Subir script i fichero para introducir queries.

RellenarOVBD.R

@@ -0,0 +1,60 @@
+library(tidyverse)
+library(RODBC)
+library(openxlsx)
+
+dta<-odbcConnectAccess2007(access.file = "C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/OVARIO.accdb", 
+                           pwd = .rs.askForPassword("Enter password:"))
+
+nhc.test<-read.xlsx("queryOV.xlsx", sheet = "NHC") %>% pull(NHC)
+
+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)
+
+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)
+
+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)]<-""
+
+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])}
+
+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)
+
+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)