diff --git a/R/ds.Boole.R b/R/ds.Boole.R index c435e4c6..881ebbb7 100644 --- a/R/ds.Boole.R +++ b/R/ds.Boole.R @@ -44,29 +44,29 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Generating Boolean indicators diff --git a/R/ds.abs.R b/R/ds.abs.R index cc4523f3..625591a8 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -22,29 +22,29 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Generate a normally distributed variable with zero mean and variance equal diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 623e43db..700b90b1 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -18,25 +18,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -44,7 +44,7 @@ #' # Converting the R object into a class character #' ds.asCharacter(x.name = "D$LAB_TSC", #' newobj = "char.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index bdfa9fdd..9126b9fc 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -17,25 +17,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -43,7 +43,7 @@ #' # Converting the R object into a matrix #' ds.asDataMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index e6b6e7ce..a8ae29f4 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -140,28 +140,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", @@ -170,14 +170,14 @@ #' #from all studies is created #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections)#all the Opal servers are used, in this case 3 +#' datasources = connections)#all the servers are used, in this case 2 #' #(see above the connection to the servers) #' ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", #' newobj.name = "fact.obj", #' forced.factor.levels = c(2,3), #the variable is split in 2 levels #' fixed.dummy.vars = TRUE, #create a matrix of dummy variables #' baseline.level = 1, -#' datasources = connections[1])#only the first Opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 0e9670df..bd5eb292 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -31,25 +31,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -57,7 +57,7 @@ #' # Converting the R object into an integer #' ds.asInteger(x.name = "D$LAB_TSC", #' newobj = "int.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "int.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asList.R b/R/ds.asList.R index 83007f5a..fb3fbdbc 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -18,25 +18,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -44,7 +44,7 @@ #' # Converting the R object into a List #' ds.asList(x.name = "D", #' newobj = "D.asList", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "D.asList", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index 85617edc..89dfb255 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -17,25 +17,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -43,7 +43,7 @@ #' # Converting the R object into a logical #' ds.asLogical(x.name = "D$LAB_TSC", #' newobj = "logical.obj", -#' datasources =connections[1]) #only the first Opal server is used ("study1") +#' datasources =connections[1]) #only the first server is used ("study1") #' ds.class(x = "logical.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index f3980377..1c97dbf1 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -20,25 +20,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -46,7 +46,7 @@ #' # Converting the R object into a matrix #' ds.asMatrix(x.name = "D", #' newobj = "mat.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 803a6308..980a7117 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -31,25 +31,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -57,7 +57,7 @@ #' # Converting the R object into a numeric class #' ds.asNumeric(x.name = "D$LAB_TSC", #' newobj = "num.obj", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' ds.class(x = "num.obj", datasources = connections[1]) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.assign.R b/R/ds.assign.R index 79c373d5..c646e378 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -22,25 +22,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -48,7 +48,7 @@ #' # Assign a variable to a name #' ds.assign(toAssign = "D$LAB_TSC", #' newobj = "labtsc", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index e02aab96..cb51d601 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -24,25 +24,25 @@ #' ### Please ensure you have a training Virtual Machine running, #' or that you have a live connection to a server. #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, diff --git a/R/ds.c.R b/R/ds.c.R index 7be360a4..8a928413 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -21,25 +21,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -48,7 +48,7 @@ #' myvect <- c("D$LAB_TSC", "D$LAB_HDL") #' ds.c(x = myvect, #' newobj = "new.vect", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.cbind.R b/R/ds.cbind.R index 0f85ca99..1af1737a 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -45,28 +45,28 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Assign the exponent of a numeric variable at each server and cbind it diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index a06ac143..ae06bd6b 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -39,28 +39,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Changing the reference group in the server-side diff --git a/R/ds.class.R b/R/ds.class.R index ab6e8937..299950a4 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -17,28 +17,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Getting the class of the R objects stored in the server-side diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 06e64728..57157421 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -18,28 +18,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Getting column names of the R objects stored in the server-side diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index 107f70de..1a3d3f5a 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -24,44 +24,44 @@ #' @examples #' \dontrun{ #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select complete cases from different R objects #' -#' ds.completeCases(x1 = "D", #data frames in the Opal servers -#' #(see above the connection to the Opal servers) +#' ds.completeCases(x1 = "D", #data frames in the servers +#' #(see above the connection to the servers) #' newobj = "D.completeCases", # name for the output object -#' # that is stored in the Opal servers -#' datasources = connections) # All Opal servers are used -#' # (see above the connection to the Opal servers) +#' # that is stored in the servers +#' datasources = connections) # All servers are used +#' # (see above the connection to the servers) #' -#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers -#' #(see above the connection to the Opal servers) +#' ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the servers +#' #(see above the connection to the servers) #' newobj = "LAB_TSC.completeCases", #name for the output variable -#' #that is stored in the Opal servers -#' datasources = connections[2]) #only the second Opal server is used ("study2") +#' #that is stored in the servers +#' datasources = connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 42084006..94dfa21b 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -61,28 +61,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Generating contour plots diff --git a/R/ds.cor.R b/R/ds.cor.R index 9c0ef8e1..8d068beb 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -43,28 +43,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Get the correlation matrix of two continuous variables diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 95b59d0c..78c80216 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -32,25 +32,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.cov.R b/R/ds.cov.R index 0aa75a3d..1fdf57f2 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -53,28 +53,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Calculate the covariance between two vectors @@ -90,7 +90,7 @@ #' y = 'gender', #' naAction = 'pairwise.complete', #' type = 'combine', -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index ccd671c4..c06322a5 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -45,30 +45,30 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Create a new data frame @@ -80,7 +80,7 @@ #' completeCases = TRUE, #only rows with not missing values are selected #' DataSHIELD.checks = FALSE, #' newobj = "df1", -#' datasources = connections[1], #only the first Opal server is used ("study1") +#' datasources = connections[1], #only the first server is used ("study1") #' notify.of.progress = FALSE) #' #' diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index f4bb080c..59caf5b0 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -26,29 +26,29 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Create two data frames with one different column diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index f8fc52f7..3e41eccd 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -41,25 +41,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -70,7 +70,7 @@ #' sort.descending = TRUE, #' sort.method = "numeric", #' newobj = "df.sort", -#' datasources = connections[1]) #only the first Opal server is used ("study1") +#' datasources = connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 9792afa4..c6603c41 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -41,25 +41,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index d617dd73..e2dcae6c 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -35,41 +35,41 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Generate the density grid #' # Example1: generate a combined grid density object (default) #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all servers are used #' #' # Example2: generate a grid density object for each study separately #' ds.densityGrid(x="D$LAB_TSC", #' y="D$LAB_HDL", #' type="split" -#' datasources = connections[1])#only the first Opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") #' #' # Example3: generate a grid density object where the number of intervals is set to 15, for #' each study separately diff --git a/R/ds.dim.R b/R/ds.dim.R index 17c5fb75..6778a646 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -37,25 +37,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -64,14 +64,14 @@ #' # Calculate the dimension #' ds.dim(x="D", #' type="combine", #global dimension -#'#' datasources = connections)#all opal servers are used +#'#' datasources = connections)#all servers are used #' ds.dim(x="D", #' type = "both",#separate dimension for each study #' #and the pooled dimension (default) -#'#' datasources = connections)#all opal servers are used +#'#' datasources = connections)#all servers are used #' ds.dim(x="D", #' type="split", #separate dimension for each study -#'#' datasources = connections[1])#only the first opal server is used ("study1") +#'#' datasources = connections[1])#only the first server is used ("study1") #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.dmtC2S.R b/R/ds.dmtC2S.R index 3c032b71..96d059e6 100644 --- a/R/ds.dmtC2S.R +++ b/R/ds.dmtC2S.R @@ -22,17 +22,17 @@ #' the name of the copied DMT defaults to "dmt.copied.C2S". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.exists.R b/R/ds.exists.R index 6dff8b4c..24c5bfa2 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -25,34 +25,34 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Check if the object exist in the server-side #' ds.exists(x = "D", -#' datasources = connections) #All opal servers are used +#' datasources = connections) #All servers are used #' ds.exists(x = "D", -#' datasources = connections[1]) #Only the first Opal server is used (study1) +#' datasources = connections[1]) #Only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.exp.R b/R/ds.exp.R index 65102600..c23fbaba 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -21,35 +21,35 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # compute exponential function of the 'PM_BMI_CONTINUOUS' variable #' ds.exp(x = "D$PM_BMI_CONTINUOUS", #' newobj = "exp.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Opal server is used (study1) +#' datasources = connections[1]) #only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.extractQuantiles.R b/R/ds.extractQuantiles.R index 4068f8f3..68900f8f 100644 --- a/R/ds.extractQuantiles.R +++ b/R/ds.extractQuantiles.R @@ -60,7 +60,7 @@ #' otherwise left behind. These are not usually needed, but could be of value #' if one were investigating a problem with the ranking. FALSE: do not delete #' the residual objects -#' @param extract.datasources specifies the particular opal object(s) to use. +#' @param extract.datasources specifies the particular connection object(s) to use. #' This is set via the argument in ds.ranksSecure. For more details #' see the associated document entitled "secure.global.ranking.docx". Also see #' the header file for ds.ranksSecure. diff --git a/R/ds.forestplot.R b/R/ds.forestplot.R index e1bc21c1..d71fafdb 100644 --- a/R/ds.forestplot.R +++ b/R/ds.forestplot.R @@ -18,22 +18,21 @@ #' \dontrun{ #' # Run a logistic regression #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.getWGSR.R b/R/ds.getWGSR.R index 80306811..f7fa79e3 100644 --- a/R/ds.getWGSR.R +++ b/R/ds.getWGSR.R @@ -63,29 +63,29 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/anthro/anthro1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "ANTHRO.anthro3", driver = "OpalDriver") +#' table = "ANTHRO.anthro2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Generate the weight-for-height (wfh) index diff --git a/R/ds.glm.R b/R/ds.glm.R index 24488e22..d6937795 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -217,31 +217,31 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the GLM @@ -284,20 +284,17 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.glmPredict.R b/R/ds.glmPredict.R index e881bb54..e7e0c02a 100644 --- a/R/ds.glmPredict.R +++ b/R/ds.glmPredict.R @@ -84,17 +84,17 @@ #' object on the serverside defaults to the name "predict_glm". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index ef366e21..b8627124 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -267,31 +267,31 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the GLM @@ -330,20 +330,17 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Fit the logistic regression model diff --git a/R/ds.glmSummary.R b/R/ds.glmSummary.R index 5a80b7fc..22ae6a96 100644 --- a/R/ds.glmSummary.R +++ b/R/ds.glmSummary.R @@ -41,17 +41,17 @@ #' object on the serverside defaults to "summary_glm.newobj". #' @param datasources specifies the particular 'connection object(s)' to use. #' e.g. if you have several data sets in the sources you are working with -#' called opals.a, opals.w2, and connection.xyz, you can choose which of +#' called connections.a, connections.w2, and connection.xyz, you can choose which of #' these to work with. The call 'datashield.connections_find()' lists all of #' the different datasets available and if one of these is called 'default.connections' #' that will be the dataset used by default if no other dataset is specified. If you #' wish to change the connections you wish to use by default the call -#' datashield.connections_default('opals.a') will set 'default.connections' -#' to be 'opals.a' and so in the absence of specific instructions to the contrary +#' datashield.connections_default('connections.a') will set 'default.connections' +#' to be 'connections.a' and so in the absence of specific instructions to the contrary #' (e.g. by specifying a particular dataset to be used via the -#' argument) all subsequent function calls will be to the datasets held in opals.a. +#' argument) all subsequent function calls will be to the datasets held in connections.a. #' If the argument is specified, it should be set without -#' inverted commas: e.g. datasources=opals.a or datasources=default.connections. +#' inverted commas: e.g. datasources=connections.a or datasources=default.connections. #' The argument also allows you to apply a function solely to a subset #' of the studies/sources you are working with. For example, the second source #' in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index 0665b24e..ed254a08 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -168,28 +168,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select all rows without missing values @@ -209,20 +209,17 @@ #' #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") +#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index 48312460..33d402aa 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -95,28 +95,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Compute the heat map plot diff --git a/R/ds.histogram.R b/R/ds.histogram.R index f9b375dd..d0f4a7f3 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -91,28 +91,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Compute the histogram diff --git a/R/ds.isNA.R b/R/ds.isNA.R index 80ffcc08..63ef2658 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -22,25 +22,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.isValid.R b/R/ds.isValid.R index 266dbca2..da48891c 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -23,25 +23,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.length.R b/R/ds.length.R index d2acd0e7..5db7d1e3 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -28,25 +28,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.levels.R b/R/ds.levels.R index 5dc650b4..337a2759 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -18,25 +18,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.lexis.R b/R/ds.lexis.R index abc019a7..5f4610d4 100644 --- a/R/ds.lexis.R +++ b/R/ds.lexis.R @@ -141,31 +141,31 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' #' # Example 1: Fitting GLM for survival analysis #' # For this analysis we need to load survival data from the server #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Example 1: Create the expanded data frame. diff --git a/R/ds.list.R b/R/ds.list.R index ebbf5749..3ec7707b 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -21,25 +21,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.listDisclosureSettings.R b/R/ds.listDisclosureSettings.R index 33c73875..04851def 100644 --- a/R/ds.listDisclosureSettings.R +++ b/R/ds.listDisclosureSettings.R @@ -62,28 +62,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Call to list current disclosure settings in all data repository servers diff --git a/R/ds.listOpals.R b/R/ds.listOpals.R index a07aaa0e..310baef5 100644 --- a/R/ds.listOpals.R +++ b/R/ds.listOpals.R @@ -3,7 +3,7 @@ #' @description ds.listOpals calls the internal DataSHIELD function getOpals() which identifies #' all Opal objects in the analytic environment. #' @details ds.listOpals calls the internal DataSHIELD function getOpals() which identifies -#' all Opal objects in the analytic environment. If there are no Opal servers in the analytic +#' all Opal objects in the analytic environment. If there are no Armadillo/Opal servers in the analytic #' environment ds.listOpalsIreminds the user that they have to login to a valid set of Opal #' login objects, if they wish to use DataSHIELD. If there is only one set of Opals, ds.listOpals #' copies that one set and names the copy 'default.opals'. This default set will then be used by diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index 97188b28..2df6630c 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -18,28 +18,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # List server-side functions diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 23192f7a..3f0f5cfc 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -164,28 +164,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") +#' table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' #Log onto the remote Opal training servers +#' #Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Select all rows without missing values diff --git a/R/ds.log.R b/R/ds.log.R index cfa2155f..ca236461 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -20,29 +20,29 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Calculating the log value of the 'PM_BMI_CONTINUOUS' variable @@ -50,7 +50,7 @@ #' ds.log(x = "D$PM_BMI_CONTINUOUS", #' base = exp(2), #' newobj = "log.PM_BMI_CONTINUOUS", -#' datasources = connections[1]) #only the first Opal server is used (study1) +#' datasources = connections[1]) #only the first server is used (study1) #' #' # clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.look.R b/R/ds.look.R index 8dffa52f..c1d005bd 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -31,25 +31,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.ls.R b/R/ds.ls.R index ce96c901..7377d59e 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -67,25 +67,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.make.R b/R/ds.make.R index 044c727a..80b22885 100644 --- a/R/ds.make.R +++ b/R/ds.make.R @@ -77,25 +77,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrix.R b/R/ds.matrix.R index 5a0ed315..5813ebe0 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -56,25 +56,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index 2f4d4960..97bcbff3 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -25,25 +25,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 4d914d5c..e2b8061c 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -24,25 +24,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index 7b78d9ba..4e03f1d0 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -64,25 +64,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index be7cb169..b5db1fee 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -23,25 +23,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index d92591c4..a8902aac 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -20,25 +20,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 35e9d711..bdef9abe 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -25,25 +25,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 4de06471..9286bb28 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -23,25 +23,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.mdPattern.R b/R/ds.mdPattern.R index af59498e..37823071 100644 --- a/R/ds.mdPattern.R +++ b/R/ds.mdPattern.R @@ -65,21 +65,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.mean.R b/R/ds.mean.R index ca91ca1d..501c3773 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -62,25 +62,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index 538ef8c8..6940c548 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -37,25 +37,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' diff --git a/R/ds.meanSdGp.R b/R/ds.meanSdGp.R index f95cdbb9..9232eeb7 100644 --- a/R/ds.meanSdGp.R +++ b/R/ds.meanSdGp.R @@ -75,25 +75,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.merge.R b/R/ds.merge.R index c2d11678..2eae9620 100644 --- a/R/ds.merge.R +++ b/R/ds.merge.R @@ -56,25 +56,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.message.R b/R/ds.message.R index eb88d8b9..361c9be6 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -31,25 +31,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 78ceb43c..2e080f01 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -17,25 +17,25 @@ #' @examples #' \dontrun{ #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.names.R b/R/ds.names.R index e348f002..1466ce8d 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -27,25 +27,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.numNA.R b/R/ds.numNA.R index 444034f7..b5ad89dc 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -20,25 +20,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index fd8145a6..4f037f1f 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -31,25 +31,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index 1759db7d..35b8a3ad 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -54,40 +54,40 @@ #' @examples #' \dontrun{ #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' #Generating the vectors in the Opal servers -#' ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different -#' size=c(10,23,5), #Bernoulli trials change in each source -#' prob=c(0.6,0.1,0.5), #Probability changes in each source +#' #Generating the vectors in the servers +#' ds.rBinom(samp.size=c(13,20), #the length of the vector created in each source is different +#' size=c(10,23), #Bernoulli trials change in each source +#' prob=c(0.6,0.1), #Probability changes in each source #' newobj="Binom.dist", #' seed.as.integer=45, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rBinom(samp.size=15, @@ -96,7 +96,7 @@ #' newobj="Binom.dist", #' seed.as.integer=324, #' return.full.seed.as.set=FALSE, -#' datasources=connections[2]) #only the second Opal server is used ("study2") +#' datasources=connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 05bb15d2..d2e035b8 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -65,41 +65,41 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers +#' # Generating the vectors in the servers #' -#' ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different -#' mean=c(1,6,4), #the mean of the Normal distribution changes in each server -#' sd=c(1,4,3), #the sd of the Normal distribution changes in each server +#' ds.rNorm(samp.size=c(10,20), #the length of the vector created in each source is different +#' mean=c(1,6), #the mean of the Normal distribution changes in each server +#' sd=c(1,4), #the sd of the Normal distribution changes in each server #' newobj="Norm.dist", #' seed.as.integer=2345, #' return.full.seed.as.set=FALSE, -#' force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different +#' force.output.to.k.decimal.places=c(4,5), #output random numbers have different #' #decimal quantity in each source -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rNorm(samp.size=10, @@ -109,7 +109,7 @@ #' seed.as.integer=2345, #' return.full.seed.as.set=FALSE, #' force.output.to.k.decimal.places=1, -#' datasources=connections[2]) #only the second Opal server is used ("study2") +#' datasources=connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rPois.R b/R/ds.rPois.R index e6ae42d4..c4d56448 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -53,46 +53,46 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers -#' ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different -#' lambda=c(2,3,4), #different mean per interval (2,3,4) in each source +#' # Generating the vectors in the servers +#' ds.rPois(samp.size=c(13,20), #the length of the vector created in each source is different +#' lambda=c(2,3), #different mean per interval (2,3) in each source #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections) #all the Opal servers are used, in this case 3 +#' datasources=connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' ds.rPois(samp.size=13, #' lambda=5, #' newobj="Pois.dist", #' seed.as.integer=1234, #' return.full.seed.as.set=FALSE, -#' datasources=connections[1]) #only the first Opal server is used ("study1") +#' datasources=connections[1]) #only the first server is used ("study1") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index bac2db04..e09ed491 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -72,41 +72,41 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' -#' # Generating the vectors in the Opal servers +#' # Generating the vectors in the servers #' -#' ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different -#' min = c(0,2,5), #different minumum value of the function in each source -#' max = c(2,5,9), #different maximum value of the function in each source +#' ds.rUnif(samp.size = c(12,20), #the length of the vector created in each source is different +#' min = c(0,2), #different minumum value of the function in each source +#' max = c(2,5), #different maximum value of the function in each source #' newobj = "Unif.dist", #' seed.as.integer = 234, #' return.full.seed.as.set = FALSE, -#' force.output.to.k.decimal.places = c(1,2,3), -#' datasources = connections) #all the Opal servers are used, in this case 3 +#' force.output.to.k.decimal.places = c(1,2), +#' datasources = connections) #all the servers are used, in this case 2 #' #(see above the connection to the servers) #' #' ds.rUnif(samp.size = 12, @@ -116,7 +116,7 @@ #' seed.as.integer = 12345, #' return.full.seed.as.set = FALSE, #' force.output.to.k.decimal.places = 2, -#' datasources = connections[2]) #only the second Opal server is used ("study2") +#' datasources = connections[2]) #only the second server is used ("study2") #' #' # Clear the Datashield R sessions and logout #' datashield.logout(connections) diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 2943312d..995b719e 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -36,40 +36,40 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Combining R objects by rows #' #' #' ds.rbind(x = "D", #data frames in the server-side to be conbined -#' #(see above the connection to the Opal servers) +#' #(see above the connection to the servers) #' DataSHIELD.checks = FALSE, #' force.colnames = NULL, #' newobj = "D.rbind", # name for the output object that is stored in the data servers -#' datasources = connections, # All Opal servers are used -#' #(see above the connection to the Opal servers) +#' datasources = connections, # All servers are used +#' #(see above the connection to the servers) #' notify.of.progress = FALSE) #' #' # Clear the Datashield R sessions and logout diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 38fa36b5..209734f2 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -40,28 +40,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") +#' table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Reshape server-side grouped data diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 32bf30e6..3d85a453 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -26,25 +26,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index c0a52c3d..81c352fb 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -32,25 +32,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rep.R b/R/ds.rep.R index 7874045f..72c9177a 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -31,28 +31,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, #' assign = TRUE, #' symbol = "D") diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 0596f2da..1ec2d3a9 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -32,28 +32,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Replace missing values in variable 'LAB_HDL' by the mean value @@ -66,7 +66,7 @@ #' #' # Replace the missing values using the mean for each study #' ds.replaceNA(x = "D$LAB_HDL", -#' forNA = list(mean[[1]][1], mean[[1]][2], mean[[1]][3]), +#' forNA = list(mean[[1]][1], mean[[1]][2]), #' newobj = "HDL.noNA", #' datasources = connections) #' @@ -79,7 +79,7 @@ #' #' # Replace the missing values with 999s #' ds.replaceNA(x = "D$PM_BMI_CATEGORICAL", -#' forNA = c(999,999,999), +#' forNA = c(999,999), #' newobj = "bmi999") #' #' # Check if the NAs have been replaced correctly diff --git a/R/ds.rm.R b/R/ds.rm.R index e977afe5..652e9e58 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -27,25 +27,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index 8d0ec804..7aecbba0 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -24,31 +24,31 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' myvar <- list("LAB_TSC","LAB_HDL") #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, #' variables = myvar, symbol = "D") #' diff --git a/R/ds.sample.R b/R/ds.sample.R index e52af826..9128a9e1 100644 --- a/R/ds.sample.R +++ b/R/ds.sample.R @@ -92,7 +92,7 @@ #' If you want to use the same starting seed in all studies but do not wish it to #' be 0, you can specify a non-zero scalar value for and then #' use the argument to generate the random number vectors one source at -#' a time (e.g. ,datasources=default.opals[2] to generate the random vector in source 2). +#' a time (e.g. ,datasources=default.connections[2] to generate the random vector in source 2). #' As an example, if the value is 78326 then the seed #' in each source will be set at 78326*1 = 78326 because the vector of datasources #' being used in each call to the function will always be of length 1 and so the @@ -110,15 +110,15 @@ #' For further details see help for \code{sample} in native R. #' @param newobj This a character string providing a name for the output #' data.frame which defaults to 'newobj.sample' if no name is specified. -#' @param datasources specifies the particular opal object(s) to use. If the -#' argument is not specified the default set of opals will be used. The default opals -#' are called default.opals and the default can be set using the function -#' \code{ds.setDefaultOpals}. If the is to be specified, it should be set without -#' inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -#' apply the function solely to e.g. the second opal server in a set of three, -#' the argument can be specified as: e.g. datasources=opals.em[2]. -#' If you wish to specify the first and third opal servers in a set you specify: -#' e.g. datasources=opals.em[c(1,3)] +#' @param datasources specifies the particular connection object(s) to use. If the +#' argument is not specified the default set of servers will be used. The default servers +#' are called default.connections and the default can be set using the function +#' \code{DSI::datashield.connections_default}. If the is to be specified, it should be set without +#' inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to +#' apply the function solely to e.g. the second server in a set of three, +#' the argument can be specified as: e.g. datasources=connections.em[2]. +#' If you wish to specify the first and third servers in a set you specify: +#' e.g. datasources=connections.em[c(1,3)] #' @param notify.of.progress specifies if console output should be produce to indicate #' progress. The default value for notify.of.progress is FALSE. #' @return the object specified by the argument (or default name diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 4d9c872d..6a76d798 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -77,30 +77,30 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Example 1: generate a scatter plot for each study separately diff --git a/R/ds.seq.R b/R/ds.seq.R index 1bb95836..13fc644a 100644 --- a/R/ds.seq.R +++ b/R/ds.seq.R @@ -65,28 +65,28 @@ #' \dontrun{ #' #' ## Version 6, for version 5 see the Wiki -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Create 3 different sequences diff --git a/R/ds.setSeed.R b/R/ds.setSeed.R index acd73f81..5192f753 100644 --- a/R/ds.setSeed.R +++ b/R/ds.setSeed.R @@ -46,28 +46,28 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Generate a pseudorandom number in the server-side diff --git a/R/ds.skewness.R b/R/ds.skewness.R index 22214612..52f0c87a 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -1,7 +1,7 @@ #' #' @title Calculates the skewness of a server-side numeric variable #' @description This function calculates the skewness of a numeric variable -#' that is stored on the server-side (Opal server). +#' that is stored on the server-side (server). #' @details This function is similar to the function \code{skewness} in R package \code{e1071}. #' #' The function calculates the skewness of an input variable \code{x} @@ -43,25 +43,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 3aef2193..76a7538e 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -22,29 +22,29 @@ #' @examples #' \dontrun{ #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' # Example 1: Get the square root of LAB_HDL variable diff --git a/R/ds.summary.R b/R/ds.summary.R index 3174023a..bac5cb62 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -26,28 +26,28 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # Connecting to the Opal servers +#' # Connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' -#' # Log onto the remote Opal training servers +#' # Log onto the remote Armadillo/Opal training servers #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #' #' #Calculate the summary of a numeric variable diff --git a/R/ds.tapply.R b/R/ds.tapply.R index 3972bf83..5342c332 100644 --- a/R/ds.tapply.R +++ b/R/ds.tapply.R @@ -77,25 +77,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.tapply.assign.R b/R/ds.tapply.assign.R index 5e2ac52f..14722a94 100644 --- a/R/ds.tapply.assign.R +++ b/R/ds.tapply.assign.R @@ -82,25 +82,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index 5b7e946a..e12799df 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -21,25 +21,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.unList.R b/R/ds.unList.R index 9af30d6b..6f98fddd 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -28,25 +28,25 @@ #' \dontrun{ #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.unique.R b/R/ds.unique.R index dd8e5e53..07ceced2 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -13,25 +13,25 @@ #' @return \code{ds.unique} returns the vector of unique R objects which are written to the server-side. #' @examples #' \dontrun{ -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/ds.var.R b/R/ds.var.R index fcf20495..4247e024 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -40,25 +40,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/R/subsetHelper.R b/R/subsetHelper.R index 62648552..2400c077 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -22,25 +22,25 @@ #' #' ## Version 6, for version 5 see the Wiki #' -#' # connecting to the Opal servers +#' # connecting to the Armadillo/Opal servers #' #' require('DSI') +#' require('DSMolgenisArmadillo') #' require('DSOpal') #' require('dsBaseClient') #' +#' armadillo_url <- "http://192.168.56.100:8080/" +#' token <- armadillo.get_credentials(armadillo_url) #' builder <- DSI::newDSLoginBuilder() #' builder$append(server = "study1", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM1", driver = "OpalDriver") +#' url = armadillo_url, +#' token = token@access_token, +#' table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") #' builder$append(server = "study2", -#' url = "http://192.168.56.100:8080/", -#' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM2", driver = "OpalDriver") -#' builder$append(server = "study3", -#' url = "http://192.168.56.100:8080/", +#' url = "https://192.168.56.100:8443/", #' user = "administrator", password = "datashield_test&", -#' table = "CNSIM.CNSIM3", driver = "OpalDriver") +#' table = "CNSIM.CNSIM2", driver = "OpalDriver", +#' options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") #' logindata <- builder$build() #' #' connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.Boole.Rd b/man/ds.Boole.Rd index af451932..33d69fd3 100644 --- a/man/ds.Boole.Rd +++ b/man/ds.Boole.Rd @@ -70,28 +70,28 @@ Server function called: \code{BooleDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Generating Boolean indicators diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index 6cd9404d..a89aea27 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -35,29 +35,29 @@ specified by the user through the argument \code{newobj}, otherwise is named by \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Generate a normally distributed variable with zero mean and variance equal diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index e557c9fc..19b2c55d 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -32,25 +32,25 @@ Server function called: \code{asCharacterDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asCharacterDS} # Converting the R object into a class character ds.asCharacter(x.name = "D$LAB_TSC", newobj = "char.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index d9e253e6..08d1bad3 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -34,25 +34,25 @@ Server function called: \code{asDataMatrixDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -60,7 +60,7 @@ Server function called: \code{asDataMatrixDS}. # Converting the R object into a matrix ds.asDataMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index 2ca4d1c4..43212e9b 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -166,28 +166,28 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", @@ -196,14 +196,14 @@ Server functions called: \code{asFactorDS1} and \code{asFactorDS2} #from all studies is created fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections)#all the Opal servers are used, in this case 3 + datasources = connections)#all the servers are used, in this case 2 #(see above the connection to the servers) ds.asFactor(input.var.name = "D$PM_BMI_CATEGORICAL", newobj.name = "fact.obj", forced.factor.levels = c(2,3), #the variable is split in 2 levels fixed.dummy.vars = TRUE, #create a matrix of dummy variables baseline.level = 1, - datasources = connections[1])#only the first Opal server is used ("study1") + datasources = connections[1])#only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 0bf7ab47..7a9cabe0 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -47,25 +47,25 @@ Server function called: \code{asIntegerDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -73,7 +73,7 @@ Server function called: \code{asIntegerDS} # Converting the R object into an integer ds.asInteger(x.name = "D$LAB_TSC", newobj = "int.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "int.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index 6af6f960..7b88cf6f 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -32,25 +32,25 @@ Server function called: \code{asListDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asListDS} # Converting the R object into a List ds.asList(x.name = "D", newobj = "D.asList", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "D.asList", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index ec539cc3..4d91cde5 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -32,25 +32,25 @@ Server function called: \code{asLogicalDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -58,7 +58,7 @@ Server function called: \code{asLogicalDS} # Converting the R object into a logical ds.asLogical(x.name = "D$LAB_TSC", newobj = "logical.obj", - datasources =connections[1]) #only the first Opal server is used ("study1") + datasources =connections[1]) #only the first server is used ("study1") ds.class(x = "logical.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index 8116ac1d..55006e5a 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -37,25 +37,25 @@ Server function called: \code{asMatrixDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -63,7 +63,7 @@ Server function called: \code{asMatrixDS} # Converting the R object into a matrix ds.asMatrix(x.name = "D", newobj = "mat.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 73f03693..7acb2e77 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -46,25 +46,25 @@ Server function called: \code{asNumericDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -72,7 +72,7 @@ Server function called: \code{asNumericDS} # Converting the R object into a numeric class ds.asNumeric(x.name = "D$LAB_TSC", newobj = "num.obj", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") ds.class(x = "num.obj", datasources = connections[1]) # Clear the Datashield R sessions and logout diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index df41057b..f66a184f 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -34,25 +34,25 @@ assigned the variable called \code{newobj} on the server-side. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -60,7 +60,7 @@ assigned the variable called \code{newobj} on the server-side. # Assign a variable to a name ds.assign(toAssign = "D$LAB_TSC", newobj = "labtsc", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 9b73d486..3f3cb16e 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -48,25 +48,25 @@ of grouping using categorical variables on the dataset (only for data frames) ### Please ensure you have a training Virtual Machine running, or that you have a live connection to a server. - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, diff --git a/man/ds.c.Rd b/man/ds.c.Rd index c0046d46..76bd4fa5 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -38,25 +38,25 @@ Server function called: \code{cDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -65,7 +65,7 @@ Server function called: \code{cDS} myvect <- c("D$LAB_TSC", "D$LAB_HDL") ds.c(x = myvect, newobj = "new.vect", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 82ddbd88..50b900ef 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -73,28 +73,28 @@ Server function called: \code{cbindDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Assign the exponent of a numeric variable at each server and cbind it diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index c20f2389..43f16ac0 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -54,28 +54,28 @@ Server function called: \code{changeRefGroupDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Changing the reference group in the server-side diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 861eeddc..3d911fdd 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -29,28 +29,28 @@ Server function called: \code{classDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting the class of the R objects stored in the server-side diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 6915dd59..f089838d 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -30,28 +30,28 @@ Server function called: \code{colnamesDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Getting column names of the R objects stored in the server-side diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index 8a8f4ea4..686b4730 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -39,44 +39,44 @@ Server function called: \code{completeCasesDS} \examples{ \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select complete cases from different R objects - ds.completeCases(x1 = "D", #data frames in the Opal servers - #(see above the connection to the Opal servers) + ds.completeCases(x1 = "D", #data frames in the servers + #(see above the connection to the servers) newobj = "D.completeCases", # name for the output object - # that is stored in the Opal servers - datasources = connections) # All Opal servers are used - # (see above the connection to the Opal servers) + # that is stored in the servers + datasources = connections) # All servers are used + # (see above the connection to the servers) - ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the Opal servers - #(see above the connection to the Opal servers) + ds.completeCases(x1 = "D$LAB_TSC", #vector (variable) of the data frames in the servers + #(see above the connection to the servers) newobj = "LAB_TSC.completeCases", #name for the output variable - #that is stored in the Opal servers - datasources = connections[2]) #only the second Opal server is used ("study2") + #that is stored in the servers + datasources = connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.contourPlot.Rd b/man/ds.contourPlot.Rd index 16529564..1ad94a2d 100644 --- a/man/ds.contourPlot.Rd +++ b/man/ds.contourPlot.Rd @@ -93,28 +93,28 @@ Server functions called: \code{heatmapPlotDS}, \code{rangeDS} and \code{densityG \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Generating contour plots diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index b7329709..90fa8af7 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -65,28 +65,28 @@ Server function called: \code{corDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Get the correlation matrix of two continuous variables diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index 1dbaf49c..25495438 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -60,25 +60,25 @@ Server function called: \code{corTestDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index a953b8e4..75cf1a98 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -76,28 +76,28 @@ and the total number of missing values aggregated from all the involved studies, \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Calculate the covariance between two vectors @@ -113,7 +113,7 @@ and the total number of missing values aggregated from all the involved studies, y = 'gender', naAction = 'pairwise.complete', type = 'combine', - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 918a5044..6feb1a74 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -81,29 +81,29 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Create a new data frame @@ -115,7 +115,7 @@ Server functions called: \code{classDS}, \code{colnamesDS}, \code{dataFrameDS} completeCases = TRUE, #only rows with not missing values are selected DataSHIELD.checks = FALSE, newobj = "df1", - datasources = connections[1], #only the first Opal server is used ("study1") + datasources = connections[1], #only the first server is used ("study1") notify.of.progress = FALSE) diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index e096223e..02adb785 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -45,29 +45,29 @@ Server function called: \code{dataFrameFillDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Create two data frames with one different column diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index af86a99f..3eb2d9e1 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -66,25 +66,25 @@ Server function called: \code{dataFrameSortDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -95,7 +95,7 @@ Server function called: \code{dataFrameSortDS}. sort.descending = TRUE, sort.method = "numeric", newobj = "df.sort", - datasources = connections[1]) #only the first Opal server is used ("study1") + datasources = connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 5d909752..62865652 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -75,25 +75,25 @@ Server functions called: \code{dataFrameSubsetDS1} and \code{dataFrameSubsetDS2} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 00fe1e91..26baa29d 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -59,41 +59,41 @@ Server function called: \code{densityGridDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Generate the density grid # Example1: generate a combined grid density object (default) ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", - datasources = connections)#all opal servers are used + datasources = connections)#all servers are used # Example2: generate a grid density object for each study separately ds.densityGrid(x="D$LAB_TSC", y="D$LAB_HDL", type="split" - datasources = connections[1])#only the first Opal server is used ("study1") + datasources = connections[1])#only the first server is used ("study1") # Example3: generate a grid density object where the number of intervals is set to 15, for each study separately diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index 1fbacddf..dacda6a6 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -51,25 +51,25 @@ Server function called: \code{dimDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") @@ -78,14 +78,14 @@ Server function called: \code{dimDS} # Calculate the dimension ds.dim(x="D", type="combine", #global dimension -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all servers are used ds.dim(x="D", type = "both",#separate dimension for each study #and the pooled dimension (default) -#' datasources = connections)#all opal servers are used +#' datasources = connections)#all servers are used ds.dim(x="D", type="split", #separate dimension for each study -#' datasources = connections[1])#only the first opal server is used ("study1") +#' datasources = connections[1])#only the first server is used ("study1") # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.dmtC2S.Rd b/man/ds.dmtC2S.Rd index bfd673b4..ce991d8d 100644 --- a/man/ds.dmtC2S.Rd +++ b/man/ds.dmtC2S.Rd @@ -16,17 +16,17 @@ the name of the copied DMT defaults to "dmt.copied.C2S".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index 2352a294..eb9795a0 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -35,34 +35,34 @@ Server function called: \code{exists} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Check if the object exist in the server-side ds.exists(x = "D", - datasources = connections) #All opal servers are used + datasources = connections) #All servers are used ds.exists(x = "D", - datasources = connections[1]) #Only the first Opal server is used (study1) + datasources = connections[1]) #Only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index dd10147a..cb6b814e 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -31,35 +31,35 @@ Server function called: \code{expDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # compute exponential function of the 'PM_BMI_CONTINUOUS' variable ds.exp(x = "D$PM_BMI_CONTINUOUS", newobj = "exp.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Opal server is used (study1) + datasources = connections[1]) #only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.extractQuantiles.Rd b/man/ds.extractQuantiles.Rd index b5a2ddad..26308f61 100644 --- a/man/ds.extractQuantiles.Rd +++ b/man/ds.extractQuantiles.Rd @@ -56,7 +56,7 @@ otherwise left behind. These are not usually needed, but could be of value if one were investigating a problem with the ranking. FALSE: do not delete the residual objects} -\item{extract.datasources}{specifies the particular opal object(s) to use. +\item{extract.datasources}{specifies the particular connection object(s) to use. This is set via the argument in ds.ranksSecure. For more details see the associated document entitled "secure.global.ranking.docx". Also see the header file for ds.ranksSecure.} diff --git a/man/ds.forestplot.Rd b/man/ds.forestplot.Rd index 66606601..79b2c6dd 100644 --- a/man/ds.forestplot.Rd +++ b/man/ds.forestplot.Rd @@ -30,22 +30,21 @@ DataSHIELD \dontrun{ # Run a logistic regression + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.getWGSR.Rd b/man/ds.getWGSR.Rd index c5a8c932..17572520 100644 --- a/man/ds.getWGSR.Rd +++ b/man/ds.getWGSR.Rd @@ -90,29 +90,29 @@ data. \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/anthro/anthro1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "ANTHRO.anthro3", driver = "OpalDriver") + table = "ANTHRO.anthro2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Generate the weight-for-height (wfh) index diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index f3a872c1..a15d9f46 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -261,31 +261,31 @@ Server functions called: \code{glmDS1} and \code{glmDS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the GLM @@ -328,20 +328,17 @@ Server functions called: \code{glmDS1} and \code{glmDS2} builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.glmPredict.Rd b/man/ds.glmPredict.Rd index 1904e0fe..58b1483f 100644 --- a/man/ds.glmPredict.Rd +++ b/man/ds.glmPredict.Rd @@ -80,17 +80,17 @@ object on the serverside defaults to the name "predict_glm".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index 4ad3ab0f..9b3430a6 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -329,31 +329,31 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the GLM @@ -392,20 +392,17 @@ Server functions called: \code{glmSLMADS1}, \code{glmSLMADS2}, \code{glmSLMADS.a builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Fit the logistic regression model diff --git a/man/ds.glmSummary.Rd b/man/ds.glmSummary.Rd index f856c148..66b93eb6 100644 --- a/man/ds.glmSummary.Rd +++ b/man/ds.glmSummary.Rd @@ -17,17 +17,17 @@ object on the serverside defaults to "summary_glm.newobj".} \item{datasources}{specifies the particular 'connection object(s)' to use. e.g. if you have several data sets in the sources you are working with -called opals.a, opals.w2, and connection.xyz, you can choose which of +called connections.a, connections.w2, and connection.xyz, you can choose which of these to work with. The call 'datashield.connections_find()' lists all of the different datasets available and if one of these is called 'default.connections' that will be the dataset used by default if no other dataset is specified. If you wish to change the connections you wish to use by default the call -datashield.connections_default('opals.a') will set 'default.connections' -to be 'opals.a' and so in the absence of specific instructions to the contrary +datashield.connections_default('connections.a') will set 'default.connections' +to be 'connections.a' and so in the absence of specific instructions to the contrary (e.g. by specifying a particular dataset to be used via the -argument) all subsequent function calls will be to the datasets held in opals.a. +argument) all subsequent function calls will be to the datasets held in connections.a. If the argument is specified, it should be set without -inverted commas: e.g. datasources=opals.a or datasources=default.connections. +inverted commas: e.g. datasources=connections.a or datasources=default.connections. The argument also allows you to apply a function solely to a subset of the studies/sources you are working with. For example, the second source in a set of three, can be specified using a call such as datasources=connection.xyz[2]. diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 3af0a748..968fa6ae 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -231,28 +231,28 @@ Server function called: \code{glmerSLMADS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select all rows without missing values @@ -272,20 +272,17 @@ Server function called: \code{glmerSLMADS2} builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") + table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index 8d140321..56f2157f 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -127,28 +127,28 @@ Server function called: \code{heatmapPlotDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Compute the heat map plot diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 181e8ef6..428c062b 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -121,28 +121,28 @@ Server function called: \code{histogramDS2} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Compute the histogram diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 5afec642..0bb07cf8 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -36,25 +36,25 @@ Server function called: \code{isNaDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index eb4f4cd9..1ae16a1f 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -37,25 +37,25 @@ Server function called: \code{isValidDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 72add869..e0183073 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -47,25 +47,25 @@ Server function called: \code{lengthDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index da714bf5..21807efc 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -29,25 +29,25 @@ Server function called: \code{levelsDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.lexis.Rd b/man/ds.lexis.Rd index 45c0afc3..79d19b1f 100644 --- a/man/ds.lexis.Rd +++ b/man/ds.lexis.Rd @@ -166,31 +166,31 @@ Server functions called: \code{lexisDS1}, \code{lexisDS2} and \code{lexisDS3} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') # Example 1: Fitting GLM for survival analysis # For this analysis we need to load survival data from the server + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Example 1: Create the expanded data frame. diff --git a/man/ds.list.Rd b/man/ds.list.Rd index 424d1023..92e8b656 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -40,25 +40,25 @@ Server function called: \code{listDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.listDisclosureSettings.Rd b/man/ds.listDisclosureSettings.Rd index 23ab83fd..5ac64a61 100644 --- a/man/ds.listDisclosureSettings.Rd +++ b/man/ds.listDisclosureSettings.Rd @@ -75,27 +75,27 @@ Server function called: \code{listDisclosureSettingsDS} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Call to list current disclosure settings in all data repository servers diff --git a/man/ds.listOpals.Rd b/man/ds.listOpals.Rd index 2ad3784f..c06b47ca 100644 --- a/man/ds.listOpals.Rd +++ b/man/ds.listOpals.Rd @@ -16,7 +16,7 @@ all Opal objects in the analytic environment. } \details{ ds.listOpals calls the internal DataSHIELD function getOpals() which identifies -all Opal objects in the analytic environment. If there are no Opal servers in the analytic +all Opal objects in the analytic environment. If there are no Armadillo/Opal servers in the analytic environment ds.listOpalsIreminds the user that they have to login to a valid set of Opal login objects, if they wish to use DataSHIELD. If there is only one set of Opals, ds.listOpals copies that one set and names the copy 'default.opals'. This default set will then be used by diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 70d9ba5d..3706a4fb 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -33,28 +33,28 @@ This function does not call any server-side function. \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # List server-side functions diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index 197e1093..0e7d89ff 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -223,28 +223,28 @@ Server function called: \code{lmerSLMADS2} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cluster/CLUSTER_SLO1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CLUSTER.CLUSTER_SLO3", driver = "OpalDriver") + table = "CLUSTER.CLUSTER_SLO2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - #Log onto the remote Opal training servers + #Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Select all rows without missing values diff --git a/man/ds.log.Rd b/man/ds.log.Rd index a48ee6aa..caa01a93 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -34,29 +34,29 @@ Server function called: \code{logDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Calculating the log value of the 'PM_BMI_CONTINUOUS' variable @@ -64,7 +64,7 @@ Server function called: \code{logDS} ds.log(x = "D$PM_BMI_CONTINUOUS", base = exp(2), newobj = "log.PM_BMI_CONTINUOUS", - datasources = connections[1]) #only the first Opal server is used (study1) + datasources = connections[1]) #only the first server is used (study1) # clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 3cecb462..bacde6f3 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -45,25 +45,25 @@ The function is a wrapper for the DSI package function \code{datashield.aggregat ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index ae54bd5c..9df57306 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -87,25 +87,25 @@ Server function called: \code{lsDS}. ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.make.Rd b/man/ds.make.Rd index 5b361b83..f8af3eb6 100644 --- a/man/ds.make.Rd +++ b/man/ds.make.Rd @@ -88,25 +88,25 @@ The \code{ds.make} function is a wrapper for the DSI package function \code{data ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index c005e7ad..260dc286 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -84,25 +84,25 @@ Server function called: \code{matrixDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 6870ae60..a46acc8e 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -40,25 +40,25 @@ Server function called: \code{matrixDetDS2} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index c9f039f0..9a7fe7a0 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -38,25 +38,25 @@ Server function called: \code{matrixDetDS1} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index ab9385f1..f2a4342f 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -87,25 +87,25 @@ Server function called: \code{matrixDiagDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index 86311432..7a991500 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -44,25 +44,25 @@ Server function called: \code{matrixDimnamesDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 6159b4f3..b73d91df 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -35,25 +35,25 @@ Server function called: \code{matrixInvertDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index e43c83d4..10f4e658 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -40,25 +40,25 @@ Server function called: \code{matrixMultDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 55fcd239..bed688b5 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -37,25 +37,25 @@ Server function called: \code{matrixTransposeDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.mdPattern.Rd b/man/ds.mdPattern.Rd index b1bacc0b..d5273049 100644 --- a/man/ds.mdPattern.Rd +++ b/man/ds.mdPattern.Rd @@ -78,21 +78,25 @@ for disclosure control: \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index 9c7d7e78..2e6cc9f3 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -80,25 +80,25 @@ Server function called: \code{meanDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index f60ba7a4..592de07c 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -55,25 +55,25 @@ parameter \code{datasources}. ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() diff --git a/man/ds.meanSdGp.Rd b/man/ds.meanSdGp.Rd index 11501f72..768bab71 100644 --- a/man/ds.meanSdGp.Rd +++ b/man/ds.meanSdGp.Rd @@ -93,25 +93,25 @@ Server function called: \code{meanSdGpDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.merge.Rd b/man/ds.merge.Rd index a99b0732..15be0af3 100644 --- a/man/ds.merge.Rd +++ b/man/ds.merge.Rd @@ -93,25 +93,25 @@ Server function called: \code{mergeDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.message.Rd b/man/ds.message.Rd index ab1dff8d..9a99f1da 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -45,25 +45,25 @@ Server function called: \code{messageDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index 0e704042..e38d0e58 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -28,25 +28,25 @@ which are non-disclosive. \examples{ \dontrun{ - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.names.Rd b/man/ds.names.Rd index 984e2596..9a00feb9 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -38,25 +38,25 @@ is formally of class "glm" and "ls" but responds TRUE to is.list(), ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index bae29ca8..76abbc4f 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -33,25 +33,25 @@ Server function called: \code{numNaDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 01cb36df..e703e0d2 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -49,25 +49,25 @@ Server functions called: \code{quantileMeanDS}, \code{length} and \code{numNaDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index 7642073a..a8423c5a 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -82,39 +82,39 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. \examples{ \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - #Generating the vectors in the Opal servers - ds.rBinom(samp.size=c(13,20,25), #the length of the vector created in each source is different - size=c(10,23,5), #Bernoulli trials change in each source - prob=c(0.6,0.1,0.5), #Probability changes in each source + #Generating the vectors in the servers + ds.rBinom(samp.size=c(13,20), #the length of the vector created in each source is different + size=c(10,23), #Bernoulli trials change in each source + prob=c(0.6,0.1), #Probability changes in each source newobj="Binom.dist", seed.as.integer=45, return.full.seed.as.set=FALSE, - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rBinom(samp.size=15, @@ -123,7 +123,7 @@ Server functions called: \code{rBinomDS} and \code{setSeedDS}. newobj="Binom.dist", seed.as.integer=324, return.full.seed.as.set=FALSE, - datasources=connections[2]) #only the second Opal server is used ("study2") + datasources=connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rNorm.Rd b/man/ds.rNorm.Rd index c278d757..c1cd7bc1 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -95,41 +95,41 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers + # Generating the vectors in the servers - ds.rNorm(samp.size=c(10,20,45), #the length of the vector created in each source is different - mean=c(1,6,4), #the mean of the Normal distribution changes in each server - sd=c(1,4,3), #the sd of the Normal distribution changes in each server + ds.rNorm(samp.size=c(10,20), #the length of the vector created in each source is different + mean=c(1,6), #the mean of the Normal distribution changes in each server + sd=c(1,4), #the sd of the Normal distribution changes in each server newobj="Norm.dist", seed.as.integer=2345, return.full.seed.as.set=FALSE, - force.output.to.k.decimal.places=c(4,5,6), #output random numbers have different + force.output.to.k.decimal.places=c(4,5), #output random numbers have different #decimal quantity in each source - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rNorm(samp.size=10, @@ -139,7 +139,7 @@ Server functions called: \code{rNormDS} and \code{setSeedDS}. seed.as.integer=2345, return.full.seed.as.set=FALSE, force.output.to.k.decimal.places=1, - datasources=connections[2]) #only the second Opal server is used ("study2") + datasources=connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index dc216bd8..5a30eee5 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -78,43 +78,43 @@ Server functions called: \code{rPoisDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers - ds.rPois(samp.size=c(13,20,25), #the length of the vector created in each source is different - lambda=c(2,3,4), #different mean per interval (2,3,4) in each source + # Generating the vectors in the servers + ds.rPois(samp.size=c(13,20), #the length of the vector created in each source is different + lambda=c(2,3), #different mean per interval (2,3) in each source newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections) #all the Opal servers are used, in this case 3 + datasources=connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rPois(samp.size=13, lambda=5, newobj="Pois.dist", seed.as.integer=1234, return.full.seed.as.set=FALSE, - datasources=connections[1]) #only the first Opal server is used ("study1") + datasources=connections[1]) #only the first server is used ("study1") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index 622c4437..234c0d9f 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -101,40 +101,40 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") - # Generating the vectors in the Opal servers + # Generating the vectors in the servers - ds.rUnif(samp.size = c(12,20,4), #the length of the vector created in each source is different - min = c(0,2,5), #different minumum value of the function in each source - max = c(2,5,9), #different maximum value of the function in each source + ds.rUnif(samp.size = c(12,20), #the length of the vector created in each source is different + min = c(0,2), #different minumum value of the function in each source + max = c(2,5), #different maximum value of the function in each source newobj = "Unif.dist", seed.as.integer = 234, return.full.seed.as.set = FALSE, - force.output.to.k.decimal.places = c(1,2,3), - datasources = connections) #all the Opal servers are used, in this case 3 + force.output.to.k.decimal.places = c(1,2), + datasources = connections) #all the servers are used, in this case 2 #(see above the connection to the servers) ds.rUnif(samp.size = 12, @@ -144,7 +144,7 @@ Server functions called: \code{rUnifDS} and \code{setSeedDS}. seed.as.integer = 12345, return.full.seed.as.set = FALSE, force.output.to.k.decimal.places = 2, - datasources = connections[2]) #only the second Opal server is used ("study2") + datasources = connections[2]) #only the second server is used ("study2") # Clear the Datashield R sessions and logout datashield.logout(connections) diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index 48315a37..63eb3b20 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -63,40 +63,40 @@ Server functions called: \code{rbindDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Combining R objects by rows ds.rbind(x = "D", #data frames in the server-side to be conbined - #(see above the connection to the Opal servers) + #(see above the connection to the servers) DataSHIELD.checks = FALSE, force.colnames = NULL, newobj = "D.rbind", # name for the output object that is stored in the data servers - datasources = connections, # All Opal servers are used - #(see above the connection to the Opal servers) + datasources = connections, # All servers are used + #(see above the connection to the servers) notify.of.progress = FALSE) # Clear the Datashield R sessions and logout diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index 7b032112..fc40cdcb 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -73,28 +73,28 @@ Server function called: \code{reShapeDS} \dontrun{ ## Version 6, for version 5 see Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/survival/EXPAND_NO_MISSING1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver") + table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Reshape server-side grouped data diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index 4fbf3402..0faa5407 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -44,25 +44,25 @@ Server function called: \code{levels()} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index 8dd60bb3..7a602591 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -59,25 +59,25 @@ Server function called: \code{recodeValuesDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index caf7e9b4..8284ffbe 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -66,28 +66,28 @@ Server function called: \code{repDS}. \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index f73a3ab5..9058b7b0 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -46,28 +46,28 @@ Server function called: \code{replaceNaDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Replace missing values in variable 'LAB_HDL' by the mean value @@ -80,7 +80,7 @@ Server function called: \code{replaceNaDS} # Replace the missing values using the mean for each study ds.replaceNA(x = "D$LAB_HDL", - forNA = list(mean[[1]][1], mean[[1]][2], mean[[1]][3]), + forNA = list(mean[[1]][1], mean[[1]][2]), newobj = "HDL.noNA", datasources = connections) @@ -93,7 +93,7 @@ Server function called: \code{replaceNaDS} # Replace the missing values with 999s ds.replaceNA(x = "D$PM_BMI_CATEGORICAL", - forNA = c(999,999,999), + forNA = c(999,999), newobj = "bmi999") # Check if the NAs have been replaced correctly diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index a6378621..2988826a 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -42,25 +42,25 @@ Server function called: \code{rmDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index 67818472..81fbfdbe 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -39,29 +39,29 @@ Server functions called: \code{classDS}, \code{dimDS} and \code{colnamesDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() myvar <- list("LAB_TSC","LAB_HDL") - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, variables = myvar, symbol = "D") diff --git a/man/ds.sample.Rd b/man/ds.sample.Rd index 2f801edc..bd6e893e 100644 --- a/man/ds.sample.Rd +++ b/man/ds.sample.Rd @@ -53,7 +53,7 @@ If is set as 0 all sources will start with the seed value If you want to use the same starting seed in all studies but do not wish it to be 0, you can specify a non-zero scalar value for and then use the argument to generate the random number vectors one source at -a time (e.g. ,datasources=default.opals[2] to generate the random vector in source 2). +a time (e.g. ,datasources=default.connections[2] to generate the random vector in source 2). As an example, if the value is 78326 then the seed in each source will be set at 78326*1 = 78326 because the vector of datasources being used in each call to the function will always be of length 1 and so the @@ -75,15 +75,15 @@ For further details see help for \code{sample} in native R.} \item{newobj}{This a character string providing a name for the output data.frame which defaults to 'newobj.sample' if no name is specified.} -\item{datasources}{specifies the particular opal object(s) to use. If the -argument is not specified the default set of opals will be used. The default opals -are called default.opals and the default can be set using the function -\code{ds.setDefaultOpals}. If the is to be specified, it should be set without -inverted commas: e.g. datasources=opals.em or datasources=default.opals. If you wish to -apply the function solely to e.g. the second opal server in a set of three, -the argument can be specified as: e.g. datasources=opals.em[2]. -If you wish to specify the first and third opal servers in a set you specify: -e.g. datasources=opals.em[c(1,3)]} +\item{datasources}{specifies the particular connection object(s) to use. If the +argument is not specified the default set of servers will be used. The default servers +are called default.connections and the default can be set using the function +\code{DSI::datashield.connections_default}. If the is to be specified, it should be set without +inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to +apply the function solely to e.g. the second server in a set of three, +the argument can be specified as: e.g. datasources=connections.em[2]. +If you wish to specify the first and third servers in a set you specify: +e.g. datasources=connections.em[c(1,3)]} \item{notify.of.progress}{specifies if console output should be produce to indicate progress. The default value for notify.of.progress is FALSE.} diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index 984cd329..9391dc8e 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -107,27 +107,27 @@ Server function called: \code{scatterPlotDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Example 1: generate a scatter plot for each study separately diff --git a/man/ds.seq.Rd b/man/ds.seq.Rd index 5ce61545..b7ce7a8a 100644 --- a/man/ds.seq.Rd +++ b/man/ds.seq.Rd @@ -92,28 +92,28 @@ Server function called: \code{seqDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Create 3 different sequences diff --git a/man/ds.setSeed.Rd b/man/ds.setSeed.Rd index c8b52a69..b4070a92 100644 --- a/man/ds.setSeed.Rd +++ b/man/ds.setSeed.Rd @@ -60,28 +60,28 @@ Server function called: \code{setSeedDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Generate a pseudorandom number in the server-side diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index cb74c721..6bd629be 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -36,7 +36,7 @@ and the number of valid observations. } \description{ This function calculates the skewness of a numeric variable -that is stored on the server-side (Opal server). +that is stored on the server-side (server). } \details{ This function is similar to the function \code{skewness} in R package \code{e1071}. @@ -65,25 +65,25 @@ Server functions called: \code{skewnessDS1} and \code{skewnessDS2} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index 95b5432c..767f9894 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -35,29 +35,29 @@ specified by the user through the argument \code{newobj}, otherwise is named by \examples{ \dontrun{ - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") # Example 1: Get the square root of LAB_HDL variable diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index 3e8da4f9..63753c15 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -38,28 +38,28 @@ server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} ## Version 6, for version 5 see the Wiki - # Connecting to the Opal servers + # Connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() - # Log onto the remote Opal training servers + # Log onto the remote Armadillo/Opal training servers connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") #Calculate the summary of a numeric variable diff --git a/man/ds.tapply.Rd b/man/ds.tapply.Rd index 5c764c2b..bd281d62 100644 --- a/man/ds.tapply.Rd +++ b/man/ds.tapply.Rd @@ -100,25 +100,25 @@ Server function called: \code{tapplyDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.tapply.assign.Rd b/man/ds.tapply.assign.Rd index 908a1555..7f09c6ca 100644 --- a/man/ds.tapply.assign.Rd +++ b/man/ds.tapply.assign.Rd @@ -105,25 +105,25 @@ Server function called: \code{ds.tapply.assign} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index ae0fb40d..47e9406d 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -36,25 +36,25 @@ Server function called: \code{testObjExistsDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 41f1665a..5a36dc26 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -43,25 +43,25 @@ Server function called: \code{unListDS} \dontrun{ ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index 18d77005..e1d6e81d 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -29,25 +29,25 @@ Server function called: \code{uniqueDS} } \examples{ \dontrun{ - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 86a89fd9..cfe9272e 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -60,25 +60,25 @@ Server function called: \code{varDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") diff --git a/man/subsetHelper.Rd b/man/subsetHelper.Rd index 6922ec94..fb6c9a99 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -38,25 +38,25 @@ Server function called: \code{dimDS} ## Version 6, for version 5 see the Wiki - # connecting to the Opal servers + # connecting to the Armadillo/Opal servers require('DSI') + require('DSMolgenisArmadillo') require('DSOpal') require('dsBaseClient') + armadillo_url <- "http://192.168.56.100:8080/" + token <- armadillo.get_credentials(armadillo_url) builder <- DSI::newDSLoginBuilder() builder$append(server = "study1", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM1", driver = "OpalDriver") + url = armadillo_url, + token = token@access_token, + table = "datashield/cnsim/CNSIM1", driver = "ArmadilloDriver") builder$append(server = "study2", - url = "http://192.168.56.100:8080/", - user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM2", driver = "OpalDriver") - builder$append(server = "study3", - url = "http://192.168.56.100:8080/", + url = "https://192.168.56.100:8443/", user = "administrator", password = "datashield_test&", - table = "CNSIM.CNSIM3", driver = "OpalDriver") + table = "CNSIM.CNSIM2", driver = "OpalDriver", + options = "list(ssl_verifyhost=0, ssl_verifypeer=0)") logindata <- builder$build() connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")