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@ -5,3 +5,129 @@ sqlDropLast<-function(conn, tablename, droplast=1){ |
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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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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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} |