From 4c27e84cbd8491f029925de0980e2395060700d4 Mon Sep 17 00:00:00 2001 From: marcelcosta Date: Tue, 10 Oct 2023 12:51:15 +0200 Subject: [PATCH] NHC as a character. --- BDAccess/app.R | 98 +++++++++++++++++++++++++------------------------- sqlFunctions.R | 10 +++--- 2 files changed, 55 insertions(+), 53 deletions(-) diff --git a/BDAccess/app.R b/BDAccess/app.R index 96c9229..87fb14c 100644 --- a/BDAccess/app.R +++ b/BDAccess/app.R @@ -299,13 +299,13 @@ 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$dbtype == "CC"){ - values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "PATID")) + values[["DF"]]<-merge(values[["DF"]], sqlFetch(dta, "PATID", as.is=T)) } print(values[["DF"]]) }) @@ -313,9 +313,9 @@ server <- function(input, output) { observeEvent(input$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$CODIGO) %>% as.numeric %>% max(na.rm=T)+1 }else{ @@ -323,7 +323,7 @@ server <- function(input, output) { } last.samp<-next.samp+(length(values[["DF"]]$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$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y") @@ -333,30 +333,30 @@ server <- function(input, output) { if (any(sapply(nhc.table$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])} @@ -367,9 +367,9 @@ 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$samples) %>% as.numeric %>% max(na.rm=T)+1 }else{ @@ -377,7 +377,7 @@ server <- function(input, output) { } last.samp<-next.samp+(length(values[["DF"]]$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$IQ_date<-format(Sys.Date(), "%d/%m/%y") @@ -386,8 +386,8 @@ server <- function(input, output) { nhc.table<-values[["DF"]] ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos - upd.clinics<-sqlFetch(dta, "CLINICS") - umid.new<-sqlFetch(dta, "OVID") %>% filter(NHC %in% values[["DF"]]$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$NHC) for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} @@ -397,9 +397,9 @@ server <- function(input, output) { } if (input$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{ @@ -407,7 +407,7 @@ 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$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y") @@ -417,30 +417,30 @@ server <- function(input, output) { if (any(sapply(nhc.table$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])} @@ -473,8 +473,8 @@ 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 @@ -487,8 +487,8 @@ 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} @@ -505,7 +505,7 @@ 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) @@ -518,7 +518,7 @@ 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){ @@ -534,7 +534,7 @@ 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() } @@ -549,14 +549,14 @@ 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() } @@ -567,13 +567,13 @@ 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() } @@ -601,8 +601,8 @@ 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 @@ -615,8 +615,8 @@ 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} @@ -633,7 +633,7 @@ 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) @@ -646,7 +646,7 @@ 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){ diff --git a/sqlFunctions.R b/sqlFunctions.R index 18915ee..3806d30 100644 --- a/sqlFunctions.R +++ b/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) @@ -75,7 +77,7 @@ 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$NHC] %>% unique() if(length(new.nhc) > 0){ @@ -91,7 +93,7 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){ if(dbtype=="UM"){ dbid<-merge(dbid, newtab, all=T) %>% select(NHC,UMID) %>% arrange(UMID) # dbid$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)