| 
																	
																	
																		
																			
																		
																	
																	
																 | 
																@ -2,7 +2,6 @@ library(shiny) | 
															
														
														
													
														
															
																 | 
																 | 
																library(rhandsontable) | 
																 | 
																 | 
																library(rhandsontable) | 
															
														
														
													
														
															
																 | 
																 | 
																
 | 
																 | 
																 | 
																
 | 
															
														
														
													
														
															
																 | 
																 | 
																print(getwd()) | 
																 | 
																 | 
																print(getwd()) | 
															
														
														
													
														
															
																 | 
																 | 
																print(file) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																source("../sqlFunctions.R", encoding = "UTF-8") | 
																 | 
																 | 
																source("../sqlFunctions.R", encoding = "UTF-8") | 
															
														
														
													
														
															
																 | 
																 | 
																
 | 
																 | 
																 | 
																
 | 
															
														
														
													
														
															
																 | 
																 | 
																DF<-data.frame("NHC"="","Samples"="") | 
																 | 
																 | 
																DF<-data.frame("NHC"="","Samples"="") | 
															
														
														
													
												
													
														
															
																| 
																	
																	
																	
																		
																			
																		
																	
																 | 
																@ -28,7 +27,7 @@ ui <- fluidPage( | 
															
														
														
													
														
															
																 | 
																 | 
																                hr(), | 
																 | 
																 | 
																                hr(), | 
															
														
														
													
														
															
																 | 
																 | 
																                fileInput(inputId = "file_query", label = "Plantilla", multiple = F), | 
																 | 
																 | 
																                fileInput(inputId = "file_query", label = "Plantilla", multiple = F), | 
															
														
														
													
														
															
																 | 
																 | 
																                actionButton("impNHC", "Importa NHC"), | 
																 | 
																 | 
																                actionButton("impNHC", "Importa NHC"), | 
															
														
														
													
														
															
																 | 
																 | 
																                actionButton("goButton", "Genera UMID"), | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                actionButton("goButton", "Genera CodiID"), | 
															
														
														
													
														
															
																 | 
																 | 
																                hr(), | 
																 | 
																 | 
																                hr(), | 
															
														
														
													
														
															
																 | 
																 | 
																                actionButton("filltemplate", "Plantilla"), | 
																 | 
																 | 
																                actionButton("filltemplate", "Plantilla"), | 
															
														
														
													
														
															
																 | 
																 | 
																                hr(), | 
																 | 
																 | 
																                hr(), | 
															
														
														
													
												
													
														
															
																| 
																	
																		
																			
																		
																	
																	
																		
																			
																		
																	
																	
																 | 
																@ -59,8 +58,17 @@ server <- function(input, output) { | 
															
														
														
													
														
															
																 | 
																 | 
																    values[["Excel"]]<-"" | 
																 | 
																 | 
																    values[["Excel"]]<-"" | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																     | 
															
														
														
													
														
															
																 | 
																 | 
																    observeEvent(input$butdbtype, { | 
																 | 
																 | 
																    observeEvent(input$butdbtype, { | 
															
														
														
													
														
															
																 | 
																 | 
																        dta<<-odbcConnectAccess2007(access.file = file,  | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																                                    pwd = .rs.askForPassword("Enter password:")) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        print(UMfile) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        print(OVfile) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "UM"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            dta<<-odbcConnectAccess2007(access.file = UMfile,  | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                                        pwd = .rs.askForPassword("Enter password:")) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "OV"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            dta<<-odbcConnectAccess2007(access.file = OVfile,  | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                                        pwd = .rs.askForPassword("Enter password:")) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																         | 
															
														
														
													
														
															
																 | 
																 | 
																        print(dta) | 
																 | 
																 | 
																        print(dta) | 
															
														
														
													
														
															
																 | 
																 | 
																        if (input$backup == T){ | 
																 | 
																 | 
																        if (input$backup == T){ | 
															
														
														
													
														
															
																 | 
																 | 
																            sqlBackUp()    | 
																 | 
																 | 
																            sqlBackUp()    | 
															
														
														
													
												
													
														
															
																| 
																	
																	
																	
																		
																			
																		
																	
																 | 
																@ -86,7 +94,7 @@ server <- function(input, output) { | 
															
														
														
													
														
															
																 | 
																 | 
																    observeEvent(input$impNHC, { | 
																 | 
																 | 
																    observeEvent(input$impNHC, { | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["DF"]]$NHC<-values[["Excel"]] | 
																 | 
																 | 
																        values[["DF"]]$NHC<-values[["Excel"]] | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																
 | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																     | 
															
														
														
													
														
															
																 | 
																 | 
																    ## Handsontable | 
																 | 
																 | 
																    ## Handsontable | 
															
														
														
													
														
															
																 | 
																 | 
																    observe({ | 
																 | 
																 | 
																    observe({ | 
															
														
														
													
														
															
																 | 
																 | 
																        if (!is.null(input$hot)) { | 
																 | 
																 | 
																        if (!is.null(input$hot)) { | 
															
														
														
													
												
													
														
															
																| 
																	
																	
																	
																		
																			
																		
																	
																 | 
																@ -109,7 +117,6 @@ server <- function(input, output) { | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																     | 
															
														
														
													
														
															
																 | 
																 | 
																    observe({ | 
																 | 
																 | 
																    observe({ | 
															
														
														
													
														
															
																 | 
																 | 
																        print(1) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (!is.null(input$samples)) { | 
																 | 
																 | 
																        if (!is.null(input$samples)) { | 
															
														
														
													
														
															
																 | 
																 | 
																            samples = hot_to_r(input$samples) | 
																 | 
																 | 
																            samples = hot_to_r(input$samples) | 
															
														
														
													
														
															
																 | 
																 | 
																        } else { | 
																 | 
																 | 
																        } else { | 
															
														
														
													
												
													
														
															
																| 
																	
																		
																			
																		
																	
																	
																		
																			
																		
																	
																	
																 | 
																@ -190,145 +197,236 @@ server <- function(input, output) { | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																     | 
															
														
														
													
														
															
																 | 
																 | 
																    observeEvent(input$goButton, { | 
																 | 
																 | 
																    observeEvent(input$goButton, { | 
															
														
														
													
														
															
																 | 
																 | 
																        print(dta) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        sqlGenOVID(nhcs = values[["DF"]]$NHC, sinc=T) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "UMID")) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																
 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        sqlGenOVID(dta, nhcs = values[["DF"]]$NHC, sinc=T) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																
 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "UM"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "UMID")) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "OV"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "OVID")) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																        print(values[["DF"]]) | 
																 | 
																 | 
																        print(values[["DF"]]) | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																
 | 
																 | 
																 | 
																
 | 
															
														
														
													
														
															
																 | 
																 | 
																    observeEvent(input$filltemplate,{ | 
																 | 
																 | 
																    observeEvent(input$filltemplate,{ | 
															
														
														
													
														
															
																 | 
																 | 
																        today=T | 
																 | 
																 | 
																        today=T | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.umid<-sqlFetch(dta, "UMID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Generar código para las nuevas muestras | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        samples<-sqlFetch(dta, "MUESTRAS") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1   | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        }else{ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            next.samp<-1 | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        last.samp<-next.samp+(length(values[["DF"]]$NHC)-1) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID"), all.x=T) %>% arrange(CODIGO) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (today==TRUE){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            samples.exp$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        nhc.table<-values[["DF"]] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (any(sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]) == T)){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            nhcs.cnag<-nhc.table[sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]),"NHC"] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            umid.cnag<-sqlFetch(dta, "UMID") %>% filter(NHC %in% nhcs.cnag) %>% pull(UMID) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            sample.cnag<-samples.exp %>% filter(UMID %in% umid.cnag) %>% pull(CODIGO) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            cnag.exp<-merge(data.frame("UMID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG") %>% slice(0), all=T) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "UM"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.umid<-sqlFetch(dta, "UMID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Generar código para las nuevas muestras | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            samples<-sqlFetch(dta, "MUESTRAS") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1   | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            }else{ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                next.samp<-1 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            last.samp<-next.samp+(length(values[["DF"]]$NHC)-1) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID"), all.x=T) %>% arrange(CODIGO) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO) | 
															
														
														
													
														
															
																 | 
																 | 
																            if (today==TRUE){ | 
																 | 
																 | 
																            if (today==TRUE){ | 
															
														
														
													
														
															
																 | 
																 | 
																                cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                samples.exp$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y") | 
															
														
														
													
														
															
																 | 
																 | 
																            } | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																        }else{ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0) %>%  | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																                mutate(across(lubridate::is.POSIXct, as.character)) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nhc.table<-values[["DF"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (any(sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]) == T)){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                nhcs.cnag<-nhc.table[sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]),"NHC"] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                umid.cnag<-sqlFetch(dta, "UMID") %>% filter(NHC %in% nhcs.cnag) %>% pull(UMID) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sample.cnag<-samples.exp %>% filter(UMID %in% umid.cnag) %>% pull(CODIGO) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                cnag.exp<-merge(data.frame("UMID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG") %>% slice(0), all=T) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                if (today==TRUE){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            }else{ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0) %>%  | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    mutate(across(lubridate::is.POSIXct, as.character)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (any(sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]) == T)){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                nhcs.rna<-nhc.table[sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]),"NHC"] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                umid.rna<-sqlFetch(dta, "UMID") %>% filter(NHC %in% nhcs.rna) %>% pull(UMID) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sample.rna<-samples.exp %>% filter(UMID %in% umid.rna) %>% pull(CODIGO) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                rna.exp<-merge(data.frame("UMID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA") %>% slice(0)%>%  | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                                   mutate(across(lubridate::is.POSIXct, as.character)), all=T) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            }else{ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                rna.exp<-sqlFetch(dta, "RNADNA") %>% slice(0) %>%  | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    mutate(across(lubridate::is.POSIXct, as.character)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-sqlFetch(dta, "CLINICOS") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.new<-sqlFetch(dta, "UMID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="UMID") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics$NHC<-as.character(upd.clinics$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["samples"]]<-samples.exp | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["CLINICS"]]<-upd.clinics | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["cnag"]]<-cnag.exp | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["rna"]]<-rna.exp | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "OV"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.umid<-sqlFetch(dta, "OVID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Generar código para las nuevas muestras | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            samples<-sqlFetch(dta, "SAMPLES") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1   | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            }else{ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                next.samp<-1 | 
															
														
														
													
														
															
																 | 
																 | 
																            } | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																        if (any(sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]) == T)){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            nhcs.rna<-nhc.table[sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]),"NHC"] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            umid.rna<-sqlFetch(dta, "UMID") %>% filter(NHC %in% nhcs.rna) %>% pull(UMID) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            sample.rna<-samples.exp %>% filter(UMID %in% umid.rna) %>% pull(CODIGO) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            rna.exp<-merge(data.frame("UMID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA") %>% slice(0)%>%  | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																                               mutate(across(lubridate::is.POSIXct, as.character)), all=T) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        }else{ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            rna.exp<-sqlFetch(dta, "RNADNA") %>% slice(0) %>%  | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																                mutate(across(lubridate::is.POSIXct, as.character)) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            last.samp<-next.samp+(length(values[["DF"]]$NHC)-1) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "samples"=new.samp) %>% merge(sqlFetch(dta,"OVID"), all.x=T) %>% arrange(samples) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (today==TRUE){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                samples.exp$IQ_date<-format(Sys.Date(), "%d/%m/%y") | 
															
														
														
													
														
															
																 | 
																 | 
																            } | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.clinics<-sqlFetch(dta, "CLINICOS") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        umid.new<-sqlFetch(dta, "UMID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="UMID") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.clinics$NHC<-as.character(upd.clinics$NHC) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["samples"]]<-samples.exp | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["CLINICS"]]<-upd.clinics | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["cnag"]]<-cnag.exp | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        values[["rna"]]<-rna.exp | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        print(values[["rna"]] %>% sapply(class)) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nhc.table<-values[["DF"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-sqlFetch(dta, "CLINICS") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.new<-sqlFetch(dta, "OVID") %>% filter(NHC %in% values[["DF"]]$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="OVID") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics$NHC<-as.character(upd.clinics$NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["samples"]]<-samples.exp %>% mutate(across(lubridate::is.POSIXct, as.character)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            values[["CLINICS"]]<-upd.clinics %>% mutate(across(lubridate::is.POSIXct, as.character)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																         | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																     | 
															
														
														
													
														
															
																 | 
																 | 
																    observeEvent(input$synctemplate,{ | 
																 | 
																 | 
																    observeEvent(input$synctemplate,{ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "UM"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            # conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en MUESTRAS | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nsamples<-values[["samples"]] %>% nrow | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.samples<-values[["samples"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(upd.samples) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                upd.samples$FECHA_RECEPCION<-lubridate::parse_date_time(upd.samples$FECHA_RECEPCION, c("d/m/Y","d/m/y")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                upd.samples$TIPO<-as.character(upd.samples$TIPO) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                upd.samples$OBS<-as.character(upd.samples$OBS) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sqlSave(dta, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                print("Tabla MUESTRAS sincronizada.") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																         | 
															
														
														
													
														
															
																 | 
																 | 
																        # conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Nuevas entradas en MUESTRAS | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        nsamples<-values[["samples"]] %>% nrow | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.samples<-values[["samples"]] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (nrow(upd.samples) > 0){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            upd.samples$FECHA_RECEPCION<-lubridate::parse_date_time(upd.samples$FECHA_RECEPCION, c("d/m/Y","d/m/y")) %>% as.Date() | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            upd.samples$TIPO<-as.character(upd.samples$TIPO) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            upd.samples$OBS<-as.character(upd.samples$OBS) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Entradas modificadas en CLINICOS | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-values[["CLINICS"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            rnames<-sqlFetch(dta, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            rownames(clinics.mod)<-rnames | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																            ### !! Atención, esto cambia la base de datos: | 
																 | 
																 | 
																            ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																            print(upd.samples) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            sqlSave(dta, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            print("Tabla MUESTRAS sincronizada.") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Entradas modificadas en CLINICOS | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        upd.clinics<-values[["CLINICS"]] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        rnames<-sqlFetch(dta, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        rownames(clinics.mod)<-rnames | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ### !! Atención, esto cambia la base de datos: | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        for (i in fechas){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            clinics.mod[,i]<-lubridate::parse_date_time(clinics.mod[,i], c("d/m/Y","d/m/y")) %>% as.Date() | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        sqlUpdate(dta, clinics.mod,"CLINICOS", index="UMID") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        print("Tabla CLINICOS modificada.") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Nuevas entradas en CLINICOS | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        nsamples.clin<-sqlFetch(dta, "CLINICOS") %>% nrow | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ### !! Atención, esto cambia la base de datos: | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        fechas<-colnames(clinics.new)[grepl("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        varTypes<-rep("Date",length(fechas)) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        names(varTypes)<-fechas | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        for (i in fechas){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            clinics.new[,i]<-lubridate::parse_date_time(clinics.new[,i], c("d/m/Y","d/m/y")) %>% as.Date() | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        sqlSave(dta, clinics.new, tablename="CLINICOS", append = T, varTypes = varTypes, rownames = F) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        print("Tabla CLINICOS sincronizada.") | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Nuevas entradas en CNAG | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (nrow(values[["cnag"]]) > 0){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            cnag.sync<-values[["cnag"]] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            fechas<-colnames(cnag.sync)[sqlFetch(dta, "CNAG") %>% sapply(lubridate::is.POSIXct)] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                clinics.mod[,i]<-lubridate::parse_date_time(clinics.mod[,i], c("d/m/Y","d/m/y")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            sqlUpdate(dta, clinics.mod,"CLINICOS", index="UMID") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print("Tabla CLINICOS modificada.") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en CLINICOS | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nsamples.clin<-sqlFetch(dta, "CLINICOS") %>% nrow | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            fechas<-colnames(clinics.new)[grepl("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)] | 
															
														
														
													
														
															
																 | 
																 | 
																            varTypes<-rep("Date",length(fechas)) | 
																 | 
																 | 
																            varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																            names(varTypes)<-fechas | 
																 | 
																 | 
																            names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																            print(fechas) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            for (i in fechas){ | 
																 | 
																 | 
																            for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																                cnag.sync[,i]<-lubridate::parse_date_time(cnag.sync[,i], c("d/m/Y","d/m/y")) %>% as.Date() | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                clinics.new[,i]<-lubridate::parse_date_time(clinics.new[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            sqlSave(dta, clinics.new, tablename="CLINICOS", append = T, varTypes = varTypes, rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print("Tabla CLINICOS sincronizada.") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en CNAG | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(values[["cnag"]]) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                cnag.sync<-values[["cnag"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                fechas<-colnames(cnag.sync)[sqlFetch(dta, "CNAG") %>% sapply(lubridate::is.POSIXct)] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                print(fechas) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    cnag.sync[,i]<-lubridate::parse_date_time(cnag.sync[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sqlSave(dta, cnag.sync, tablename="CNAG", append = T, varTypes = varTypes, rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en RNADNA | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(values[["rna"]]) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                rna.sync<-values[["rna"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA") %>% sapply(lubridate::is.POSIXct)] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    rna.sync[,i]<-lubridate::parse_date_time(rna.sync[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sqlSave(dta, rna.sync, tablename="RNADNA", append = T, varTypes = varTypes, rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																            } | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																            sqlSave(dta, cnag.sync, tablename="CNAG", append = T, varTypes = varTypes, rownames = F) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																         | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        ## Nuevas entradas en RNADNA | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																        if (nrow(values[["rna"]]) > 0){ | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            rna.sync<-values[["rna"]] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																            fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA") %>% sapply(lubridate::is.POSIXct)] | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																        if (input$dbtype == "OV"){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en SAMPLES | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nsamples<-values[["samples"]] %>% nrow | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.samples<-values[["samples"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (nrow(upd.samples) > 0){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                fechas<-colnames(upd.samples)[sqlFetch(dta, "SAMPLES") %>% sapply(lubridate::is.POSIXct)] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                    upd.samples[,i]<-lubridate::parse_date_time(upd.samples[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                # upd.samples$TIPO<-as.character(upd.samples$TIPO) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                # upd.samples$OBS<-as.character(upd.samples$OBS) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                sqlSave(dta, upd.samples, tablename="SAMPLES", append = T, varTypes = varTypes, rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                print("Tabla SAMPLES sincronizada.") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Entradas modificadas en CLINICOS | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            upd.clinics<-values[["CLINICS"]] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            rnames<-sqlFetch(dta, "CLINICS") %>% filter(OVID %in% umid.mod) %>% rownames | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            clinics.mod<-upd.clinics %>% filter(OVID %in% umid.mod) %>% select(-NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            rownames(clinics.mod)<-rnames | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print(clinics.mod) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            fechas<-colnames(clinics.mod)[sqlFetch(dta, "CLINICS") %>% sapply(lubridate::is.POSIXct)] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                clinics.mod[,i]<-lubridate::parse_date_time(clinics.mod[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																            varTypes<-rep("Date",length(fechas)) | 
																 | 
																 | 
																            varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																            names(varTypes)<-fechas | 
																 | 
																 | 
																            names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print(clinics.mod) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            sqlUpdate(dta, clinics.mod,"CLINICS", index="OVID") | 
															
														
														
													
														
															
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																 | 
																 | 
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																 | 
																            print("Tabla CLINICS modificada.") | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ## Nuevas entradas en CLINICOS | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            nsamples.clin<-sqlFetch(dta, "CLINICS") %>% nrow | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            umid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))] | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            clinics.new<-upd.clinics %>% filter(OVID %in% umid.new) %>% select(-NHC) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																             | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            ### !! Atención, esto cambia la base de datos: | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            fechas<-colnames(clinics.new)[sqlFetch(dta, "CLINICS") %>% sapply(lubridate::is.POSIXct)] | 
															
														
														
													
														
															
																 | 
																 | 
																            for (i in fechas){ | 
																 | 
																 | 
																            for (i in fechas){ | 
															
														
														
													
														
															
																 | 
																 | 
																                rna.sync[,i]<-lubridate::parse_date_time(rna.sync[,i], c("d/m/Y","d/m/y")) %>% as.Date() | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																                clinics.new[,i]<-lubridate::parse_date_time(clinics.new[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date() | 
															
														
														
													
														
															
																 | 
																 | 
																            } | 
																 | 
																 | 
																            } | 
															
														
														
													
														
															
																 | 
																 | 
																            sqlSave(dta, rna.sync, tablename="RNADNA", append = T, varTypes = varTypes, rownames = F) | 
																 | 
																 | 
																 | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            varTypes<-rep("Date",length(fechas)) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            names(varTypes)<-fechas | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print(varTypes) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print(clinics.new) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            sqlSave(dta, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes, rownames = F) | 
															
														
														
													
														
															
																 | 
																 | 
																 | 
																 | 
																 | 
																            print("Tabla CLINICS sincronizada.") | 
															
														
														
													
														
															
																 | 
																 | 
																        } | 
																 | 
																 | 
																        } | 
															
														
														
													
														
															
																 | 
																 | 
																    }) | 
																 | 
																 | 
																    }) | 
															
														
														
													
														
															
																 | 
																 | 
																     | 
																 | 
																 | 
																     | 
															
														
														
													
												
													
														
															
																| 
																	
																		
																			
																		
																	
																	
																	
																 | 
																
 |