BDAccess/Docs/sqlFunctions-doc.Rmd

---
title: "sqlFunctions-Doc"
output:
  html_document:
    toc: true
    toc_depth: 2
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

---

## sqlDropLast

### Description
Removes from Database the last (or the amount specified) entry.

### Usage
sqlDropLast(conn, tablename, droplast=1, dbtype=NULL)

### Arguments
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.

### Value
Invisibly for success (and failures cause errors).

### Examples
```r
dta<-odbcConnect("test")
sqlDropLast(dta, "TableTest")
```

### Function
```r
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),]
  
  if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)}
  if (dbtype == "UM"){
    sqlDrop(conn, tablename)
    sqlSave(conn, table, tablename = tablename, safer = F)}
}
```

---

## sqlInitizalize

### Description
Loads required libraries and gets the db location.

### Usage
sqlInitialize()

### Arguments
Argument|Description
---|---

### Details
Loads required libraries and gets the db location from "ruta_database.R" file.

### Value
Invisibly for success (and failures cause errors).

### Examples
```r
sqlInitialize()
```

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

---

## sqlBackUp

### Description
Creates a Back Up copy of the database.

### Usage
sqlBackUp(dbfile=file,conn=dta,bu.dir=NULL)

### Arguments
Argument|Description
---|---
dbfile| Database File location.
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.

### Value
Invisibly for success (and failures cause errors).

### Examples
```r
sqlInitialize()
sqlBackUp()
```

### Function
```r
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)){
    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

### Description
Shows if there are already samples from the specified NHCs.

### Usage
sqlShowSamples(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL)

### Arguments
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.

### Value
A data.frame with information about the patients.

### Examples
```r
dta<-odbcConnect("test")
nhc.test<-c("XXXXXXXX","XXXXXXX")
sqlShowSamples()
```

### Function
```r
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 = nhcs)) %>% arrange(NHC)
  }else{
    sqlQuery(conn, query) %>% filter(NHC %in% nhcs)
  }
}
```

---

## sqlGenOVID

### Description
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, dbtype=NULL)

### Arguments
Argument|Description
---|---
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 or UMID code for the patients that are not found in the DB.

### Value
If verb is TRUE, it returns a data.frame.

### Examples
```r
dta<-odbcConnect("test")
nhc.test<-c("XXXXXXXX","XXXXXXX")
sqlGenOVID(sinc=T)
```

### Function
```r
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 (dbtype == "OV"){
    db<-c("dbcode"="OVID")
  }
  if (dbtype == "UM"){
    db<-c("dbcode"="UMID")
  }
  
  dbid<-sqlFetch(conn,db["dbcode"])
  
  new.nhc<-nhcs[!nhcs %in% dbid$NHC]
  next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
  last.num<-next.num+(length(new.nhc)-1)
  newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
  if(dbtype=="OV"){
    dbid<-rbind(dbid,newtab)
  }
  if(dbtype=="UM"){
    dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id)
    dbid$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)
  }
}
```

---

## sqlWriteTemp

### Description
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, dbtype=NULL)

### Arguments
Argument|Description
---|---
conn|connection handle returned by odbcConnect.
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 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).

### Examples
```r
dta<-odbcConnect("test")
nhc.test<-c("XXXXXXXX","XXXXXXX")
sqlGenOVID(sinc=T)
sqlWriteTemp()
```

### Function
```r
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])}
    }
  
    ## 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)
  }
}
```

---

## sqlSincBD

### Description
Updates the DB with the information filled in the template file.

### Usage
sqlSincBD(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL)

### Arguments
Argument|Description
---|---
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.

### Value
Invisibly for success (and failures cause errors).

### Examples
```r
dta<-odbcConnect("test")
nhc.test<-c("XXXXXXXX","XXXXXXX")
sqlGenOVID(sinc=T)
sqlWriteTemp()
sqlSincBD(sinc.samples=T, sinc.clinics=T)
```

### Function
```r
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")
      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)
      print("Tabla CLINICOS 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)
    }
}
```