BDAccess/sqlFunctions.R

require(RODBC)

sqlLastDrop<-function(conn, tablename, droplast=1,dbtype=NULL){
  if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  
  table<-sqlFetch(conn, tablename)
  table<-table[1:(nrow(table)-droplast),]
  
  if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
  if (dbtype == "UM"){
    sqlDrop(conn, tablename)
    sqlSave(conn, table, tablename = tablename, safer = F)}
}


sqlInitialize<-function(ruta="ruta_database.R"){
  library(tidyverse)
  library(RODBC)
  library(openxlsx)
  
  ## Conexión a la base de datos
  source(ruta, encoding = "UTF-8")
}

sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){
  if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){bu.dir<-"BU_UM"}
  if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){bu.dir<-"BU_OVARIO"}
  
  db=strsplit(dbfile, "/")[[1]]%>% tail(n=1)
  bu_path<-gsub(db,bu.dir,dbfile)
  if (!dir.exists(bu_path)){
    dir.create(bu_path)
    print(paste0("Back Up directory ", bu_path, " created"))
  }
  cp_bu<-paste0(bu_path, "/", format(Sys.time(), format="%Y%m%d"),"-",db)
  file.copy(dbfile, cp_bu)
}

sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  
  if (dbtype == "OV"){
    db<-c("dbtables"="SAMPLES", "dbcode"="OVID", "dbsamples"="samples")
    query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
  }
  if (dbtype == "UM"){
    db<-c("dbtables"="MUESTRAS", "dbcode"="UMID", "dbsamples"="CODIGO")
    query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"])
  }
  if (nrow(sqlQuery(conn, query) %>% filter(NHC %in% nhcs)) == 0){
    return("No hay muestras de ningún paciente.")
  }
  if (isFALSE(verb)){
    sqlQuery(conn, query) %>% filter(NHC %in% nhcs) %>% 
    group_by(NHC,UQ(rlang::sym(db["dbcode"]))) %>% summarise(Samples=length(UQ(rlang::sym(db["dbsamples"]))), Names=paste0(UQ(rlang::sym(db["dbsamples"])), collapse = ";")) %>% 
      merge(data.frame(NHC=nhcs),all=T) %>% mutate(NHC=factor(NHC,levels = unique(nhcs))) %>% arrange(NHC)
  }else{
    sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
  }
}

sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
  if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  
  if (dbtype == "OV"){
    db<-c("dbcode"="OVID")
  }
  if (dbtype == "UM"){
    db<-c("dbcode"="UMID")
  }
  
  dbid<-sqlFetch(conn,db["dbcode"])
  
  new.nhc<-nhcs[!nhcs %in% dbid$NHC] %>% unique()
  if(length(new.nhc) > 0){
    next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
    last.num<-next.num+(length(new.nhc)-1)
    newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
    if(dbtype=="OV"){
      dbid<-rbind(dbid,newtab)
    }
    if(dbtype=="UM"){
      dbid<-merge(dbid, newtab, all=T) %>% select(NHC,UMID) %>% arrange(UMID)
      # dbid$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, rownames = F)
      print("La base ha sido actualizada.")
    }
    if (verb){
      return(dbid)
    }
  }else{
    print("No hay pacientes nuevos.")
  }
}

sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL, today=F){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  
  if (dbtype=="OV"){
    upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples<-sqlFetch(conn, "SAMPLES")
      if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){
        next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1  
      }else{
        next.samp<-1
      }
      last.samp<-next.samp+(length(nhcs)-1)
      new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
      new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp))
      samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples)
    }
    
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics<-sqlFetch(conn, "CLINICS")
      ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs)
      upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID")
      upd.clinics$NHC<-as.character(upd.clinics$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
    }
  
    ## Exportar tablas a la plantilla de entrada para su rellenado
    wb <- loadWorkbook(file)
    writeData(wb, "NHC", upd.ovid)
    if (samples.mod){writeData(wb,"samples",samples.exp)}
    if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
    saveWorkbook(wb,file,overwrite = TRUE)
  }
  if (dbtype=="UM"){
    upd.umid<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
    if (samples.mod){
      ## Generar código para las nuevas muestras
      samples<-sqlFetch(conn, "MUESTRAS")
      if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){
        next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1  
      }else{
        next.samp<-1
      }
      last.samp<-next.samp+(length(nhcs)-1)
      new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp)
      new.samp.df<-data.frame("NHC"=nhcs, "CODIGO"=new.samp) %>% merge(sqlFetch(dta,"UMID"), all.x=T) %>% arrange(CODIGO)
      samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO)
      if (today==TRUE){
        samples.exp$FECHA_RECEPCION<-format(Sys.Date(), "%d/%m/%y")
      }
    }
    
    nhc.table<-read.xlsx(file, sheet = "NHC")
    
    if (any(sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]) == T)){
      nhcs.cnag<-nhc.table[sapply(nhc.table$Samples, function(x) "cnag" %in% strsplit(x,",")[[1]]),"NHC"]
      umid.cnag<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs.cnag) %>% pull(UMID)
      sample.cnag<-samples.exp %>% filter(UMID %in% umid.cnag) %>% pull(CODIGO)
      cnag.exp<-merge(data.frame("UMID"=umid.cnag, "CODIGO"=sample.cnag), sqlFetch(dta, "CNAG") %>% slice(0), all=T)
      if (today==TRUE){
        cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
      }
    }else{cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0)}
    if (any(sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]) == T)){
      nhcs.rna<-nhc.table[sapply(nhc.table$Samples, function(x) "rna" %in% strsplit(x,",")[[1]]),"NHC"]
      umid.rna<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs.rna) %>% pull(UMID)
      sample.rna<-samples.exp %>% filter(UMID %in% umid.rna) %>% pull(CODIGO)
      rna.exp<-merge(data.frame("UMID"=umid.rna, "CODIGO"=sample.rna), sqlFetch(dta, "RNADNA") %>% slice(0), all=T)
    }else{rna.exp<- sqlFetch(dta, "RNADNA") %>% slice(0)}
    if (clinics.mod){
      ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
      upd.clinics<-sqlFetch(conn, "CLINICOS")
      umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs)
      upd.clinics<-merge(umid.new,upd.clinics, all.x=T, by="UMID")
      upd.clinics$NHC<-as.character(upd.clinics$NHC)
      for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])}
    }
    
    ## Exportar tablas a la plantilla de entrada para su rellenado
    wb <- createWorkbook(file)
    addWorksheet(wb, "NHC")
    addWorksheet(wb, "samples")
    addWorksheet(wb, "CLINICS")
    addWorksheet(wb, "CNAG")
    addWorksheet(wb, "RNADNA")
    writeData(wb, "NHC", merge(nhc.table, upd.umid, sort = F))
    if (samples.mod){writeData(wb,"samples",samples.exp)}
    if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
    writeData(wb,"CNAG",cnag.exp)
    writeData(wb,"RNADNA",rna.exp)
    saveWorkbook(wb,file,overwrite = TRUE)
  }
}

sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){
  if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
  
  ## Añadir código de muestra nueva a la base de datos
  if (dbtype == "OV"){
    print("DB OV detectada")
    nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow
    upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
    if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
    
    if (sinc.samples & nrow(upd.samples) > 0){
      upd.samples$IQ_date<-as.Date(upd.samples$IQ_date)
      upd.samples$TIL_date<-as.Date(upd.samples$TIL_date)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date"))
      print("Tabla SAMPLES sincronizada.")
    }
  }
  if (dbtype == "UM"){
    print("DB UM detectada")
    nsamples<-sqlFetch(conn, "MUESTRAS") %>% nrow
    upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T)
    if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character}
    
    if (sinc.samples & nrow(upd.samples) > 0){
      upd.samples$FECHA_RECEPCION<-as.Date(upd.samples$FECHA_RECEPCION)
      upd.samples$TIPO<-as.character(upd.samples$TIPO)
      upd.samples$OBS<-as.character(upd.samples$OBS)
      ### !! Atención, esto cambia la base de datos:
      sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F)
      print("Tabla MUESTRAS sincronizada.")
    }
  }
  
  ## Añadir datos clínicos modificados a la base de datos
  if (dbtype == "OV"){
    upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
    ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))]
    rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames
    clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC)
    rownames(clinics.mod)<-rnames
    
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))]
      for (i in fechas){
        clinics.mod[,i]<-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,"CLINICS")
      print("Tabla CLINICS modificada.")
    }
  }
  if (dbtype == "UM"){
    upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T)
    umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))]
    rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames
    clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC)
    rownames(clinics.mod)<-rnames
    
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)]
      for (i in fechas){
        clinics.mod[,i]<-as.Date(clinics.mod[,i])
      }
      sqlUpdate(conn, clinics.mod,"CLINICOS", index="UMID")
      print("Tabla CLINICOS modificada.")
    }
  }
  
  ## Añadir datos clínicos nuevos a la base de datos
  if (dbtype == "OV"){
    nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow
    ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))]
    clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC)
    if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
    
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))]
      varTypes<-rep("Date",length(fechas))
      names(varTypes)<-fechas
      for (i in fechas){
        clinics.new[,i]<-as.Date(clinics.new[,i])
      }
      sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes)
      print("Tabla CLINICS sincronizada.")
    }
  }
  if (dbtype == "UM"){
    nsamples.clin<-sqlFetch(conn, "CLINICOS") %>% nrow
    umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(conn, "CLINICOS") %>% pull(UMID))]
    clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC)
    if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character}
    
    ### !! Atención, esto cambia la base de datos:
    if (sinc.clinics){
      fechas<-colnames(clinics.new)[grepl("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)]
      varTypes<-rep("Date",length(fechas))
      names(varTypes)<-fechas
      for (i in fechas){
        clinics.new[,i]<-as.Date(clinics.new[,i])
      }
      sqlSave(conn, clinics.new, tablename="CLINICOS", append = T, varTypes = varTypes, rownames = F)
      print("Tabla CLINICOS sincronizada.")
    }
  }
}

sqlMultiSamples<-function(kbl=F, NHC=F, full=F){
  query<-sqlQuery(dta, "SELECT U.UMID,U.NHC,M.FECHA_RECEPCION,M.TIPO,M.CODIGO,C.CODIGO,R.CODIGO,R.ESTADO 
         FROM ((UMID U
         LEFT OUTER JOIN MUESTRAS M ON U.UMID=M.UMID)
         LEFT OUTER JOIN CNAG C ON M.CODIGO=C.CODIGO)
         LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2")
  
  if (full==F){query<- query %>% filter(!is.na(CODIGO))}
  if (NHC==F){query<- query %>% select(-NHC)}
  
  query<-query %>% mutate(
    CNAG=case_when(!is.na(CNAG)~"X",TRUE~""),
    RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X",
                     (!is.na(RNADNA) & (is.na(ESTADO)))~".",
                     TRUE~"")
  ) %>% select(-ESTADO)
  if (kbl==T){
    query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped"))
  }else{
    return(query)
    }
}