Initial commit.

UnCover_DS_Workshop0_code.R

+############################################################
+###          DS ANALYSIS ENVIRONMENT: SET UP             ###
+############################################################
+
+# List of required packages
+packages = c("DSI", 
+             "DSOpal", 
+             "dsBaseClient", 
+             "ggplot2")
+
+# Requirement exclusive of Windows Systems
+if(Sys.info()["sysname"] == "Windows"){
+  packages[length(packages)+1] = "Rtools"
+}
+
+# This loop checks whether or not the required packages are already installed or not, and only executes the installation procedure in negative case.
+for(p in packages){
+  
+  print(sprintf("Checking package %s", p))
+  
+  # This condition check whether or not package 'p' is already installed.
+  if(require(p, character.only = T) == FALSE){
+    
+    installation_repo <- "http://cran.us.r-project.org"
+    
+    # dsBaseClient package requires an specific repository to be installed from.
+    if(p == "dsBaseClient"){
+      
+      installation_repo <- "http://cran.obiba.org"
+    }
+    
+    install.packages(p, repos = installation_repo, dependencies = TRUE)
+  }
+  
+  
+  # Load packages (Rtools only requires installation, not loading).
+  if(p != "Rtools"){
+  
+      library(p, character.only = T)
+  }   
+  
+}
+
+
+############################################################
+############################################################
+###           CONNECTING TO 1+ DATA SOURCES              ###
+############################################################
+
+# Variables to be set prior to any execution
+
+urls <- c( "http://192.168.1.50:8880",# UPM's test server 
+          "http://192.168.1.101:8888") # Baskent University
+
+project_names <- c("DRAFT_TEST",
+                   "DRAFT_TEST")
+
+view_names <- c("DRAFT_VIEW",
+                "DRAFT_TEST")
+
+users <- c("administrator",
+           "DRAFT_TEST")
+
+passwords <- c("password",
+               "DRAFT_TEST")
+
+# Name for the dataframe to generate on server side. It will contain the aggregation of data from all sources. Not locally available.
+myDFName <- "D"
+
+# Variable in which connections to each server will be stored.
+builder <- DSI::newDSLoginBuilder()
+
+url_ctr <- 0
+# This loop will add each server-connection configuration to the "builder" variable.
+for(i in 1:length(urls)){
+  
+  print(sprintf("Connecting to Server with URL: %s", urls[i]))
+  
+  builder$append(server = sprintf("study%s", url_ctr), url = urls[i],
+                 user = users[i], password = passwords[i],
+                 table = sprintf("%s.%s", project_names[i], view_names[i]),
+                 driver = "OpalDriver", options="list(ssl_verifyhost=0,ssl_verifypeer=0)")
+  
+  url_ctr <- url_ctr+1
+}
+
+# Set up the connections previously defined and stored in "builder". Also, store data aggregation on server-side dataframe with name "myDFName".
+logindata <- builder$build()
+connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = myDFName)
+
+
+############################################################
+############################################################
+###                    CUSTOM QUERIES                    ###
+############################################################
+
+mycustom_f  <- function (x = NULL, datasources = NULL){
+  
+  if (is.null(datasources)) {
+    datasources <- datashield.connections_find()
+  }
+  
+  if (!(is.list(datasources) && all(unlist(lapply(datasources, 
+                                                  function(d) {
+                                                    methods::is(d, "DSConnection")
+                                                  }))))) {
+    
+    stop("The 'datasources' were expected to be a list of DSConnection-class objects", call. = FALSE)
+  }
+  
+  if (is.null(x)) {
+    
+    stop("Please provide the name of a data.frame or matrix!", call. = FALSE)
+  }
+  
+  cally <- call("TEST", x)
+  
+  dimensions <- DSI::datashield.aggregate(datasources, cally)
+  
+  stdnames <- names(datasources)
+  
+  outputnames <- c()
+  for (i in 1:length(datasources)) {
+    outputnames[i] <- paste0("dimensions of ", x, " in ", stdnames[i])
+  }
+  
+  global.dim1 <- 0
+  global.dim2 <- dimensions[[1]][2]
+  
+  for (i in 1:length(datasources)) {
+    global.dim1 <- global.dim1 + dimensions[[i]][1]
+  }
+  pooled.dim <- list(c(global.dim1, global.dim2))
+  
+  out <- c(dimensions, pooled.dim)
+  names(out) <- c(outputnames, paste0("dimensions of ", 
+                                      x, " in combined studies"))
+
+  return(out)
+}
+
+
+############################################################
+############################################################
+###                    BASIC QUERIES                     ###
+############################################################
+
+# Inspect dimensions of each data source
+dim_info <- ds.dim(x="D", datasources= connections)
+
+# Inspect variables stored in each data source
+colname_info <- ds.colnames(x="D", datasources= connections)
+
+# Get info about data types in each data source
+variables_type_inspect <- c("DMRAGEYR", "DMRGENDR")
+variable_type_info <- c()
+for(var in variables_type_inspect){
+  
+  variable_type_info[length(variable_type_info)+1] <-
+    ds.class(x=sprintf("%s$%s", myDFName, var), datasources = connections)
+}
+
+# Numeric-specific functions
+ds.mean(x=sprintf("%s$DMRAGEYR", myDFName), datasources = connections)
+
+ds.quantileMean(x=sprintf("%s$DMRAGEYR", myDFName), datasources = connections[1])
+
+# Categorical-specific functions
+ds.table(sprintf("%s$DMRGENDR", myDFName), datasources = connections)
+
+
+############################################################
+############################################################
+###        BASIC MACHINE LEARNING - LINEAR MODEL         ###
+############################################################
+
+ds.scatterPlot(x = sprintf("%s$DMRAGEYR", myDFName), y = sprintf("%s$DATLGT", myDFName), datasources = connections)
+ds.boxPlot(x = sprintf("%s$DMRAGEYR", myDFName), datasources = connections)
+
+linear_model = ds.glmSLMA(formula = sprintf("%s$DMRAGEYR~%s$DATLGT", myDFName, myDFName), family = "gaussian", datasources = connections, newobj = "ws")
+
+
+############################################################
+############################################################
+###                       LOG-OUT                        ###
+############################################################
+
+# Always execute this command after closing your IDE to free server-side resources.
+datashield.logout(connections) 

UnCover_DS_Workshop1_code.R

+############################################################
+###          DS ANALYSIS ENVIRONMENT: SET UP             ###
+############################################################
+
+# List of required packages
+packages = c("DSI", 
+             "DSOpal", 
+             "dsBaseClient", 
+             "ggplot2")
+
+# Requirement exclusive of Windows Systems
+if(Sys.info()["sysname"] == "Windows"){
+  packages[length(packages)+1] = "Rtools"
+}
+
+# This loop checks whether or not the required packages are already installed or not, and only executes the installation procedure in negative case.
+for(p in packages){
+  
+  print(sprintf("Checking package %s", p))
+  
+  # This condition check whether or not package 'p' is already installed.
+  if(require(p, character.only = T) == FALSE){
+    
+    installation_repo <- "http://cran.us.r-project.org"
+    
+    # dsBaseClient package requires an specific repository to be installed from.
+    if(p == "dsBaseClient"){
+      
+      installation_repo <- "http://cran.obiba.org"
+    }
+    
+    install.packages(p, repos = installation_repo, dependencies = TRUE)
+  }
+  
+  
+  # Load packages (Rtools only requires installation, not loading).
+  if(p != "Rtools"){
+    
+    library(p, character.only = T)
+  }   
+  
+}
+
+
+############################################################
+############################################################
+###           CONNECTING TO 1+ DATA SOURCES              ###
+############################################################
+
+# Variables to be set prior to any execution
+
+urls <- c("https://uncover.itg.be")
+
+project_names <- c("name of your project")
+
+resource_names <- c("name of your resource")
+
+users <- c("administrator")
+
+passwords <- c("your password")
+
+
+# Variable in which connections to each server will be stored.
+builder <- DSI::newDSLoginBuilder()
+
+url_ctr <- 0
+# This loop will add each server-connection configuration to the "builder" variable.
+for(i in 1:length(urls)){
+  
+  print(sprintf("Connecting to Server with URL: %s", urls[i]))
+  
+  builder$append(server = sprintf("study%s", url_ctr), url = urls[i],
+                 user = users[i], password = passwords[i],
+                 resource = sprintf("%s.%s", project_names[i], resource_names[i]),
+                 driver = "OpalDriver", options="list(ssl_verifyhost=0,ssl_verifypeer=0)")
+  
+  url_ctr <- url_ctr+1
+}
+
+# Set up the connections previously defined and stored in "builder". Also, store data aggregation on server-side dataframe with name "myDFName".
+logindata <- builder$build()
+connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
+
+datashield.assign.expr(connections, symbol = 'data', expr = quote(as.resource.data.frame(D)))
+
+
+ds.colnames(x='data', datasources= connections)
+
+ds.class('data$DMRAGEYR', datasources = connections)
+############################################################
+############################################################
+###                       LOG-OUT                        ###
+############################################################
+
+# Always execute this command after closing your IDE to free server-side resources.
+datashield.logout(connections) 
+