This tutorial illustrates how to login to two datashield example servers and assign data for use in other tutorials.
library(DSI)
library(DSMolgenisArmadillo)
library(DSOpal)
armadillo_url <- "https://armadillo-playground.molgenis.net/"
token <- armadillo.get_token(armadillo_url)
## [1] "We're opening a browser so you can log in with code MRH4NR"
A browser page will open, press the 'submit' button. On the next screen, enter the below details and press 'submit'.
| Credential | Value |
|---|---|
| User | dsuser@datashield.org |
| Password | P@ssw0rd |
When you see the message 'Successfully connected device' you can close the browser window and return to RStudio.
builder <- DSI::newDSLoginBuilder()
builder$append(server = "server1", url = "https://armadillo-playground.molgenis.net/",
token = token, driver = "ArmadilloDriver")
builder$append(server = "server2", url = "https://opal-demo.obiba.org/",
user = "dsuser", password = "P@ssw0rd", driver = "OpalDriver")
logindata <- builder$build()
conns <- datashield.login(logins = logindata, assign = FALSE)
##
## Logging into the collaborating servers
##
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Login server1 [=======================>------------------------------------------------] 33% / 0s
Login server2 [===============================================>------------------------] 67% / 2s
Logged in all servers [================================================================] 100% / 3s
The tutorials in this wiki make use of three test datasets: mtcars, titanic, and iris. We need to assign these three datasets so that the data is available for analysis. Because Armadillo and Opal
use different storage systems, the path of these tables is different:
datashield.assign.table(conns["server1"], "mtcars", "example-datasets/mtcars/mtcars")
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Checking server1 (mtcars <- `example-datasets/mtcars/mtcars`) [------------------------] 0% / 0s
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Checking server1 (mtcars <- `example-datasets/mtcars/mtcars`) [------------------------] 0% / 0s
Finalizing assignment server1 (mtcars <- `example-datasets/mtcars/mtcars`) [=====>-----] 50% / 0s
Assigned all table (mtcars <- ...) [===================================================] 100% / 1s
datashield.assign.table(conns["server1"], "titanic", "example-datasets/titanic_train/titanic_train")
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Checking server1 (titanic <- `example-datasets/titanic_train/titanic_train`) [---------] 0% / 0s
Finalizing assignment server1 (titanic <- `example-datasets/titanic_train/titanic_train`) [] 5...
Assigned all table (titanic <- ...) [==================================================] 100% / 0s
datashield.assign.table(conns["server1"], "iris", "example-datasets/iris/iris")
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Checking server1 (iris <- `example-datasets/iris/iris`) [------------------------------] 0% / 0s
Finalizing assignment server1 (iris <- `example-datasets/iris/iris`) [=======>---------] 50% / 0s
Assigned all table (iris <- ...) [=====================================================] 100% / 0s
datashield.assign.table(conns["server2"], "mtcars", "example-datasets.mtcars")
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Checking server2 (mtcars <- `example-datasets.mtcars`) [-------------------------------] 0% / 0s
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datashield.assign.table(conns["server2"], "titanic", "example-datasets.titanic_train")
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Assigned all table (titanic <- ...) [==================================================] 100% / 0s
datashield.assign.table(conns["server2"], "iris", "example-datasets.iris")
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Checking server2 (iris <- `example-datasets.iris`) [-----------------------------------] 0% / 0s
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Finalizing assignment server2 (iris <- `example-datasets.iris`) [==========>-----------] 50% / 0s
Assigned all table (iris <- ...) [=====================================================] 100% / 0s