Correction of conflicts for merging UM to main.

Merge branch 'UM' # Conflicts: # workflow.R
2 years ago · 4ba729e6c6
5 changed files with 1200 additions and 395 deletions
--- a/Docs/Readme.md
+++ b/Docs/Readme.md
@ -8,6 +8,7 @@
 <li><a href="#sqlgenovid">sqlGenOVID</a></li>
 <li><a href="#sqlwritetemp">sqlWriteTemp</a></li>
 <li><a href="#sqlsincbd">sqlSincBD</a></li>
 <li><a href="#sqlmultisamples">sqlMultiSamples</a></li>
 </ul>
 </div>
@ -19,7 +20,7 @@
 Removes from Database the last (or the amount specified) entry.
 ### Usage
 sqlDropLast(conn, tablename, droplast=1)
 sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -27,6 +28,7 @@ Argument|Description
 conn|connection handle returned by odbcConnect.
 tablename|character: a database table name accessible from the connected DSN.
 droplast|the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Removes from Database the last (or the amount specified) entry.
@ -42,10 +44,17 @@ sqlDropLast(dta, "TableTest")
 ### Function
 ```r
 sqlDropLast<-function(conn, tablename, droplast=1){
 sqlDropLast<-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),]
  sqlSave(conn, table, tablename = tablename, safer = F)
  if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
  if (dbtype == "UM"){
    sqlDrop(conn, tablename)
    sqlSave(conn, table, tablename = tablename, safer = F)}
 }
 ```
@ -94,13 +103,14 @@ sqlInitialize<-function(){
 Creates a Back Up copy of the database.
 ### Usage
 sqlBackUp(dbfile=file,bu.dir="BU_OVARIO")
 sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)
 ### Arguments
 Argument|Description
 ---|---
 dbfile| Database File location.
 bu.dir| Directory under the DB file where the back up will be placed.
 conn|connection handle returned by odbcConnect.
 bu.dir|Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database.
 ### Details
 Creates a Back Up copy of the database. It adds the date in front of the back up file.
@ -116,7 +126,10 @@ sqlBackUp()
 ### Function
 ```r
 sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
 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){dbtype<-"BU_OVARIO"}
  db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
  bu_path<-gsub(db,bu.dir,dbfile)
  if (!dir.exists(bu_path)){
@ -136,7 +149,7 @@ sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
 Shows if there are already samples from the specified NHCs.
 ### Usage
 sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)
 sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -144,6 +157,7 @@ Argument|Description
 conn|connection handle returned by odbcConnect.
 nhcs|Character vector with the NHCs to test.
 verb|Verbose: if TRUE, all the columns from "SAMPLES" table are printed.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Takes the NHCs listed in the nhcs vector and checks if there are already samples from those patients.
@ -160,18 +174,27 @@ sqlShowSamples()
 ### Function
 ```r
 sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
 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, "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)
    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 = nhcs)) %>% arrange(NHC)
  }else{
    sqlQuery(conn, "SELECT O.NHC,S.* 
         FROM SAMPLES S 
         INNER JOIN OVID O 
         ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
    sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
  }
 }
 ```
@ -181,10 +204,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
 ## sqlGenOVID
 ### Description
 Generates new consecutive OVID code for the patients that are not found in the DB.
 Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
 ### Usage
 sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)
 sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -193,9 +216,10 @@ conn|connection handle returned by odbcConnect.
 nhcs|Character vector with the NHCs to test.
 verb|Verbose: if TRUE (default), it prints the data.frame with the generated OVID codes.
 sinc|If TRUE (default is FALSE for security), it adds the new entries to the "OVID" table in the DB.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Generates new consecutive OVID code for the patients that are not found in the DB.
 Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
 ### Value
 If verb is TRUE, it returns a data.frame.
@ -209,23 +233,41 @@ sqlGenOVID(sinc=T)
 ### Function
 ```r
 sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
  ovid<-sqlFetch(conn,"OVID")
 sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=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"}
  new.nhc<-nhcs[!nhcs %in% ovid$NHC]
  next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
  if (dbtype == "OV"){
    db<-c("dbcode"="OVID")
  }
  if (dbtype == "UM"){
    db<-c("dbcode"="UMID")
  }
  dbid<-sqlFetch(conn,db["dbcode"])
  new.nhc<-nhcs[!nhcs %in% dbid$NHC]
  next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
  last.num<-next.num+(length(new.nhc)-1)
  upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
  rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
  upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
  newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
  if(dbtype=="OV"){
    dbid<-rbind(dbid,newtab)
  }
  if(dbtype=="UM"){
    dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
    dbid$Id<-as.numeric(rownames(dbid))
    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, upd.ovid, tablename="OVID", append = T)
    sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
    print("La base ha sido actualizada.")
  }
  if (verb){
    return(upd.ovid)
    return(dbid)
  }
 }
 ```
@ -235,10 +277,10 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
 ## sqlWriteTemp
 ### Description
 Fills the Query Template file with the OVID and OV newly generated codes.
 Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.
 ### Usage
 sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T)
 sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -248,9 +290,10 @@ nhcs|Character vector with the NHCs to test.
 file|Template file that will be used to interact with the DB.
 samples.mod|If TRUE (default), it fills the "samples" template sheet.
 clinics.mod|If TRUE (default), it fills the "CLINICS" template sheet.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.
 Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.
 ### Value
 Invisibly for success (and failures cause errors).
@ -265,37 +308,74 @@ sqlWriteTemp()
 ### Function
 ```r
 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
 sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, 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"){
    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])}
    }
    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<-merge(sqlFetch(dta,"UMID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "CODIGO"=new.samp))
      samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
    }
    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 %>% select(-Id), 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 <- loadWorkbook(file)
    writeData(wb, "NHC", upd.umid)
    if (samples.mod){writeData(wb,"samples",samples.exp)}
    if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  ## 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)
 }
 ```
@ -307,7 +387,7 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
 Updates the DB with the information filled in the template file.
 ### Usage
 sqlSincBD(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F)
 sqlSincBD(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -316,6 +396,7 @@ conn|connection handle returned by odbcConnect.
 filetemp|Template file that will be used to interact with the DB.
 sinc.samples|If TRUE (default is FALSE for security), it updates the SAMPLES table in the DB with the information in the "samples" template sheet.
 clinics.mod|If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the "CLINICS" template sheet.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Updates the DB with the information filled in the template file. All the "samples" entries are added as new rows (as all samples are new even if the patient was already in the DB). The new patients included in the "CLINICS" sheet are introduced in the DB as new rows and the ones that were already there are modified in its previous row location.
@ -334,52 +415,168 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
 ### Function
 ```r
 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}
 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"}
  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 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
  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])
  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")
      print("Tabla CLINICOS modificada.")
    }
    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])
  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)
      print("Tabla CLINICOS sincronizada.")
    }
    sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
    print("Tabla CLINICS sincronizada.")
  }
 }
 ```
 ```
 ---
 ## sqlMultiSamples
 ### Description
 Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
 ### Usage
 sqlMultiSamples(kbl=F, NHC=F, full=F)
 ### Arguments
 Argument|Description
 ---|---
 kbl|formats the output table with the kableEstra style. Defaults to F.
 NHC|adds the NHC to the table in addition to the UMID. Defaults to F.
 full|prints also the patients that doesn't appear in the MUESTRAS table. Defaults to F.
 ### Details
 Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
 ### Value
 A data.frame or a kableExtra table.
 ### Examples
 ```r
 dta<-odbcConnect("test")
 sqlMultiSamples()
 ```
 ### Function
 ```r
 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)
    }
 }
 ```
--- a/Docs/sqlFunctions-doc.Rmd
+++ b/Docs/sqlFunctions-doc.Rmd
@ -18,7 +18,7 @@ knitr::opts_chunk$set(echo = TRUE)
 Removes from Database the last (or the amount specified) entry.
 ### Usage
 sqlDropLast(conn, tablename, droplast=1)
 sqlLastDrop(conn, tablename, droplast=1, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -26,6 +26,7 @@ Argument|Description
 conn|connection handle returned by odbcConnect.
 tablename|character: a database table name accessible from the connected DSN.
 droplast|the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Removes from Database the last (or the amount specified) entry.
@ -36,15 +37,22 @@ Invisibly for success (and failures cause errors).
 ### Examples
 ```r
 dta<-odbcConnect("test")
 sqlDropLast(dta, "TableTest")
 sqlLastDrop(dta, "TableTest")
 ```
 ### Function
 ```r
 sqlDropLast<-function(conn, tablename, droplast=1){
 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),]
  sqlSave(conn, table, tablename = tablename, safer = F)
  if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
  if (dbtype == "UM"){
    sqlDrop(conn, tablename)
    sqlSave(conn, table, tablename = tablename, safer = F)}
 }
 ```
@ -93,13 +101,14 @@ sqlInitialize<-function(){
 Creates a Back Up copy of the database.
 ### Usage
 sqlBackUp(dbfile=file,bu.dir="BU_OVARIO")
 sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)
 ### Arguments
 Argument|Description
 ---|---
 dbfile| Database File location.
 bu.dir| Directory under the DB file where the back up will be placed.
 conn|connection handle returned by odbcConnect.
 bu.dir|Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database.
 ### Details
 Creates a Back Up copy of the database. It adds the date in front of the back up file.
@ -115,7 +124,10 @@ sqlBackUp()
 ### Function
 ```r
 sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
 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){dbtype<-"BU_OVARIO"}
  db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
  bu_path<-gsub(db,bu.dir,dbfile)
  if (!dir.exists(bu_path)){
@ -135,7 +147,7 @@ sqlBackUp<-function(dbfile=file,bu.dir="BU_OVARIO"){
 Shows if there are already samples from the specified NHCs.
 ### Usage
 sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)
 sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -143,6 +155,7 @@ Argument|Description
 conn|connection handle returned by odbcConnect.
 nhcs|Character vector with the NHCs to test.
 verb|Verbose: if TRUE, all the columns from "SAMPLES" table are printed.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Takes the NHCs listed in the nhcs vector and checks if there are already samples from those patients.
@ -159,18 +172,27 @@ sqlShowSamples()
 ### Function
 ```r
 sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
 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, "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)
    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 = nhcs)) %>% arrange(NHC)
  }else{
    sqlQuery(conn, "SELECT O.NHC,S.* 
         FROM SAMPLES S 
         INNER JOIN OVID O 
         ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
    sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
  }
 }
 ```
@ -180,10 +202,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
 ## sqlGenOVID
 ### Description
 Generates new consecutive OVID code for the patients that are not found in the DB.
 Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
 ### Usage
 sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)
 sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -192,9 +214,10 @@ conn|connection handle returned by odbcConnect.
 nhcs|Character vector with the NHCs to test.
 verb|Verbose: if TRUE (default), it prints the data.frame with the generated OVID codes.
 sinc|If TRUE (default is FALSE for security), it adds the new entries to the "OVID" table in the DB.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Generates new consecutive OVID code for the patients that are not found in the DB.
 Generates new consecutive OVID or UMID code for the patients that are not found in the DB.
 ### Value
 If verb is TRUE, it returns a data.frame.
@ -208,23 +231,41 @@ sqlGenOVID(sinc=T)
 ### Function
 ```r
 sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
  ovid<-sqlFetch(conn,"OVID")
 sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=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"}
  new.nhc<-nhcs[!nhcs %in% ovid$NHC]
  next.num<-gsub("OVID","",ovid$OVID) %>% as.numeric %>% max(na.rm=T)+1
  if (dbtype == "OV"){
    db<-c("dbcode"="OVID")
  }
  if (dbtype == "UM"){
    db<-c("dbcode"="UMID")
  }
  dbid<-sqlFetch(conn,db["dbcode"])
  new.nhc<-nhcs[!nhcs %in% dbid$NHC]
  next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% 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))
  newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],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(Id,NHC,UMID) %>% arrange(Id)
    dbid$Id<-as.numeric(rownames(dbid))
    dbid$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, upd.ovid, tablename="OVID", append = T)
    sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
    print("La base ha sido actualizada.")
  }
  if (verb){
    return(upd.ovid)
    return(dbid)
  }
 }
 ```
@ -234,10 +275,10 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
 ## sqlWriteTemp
 ### Description
 Fills the Query Template file with the OVID and OV newly generated codes.
 Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.
 ### Usage
 sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T)
 sqlWriteTemp(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -247,9 +288,10 @@ nhcs|Character vector with the NHCs to test.
 file|Template file that will be used to interact with the DB.
 samples.mod|If TRUE (default), it fills the "samples" template sheet.
 clinics.mod|If TRUE (default), it fills the "CLINICS" template sheet.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.
 Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of "CLINICS" table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.
 ### Value
 Invisibly for success (and failures cause errors).
@ -264,37 +306,74 @@ sqlWriteTemp()
 ### Function
 ```r
 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$samples) %>% as.numeric %>% max(na.rm=T)+1  
    }else{
      next.samp<-1
 sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  if (dbtype=="OV"){
    upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples<-sqlFetch(conn, "SAMPLES")
      if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$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$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
    }
    last.samp<-next.samp+(length(nhcs)-1)
    new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
    new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
    samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
  }
  if (clinics.mod){
    ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
    upd.clinics<-sqlFetch(conn, "CLINICS")
    ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
    upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
    upd.clinics$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$CODIGO) %>% as.numeric %>% max(na.rm=T)+1  
      }else{
        next.samp<-1
      }
      last.samp<-next.samp+(length(nhcs)-1)
      new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
      new.samp.df<-merge(sqlFetch(dta,"UMID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "CODIGO"=new.samp))
      samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
    }
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics<-sqlFetch(conn, "CLINICOS")
      umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
      upd.clinics<-merge(umid.new,upd.clinics %>% select(-Id), all.x=T, by="UMID")
      upd.clinics$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 <- loadWorkbook(file)
    writeData(wb, "NHC", upd.umid)
    if (samples.mod){writeData(wb,"samples",samples.exp)}
    if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  ## 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)
 }
 ```
@ -306,7 +385,7 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
 Updates the DB with the information filled in the template file.
 ### Usage
 sqlSincBD(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F)
 sqlSincBD(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL)
 ### Arguments
 Argument|Description
@ -315,6 +394,7 @@ conn|connection handle returned by odbcConnect.
 filetemp|Template file that will be used to interact with the DB.
 sinc.samples|If TRUE (default is FALSE for security), it updates the SAMPLES table in the DB with the information in the "samples" template sheet.
 clinics.mod|If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the "CLINICS" template sheet.
 dbtype|used to manually specify the database type. It defaults to NULL and the type is deduced.
 ### Details
 Updates the DB with the information filled in the template file. All the "samples" entries are added as new rows (as all samples are new even if the patient was already in the DB). The new patients included in the "CLINICS" sheet are introduced in the DB as new rows and the ones that were already there are modified in its previous row location.
@ -333,52 +413,168 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
 ### Function
 ```r
 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}
 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"}
  if (sinc.samples & nrow(upd.samples) > 0){
    upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
    ### !! Atención, esto cambia la base de datos:
    sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date"))
    print("Tabla SAMPLES sincronizada.")
  ## Añadir código de muestra nueva a la base de datos
  if (dbtype == "OV"){
    print("DB OV detectada")
    nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
    upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
    if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
    if (sinc.samples & nrow(upd.samples) > 0){
      upd.samples$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$OBS)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
      print("Tabla MUESTRAS sincronizada.")
    }
  }
  ## Añadir datos clínicos modificados a la base de datos
  upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
  ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
  rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
  clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
  rownames(clinics.mod)<-rnames
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
    for (i in fechas){
      clinics.mod[,i]<-as.Date(clinics.mod[,i])
  if (dbtype == "OV"){
    upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
    ovid.mod<-upd.clinics$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$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
    rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
    clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
    rownames(clinics.mod)<-rnames
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
      for (i in fechas){
        clinics.mod[,i]<-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,"CLINICOS")
      print("Tabla CLINICOS modificada.")
    }
    sqlUpdate(conn, clinics.mod,"CLINICS")
    print("Tabla CLINICS modificada.")
  }
  ## Añadir datos clínicos nuevos a la base de datos
  nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
  ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
  clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
  if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
    varTypes<-rep("Date",length(fechas))
    names(varTypes)<-fechas
    for (i in fechas){
      clinics.new[,i]<-as.Date(clinics.new[,i])
  if (dbtype == "OV"){
    nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
    ovid.new<-upd.clinics$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)
      print("Tabla CLINICOS sincronizada.")
    }
    sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
    print("Tabla CLINICS sincronizada.")
  }
 }
 ```
 ```
 ---
 ## sqlMultiSamples
 ### Description
 Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
 ### Usage
 sqlMultiSamples(kbl=F, NHC=F, full=F)
 ### Arguments
 Argument|Description
 ---|---
 kbl|formats the output table with the kableEstra style. Defaults to F.
 NHC|adds the NHC to the table in addition to the UMID. Defaults to F.
 full|prints also the patients that doesn't appear in the MUESTRAS table. Defaults to F.
 ### Details
 Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.
 ### Value
 A data.frame or a kableExtra table.
 ### Examples
 ```r
 dta<-odbcConnect("test")
 sqlMultiSamples()
 ```
 ### Function
 ```r
 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)
    }
 }
 ```
--- a/Docs/sqlFunctions-doc.html
+++ b/Docs/sqlFunctions-doc.html
@ -176,6 +176,7 @@ pre code {
 <li><a href="#sqlgenovid">sqlGenOVID</a></li>
 <li><a href="#sqlwritetemp">sqlWriteTemp</a></li>
 <li><a href="#sqlsincbd">sqlSincBD</a></li>
 <li><a href="#sqlmultisamples">sqlMultiSamples</a></li>
 </ul>
 </div>
@ -188,7 +189,7 @@ pre code {
 </div>
 <div id="usage" class="section level3">
 <h3>Usage</h3>
 <p>sqlDropLast(conn, tablename, droplast=1)</p>
 <p>sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)</p>
 </div>
 <div id="arguments" class="section level3">
 <h3>Arguments</h3>
@ -216,6 +217,10 @@ pre code {
 <td>droplast</td>
 <td>the amount of lines to be removed from the table strating from tail. By default, it removes only 1 line.</td>
 </tr>
 <tr class="even">
 <td>dbtype</td>
 <td>used to manually specify the database type. It defaults to NULL and the type is deduced.</td>
 </tr>
 </tbody>
 </table>
 </div>
@ -234,10 +239,17 @@ sqlDropLast(dta, "TableTest")
 </div>
 <div id="function" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlDropLast&lt;-function(conn, tablename, droplast=1){
 <pre class="r"><code>sqlDropLast&lt;-function(conn, tablename, droplast=1,dbtype=NULL){
  if(sqlTables(conn) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;UM&quot;}
  if(sqlTables(conn) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;OV&quot;}
  table&lt;-sqlFetch(conn, tablename)
  table&lt;-table[1:(nrow(table)-droplast),]
  sqlSave(conn, table, tablename = tablename, safer = F)
  if (dbtype == &quot;OV&quot;){sqlSave(conn, table, tablename = tablename, safer = F)}
  if (dbtype == &quot;UM&quot;){
    sqlDrop(conn, tablename)
    sqlSave(conn, table, tablename = tablename, safer = F)}
 }</code></pre>
 <hr />
 </div>
@ -298,11 +310,15 @@ sqlDropLast(dta, "TableTest")
 </div>
 <div id="usage-2" class="section level3">
 <h3>Usage</h3>
 <p>sqlBackUp(dbfile=file,bu.dir=“BU_OVARIO”)</p>
 <p>sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)</p>
 </div>
 <div id="arguments-2" class="section level3">
 <h3>Arguments</h3>
 <table>
 <colgroup>
 <col width="50%" />
 <col width="50%" />
 </colgroup>
 <thead>
 <tr class="header">
 <th>Argument</th>
@ -315,8 +331,12 @@ sqlDropLast(dta, "TableTest")
 <td>Database File location.</td>
 </tr>
 <tr class="even">
 <td>conn</td>
 <td>connection handle returned by odbcConnect.</td>
 </tr>
 <tr class="odd">
 <td>bu.dir</td>
 <td>Directory under the DB file where the back up will be placed.</td>
 <td>Directory under the DB file where the back up will be placed. It defaults to NULL and is deduced from conn database.</td>
 </tr>
 </tbody>
 </table>
@ -336,7 +356,10 @@ sqlBackUp()
 </div>
 <div id="function-2" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlBackUp&lt;-function(dbfile=file,bu.dir=&quot;BU_OVARIO&quot;){
 <pre class="r"><code>sqlBackUp&lt;-function(dbfile=file,conn=dta,bu.dir=NULL){
  if(sqlTables(conn) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){bu.dir&lt;-&quot;BU_UM&quot;}
  if(sqlTables(conn) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;BU_OVARIO&quot;}
  db=strsplit(dbfile, &quot;/&quot;)[[1]]%&gt;% tail(n=1)
  bu_path&lt;-gsub(db,bu.dir,dbfile)
  if (!dir.exists(bu_path)){
@ -357,11 +380,15 @@ sqlBackUp()
 </div>
 <div id="usage-3" class="section level3">
 <h3>Usage</h3>
 <p>sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F)</p>
 <p>sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)</p>
 </div>
 <div id="arguments-3" class="section level3">
 <h3>Arguments</h3>
 <table>
 <colgroup>
 <col width="50%" />
 <col width="50%" />
 </colgroup>
 <thead>
 <tr class="header">
 <th>Argument</th>
@ -381,6 +408,10 @@ sqlBackUp()
 <td>verb</td>
 <td>Verbose: if TRUE, all the columns from “SAMPLES” table are printed.</td>
 </tr>
 <tr class="even">
 <td>dbtype</td>
 <td>used to manually specify the database type. It defaults to NULL and the type is deduced.</td>
 </tr>
 </tbody>
 </table>
 </div>
@ -400,18 +431,27 @@ sqlShowSamples()
 </div>
 <div id="function-3" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlShowSamples&lt;-function(conn=dta, nhcs=nhc.test, verb=F){
 <pre class="r"><code>sqlShowSamples&lt;-function(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL){
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;UM&quot;}
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;OV&quot;}
  if (dbtype == &quot;OV&quot;){
    db&lt;-c(&quot;dbtables&quot;=&quot;SAMPLES&quot;, &quot;dbcode&quot;=&quot;OVID&quot;, &quot;dbsamples&quot;=&quot;samples&quot;)
    query&lt;-paste0(&quot;SELECT O.NHC,S.* FROM &quot;,db[&quot;dbtables&quot;],&quot; S INNER JOIN &quot;,db[&quot;dbcode&quot;],&quot; O ON O.&quot;,db[&quot;dbcode&quot;],&quot;=S.&quot;,db[&quot;dbcode&quot;])
  }
  if (dbtype == &quot;UM&quot;){
    db&lt;-c(&quot;dbtables&quot;=&quot;MUESTRAS&quot;, &quot;dbcode&quot;=&quot;UMID&quot;, &quot;dbsamples&quot;=&quot;CODIGO&quot;)
    query&lt;-paste0(&quot;SELECT O.NHC,S.* FROM &quot;,db[&quot;dbtables&quot;],&quot; S INNER JOIN &quot;,db[&quot;dbcode&quot;],&quot; O ON O.&quot;,db[&quot;dbcode&quot;],&quot;=S.&quot;,db[&quot;dbcode&quot;])
  }
  if (nrow(sqlQuery(conn, query) %&gt;% filter(NHC %in% nhcs)) == 0){
    return(&quot;No hay muestras de ningún paciente.&quot;)
  }
  if (isFALSE(verb)){
    sqlQuery(conn, &quot;SELECT O.NHC,S.* 
         FROM SAMPLES S 
         INNER JOIN OVID O 
         ON O.OVID=S.OVID&quot;) %&gt;% filter(NHC %in% nhcs) %&gt;% 
    group_by(NHC,OVID) %&gt;% summarise(Samples=length(samples), Names=paste0(samples, collapse = &quot;;&quot;)) %&gt;% merge(data.frame(NHC=nhcs),all=T)
    sqlQuery(conn, query) %&gt;% filter(NHC %in% nhcs) %&gt;% 
    group_by(NHC,UQ(rlang::sym(db[&quot;dbcode&quot;]))) %&gt;% summarise(Samples=length(UQ(rlang::sym(db[&quot;dbsamples&quot;]))), Names=paste0(UQ(rlang::sym(db[&quot;dbsamples&quot;])), collapse = &quot;;&quot;)) %&gt;% 
      merge(data.frame(NHC=nhcs),all=T) %&gt;% mutate(NHC=factor(NHC,levels = nhcs)) %&gt;% arrange(NHC)
  }else{
    sqlQuery(conn, &quot;SELECT O.NHC,S.* 
         FROM SAMPLES S 
         INNER JOIN OVID O 
         ON O.OVID=S.OVID&quot;) %&gt;% filter(NHC %in% nhcs)
    sqlQuery(conn, query) %&gt;% filter(NHC %in% nhcs)
  }
 }</code></pre>
 <hr />
@ -421,11 +461,11 @@ sqlShowSamples()
 <h2>sqlGenOVID</h2>
 <div id="description-4" class="section level3">
 <h3>Description</h3>
 <p>Generates new consecutive OVID code for the patients that are not found in the DB.</p>
 <p>Generates new consecutive OVID or UMID code for the patients that are not found in the DB.</p>
 </div>
 <div id="usage-4" class="section level3">
 <h3>Usage</h3>
 <p>sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F)</p>
 <p>sqlGenOVID(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL)</p>
 </div>
 <div id="arguments-4" class="section level3">
 <h3>Arguments</h3>
@ -457,12 +497,16 @@ sqlShowSamples()
 <td>sinc</td>
 <td>If TRUE (default is FALSE for security), it adds the new entries to the “OVID” table in the DB.</td>
 </tr>
 <tr class="odd">
 <td>dbtype</td>
 <td>used to manually specify the database type. It defaults to NULL and the type is deduced.</td>
 </tr>
 </tbody>
 </table>
 </div>
 <div id="details-4" class="section level3">
 <h3>Details</h3>
 <p>Generates new consecutive OVID code for the patients that are not found in the DB.</p>
 <p>Generates new consecutive OVID or UMID code for the patients that are not found in the DB.</p>
 </div>
 <div id="value-4" class="section level3">
 <h3>Value</h3>
@ -476,23 +520,41 @@ sqlGenOVID(sinc=T)
 </div>
 <div id="function-4" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlGenOVID&lt;-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F){
  ovid&lt;-sqlFetch(conn,&quot;OVID&quot;)
 <pre class="r"><code>sqlGenOVID&lt;-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;UM&quot;}
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;OV&quot;}
  if (dbtype == &quot;OV&quot;){
    db&lt;-c(&quot;dbcode&quot;=&quot;OVID&quot;)
  }
  if (dbtype == &quot;UM&quot;){
    db&lt;-c(&quot;dbcode&quot;=&quot;UMID&quot;)
  }
  new.nhc&lt;-nhcs[!nhcs %in% ovid$NHC]
  next.num&lt;-gsub(&quot;OVID&quot;,&quot;&quot;,ovid$OVID) %&gt;% as.numeric %&gt;% max(na.rm=T)+1
  dbid&lt;-sqlFetch(conn,db[&quot;dbcode&quot;])
  new.nhc&lt;-nhcs[!nhcs %in% dbid$NHC]
  next.num&lt;-gsub(db[&quot;dbcode&quot;],&quot;&quot;,dbid[,db[&quot;dbcode&quot;]]) %&gt;% as.numeric %&gt;% max(na.rm=T)+1
  last.num&lt;-next.num+(length(new.nhc)-1)
  upd.ovid&lt;-rbind(ovid,data.frame(&quot;NHC&quot;=new.nhc, &quot;OVID&quot;=sprintf(&quot;OVID%04d&quot;,next.num:last.num)))
  rownames(upd.ovid)&lt;-as.character(1:nrow(upd.ovid))
  upd.ovid&lt;-filter(upd.ovid, NHC %in% new.nhc) %&gt;% mutate(NHC=as.character(NHC))
  newtab&lt;-data.frame(&quot;NHC&quot;=new.nhc, &quot;ID&quot;=sprintf(&quot;%s%04d&quot;,db[&quot;dbcode&quot;],next.num:last.num)) %&gt;% rename(!!db[&quot;dbcode&quot;]:=&quot;ID&quot;)
  if(dbtype==&quot;OV&quot;){
    dbid&lt;-rbind(dbid,newtab)
  }
  if(dbtype==&quot;UM&quot;){
    dbid&lt;-merge(dbid, newtab, all=T) %&gt;% select(Id,NHC,UMID) %&gt;% arrange(Id)
    dbid$Id&lt;-as.numeric(rownames(dbid))
    dbid$NHC&lt;-as.numeric(dbid$NHC)
  }
  rownames(dbid)&lt;-as.character(1:nrow(dbid))
  dbid&lt;-filter(dbid, NHC %in% new.nhc) %&gt;% mutate(NHC=as.character(NHC))
  if (sinc){
    ### !! Atención, esto cambia la base de datos:
    sqlSave(conn, upd.ovid, tablename=&quot;OVID&quot;, append = T)
    sqlSave(conn, dbid, tablename=db[&quot;dbcode&quot;], append = T)
    print(&quot;La base ha sido actualizada.&quot;)
  }
  if (verb){
    return(upd.ovid)
    return(dbid)
  }
 }</code></pre>
 <hr />
@ -502,15 +564,19 @@ sqlGenOVID(sinc=T)
 <h2>sqlWriteTemp</h2>
 <div id="description-5" class="section level3">
 <h3>Description</h3>
 <p>Fills the Query Template file with the OVID and OV newly generated codes.</p>
 <p>Fills the Query Template file with the OVID or UMID and OV or UM newly generated codes.</p>
 </div>
 <div id="usage-5" class="section level3">
 <h3>Usage</h3>
 <p>sqlWriteTemp(conn=dta, nhcs=nhc.test, file=“queryOV.xlsx”, samples.mod=T, clinics.mod=T)</p>
 <p>sqlWriteTemp(conn=dta, nhcs=nhc.test, file=“queryOV.xlsx”, samples.mod=T, clinics.mod=T, dbtype=NULL)</p>
 </div>
 <div id="arguments-5" class="section level3">
 <h3>Arguments</h3>
 <table>
 <colgroup>
 <col width="50%" />
 <col width="50%" />
 </colgroup>
 <thead>
 <tr class="header">
 <th>Argument</th>
@ -538,12 +604,16 @@ sqlGenOVID(sinc=T)
 <td>clinics.mod</td>
 <td>If TRUE (default), it fills the “CLINICS” template sheet.</td>
 </tr>
 <tr class="even">
 <td>dbtype</td>
 <td>used to manually specify the database type. It defaults to NULL and the type is deduced.</td>
 </tr>
 </tbody>
 </table>
 </div>
 <div id="details-5" class="section level3">
 <h3>Details</h3>
 <p>Fills the Query Template file with the OVID and OV newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of “CLINICS” table, if there were already an entry in the DB for that OVID code, the template file is filled with that information.</p>
 <p>Fills the Query Template file with the OVID and OV or UMID and UM newly generated codes. It is required that the DB has been updated with the sqlGenOVID function. It replaces previous content in the template file sheets that are filled. In the case of “CLINICS” table, if there were already an entry in the DB for that OVID/UMID code, the template file is filled with that information.</p>
 </div>
 <div id="value-5" class="section level3">
 <h3>Value</h3>
@ -558,37 +628,74 @@ sqlWriteTemp()
 </div>
 <div id="function-5" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlWriteTemp&lt;-function(conn=dta, nhcs=nhc.test, file=&quot;queryOV.xlsx&quot;, samples.mod=T, clinics.mod=T){
  upd.ovid&lt;-sqlFetch(conn, &quot;OVID&quot;) %&gt;% filter(NHC %in% nhcs)
  if (samples.mod){
    ## Generar código para las nuevas muestras
    samples&lt;-sqlFetch(conn, &quot;SAMPLES&quot;)
    if(sum(grepl(paste0(&quot;OV&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)), samples$samples)) &gt; 0){
      next.samp&lt;-gsub(paste0(&quot;OV&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)),&quot;&quot;, samples$samples) %&gt;% as.numeric %&gt;% max(na.rm=T)+1  
    }else{
      next.samp&lt;-1
 <pre class="r"><code>sqlWriteTemp&lt;-function(conn=dta, nhcs=nhc.test, file=&quot;queryOV.xlsx&quot;, samples.mod=T, clinics.mod=T, dbtype=NULL){
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;UM&quot;}
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;OV&quot;}
  if (dbtype==&quot;OV&quot;){
    upd.ovid&lt;-sqlFetch(conn, &quot;OVID&quot;) %&gt;% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples&lt;-sqlFetch(conn, &quot;SAMPLES&quot;)
      if(sum(grepl(paste0(&quot;OV&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)), samples$samples)) &gt; 0){
        next.samp&lt;-gsub(paste0(&quot;OV&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)),&quot;&quot;, samples$samples) %&gt;% as.numeric %&gt;% max(na.rm=T)+1  
      }else{
        next.samp&lt;-1
      }
      last.samp&lt;-next.samp+(length(nhcs)-1)
      new.samp&lt;-sprintf(&quot;OV%s%02d&quot;,Sys.time() %&gt;% format(&quot;%y&quot;),next.samp:last.samp)
      new.samp.df&lt;-merge(sqlFetch(dta,&quot;OVID&quot;) %&gt;% merge(data.frame(&quot;NHC&quot;=nhcs)), data.frame(&quot;NHC&quot;=nhcs, &quot;samples&quot;=new.samp))
      samples.exp&lt;-merge(samples %&gt;% slice(0), new.samp.df %&gt;% select(-NHC), all=T) %&gt;% select(colnames(samples)) %&gt;% arrange(samples)
    }
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics&lt;-sqlFetch(conn, &quot;CLINICS&quot;)
      ovid.new&lt;-sqlFetch(conn, &quot;OVID&quot;) %&gt;% filter(NHC %in% nhcs)
      upd.clinics&lt;-merge(ovid.new,upd.clinics, all.x=T, by=&quot;OVID&quot;)
      upd.clinics$NHC&lt;-as.character(upd.clinics$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]&lt;-as.Date(upd.clinics[,i])}
    }
    last.samp&lt;-next.samp+(length(nhcs)-1)
    new.samp&lt;-sprintf(&quot;OV%s%02d&quot;,Sys.time() %&gt;% format(&quot;%y&quot;),next.samp:last.samp)
    new.samp.df&lt;-merge(sqlFetch(dta,&quot;OVID&quot;) %&gt;% merge(data.frame(&quot;NHC&quot;=nhcs)), data.frame(&quot;NHC&quot;=nhcs, &quot;samples&quot;=new.samp))
    samples.exp&lt;-merge(samples %&gt;% slice(0), new.samp.df %&gt;% select(-NHC), all=T) %&gt;% select(colnames(samples)) %&gt;% arrange(samples)
  }
  if (clinics.mod){
    ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
    upd.clinics&lt;-sqlFetch(conn, &quot;CLINICS&quot;)
    ovid.new&lt;-sqlFetch(conn, &quot;OVID&quot;) %&gt;% filter(NHC %in% nhcs)
    upd.clinics&lt;-merge(ovid.new,upd.clinics, all.x=T, by=&quot;OVID&quot;)
    upd.clinics$NHC&lt;-as.character(upd.clinics$NHC)
    for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]&lt;-as.Date(upd.clinics[,i])}
    ## Exportar tablas a la plantilla de entrada para su rellenado
    wb &lt;- loadWorkbook(file)
    writeData(wb, &quot;NHC&quot;, upd.ovid)
    if (samples.mod){writeData(wb,&quot;samples&quot;,samples.exp)}
    if (clinics.mod){writeData(wb,&quot;CLINICS&quot;,upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  if (dbtype==&quot;UM&quot;){
    upd.umid&lt;-sqlFetch(conn, &quot;UMID&quot;) %&gt;% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples&lt;-sqlFetch(conn, &quot;MUESTRAS&quot;)
      if(sum(grepl(paste0(&quot;UM&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)), samples$CODIGO)) &gt; 0){
        next.samp&lt;-gsub(paste0(&quot;UM&quot;,Sys.time() %&gt;% format(&quot;%y&quot;)),&quot;&quot;, samples$CODIGO) %&gt;% as.numeric %&gt;% max(na.rm=T)+1  
      }else{
        next.samp&lt;-1
      }
      last.samp&lt;-next.samp+(length(nhcs)-1)
      new.samp&lt;-sprintf(&quot;UM%s%02d&quot;,Sys.time() %&gt;% format(&quot;%y&quot;),next.samp:last.samp)
      new.samp.df&lt;-merge(sqlFetch(dta,&quot;UMID&quot;) %&gt;% merge(data.frame(&quot;NHC&quot;=nhcs)), data.frame(&quot;NHC&quot;=nhcs, &quot;CODIGO&quot;=new.samp))
      samples.exp&lt;-merge(samples %&gt;% slice(0), new.samp.df %&gt;% select(-NHC), all=T) %&gt;% select(colnames(samples)) %&gt;% arrange(CODIGO)
    }
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics&lt;-sqlFetch(conn, &quot;CLINICOS&quot;)
      umid.new&lt;-sqlFetch(conn, &quot;UMID&quot;) %&gt;% filter(NHC %in% nhcs)
      upd.clinics&lt;-merge(umid.new,upd.clinics %&gt;% select(-Id), all.x=T, by=&quot;UMID&quot;)
      upd.clinics$NHC&lt;-as.character(upd.clinics$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]&lt;-as.Date(upd.clinics[,i])}
    }
    ## Exportar tablas a la plantilla de entrada para su rellenado
    wb &lt;- loadWorkbook(file)
    writeData(wb, &quot;NHC&quot;, upd.umid)
    if (samples.mod){writeData(wb,&quot;samples&quot;,samples.exp)}
    if (clinics.mod){writeData(wb,&quot;CLINICS&quot;,upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  ## Exportar tablas a la plantilla de entrada para su rellenado
  wb &lt;- loadWorkbook(file)
  writeData(wb, &quot;NHC&quot;, upd.ovid)
  if (samples.mod){writeData(wb,&quot;samples&quot;,samples.exp)}
  if (clinics.mod){writeData(wb,&quot;CLINICS&quot;,upd.clinics)}
  saveWorkbook(wb,file,overwrite = TRUE)
 }</code></pre>
 <hr />
 </div>
@ -601,7 +708,7 @@ sqlWriteTemp()
 </div>
 <div id="usage-6" class="section level3">
 <h3>Usage</h3>
 <p>sqlSincBD(conn=dta, filetemp=“QueryOV.xlsx”, sinc.samples=F, sinc.clinics=F)</p>
 <p>sqlSincBD(conn=dta, filetemp=“queryOV.xlsx”, sinc.samples=F, sinc.clinics=F, dbtype=NULL)</p>
 </div>
 <div id="arguments-6" class="section level3">
 <h3>Arguments</h3>
@ -633,6 +740,10 @@ sqlWriteTemp()
 <td>clinics.mod</td>
 <td>If TRUE (default is FALSE for security), it updates the CLINICS table in the DB with the information in the “CLINICS” template sheet.</td>
 </tr>
 <tr class="odd">
 <td>dbtype</td>
 <td>used to manually specify the database type. It defaults to NULL and the type is deduced.</td>
 </tr>
 </tbody>
 </table>
 </div>
@ -654,53 +765,193 @@ sqlSincBD(sinc.samples=T, sinc.clinics=T)
 </div>
 <div id="function-6" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlSincBD&lt;-function(conn=dta, filetemp=&quot;QueryOV.xlsx&quot;, sinc.samples=F, sinc.clinics=F){
  ## Añadir código de muestra nueva a la base de datos
  nsamples&lt;-sqlFetch(conn, &quot;SAMPLES&quot;) %&gt;% nrow
  upd.samples&lt;-read.xlsx(filetemp, sheet = &quot;samples&quot;, detectDates = T)
  if (nrow(upd.samples) &gt; 0){rownames(upd.samples)&lt;-(nsamples+1):(nsamples+nrow(upd.samples)) %&gt;% as.character}
 <pre class="r"><code>sqlSincBD&lt;-function(conn=dta, filetemp=&quot;queryOV.xlsx&quot;, sinc.samples=F, sinc.clinics=F, dbtype=NULL){
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;UMID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;UM&quot;}
  if(sqlTables(dta) %&gt;% filter(TABLE_NAME == &quot;OVID&quot;) %&gt;% nrow &gt; 0){dbtype&lt;-&quot;OV&quot;}
  if (sinc.samples &amp; nrow(upd.samples) &gt; 0){
    upd.samples$IQ_date&lt;-as.Date(upd.samples$IQ_date)
    ### !! Atención, esto cambia la base de datos:
    sqlSave(conn, upd.samples, tablename=&quot;SAMPLES&quot;, append = T, varTypes = c(&quot;IQ_date&quot;=&quot;date&quot;))
    print(&quot;Tabla SAMPLES sincronizada.&quot;)
  ## Añadir código de muestra nueva a la base de datos
  if (dbtype == &quot;OV&quot;){
    print(&quot;DB OV detectada&quot;)
    nsamples&lt;-sqlFetch(conn, &quot;SAMPLES&quot;) %&gt;% nrow
    upd.samples&lt;-read.xlsx(filetemp, sheet = &quot;samples&quot;, detectDates = T)
    if (nrow(upd.samples) &gt; 0){rownames(upd.samples)&lt;-(nsamples+1):(nsamples+nrow(upd.samples)) %&gt;% as.character}
    if (sinc.samples &amp; nrow(upd.samples) &gt; 0){
      upd.samples$IQ_date&lt;-as.Date(upd.samples$IQ_date)
      upd.samples$TIL_date&lt;-as.Date(upd.samples$TIL_date)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename=&quot;SAMPLES&quot;, append = T, varTypes = c(&quot;IQ_date&quot;=&quot;date&quot;,&quot;TIL_date&quot;=&quot;date&quot;))
      print(&quot;Tabla SAMPLES sincronizada.&quot;)
    }
  }
  if (dbtype == &quot;UM&quot;){
    print(&quot;DB UM detectada&quot;)
    nsamples&lt;-sqlFetch(conn, &quot;MUESTRAS&quot;) %&gt;% nrow
    upd.samples&lt;-read.xlsx(filetemp, sheet = &quot;samples&quot;, detectDates = T)
    if (nrow(upd.samples) &gt; 0){rownames(upd.samples)&lt;-(nsamples+1):(nsamples+nrow(upd.samples)) %&gt;% as.character}
    if (sinc.samples &amp; nrow(upd.samples) &gt; 0){
      upd.samples$FECHA_RECEPCION&lt;-as.Date(upd.samples$FECHA_RECEPCION)
      upd.samples$TIPO&lt;-as.character(upd.samples$TIPO)
      upd.samples$OBS&lt;-as.character(upd.samples$OBS)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename=&quot;MUESTRAS&quot;, append = T, varTypes = c(&quot;FECHA_RECEPCION&quot;=&quot;Date&quot;), rownames = F)
      print(&quot;Tabla MUESTRAS sincronizada.&quot;)
    }
  }
  ## Añadir datos clínicos modificados a la base de datos
  upd.clinics&lt;-read.xlsx(filetemp, sheet = &quot;CLINICS&quot;,detectDates = T)
  ovid.mod&lt;-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, &quot;CLINICS&quot;) %&gt;% pull(OVID))]
  rnames&lt;-sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% filter(OVID %in% ovid.mod) %&gt;% rownames
  clinics.mod&lt;-upd.clinics %&gt;% filter(OVID %in% ovid.mod) %&gt;% select(-NHC)
  rownames(clinics.mod)&lt;-rnames
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas&lt;-colnames(clinics.mod)[grepl(&quot;DO|date&quot;, colnames(clinics.mod))]
    for (i in fechas){
      clinics.mod[,i]&lt;-as.Date(clinics.mod[,i])
  if (dbtype == &quot;OV&quot;){
    upd.clinics&lt;-read.xlsx(filetemp, sheet = &quot;CLINICS&quot;,detectDates = T)
    ovid.mod&lt;-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, &quot;CLINICS&quot;) %&gt;% pull(OVID))]
    rnames&lt;-sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% filter(OVID %in% ovid.mod) %&gt;% rownames
    clinics.mod&lt;-upd.clinics %&gt;% filter(OVID %in% ovid.mod) %&gt;% select(-NHC)
    rownames(clinics.mod)&lt;-rnames
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas&lt;-colnames(clinics.mod)[grepl(&quot;DO|date&quot;, colnames(clinics.mod))]
      for (i in fechas){
        clinics.mod[,i]&lt;-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,&quot;CLINICS&quot;)
      print(&quot;Tabla CLINICS modificada.&quot;)
    }
  }
  if (dbtype == &quot;UM&quot;){
    upd.clinics&lt;-read.xlsx(filetemp, sheet = &quot;CLINICS&quot;,detectDates = T)
    umid.mod&lt;-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, &quot;CLINICOS&quot;) %&gt;% pull(UMID))]
    rnames&lt;-sqlFetch(conn, &quot;CLINICOS&quot;) %&gt;% filter(UMID %in% umid.mod) %&gt;% rownames
    clinics.mod&lt;-upd.clinics %&gt;% filter(UMID %in% umid.mod) %&gt;% select(-NHC)
    rownames(clinics.mod)&lt;-rnames
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas&lt;-colnames(clinics.mod)[grepl(&quot;date|MET_DX|DoB&quot;, colnames(clinics.mod), ignore.case = T)]
      for (i in fechas){
        clinics.mod[,i]&lt;-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,&quot;CLINICOS&quot;)
      print(&quot;Tabla CLINICOS modificada.&quot;)
    }
    sqlUpdate(conn, clinics.mod,&quot;CLINICS&quot;)
    print(&quot;Tabla CLINICS modificada.&quot;)
  }
  ## Añadir datos clínicos nuevos a la base de datos
  nsamples.clin&lt;-sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% nrow
  ovid.new&lt;-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% pull(OVID))]
  clinics.new&lt;-upd.clinics %&gt;% filter(OVID %in% ovid.new) %&gt;% select(-NHC)
  if (length(ovid.new) &gt; 0){rownames(clinics.new)&lt;-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %&gt;% as.character}
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas&lt;-colnames(clinics.new)[grepl(&quot;DO|date&quot;, colnames(clinics.new))]
    varTypes&lt;-rep(&quot;Date&quot;,length(fechas))
    names(varTypes)&lt;-fechas
    for (i in fechas){
      clinics.new[,i]&lt;-as.Date(clinics.new[,i])
  if (dbtype == &quot;OV&quot;){
    nsamples.clin&lt;-sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% nrow
    ovid.new&lt;-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, &quot;CLINICS&quot;) %&gt;% pull(OVID))]
    clinics.new&lt;-upd.clinics %&gt;% filter(OVID %in% ovid.new) %&gt;% select(-NHC)
    if (length(ovid.new) &gt; 0){rownames(clinics.new)&lt;-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %&gt;% as.character}
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas&lt;-colnames(clinics.new)[grepl(&quot;DO|date&quot;, colnames(clinics.new))]
      varTypes&lt;-rep(&quot;Date&quot;,length(fechas))
      names(varTypes)&lt;-fechas
      for (i in fechas){
        clinics.new[,i]&lt;-as.Date(clinics.new[,i])
      }
      sqlSave(conn, clinics.new, tablename=&quot;CLINICS&quot;, append = T, varTypes = varTypes)
      print(&quot;Tabla CLINICS sincronizada.&quot;)
    }
    sqlSave(conn, clinics.new, tablename=&quot;CLINICS&quot;, append = T, varTypes = varTypes)
    print(&quot;Tabla CLINICS sincronizada.&quot;)
  }
  if (dbtype == &quot;UM&quot;){
    nsamples.clin&lt;-sqlFetch(conn, &quot;CLINICOS&quot;) %&gt;% nrow
    umid.new&lt;-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(conn, &quot;CLINICOS&quot;) %&gt;% pull(UMID))]
    clinics.new&lt;-upd.clinics %&gt;% filter(UMID %in% umid.new) %&gt;% select(-NHC)
    if (length(umid.new) &gt; 0){rownames(clinics.new)&lt;-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %&gt;% as.character}
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas&lt;-colnames(clinics.new)[grepl(&quot;date|MET_DX|DoB&quot;, colnames(clinics.new), ignore.case = T)]
      varTypes&lt;-rep(&quot;Date&quot;,length(fechas))
      names(varTypes)&lt;-fechas
      for (i in fechas){
        clinics.new[,i]&lt;-as.Date(clinics.new[,i])
      }
      sqlSave(conn, clinics.new, tablename=&quot;CLINICOS&quot;, append = T, varTypes = varTypes)
      print(&quot;Tabla CLINICOS sincronizada.&quot;)
    }
  }
 }</code></pre>
 <hr />
 </div>
 </div>
 <div id="sqlmultisamples" class="section level2">
 <h2>sqlMultiSamples</h2>
 <div id="description-7" class="section level3">
 <h3>Description</h3>
 <p>Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.</p>
 </div>
 <div id="usage-7" class="section level3">
 <h3>Usage</h3>
 <p>sqlMultiSamples(kbl=F, NHC=F, full=F)</p>
 </div>
 <div id="arguments-7" class="section level3">
 <h3>Arguments</h3>
 <table>
 <colgroup>
 <col width="50%" />
 <col width="50%" />
 </colgroup>
 <thead>
 <tr class="header">
 <th>Argument</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
 <td>kbl</td>
 <td>formats the output table with the kableEstra style. Defaults to F.</td>
 </tr>
 <tr class="even">
 <td>NHC</td>
 <td>adds the NHC to the table in addition to the UMID. Defaults to F.</td>
 </tr>
 <tr class="odd">
 <td>full</td>
 <td>prints also the patients that doesn’t appear in the MUESTRAS table. Defaults to F.</td>
 </tr>
 </tbody>
 </table>
 </div>
 <div id="details-7" class="section level3">
 <h3>Details</h3>
 <p>Prints a table compiling information about laboratory samples, scRNAseq samples and RNA/DNA samples.</p>
 </div>
 <div id="value-7" class="section level3">
 <h3>Value</h3>
 <p>A data.frame or a kableExtra table.</p>
 </div>
 <div id="examples-7" class="section level3">
 <h3>Examples</h3>
 <pre class="r"><code>dta&lt;-odbcConnect(&quot;test&quot;)
 sqlMultiSamples()</code></pre>
 </div>
 <div id="function-7" class="section level3">
 <h3>Function</h3>
 <pre class="r"><code>sqlMultiSamples&lt;-function(kbl=F, NHC=F, full=F){
  query&lt;-sqlQuery(dta, &quot;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&quot;) %&gt;% rename(&quot;CNAG&quot;=&quot;CODIGO.1&quot;,&quot;RNADNA&quot;=&quot;CODIGO.2&quot;)
  if (full==F){query&lt;- query %&gt;% filter(!is.na(CODIGO))}
  if (NHC==F){query&lt;- query %&gt;% select(-NHC)}
  query&lt;-query %&gt;% mutate(
    CNAG=case_when(!is.na(CNAG)~&quot;X&quot;,TRUE~&quot;&quot;),
    RNADNA=case_when((!is.na(RNADNA) &amp; (ESTADO==&quot;ENV&quot;))~&quot;X&quot;,
                     (!is.na(RNADNA) &amp; (is.na(ESTADO)))~&quot;.&quot;,
                     TRUE~&quot;&quot;)
  ) %&gt;% select(-ESTADO)
  if (kbl==T){
    query %&gt;% kableExtra::kbl() %&gt;% kableExtra::kable_styling(full_width = F, bootstrap_options = c(&quot;striped&quot;))
  }else{
    return(query)
    }
 }</code></pre>
 </div>
 </div>
--- a/sqlFunctions.R
+++ b/sqlFunctions.R
@ -1,9 +1,16 @@
 require(RODBC)
 sqlDropLast<-function(conn, tablename, droplast=1){
 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),]
  sqlSave(conn, table, tablename = tablename, safer = F)
  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(){
@ -15,7 +22,10 @@ sqlInitialize<-function(){
  source("ruta_database.R", encoding = "UTF-8")
 }
 sqlBackUp<-function(dbfile=file,bu.dir){
 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){dbtype<-"BU_OVARIO"}
  db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
  bu_path<-gsub(db,bu.dir,dbfile)
  if (!dir.exists(bu_path)){
@ -26,120 +36,271 @@ sqlBackUp<-function(dbfile=file,bu.dir){
  file.copy(dbfile, cp_bu)
 }
 sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F){
 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, "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)
    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 = nhcs)) %>% arrange(NHC)
  }else{
    sqlQuery(conn, "SELECT O.NHC,S.* 
         FROM SAMPLES S 
         INNER JOIN OVID O 
         ON O.OVID=S.OVID") %>% filter(NHC %in% nhcs)
    sqlQuery(conn, query) %>% 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$OVID) %>% as.numeric %>% max(na.rm=T)+1
  last.num<-next.num+(length(new.nhc)-1)
  upd.ovid<-rbind(ovid,data.frame("NHC"=new.nhc, "OVID"=sprintf("OVID%04d",next.num:last.num)))
  rownames(upd.ovid)<-as.character(1:nrow(upd.ovid))
  upd.ovid<-filter(upd.ovid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
 sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  if (sinc){
    ### !! Atención, esto cambia la base de datos:
    sqlSave(conn, upd.ovid, tablename="OVID", append = T)
    print("La base ha sido actualizada.")
  if (dbtype == "OV"){
    db<-c("dbcode"="OVID")
  }
  if (verb){
    return(upd.ovid)
  if (dbtype == "UM"){
    db<-c("dbcode"="UMID")
  }
  dbid<-sqlFetch(conn,db["dbcode"])
  new.nhc<-nhcs[!nhcs %in% dbid$NHC]
  if(length(new.nhc) > 0){
    next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
    last.num<-next.num+(length(new.nhc)-1)
    newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],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(Id,NHC,UMID) %>% arrange(Id)
      dbid$Id<-as.numeric(rownames(dbid))
      dbid$NHC<-as.numeric(dbid$NHC)
    }
    rownames(dbid)<-as.character(1:nrow(dbid))
    dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC))
    if (sinc){
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, dbid, tablename=db["dbcode"], append = T)
      print("La base ha sido actualizada.")
    }
    if (verb){
      return(dbid)
    }
  }else{
    print("No hay pacientes nuevos.")
  }
 }
 sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T){
  upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
  if (samples.mod){
    ## Generar código para las nuevas muestras
    samples<-sqlFetch(conn, "SAMPLES")
    if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
      next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1  
    }else{
      next.samp<-1
 sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  if (dbtype=="OV"){
    upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples<-sqlFetch(conn, "SAMPLES")
      if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$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$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
    }
    last.samp<-next.samp+(length(nhcs)-1)
    new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
    new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
    samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
  }
  if (clinics.mod){
    ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
    upd.clinics<-sqlFetch(conn, "CLINICS")
    ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
    upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
    upd.clinics$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$CODIGO) %>% as.numeric %>% max(na.rm=T)+1  
      }else{
        next.samp<-1
      }
      last.samp<-next.samp+(length(nhcs)-1)
      new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
      new.samp.df<-merge(sqlFetch(dta,"UMID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "CODIGO"=new.samp))
      samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
    }
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics<-sqlFetch(conn, "CLINICOS")
      umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
      upd.clinics<-merge(umid.new,upd.clinics %>% select(-Id), all.x=T, by="UMID")
      upd.clinics$NHC<-as.character(upd.clinics$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
    }
    ## Exportar tablas a la plantilla de entrada para su rellenado
    wb <- loadWorkbook(file)
    writeData(wb, "NHC", upd.umid)
    if (samples.mod){writeData(wb,"samples",samples.exp)}
    if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  ## Exportar tablas a la plantilla de entrada para su rellenado
  wb <- loadWorkbook(file)
  writeData(wb, "NHC", upd.ovid)
  if (samples.mod){writeData(wb,"samples",samples.exp)}
  if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
  saveWorkbook(wb,file,overwrite = TRUE)
 }
 sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){
  ## Añadir código de muestra nueva a la base de datos
  nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
  upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
  if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
 sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  if (sinc.samples & nrow(upd.samples) > 0){
    upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
    upd.samples$TIL_date<-as.Date(upd.samples$TIL_date)
    ### !! Atención, esto cambia la base de datos:
    sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date"))
    print("Tabla SAMPLES sincronizada.")
  ## Añadir código de muestra nueva a la base de datos
  if (dbtype == "OV"){
    print("DB OV detectada")
    nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
    upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
    if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
    if (sinc.samples & nrow(upd.samples) > 0){
      upd.samples$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$OBS)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
      print("Tabla MUESTRAS sincronizada.")
    }
  }
  ## Añadir datos clínicos modificados a la base de datos
  upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
  ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
  rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
  clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
  rownames(clinics.mod)<-rnames
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
    for (i in fechas){
      clinics.mod[,i]<-as.Date(clinics.mod[,i])
  if (dbtype == "OV"){
    upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
    ovid.mod<-upd.clinics$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$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
    rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
    clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
    rownames(clinics.mod)<-rnames
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
      for (i in fechas){
        clinics.mod[,i]<-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,"CLINICOS")
      print("Tabla CLINICOS modificada.")
    }
    sqlUpdate(conn, clinics.mod,"CLINICS")
    print("Tabla CLINICS modificada.")
  }
  ## Añadir datos clínicos nuevos a la base de datos
  nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
  ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
  clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
  if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
  ### !! Atención, esto cambia la base de datos:
  if (sinc.clinics){
    fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
    varTypes<-rep("Date",length(fechas))
    names(varTypes)<-fechas
    for (i in fechas){
      clinics.new[,i]<-as.Date(clinics.new[,i])
  if (dbtype == "OV"){
    nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
    ovid.new<-upd.clinics$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)
      print("Tabla CLINICOS sincronizada.")
    }
    sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
    print("Tabla CLINICS 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)
    }
 }
--- a/workflow.R
+++ b/workflow.R
@ -1,4 +1,4 @@
 source("sqlFunctions.R")
 source("sqlFunctions.R", encoding = "UTF-8")
 # Cargar dependencias
 sqlInitialize()
@ -6,13 +6,13 @@ sqlInitialize()
 ## Asegurarse de que la variable file sea la que nos corresponde:
 file
 # Crear copia de seguridad
 sqlBackUp()
 # Inicializar conexión
 dta<-odbcConnectAccess2007(access.file = file, 
                           pwd = .rs.askForPassword("Enter password:"))
 # Crear copia de seguridad
 sqlBackUp()
 ## Importamos los NHC de las muestras nuevas
 nhc.test<-read.xlsx("queryOV.xlsx", sheet = "NHC") %>% pull(NHC)