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- 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)
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