Limpieza de código.

BDAccess/app.R

@@ -88,6 +88,7 @@ ui <- fluidPage(
                      tabsetPanel(
                          tabPanel("Entrada",
                              actionButton("goButtonDir","Selecciona directorio fenotipo"),
+                             textInput("cytopath", label="Directorio fenotipo", value=""),
                              textOutput("session"),
                              hr(),
                              actionButton("fcsconvert", "Convertir a fcs"),
@@ -143,37 +144,31 @@ server <- function(input, output) {
         print(CCfile)
         if (input$dbtype == "UM"){
             dta<<-odbcConnectAccess2007(access.file = UMfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         if (input$dbtype == "OV"){
             dta<<-odbcConnectAccess2007(access.file = OVfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         if (input$dbtype == "CC"){
             dta<<-odbcConnectAccess2007(access.file = CCfile, 
-                                        pwd = .rs.askForPassword("Enter password:"))
+                                        pwd = getPass::getPass("Enter password:"))
         }
         print(dta)
         if (input$backup == T){
             if (! input$dbtype %in% c("UM","OV")){
-                sqlBackUp(bu.dir="CC_BU")
-            }else{
-                sqlBackUp()   
+              sqlBackUp(dbfile = CCfile, bu.dir="CC_BU")
             }
-                
+            if (input$dbtype == "UM"){
+              sqlBackUp(dbfile = UMfile)
+            }
+            if (input$dbtype == "OV"){
+              sqlBackUp(dbfile = OVfile)
+            }
+            print("Back up realizado.")   
         }
     })
     
-    # observe({
-    #     if (!is.null(input$file_access)){ 
-    #         # Inicializar conexión
-    #         dta<<-odbcConnectAccess2007(access.file = file, 
-    #                                    pwd = .rs.askForPassword("Enter password:"))
-    #         print(dta)
-    #         sqlBackUp()
-    #     }
-    # })
-    
     observe({
         if (!is.null(input$file_query)){
             ## Importamos los NHC de las muestras nuevas
@@ -298,13 +293,13 @@ server <- function(input, output) {
         }
             
         if (input$dbtype == "UM"){
-            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "UMID"))
+            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "UMID", as.is=T))
         }
         if (input$dbtype == "OV"){
-            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "OVID"))
+            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "OVID", as.is=T))
         }
         if (input$dbtype == "CC"){
-            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "PATID"))
+            values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "PATID", as.is=T))
         }
         print(values[["DF"]])
     })
@@ -312,9 +307,9 @@ server <- function(input, output) {
     observeEvent(input$filltemplate,{
         today=T
         if (input$dbtype == "UM"){
-            upd.umid<-sqlFetch(dta, "UMID") %>% filter(NHC %in% values[["DF"]]$NHC)
+            upd.umid<-sqlFetch(dta, "UMID", as.is=T) %>% filter(NHC %in% values[["DF"]]$NHC)
             ## Generar código para las nuevas muestras
-            samples<-sqlFetch(dta, "MUESTRAS")
+            samples<-sqlFetch(dta, "MUESTRAS", as.is=T)
             if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){
                 next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1  
             }else{
@@ -322,7 +317,7 @@ server <- function(input, output) {
             }
             last.samp<-next.samp+(length(values[["DF"]]$NHC)-1)
             new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
-            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID"), all.x=T) %>% arrange(CODIGO)
+            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID", as.is=T), 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")
@@ -332,30 +327,30 @@ server <- function(input, output) {
             
             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)
+                umid.cnag<-sqlFetch(dta, "UMID", as.is=T) %>% 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)
+                cnag.exp<-merge(data.frame("UMID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG", as.is=T) %>% slice(0), all=T)
                 if (today==TRUE){
                     cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
                 }
             }else{
-                cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0) %>% 
+                cnag.exp<-sqlFetch(dta, "CNAG", as.is=T) %>% slice(0) %>% 
                     mutate(across(lubridate::is.POSIXct, as.character))
                 }
             if (any(sapply(nhc.table$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)
+                umid.rna<-sqlFetch(dta, "UMID", as.is=T) %>% 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)%>% 
+                rna.exp<-merge(data.frame("UMID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA", as.is=T) %>% slice(0)%>% 
                                    mutate(across(lubridate::is.POSIXct, as.character)), all=T)
             }else{
-                rna.exp<-sqlFetch(dta, "RNADNA") %>% slice(0) %>% 
+                rna.exp<-sqlFetch(dta, "RNADNA", as.is=T) %>% 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"]]$NHC)
+            upd.clinics<-sqlFetch(dta, "CLINICOS", as.is=T)
+            umid.new<-sqlFetch(dta, "UMID", as.is=T) %>% filter(NHC %in% values[["DF"]]$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])}
@@ -366,9 +361,9 @@ server <- function(input, output) {
             values[["rna"]]<-rna.exp
         }
         if (input$dbtype == "OV"){
-            upd.umid<-sqlFetch(dta, "OVID") %>% filter(NHC %in% values[["DF"]]$NHC)
+            upd.umid<-sqlFetch(dta, "OVID", as.is=T) %>% filter(NHC %in% values[["DF"]]$NHC)
             ## Generar código para las nuevas muestras
-            samples<-sqlFetch(dta, "SAMPLES")
+            samples<-sqlFetch(dta, "SAMPLES", as.is=T)
             if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
                 next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1  
             }else{
@@ -376,17 +371,17 @@ server <- function(input, output) {
             }
             last.samp<-next.samp+(length(values[["DF"]]$NHC)-1)
             new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
-            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "samples"=new.samp) %>% merge(sqlFetch(dta,"OVID"), all.x=T) %>% arrange(samples)
+            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "samples"=new.samp) %>% merge(sqlFetch(dta,"OVID", as.is=T), 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$IQ_date<-format(Sys.Date(), "%d/%m/%y")
+                samples.exp$Date_extraction<-format(Sys.Date(), "%d/%m/%y")
             }
             
             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"]]$NHC)
+            upd.clinics<-sqlFetch(dta, "CLINICS", as.is=T)
+            umid.new<-sqlFetch(dta, "OVID", as.is=T) %>% filter(NHC %in% values[["DF"]]$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])}
@@ -396,9 +391,9 @@ server <- function(input, output) {
         }
         
         if (input$dbtype %in% c("CC")){
-            upd.umid<-sqlFetch(dta, "PATID") %>% filter(NHC %in% values[["DF"]]$NHC)
+            upd.umid<-sqlFetch(dta, "PATID", as.is=T) %>% filter(NHC %in% values[["DF"]]$NHC)
             ## Generar código para las nuevas muestras
-            samples<-sqlFetch(dta, "MUESTRAS")
+            samples<-sqlFetch(dta, "MUESTRAS", as.is=T)
             if(sum(grepl(paste0(input$dbtype,Sys.time() %>% format("%y")), samples$CODIGO)) > 0){
                 next.samp<-gsub(paste0(input$dbtype,Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1  
             }else{
@@ -406,7 +401,7 @@ server <- function(input, output) {
             }
             last.samp<-next.samp+(length(values[["DF"]]$NHC)-1)
             new.samp<-sprintf("%s%s%02d",input$dbtype,Sys.time() %>% format("%y"),next.samp:last.samp)
-            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"PATID"), all.x=T) %>% arrange(CODIGO)
+            new.samp.df<-data.frame("NHC"=values[["DF"]]$NHC, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"PATID", as.is=T), all.x=T) %>% arrange(CODIGO)
             samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
             if (today==TRUE){
                 samples.exp$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y")
@@ -416,30 +411,30 @@ server <- function(input, output) {
             
             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, "PATID") %>% filter(NHC %in% nhcs.cnag) %>% pull(PATID)
+                umid.cnag<-sqlFetch(dta, "PATID", as.is=T) %>% filter(NHC %in% nhcs.cnag) %>% pull(PATID)
                 sample.cnag<-samples.exp %>% filter(PATID %in% umid.cnag) %>% pull(CODIGO)
-                cnag.exp<-merge(data.frame("PATID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG") %>% slice(0), all=T)
+                cnag.exp<-merge(data.frame("PATID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG", as.is=T) %>% slice(0), all=T)
                 if (today==TRUE){
                     cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
                 }
             }else{
-                cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0) %>% 
+                cnag.exp<-sqlFetch(dta, "CNAG", as.is=T) %>% slice(0) %>% 
                     mutate(across(lubridate::is.POSIXct, as.character))
             }
             if (any(sapply(nhc.table$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, "PATID") %>% filter(NHC %in% nhcs.rna) %>% pull(PATID)
+                umid.rna<-sqlFetch(dta, "PATID", as.is=T) %>% filter(NHC %in% nhcs.rna) %>% pull(PATID)
                 sample.rna<-samples.exp %>% filter(PATID %in% umid.rna) %>% pull(CODIGO)
-                rna.exp<-merge(data.frame("PATID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA") %>% slice(0)%>% 
+                rna.exp<-merge(data.frame("PATID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA", as.is=T) %>% slice(0)%>% 
                                    mutate(across(lubridate::is.POSIXct, as.character)), all=T)
             }else{
-                rna.exp<-sqlFetch(dta, "RNADNA") %>% slice(0) %>% 
+                rna.exp<-sqlFetch(dta, "RNADNA", as.is=T) %>% 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, "PATID") %>% filter(NHC %in% values[["DF"]]$NHC)
+            upd.clinics<-sqlFetch(dta, "CLINICOS", as.is=T)
+            umid.new<-sqlFetch(dta, "PATID", as.is=T) %>% filter(NHC %in% values[["DF"]]$NHC)
             upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="PATID")
             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])}
@@ -472,8 +467,8 @@ server <- function(input, output) {
         
             ## 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
+            umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS", as.is=T) %>% pull(UMID))]
+            rnames<-sqlFetch(dta, "CLINICOS", as.is=T) %>% filter(UMID %in% umid.mod) %>% rownames
             clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
             rownames(clinics.mod)<-rnames
             
@@ -486,8 +481,8 @@ server <- function(input, output) {
             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))]
+            nsamples.clin<-sqlFetch(dta, "CLINICOS", as.is=T) %>% nrow
+            umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS", as.is=T) %>% 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}
             
@@ -504,7 +499,7 @@ server <- function(input, output) {
             ## 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(cnag.sync)[sqlFetch(dta, "CNAG", as.is=T) %>% sapply(lubridate::is.POSIXct)]
                 varTypes<-rep("Date",length(fechas))
                 names(varTypes)<-fechas
                 print(fechas)
@@ -517,7 +512,7 @@ server <- function(input, output) {
             ## Nuevas entradas en RNADNA
             if (nrow(values[["rna"]]) > 0){
                 rna.sync<-values[["rna"]]
-                fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA") %>% sapply(lubridate::is.POSIXct)]
+                fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA", as.is=T) %>% sapply(lubridate::is.POSIXct)]
                 varTypes<-rep("Date",length(fechas))
                 names(varTypes)<-fechas
                 for (i in fechas){
@@ -533,7 +528,7 @@ server <- function(input, output) {
             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)]
+                fechas<-colnames(upd.samples)[sqlFetch(dta, "SAMPLES", as.is=T) %>% 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()
                 }
@@ -548,14 +543,14 @@ server <- function(input, output) {
             
             ## 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
+            umid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS", as.is=T) %>% pull(OVID))]
+            rnames<-sqlFetch(dta, "CLINICS", as.is=T) %>% 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)]
+            fechas<-colnames(clinics.mod)[sqlFetch(dta, "CLINICS", as.is=T) %>% 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()
             }
@@ -566,13 +561,13 @@ server <- function(input, output) {
             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))]
+            nsamples.clin<-sqlFetch(dta, "CLINICS", as.is=T) %>% nrow
+            umid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS", as.is=T) %>% 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)]
+            fechas<-colnames(clinics.new)[sqlFetch(dta, "CLINICS", as.is=T) %>% sapply(lubridate::is.POSIXct)]
             for (i in fechas){
                 clinics.new[,i]<-lubridate::parse_date_time(clinics.new[,i], c("d/m/Y","d/m/y","Y-m-d")) %>% as.Date()
             }
@@ -600,8 +595,8 @@ server <- function(input, output) {
             
             ## Entradas modificadas en CLINICOS
             upd.clinics<-values[["CLINICS"]]
-            PATID.mod<-upd.clinics$PATID[upd.clinics$PATID %in% (sqlFetch(dta, "CLINICOS") %>% pull(PATID))]
-            rnames<-sqlFetch(dta, "CLINICOS") %>% filter(PATID %in% PATID.mod) %>% rownames
+            PATID.mod<-upd.clinics$PATID[upd.clinics$PATID %in% (sqlFetch(dta, "CLINICOS", as.is=T) %>% pull(PATID))]
+            rnames<-sqlFetch(dta, "CLINICOS", as.is=T) %>% filter(PATID %in% PATID.mod) %>% rownames
             clinics.mod<-upd.clinics %>% filter(PATID %in% PATID.mod) %>% select(-NHC)
             rownames(clinics.mod)<-rnames
             
@@ -614,8 +609,8 @@ server <- function(input, output) {
             print("Tabla CLINICOS modificada.")
             
             ## Nuevas entradas en CLINICOS
-            nsamples.clin<-sqlFetch(dta, "CLINICOS") %>% nrow
-            PATID.new<-upd.clinics$PATID[!upd.clinics$PATID %in% (sqlFetch(dta, "CLINICOS") %>% pull(PATID))]
+            nsamples.clin<-sqlFetch(dta, "CLINICOS", as.is=T) %>% nrow
+            PATID.new<-upd.clinics$PATID[!upd.clinics$PATID %in% (sqlFetch(dta, "CLINICOS", as.is=T) %>% pull(PATID))]
             clinics.new<-upd.clinics %>% filter(PATID %in% PATID.new) %>% select(-NHC)
             if (length(PATID.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
             
@@ -632,7 +627,7 @@ server <- function(input, output) {
             ## 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(cnag.sync)[sqlFetch(dta, "CNAG", as.is=T) %>% sapply(lubridate::is.POSIXct)]
                 varTypes<-rep("Date",length(fechas))
                 names(varTypes)<-fechas
                 print(fechas)
@@ -645,7 +640,7 @@ server <- function(input, output) {
             ## Nuevas entradas en RNADNA
             if (nrow(values[["rna"]]) > 0){
                 rna.sync<-values[["rna"]]
-                fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA") %>% sapply(lubridate::is.POSIXct)]
+                fechas<-colnames(rna.sync)[sqlFetch(dta, "RNADNA", as.is=T) %>% sapply(lubridate::is.POSIXct)]
                 varTypes<-rep("Date",length(fechas))
                 names(varTypes)<-fechas
                 for (i in fechas){
@@ -753,6 +748,7 @@ server <- function(input, output) {
                 sqlFetch(dta, "NITROGEN"),
                 file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","UM-Nitrogen.xlsx")
             )
+            print("Backup Creado.")
             
             table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
             
@@ -783,6 +779,7 @@ server <- function(input, output) {
             
             sqlDrop(dta, "NITROGEN")
             sqlSave(dta, table.um %>% select(-FECHA) %>% filter(!is.na(CODIGO)), tablename="NITROGEN", rownames=F)
+            print("Tabla Actualizada.")
         }
         if (input$dbtype == "OV"){
             ## Copia de backup
@@ -796,6 +793,7 @@ server <- function(input, output) {
                 sqlFetch(dta, "NITROGEN"),
                 file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","OV-Nitrogen.xlsx")
             )
+            print("Backup Creado.")
             
             ## Lectura del excel
             table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
@@ -821,6 +819,7 @@ server <- function(input, output) {
             
             sqlDrop(dta, "NITROGEN")
             sqlSave(dta, table.ov, tablename="NITROGEN", rownames=F)
+            print("Tabla Actualizada.")
         }
 
     })
@@ -923,9 +922,14 @@ server <- function(input, output) {
             
             pops<-sqlFetch(dta, "POPULATIONS")
             
-            g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>%
-                mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
-                                                "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+            g_pop<-pops %>% 
+              dplyr::filter(sample == input$id) %>% 
+              gather(pop,value,-sample, -code, -fc_time) %>%
+                # mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
+                #                                 "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+              # mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells",
+                                              # "CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>%
+                mutate(value=as.numeric(gsub(",",".",value))) %>% 
                 ggplot(aes(pop, value))+
                     geom_bar(stat="identity", color="black", fill="grey70")+
                     labs(title = input$id, y="% parent", x="")+
@@ -969,7 +973,11 @@ server <- function(input, output) {
 
     observe({
         if(input$goButtonDir > 0){
+            if (input$cytopath == ""){
                 cito_dir<<-choose.dir() %>% gsub("\\","/",. ,fixed=T) %>% paste0("/")
+            }else{
+                cito_dir<<-input$cytopath %>% gsub("\\","/",. ,fixed=T) %>% gsub("/$", "", .) %>% paste0("/")
+            }
 
             output$session <- renderText(
                     cito_dir
@@ -1008,7 +1016,7 @@ server <- function(input, output) {
         }
         
         if (input$phenotype == "IC"){
-            route<-cito_dir
+            route<-stringi::stri_enc_tonative(cito_dir)
 
             ws<-open_flowjo_xml(paste0(route,"IC.wsp"))
             gs<-flowjo_to_gatingset(ws, name="All Samples")
@@ -1169,6 +1177,11 @@ server <- function(input, output) {
                           # plot.margin = margin(-200,0,0,0),
                           axis.text = element_blank())
                 
+                nodes<-gs_get_pop_paths(gs)
+                nodes_parent<-nodes[!grepl("CTLA4|LAG3|PD1|TIGIT|TIM3|root$", nodes)]
+                nodes_cd4<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD4/",nodes)]
+                nodes_cd8<-nodes[grepl("CTLA4$|LAG3$|PD1$|TIGIT$|TIM3$", nodes) & grepl("/CD8/",nodes)]
+                
                 # g1<-ggcyto_arrange(autoplot(gs[[ab]], nodes_parent, bins=128), nrow=1)
                 # g2<-ggcyto_arrange(autoplot(gs[[iso]], nodes_cd8, bins=64), nrow=1)
                 # g3<-ggcyto_arrange(autoplot(gs[[ab]], nodes_cd8, bins=64), nrow=1)

sqlFunctions.R

@@ -15,7 +15,7 @@ sqlLastDrop<-function(conn, tablename, droplast=1,dbtype=NULL){
 
 
 sqlInitialize<-function(ruta="ruta_database.R"){
-  library(tidyverse)
+  # library(tidyverse)
   library(RODBC)
   library(openxlsx)
   
@@ -24,10 +24,12 @@ sqlInitialize<-function(ruta="ruta_database.R"){
 }
 
 sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){
+  print(dbfile)
   if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){bu.dir<-"BU_UM"}
   if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){bu.dir<-"BU_OVARIO"}
   
-  db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
+  db=tail(strsplit(dbfile, "/")[[1]], n=1)
+  print(db)
   bu_path<-gsub(db,bu.dir,dbfile)
   if (!dir.exists(bu_path)){
     dir.create(bu_path)
@@ -75,12 +77,12 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
     db<-c("dbcode"="PATID", "dbpref"="CCID")
   }
   
-  dbid<-sqlFetch(conn,db["dbcode"])
+  dbid<-sqlFetch(conn,db["dbcode"], as.is=T)
   new.nhc<-nhcs[!nhcs %in% dbid$NHC] %>% unique()
 
   if(length(new.nhc) > 0){
     if (nrow(dbid) == 0){next.num<-1}else{
-    next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
+    next.num<-gsub(db["dbpref"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
     }
     print(next.num)
     last.num<-next.num+(length(new.nhc)-1)
@@ -91,7 +93,7 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
     if(dbtype=="UM"){
       dbid<-merge(dbid, newtab, all=T) %>% select(NHC,UMID) %>% arrange(UMID)
       # dbid$Id<-as.numeric(rownames(dbid))
-      dbid$NHC<-as.numeric(dbid$NHC)
+      # dbid$NHC<-dbid$NHC
     }
     if (dbtype=="CC"){
       dbid<-merge(dbid, newtab, all=T) %>% select(NHC,PATID) %>% arrange(PATID)