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