########### ### 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)