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Añadir comentarios informativos del script.

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Costa
2021-10-18 15:25:26 +02:00
parent 260737bb1c
commit 29e6ff8479
1 changed files with 8 additions and 0 deletions
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RellenarOVBD.R
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@@ -2,17 +2,21 @@ library(tidyverse)
library(RODBC) library(RODBC)
library(openxlsx) 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", dta<-odbcConnectAccess2007(access.file = "C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/OVARIO.accdb",
pwd = .rs.askForPassword("Enter password:")) pwd = .rs.askForPassword("Enter password:"))
## Importamos los NHC de las muestras nuevas
nhc.test<-read.xlsx("queryOV.xlsx", sheet = "NHC") %>% pull(NHC) nhc.test<-read.xlsx("queryOV.xlsx", sheet = "NHC") %>% pull(NHC)
## Mostramos si ya hay muestras del mismo paciente
sqlQuery(dta, "SELECT O.NHC,S.* sqlQuery(dta, "SELECT O.NHC,S.*
FROM SAMPLES S FROM SAMPLES S
INNER JOIN OVID O INNER JOIN OVID O
ON O.OVID=S.OVID") %>% filter(NHC %in% nhc.test) %>% 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) 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.* sqlQuery(dta, "SELECT O.NHC,S.*
FROM SAMPLES S FROM SAMPLES S
INNER JOIN OVID O INNER JOIN OVID O
@@ -30,6 +34,7 @@ rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) upd.ovid<-filter(upd.ovid, NHC %in% new.nhc)
sqlSave(dta, upd.ovid, tablename="OVID", append = T) sqlSave(dta, upd.ovid, tablename="OVID", append = T)
## Generar código para las nuevas muestras
samples<-sqlFetch(dta, "SAMPLES") samples<-sqlFetch(dta, "SAMPLES")
if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){ if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1 next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1
@@ -42,18 +47,21 @@ new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhc.test)), d
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) 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") upd.clinics<-sqlFetch(dta, "CLINICS")
ovid.new<-sqlFetch(dta, "OVID") %>% filter(NHC %in% nhc.test) ovid.new<-sqlFetch(dta, "OVID") %>% filter(NHC %in% nhc.test)
upd.clinics<-merge(ovid.new,upd.clinics, all.x=T) upd.clinics<-merge(ovid.new,upd.clinics, all.x=T)
upd.clinics$NHC<-as.character(upd.clinics$NHC) 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])} 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") wb <- loadWorkbook("queryOV.xlsx")
writeData(wb, "NHC", upd.ovid) writeData(wb, "NHC", upd.ovid)
writeData(wb,"samples",samples.exp) writeData(wb,"samples",samples.exp)
writeData(wb,"CLINICS",upd.clinics) writeData(wb,"CLINICS",upd.clinics)
saveWorkbook(wb,"queryOV.xlsx",overwrite = TRUE) saveWorkbook(wb,"queryOV.xlsx",overwrite = TRUE)
## Añadir código de muestra nueva a la base de datos
nsamples<-sqlFetch(dta, "SAMPLES") %>% nrow nsamples<-sqlFetch(dta, "SAMPLES") %>% nrow
upd.samples<-read.xlsx("QuerySamplesOV.xlsx") upd.samples<-read.xlsx("QuerySamplesOV.xlsx")
rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character