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144 lines
5.7 KiB
144 lines
5.7 KiB
require(RODBC)
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sqlDropLast<-function(conn, tablename, droplast=1){
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table<-sqlFetch(conn, tablename)
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table<-table[1:(nrow(table)-droplast),]
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sqlSave(conn, table, tablename = tablename, safer = F)
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}
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sqlInitialize<-function(){
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library(tidyverse)
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library(RODBC)
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library(openxlsx)
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## Conexión a la base de datos
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source("ruta_database.R", encoding = "UTF-8")
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}
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sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
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db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
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bu_path<-gsub(db,bu.dir,dbfile)
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if (!dir.exists(bu_path)){
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dir.create(bu_path)
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print(paste0("Back Up directory ", bu_path, " created"))
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}
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cp_bu<-paste0(bu_path, "/", format(Sys.time(), format="%Y%m%d"),"-",db)
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file.copy(dbfile, cp_bu)
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}
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sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
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if (isFALSE(verb)){
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sqlQuery(conn, "SELECT O.NHC,S.*
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FROM SAMPLES S
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INNER JOIN OVID O
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ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs) %>%
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group_by(NHC,OVID) %>% summarise(Samples=length(samples), Names=paste0(samples, collapse = ";")) %>% merge(data.frame(NHC=nhcs),all=T)
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}else{
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sqlQuery(conn, "SELECT O.NHC,S.*
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FROM SAMPLES S
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INNER JOIN OVID O
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ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
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}
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}
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sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
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ovid<-sqlFetch(conn,"OVID")
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new.nhc<-nhcs[!nhcs %in% ovid$NHC]
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next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
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last.num<-next.num+(length(new.nhc)-1)
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upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
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rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
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upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
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if (sinc){
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### !! Atención, esto cambia la base de datos:
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sqlSave(conn, upd.ovid, tablename="OVID", append = T)
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print("La base ha sido actualizada.")
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}
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if (verb){
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return(upd.ovid)
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}
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}
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sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T){
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upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
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if (samples.mod){
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## Generar código para las nuevas muestras
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samples<-sqlFetch(conn, "SAMPLES")
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if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
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next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1
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}else{
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next.samp<-1
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}
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last.samp<-next.samp+(length(nhcs)-1)
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new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
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new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
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samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
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}
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if (clinics.mod){
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## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
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upd.clinics<-sqlFetch(conn, "CLINICS")
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ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
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upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
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upd.clinics$NHC<-as.character(upd.clinics$NHC)
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for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
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}
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## Exportar tablas a la plantilla de entrada para su rellenado
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wb <- loadWorkbook(file)
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writeData(wb, "NHC", upd.ovid)
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if (samples.mod){writeData(wb,"samples",samples.exp)}
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if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
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saveWorkbook(wb,file,overwrite = TRUE)
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}
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sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){
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## Añadir código de muestra nueva a la base de datos
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nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
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upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
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if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
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if (sinc.samples & nrow(upd.samples) > 0){
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upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
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### !! Atención, esto cambia la base de datos:
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sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date"))
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print("Tabla SAMPLES sincronizada.")
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}
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## Añadir datos clínicos modificados a la base de datos
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upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
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ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
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rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
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clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
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rownames(clinics.mod)<-rnames
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### !! Atención, esto cambia la base de datos:
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if (sinc.clinics){
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fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
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for (i in fechas){
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clinics.mod[,i]<-as.Date(clinics.mod[,i])
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}
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sqlUpdate(conn, clinics.mod,"CLINICS")
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print("Tabla CLINICS modificada.")
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}
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## Añadir datos clínicos nuevos a la base de datos
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nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
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ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
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clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
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if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
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### !! Atención, esto cambia la base de datos:
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if (sinc.clinics){
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fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
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varTypes<-rep("Date",length(fechas))
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names(varTypes)<-fechas
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for (i in fechas){
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clinics.new[,i]<-as.Date(clinics.new[,i])
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}
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sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
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print("Tabla CLINICS sincronizada.")
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}
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}
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