Browse Source

Generación de funciones a partir del script y creación de un ejemplo en "workflow.R".

main
Costa 3 years ago
parent
commit
05962b66eb
3 changed files with 147 additions and 1 deletions
  1. +1
    -1
      RellenarOVBD.R
  2. +126
    -0
      sqlFunctions.R
  3. +20
    -0
      workflow.R

+ 1
- 1
RellenarOVBD.R

@ -56,7 +56,7 @@ 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)]<-""
# samples.exp[is.na(samples.exp)]<-""
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(dta, "CLINICS")

+ 126
- 0
sqlFunctions.R

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

+ 20
- 0
workflow.R

@ -0,0 +1,20 @@
source("sqlFunctions.R")
# Cargar dependencias
sqlInitialize()
# Inicializar conexión
dta<-odbcConnectAccess2007(access.file = file,
pwd = .rs.askForPassword("Enter password:"))
# Ver si ya hay muestras de los pacientes (opcional, para uno mismo)
sqlShowSamples()
# Generar código OVID para muestras nuevas
sqlGenOVID(sinc=T)
# Rellenar fichero plantilla "QueryOV.xlsx"
sqlWriteTemp()
# Sincronizar lo rellenado en las pestañas samples y clinics
sqlSincBD(sinc.samples = T, sinc.clinics = T)

Loading…
Cancel
Save