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