You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
68 lines
3.0 KiB
68 lines
3.0 KiB
library(tidyverse)
|
|
library(RODBC)
|
|
library(openxlsx)
|
|
|
|
## Conexión a la base de datos
|
|
dta<-odbcConnectAccess2007(access.file = "C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/OVARIO.accdb",
|
|
pwd = .rs.askForPassword("Enter password:"))
|
|
|
|
## Importamos los NHC de las muestras nuevas
|
|
nhc.test<-read.xlsx("queryOV.xlsx", sheet = "NHC") %>% pull(NHC)
|
|
|
|
## Mostramos si ya hay muestras del mismo paciente
|
|
sqlQuery(dta, "SELECT O.NHC,S.*
|
|
FROM SAMPLES S
|
|
INNER JOIN OVID O
|
|
ON O.OVID=S.OVID") %>% filter(NHC %in% nhc.test) %>%
|
|
group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhc.test),all=T)
|
|
|
|
## Versión más extensa
|
|
sqlQuery(dta, "SELECT O.NHC,S.*
|
|
FROM SAMPLES S
|
|
INNER JOIN OVID O
|
|
ON O.OVID=S.OVID") %>% filter(NHC %in% nhc.test)
|
|
|
|
|
|
## Generar OVIDs para nuevos NHC
|
|
ovid<-sqlFetch(dta,"OVID")
|
|
|
|
new.nhc<-nhc.test[!nhc.test %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)
|
|
sqlSave(dta, upd.ovid, tablename="OVID", append = T)
|
|
|
|
## 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
|
|
}
|
|
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)]<-""
|
|
|
|
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
|
|
upd.clinics<-sqlFetch(dta, "CLINICS")
|
|
ovid.new<-sqlFetch(dta, "OVID") %>% filter(NHC %in% nhc.test)
|
|
upd.clinics<-merge(ovid.new,upd.clinics, all.x=T)
|
|
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("queryOV.xlsx")
|
|
writeData(wb, "NHC", upd.ovid)
|
|
writeData(wb,"samples",samples.exp)
|
|
writeData(wb,"CLINICS",upd.clinics)
|
|
saveWorkbook(wb,"queryOV.xlsx",overwrite = TRUE)
|
|
|
|
## Añadir código de muestra nueva a la base de datos
|
|
nsamples<-sqlFetch(dta, "SAMPLES") %>% nrow
|
|
upd.samples<-read.xlsx("QuerySamplesOV.xlsx")
|
|
rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character
|
|
sqlSave(dta, upd.samples, tablename="SAMPLES", append = T)
|