diff --git a/RellenarOVBD.R b/RellenarOVBD.R index 55459f6..76f634a 100644 --- a/RellenarOVBD.R +++ b/RellenarOVBD.R @@ -56,7 +56,7 @@ last.samp<-next.samp+(length(nhc.test)-1) new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhc.test)), data.frame("NHC"=nhc.test, "samples"=new.samp)) samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) -samples.exp[is.na(samples.exp)]<-"" +# samples.exp[is.na(samples.exp)]<-"" ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos upd.clinics<-sqlFetch(dta, "CLINICS") diff --git a/sqlFunctions.R b/sqlFunctions.R index a1f35d4..4414782 100644 --- a/sqlFunctions.R +++ b/sqlFunctions.R @@ -5,3 +5,129 @@ sqlDropLast<-function(conn, tablename, droplast=1){ table<-table[1:(nrow(table)-droplast),] sqlSave(conn, table, tablename = tablename, safer = F) } + +sqlInitialize<-function(){ + library(tidyverse) + library(RODBC) + library(openxlsx) + + ## Conexión a la base de datos + source("ruta_database.R", encoding = "UTF-8") +} + +sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){ + if (isFALSE(verb)){ + sqlQuery(conn, "SELECT O.NHC,S.* + FROM SAMPLES S + INNER JOIN OVID O + ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) %>% + group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhcs),all=T) + }else{ + sqlQuery(conn, "SELECT O.NHC,S.* + FROM SAMPLES S + INNER JOIN OVID O + ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) + } +} + +sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){ + ovid<-sqlFetch(conn,"OVID") + + new.nhc<-nhcs[!nhcs %in% ovid$NHC] + next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1 + last.num<-next.num+(length(new.nhc)-1) + upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num))) + rownames(upd.ovid)<-as.character(1:nrow(upd.ovid)) + upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC)) + + if (sinc){ + ### !! Atención, esto cambia la base de datos: + sqlSave(conn, upd.ovid, tablename="OVID", append = T) + print("La base ha sido actualizada.") + } + if (verb){ + return(upd.ovid) + } +} + +sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T){ + upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) + if (samples.mod){ + ## Generar código para las nuevas muestras + samples<-sqlFetch(conn, "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 + } + last.samp<-next.samp+(length(nhcs)-1) + new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) + new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp)) + samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) + } + + if (clinics.mod){ + ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos + upd.clinics<-sqlFetch(conn, "CLINICS") + ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) + upd.clinics<-merge(ovid.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])} + } + + ## Exportar tablas a la plantilla de entrada para su rellenado + wb <- loadWorkbook(file) + writeData(wb, "NHC", upd.ovid) + if (samples.mod){writeData(wb,"samples",samples.exp)} + if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)} + saveWorkbook(wb,file,overwrite = TRUE) +} + +sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){ + ## Añadir código de muestra nueva a la base de datos + nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow + upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T) + if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} + + if (sinc.samples & nrow(upd.samples) > 0){ + upd.samples$IQ_date<-as.Date(upd.samples$IQ_date) + ### !! Atención, esto cambia la base de datos: + sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date")) + print("Tabla SAMPLES sincronizada.") + } + + ## Añadir datos clínicos modificados a la base de datos + upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T) + ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))] + rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames + clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC) + rownames(clinics.mod)<-rnames + + ### !! Atención, esto cambia la base de datos: + if (sinc.clinics){ + fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))] + for (i in fechas){ + clinics.mod[,i]<-as.Date(clinics.mod[,i]) + } + sqlUpdate(conn, clinics.mod,"CLINICS") + print("Tabla CLINICS modificada.") + } + + ## Añadir datos clínicos nuevos a la base de datos + nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow + ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))] + clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC) + if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} + + ### !! Atención, esto cambia la base de datos: + if (sinc.clinics){ + fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))] + varTypes<-rep("Date",length(fechas)) + names(varTypes)<-fechas + for (i in fechas){ + clinics.new[,i]<-as.Date(clinics.new[,i]) + } + sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes) + print("Tabla CLINICS sincronizada.") + } +} diff --git a/workflow.R b/workflow.R new file mode 100644 index 0000000..51c389c --- /dev/null +++ b/workflow.R @@ -0,0 +1,20 @@ +source("sqlFunctions.R") + +# Cargar dependencias +sqlInitialize() + +# Inicializar conexión +dta<-odbcConnectAccess2007(access.file = file, + pwd = .rs.askForPassword("Enter password:")) + +# Ver si ya hay muestras de los pacientes (opcional, para uno mismo) +sqlShowSamples() + +# Generar código OVID para muestras nuevas +sqlGenOVID(sinc=T) + +# Rellenar fichero plantilla "QueryOV.xlsx" +sqlWriteTemp() + +# Sincronizar lo rellenado en las pestañas samples y clinics +sqlSincBD(sinc.samples = T, sinc.clinics = T) \ No newline at end of file