Scripts relacionados con el acceso y análisis en bases de datos Access.
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require(RODBC)
sqlLastDrop<-function(conn, tablename, droplast=1,dbtype=NULL){
if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
table<-sqlFetch(conn, tablename)
table<-table[1:(nrow(table)-droplast),]
if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
if (dbtype == "UM"){
sqlDrop(conn, tablename)
sqlSave(conn, table, tablename = tablename, safer = F)}
}
sqlInitialize<-function(ruta="ruta_database.R"){
library(tidyverse)
library(RODBC)
library(openxlsx)
## Conexión a la base de datos
source(ruta, encoding = "UTF-8")
}
sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){
if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){bu.dir<-"BU_UM"}
if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){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, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype == "OV"){
db<-c("dbtables"="SAMPLES", "dbcode"="OVID", "dbsamples"="samples")
query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
}
if (dbtype == "UM"){
db<-c("dbtables"="MUESTRAS", "dbcode"="UMID", "dbsamples"="CODIGO")
query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
}
if (nrow(sqlQuery(conn, query) %>% filter(NHC %in% nhcs)) == 0){
return("No hay muestras de ningún paciente.")
}
if (isFALSE(verb)){
sqlQuery(conn, query) %>% filter(NHC %in% nhcs) %>%
group_by(NHC,UQ(rlang::sym(db["dbcode"]))) %>% summarise(Samples=length(UQ(rlang::sym(db["dbsamples"]))), Names=paste0(UQ(rlang::sym(db["dbsamples"])), collapse = ";")) %>%
merge(data.frame(NHC=nhcs),all=T) %>% mutate(NHC=factor(NHC,levels = unique(nhcs))) %>% arrange(NHC)
}else{
sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
}
}
sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype == "OV"){
db<-c("dbcode"="OVID", "dbpref"="OVID")
}
if (dbtype == "UM"){
db<-c("dbcode"="UMID","dbpref"="UMID")
}
if (dbtype == "CC"){
db<-c("dbcode"="PATID", "dbpref"="CCID")
}
dbid<-sqlFetch(conn,db["dbcode"])
new.nhc<-nhcs[!nhcs %in% dbid$NHC] %>% unique()
if(length(new.nhc) > 0){
if (nrow(dbid) == 0){next.num<-1}else{
next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
}
print(next.num)
last.num<-next.num+(length(new.nhc)-1)
newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbpref"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
if(dbtype=="OV"){
dbid<-rbind(dbid,newtab)
}
if(dbtype=="UM"){
dbid<-merge(dbid, newtab, all=T) %>% select(NHC,UMID) %>% arrange(UMID)
# dbid$Id<-as.numeric(rownames(dbid))
dbid$NHC<-as.numeric(dbid$NHC)
}
if (dbtype=="CC"){
dbid<-merge(dbid, newtab, all=T) %>% select(NHC,PATID) %>% arrange(PATID)
dbid$NHC<-as.numeric(dbid$NHC)
}
rownames(dbid)<-as.character(1:nrow(dbid))
dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
if (sinc){
### !! Atención, esto cambia la base de datos:
sqlSave(conn, dbid, tablename=db["dbcode"], append = T, rownames = F)
print("La base ha sido actualizada.")
}
if (verb){
return(dbid)
}
}else{
print("No hay pacientes nuevos.")
}
}
sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL, today=F){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
if (dbtype=="OV"){
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)
}
if (dbtype=="UM"){
upd.umid<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
if (samples.mod){
## Generar código para las nuevas muestras
samples<-sqlFetch(conn, "MUESTRAS")
if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){
next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1
}else{
next.samp<-1
}
last.samp<-next.samp+(length(nhcs)-1)
new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
new.samp.df<-data.frame("NHC"=nhcs, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID"), all.x=T) %>% arrange(CODIGO)
samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
if (today==TRUE){
samples.exp$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y")
}
}
nhc.table<-read.xlsx(file, sheet = "NHC")
if (any(sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]) == T)){
nhcs.cnag<-nhc.table[sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]),"NHC"]
umid.cnag<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs.cnag) %>% pull(UMID)
sample.cnag<-samples.exp %>% filter(UMID %in% umid.cnag) %>% pull(CODIGO)
cnag.exp<-merge(data.frame("UMID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG") %>% slice(0), all=T)
if (today==TRUE){
cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
}
}else{cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0)}
if (any(sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]) == T)){
nhcs.rna<-nhc.table[sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]),"NHC"]
umid.rna<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs.rna) %>% pull(UMID)
sample.rna<-samples.exp %>% filter(UMID %in% umid.rna) %>% pull(CODIGO)
rna.exp<-merge(data.frame("UMID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA") %>% slice(0), all=T)
}else{rna.exp<- sqlFetch(dta, "RNADNA") %>% slice(0)}
if (clinics.mod){
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(conn, "CLINICOS")
umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="UMID")
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 <- createWorkbook(file)
addWorksheet(wb, "NHC")
addWorksheet(wb, "samples")
addWorksheet(wb, "CLINICS")
addWorksheet(wb, "CNAG")
addWorksheet(wb, "RNADNA")
writeData(wb, "NHC", merge(nhc.table, upd.umid, sort = F))
if (samples.mod){writeData(wb,"samples",samples.exp)}
if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
writeData(wb,"CNAG",cnag.exp)
writeData(wb,"RNADNA",rna.exp)
saveWorkbook(wb,file,overwrite = TRUE)
}
}
sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){
if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
## Añadir código de muestra nueva a la base de datos
if (dbtype == "OV"){
print("DB OV detectada")
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)
upd.samples$TIL_date<-as.Date(upd.samples$TIL_date)
### !! Atención, esto cambia la base de datos:
sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date"))
print("Tabla SAMPLES sincronizada.")
}
}
if (dbtype == "UM"){
print("DB UM detectada")
nsamples<-sqlFetch(conn, "MUESTRAS") %>% 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$FECHA_RECEPCION<-as.Date(upd.samples$FECHA_RECEPCION)
upd.samples$TIPO<-as.character(upd.samples$TIPO)
upd.samples$OBS<-as.character(upd.samples$OBS)
### !! Atención, esto cambia la base de datos:
sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
print("Tabla MUESTRAS sincronizada.")
}
}
## Añadir datos clínicos modificados a la base de datos
if (dbtype == "OV"){
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.")
}
}
if (dbtype == "UM"){
upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
rownames(clinics.mod)<-rnames
### !! Atención, esto cambia la base de datos:
if (sinc.clinics){
fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
for (i in fechas){
clinics.mod[,i]<-as.Date(clinics.mod[,i])
}
sqlUpdate(conn, clinics.mod,"CLINICOS", index="UMID")
print("Tabla CLINICOS modificada.")
}
}
## Añadir datos clínicos nuevos a la base de datos
if (dbtype == "OV"){
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.")
}
}
if (dbtype == "UM"){
nsamples.clin<-sqlFetch(conn, "CLINICOS") %>% nrow
umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(conn, "CLINICOS") %>% pull(UMID))]
clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC)
if (length(umid.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("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)]
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="CLINICOS", append = T, varTypes = varTypes, rownames = F)
print("Tabla CLINICOS sincronizada.")
}
}
}
sqlMultiSamples<-function(kbl=F, NHC=F, full=F){
query<-sqlQuery(dta, "SELECT U.UMID,U.NHC,M.FECHA_RECEPCION,M.TIPO,M.CODIGO,C.CODIGO,R.CODIGO,R.ESTADO
FROM ((UMID U
LEFT OUTER JOIN MUESTRAS M ON U.UMID=M.UMID)
LEFT OUTER JOIN CNAG C ON M.CODIGO=C.CODIGO)
LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2")
if (full==F){query<- query %>% filter(!is.na(CODIGO))}
if (NHC==F){query<- query %>% select(-NHC)}
query<-query %>% mutate(
CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
(!is.na(RNADNA) & (is.na(ESTADO)))~".",
TRUE~"")
) %>% select(-ESTADO)
if (kbl==T){
query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
}else{
return(query)
}
}