script peñalvo

20230411_Script_Connections.R

+
+###########
+### CONNECTING TO unCoVer OPAL SERVERS ###
+### Last edit: 20230120/JP
+###########
+
+#RStudio 2022.12.0+353 [Mac OS Monterey 12.6.3]
+
+.rs.restartR()
+
+###########
+###1. install required packages [You only need to install this the first time]
+###2. make sure you are connected to Open VPN ONLY and check which hospitals are unavailable from daily email
+###3. prep login to the servers (# servers that are down, or those that doesn't interest)
+###4. login
+###5. check available project/resources per partner (and logout) 
+###6. printing connection's details
+###7. specify paths to resources (comment out those that are not available or not interested)
+###8. resolve object to load datasets
+###9. describe uploads
+###10. logout from all servers 
+###########
+
+###1. install required packages [You only need to install this the first time]
+
+# install.packages("devtools")
+
+# devtools::install_version("opalr", version = "3.1.0", repos = 'https://cran.r-project.org/')
+# devtools::install_version("DSI", version = "1.4.0", repos = 'https://cran.r-project.org/')
+# devtools::install_version("DSOpal", version = "1.3.0", repos = 'https://cran.r-project.org/')
+# devtools::install_github("datashield/dsBaseClient", "6.1.1")
+# devtools::install_github("lifecycle-project/ds-helper", "0.4.12")
+# devtools::install_github("neelsoumya/dsSurvivalClient")
+# devtools::install_github("transbioZI/dsMTLClient")
+# devtools::install_github("isglobal-brge/dsDatesClient")
+
+# load the required libraries
+
+library(DSI)
+library(DSOpal)
+library(dsBaseClient)
+library(httr)
+
+###2. make sure you are connected to Open VPN ONLY and check which hospitals are unavailable from daily email
+
+# not available on 20230120:
+
+# Hospital_Princesa
+# Hospital_CIPH
+# Hospital_TU
+# Hospital_SMUC
+# Hospital_ASPEUR
+# Hospital_Oporto
+# Hospital_UDEA
+
+###3. prep login to the servers (# servers that are down, or those that doesnt interest)
+
+builder <- DSI::newDSLoginBuilder()
+
+#### BELGIUM ####
+builder$append(server = "UZA", url = "https://uncover.itg.be", user = "emertens", password = "3^z4AV.)hG5~PT/]")
+
+#### BRAZIL ##
+builder$append(server = "ASPEUR", url = "https://uncover.itg.be", user = "emertens", password = "3^z4AV.)hG5~PT/]")
+
+#### BOSNIA ####
+#builder$append(server = "UNSA_Inpatient", url = "https://192.168.1.200:8008", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### COLOMBIA ####
+#builder$append(server = "UDEA", url = "https://fenfisdi.udea.edu.co/opal", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### CROATIA ####
+#builder$append(server = "CIPH", url = "https://192.168.1.200:8002", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "INANTRO", url = "https://192.168.1.200:8007", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### ITALY ####
+#builder$append(server = "Sacrocuore_emergency", url = "https://192.168.1.50:8890", user = "user_analisis", password = "Ekfl07UUgz")
+#builder$append(server = "Sacrocuore_employees", url = "https://192.168.1.50:8890", user = "user_analisis", password = "Ekfl07UUgz")
+#builder$append(server = "Sacrocuore_Verona", url = "https://192.168.1.50:8890", user = "user_analisis", password = "Ekfl07UUgz")
+#builder$append(server = "Sacrocuore_ISARIC", url = "https://192.168.1.50:8890", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "ULSS6", url = "https://opal.aulss6.veneto.it", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### IRELAND ####
+builder$append(server = "TUDublin", url = "https://uncover.itg.be", user = "emertens", password = "3^z4AV.)hG5~PT/]")
+
+#### LUXEMBOURG ###
+
+
+#### PORTUGAL ####
+#builder$append(server = "Porto", url = "https://192.168.1.102", user = "user_analisis", password = "Ekfl07UUgz")
+#builder$append(server = "Coimbra", url = "https://uncover.itg.be", user = "emertens", password = "3^z4AV.)hG5~PT/]")
+
+#### ROMANIA ####
+builder$append(server = "UMF_Iasi", url = "https://192.168.1.200:8003", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "UMF_Cluj", url = "https://192.168.1.200:8005", user = "user_analisis", password = "Ekfl07UUgz")
+
+### SLOVAKIA ###
+builder$append(server = "TU", url = "https://192.168.1.200:8004", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### SPAIN ####
+builder$append(server = "hm_hospitales", url = "https://192.168.1.50:9002", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "FJD", url = "https://uncover.itg.be", user = "emertens", password = "3^z4AV.)hG5~PT/]")
+builder$append(server = "UNAV", url = "https://192.168.1.50:9001", user = "user_analisis", password = "Ekfl07UUgz")
+#builder$append(server = "princesa", url = "https://192.168.1.200:8001", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### TURKEY ####
+builder$append(server = "Ankara_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Ankara_outpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Ankara_icu_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Ankara_icu_outpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Konya_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Instanbul_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Instanbul_outpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Izmir_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Alanya_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Alanya_outpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Adana_inpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+builder$append(server = "Adana_outpatient", url = "https://192.168.1.101:8443", user = "user_analisis", password = "Ekfl07UUgz")
+
+#### UK ####
+#builder$append(server = "SMUC", url = "https://192.168.1.200:8006", user = "user_analisis", password = "Ekfl07UUgz")
+
+###4.login
+
+logindata <- builder$build()
+set_config(config(ssl_verifypeer = 0L, ssl_verifyhost = 0L))
+connections <- DSI::datashield.login(logins = logindata, failSafe = T)
+
+###6. printing connection's details
+#connections 
+
+###7. specify paths to resources (comment out those that are not available or not interested)
+
+### BELGIUM ###
+DSI::datashield.assign.resource(connections$UZA, "resource", "UZA.20220919_UZA")
+
+### BOSNIA ###
+#DSI::datashield.assign.resource(connections$UNSA_Inpatient, "resource", "UnCoVer-BiH-Final.20220919_UNSAInpatient")
+
+### BRAZIL ###
+DSI::datashield.assign.resource(connections$ASPEUR, "resource", "ASPEUR.20220919_ASPEUR")
+
+### COLOMBIA ###
+# DSI::datashield.assign.resource(connections$UDEA, "resource", "INS_Data.colombia_all")
+
+### CROATIA ###
+DSI::datashield.assign.resource(connections$INANTRO, "resource", "INANTRO.20220919_INANTRO")
+
+### ITALY ###
+#DSI::datashield.assign.resource(connections$Sacrocuore_Verona, "resource", "S_uncover.20220919_Verona")
+#DSI::datashield.assign.resource(connections$Sacrocuore_emergency, "resource", "S_uncover.20220919_SacroCuoreEmergency")
+#DSI::datashield.assign.resource(connections$Sacrocuore_employees, "resource", "S_uncover.employees")
+#DSI::datashield.assign.resource(connections$Sacrocuore_ISARIC, "resource", "S_uncover.20220919_ISARIC")
+#DSI::datashield.assign.resource(connections$ULSS6, "resource", "ULSS6.20220919_ULSS6")
+
+### IRELAND ###
+DSI::datashield.assign.resource(connections$TUDublin, "resource", "TUDublin.20220919_TUDublin")
+
+### LUXEMBOURG ###
+
+### PORTUGAL ###
+# DSI::datashield.assign.resource(connections$Porto, "resource", "uncover-up.Resource_derived")
+# DSI::datashield.assign.resource(connections$Coimbra, "resource", "IPC.IPC_Harmonised")
+
+### ROMANIA ###
+DSI::datashield.assign.resource(connections$UMF_Iasi, "resource", "umfiasi.20220919_UMFIasi")
+DSI::datashield.assign.resource(connections$UMF_Cluj, "resource", "UMF_Cluj.Romania")
+
+### SPAIN ###
+DSI::datashield.assign.resource(connections$hm_hospitales, "resource", "FiHM.20220919_FiHM")
+DSI::datashield.assign.resource(connections$UNAV, "resource", "unCOVer-UNAV.20230411_UNAV")
+DSI::datashield.assign.resource(connections$FJD, "resource", "IISFJD.20220919_IISFJD")
+
+### SLOVAKIA ###
+DSI::datashield.assign.resource(connections$TU, "resource", "TU_Uncover.20220919_TU")
+
+### TURKEY ###
+DSI::datashield.assign.resource(connections$Ankara_inpatient, "resource", "BU.20230423_ankara_inpatient")
+DSI::datashield.assign.resource(connections$Ankara_outpatient, "resource", "BU.20230423_ankara_outpatient")
+DSI::datashield.assign.resource(connections$Ankara_icu_inpatient, "resource", "BU.20230423_ankara_icu_inpatient")
+DSI::datashield.assign.resource(connections$Ankara_icu_outpatient, "resource", "BU.20230423_ankara_icu_outpatient")
+DSI::datashield.assign.resource(connections$Konya_inpatient, "resource", "BU.20230423_konya_inpatient")
+DSI::datashield.assign.resource(connections$Instanbul_inpatient, "resource", "BU.20230423_istanbul_inpatient")
+DSI::datashield.assign.resource(connections$Instanbul_outpatient, "resource", "BU.20230423_istanbul_outpatient")
+DSI::datashield.assign.resource(connections$Izmir_inpatient, "resource", "BU.20230423_izmir_inpatient")
+DSI::datashield.assign.resource(connections$Alanya_inpatient, "resource", "BU.20230423_alanya_inpatient")
+DSI::datashield.assign.resource(connections$Alanya_outpatient, "resource", "BU.20230423_alanya_outpatient")
+DSI::datashield.assign.resource(connections$Adana_inpatient, "resource", "BU.20230423_adana_inpatient")
+DSI::datashield.assign.resource(connections$Adana_outpatient, "resource", "BU.20230423_adana_outpatient")
+
+### UK ###
+# DSI::datashield.assign.resource(connections$SMUC, "resource", "SMUC.20220919_SMUC")
+
+
+###8. resolve object to load datasets
+
+DSI::datashield.assign.expr(conns = connections, symbol = "data", 
+                            expr = "as.resource.data.frame(resource)")
+
+###9. describe uploads
+
+ds.class("data")
+ds.dim("data")
+
+###10. logout from all servers [after done with analysis, this is NEEDED]
+
+datashield.logout(connections)
+
+# Log out Hospital by hospital
+# datashield.logout(connections$hm_hospitales)
+# datashield.logout(connections$princesa)
+# datashield.logout(connections$CIPH)
+# datashield.logout(connections$Porto)
+# datashield.logout(connections$Ankara_inpatient)
+# datashield.logout(connections$Ankara_outpatient)
+# datashield.logout(connections$Konya_inpatient)
+# datashield.logout(connections$Konya_outpatient)
+# datashield.logout(connections$Instanbul_outpatient)
+# datashield.logout(connections$Instanbul_inpatient)
+# datashield.logout(connections$Izmir_inpatient)
+# datashield.logout(connections$Izmir_outpatient)
+# datashield.logout(connections$Alanya_inpatient)
+# datashield.logout(connections$Alanya_outpatient)
+# datashield.logout(connections$Adana_inpatient)
+# datashield.logout(connections$UMF_Iasi)
+# datashield.logout(connections$Sacrocuore_Verona)
+# datashield.logout(connections$Sacrocuore_emergency)
+# datashield.logout(connections$Sacrocuore_employees)
+# datashield.logout(connections$Sacrocuore_ISARIC)
+# datashield.logout(connections$UDEA)
+# datashield.logout(connections$FJD)
+# datashield.logout(connections$Coimbra)
+# datashield.logout(connections$UNAV)
+# datashield.logout(connections$SMUC)
+# datashield.logout(connections$TU)
+# datashield.logout(connections$TUDublin)
+# datashield.logout(connections$UNSA_Inpatient)
+# datashield.logout(connections$UNSA_Outpatient)
+# datashield.logout(connections$UZA)
+# datashield.logout(connections$INANTRO)
+# datashield.logout(connections$UMF_Cluj)
+# datashield.logout(connections$ULSS6)

remote_execute_as_admin.R

 # load opal library
 library(opalr)
 
-o <- opal.login('opal_admin','nK5&@WC1A13M', url = 'https://opal.aulss6.veneto.it')
+o <- opal.login('pepe','7G9b!!2IyJs$', url = 'https://uncover.itg.be')
 
 
 dir_name <- readline("Introduce the name of the directory please: ")
 
 setwd(dir_name)
 
+file_name <- readline("Introduce the name of the file to check the values: ")
+harmonized_data <- ""
+
+setwd(paste(dir_name ,"/harmonized_data", sep=""))
+
+if (grepl(".csv" , file_name , fixed = TRUE)){
+  harmonized_data <- read.csv(file_name)
+  #harmonized_data <- read.csv(file_name, sep = ";")
+}else if (grepl(".xlsx" , file_name , fixed = TRUE)){
+  harmonized_data <- read.xlsx(file_name)
+}
+
+#opal.assign.resource(o , "harmonized_data" , "UZA.20220919_UZA" )
+#opal.assign.resource(o , "harmonized_data_2" , "ASPEUR.20220919_ASPEUR" )
+#opal.execute(o, "class(harmonized_data)")
+#opal.execute(o, "class(harmonized_data_2)")
+
+
+
+
 rval <- opal.execute.source(o, paste(dir_name , "script.R" , sep = "/"))

script.R

-packageVersion("dsDates")
+paste("hola" , dim.data.frame(harmonized_data_2) , collapse = " ")