.logout(conns)

## 
  Logged out from all servers [==========================================================] 100% / 1s

conns <- datashield.login(logins = logindata)

## 
## Logging into the collaborating servers

datashield.assign.table(conns = conns,
                        table = "gecko/2_1-core-1_0/nonrep",
                        symbol = "H")

## 
  Assigned all table (H <- ...) [========================================================] 100% / 0s

datashield.workspace_save(conns, "my-workspace-overwritten")
datashield.workspace_save(conns, "my-workspace-overwritten")

You can list the workspaces as well.

datashield.workspaces(conns$armadillo)

##             lastAccessDate                               ETag                               name   size user
## 1 2020-09-08T10:14:42.345Z "79ea8e26a41a0f43716040c5f09466c0" armadillo:my-workspace-overwritten 172072     
## 2 2020-09-08T10:14:40.907Z "7de51b96e6d15e9ab13b9ef52fe3547f"   armadillo:my-workspace-version-2   3610     
## 3 2020-09-08T10:14:40.524Z "7de51b96e6d15e9ab13b9ef52fe3547f"             armadillo:my-workspace   3610

Remove workspaces.

datashield.workspace_rm(conns, "my-workspace-overwritten")
datashield.workspaces(conns)

##      server name..armadillo.my.workspace.version.2. name..armadillo.my.workspace. user
## 1 armadillo        armadillo:my-workspace-version-2        armadillo:my-workspace     
## 2 armadillo        armadillo:my-workspace-version-2        armadillo:my-workspace     
##   lastAccessDate..2020.09.08T10.14.40.907Z. lastAccessDate..2020.09.08T10.14.40.524Z. size.3610L size.3610L.1
## 1                  2020-09-08T10:14:40.907Z                  2020-09-08T10:14:40.524Z       3610         3610
## 2                  2020-09-08T10:14:40.907Z                  2020-09-08T10:14:40.524Z       3610         3610