Añadir soporte para asignar CNAG y RNADNA. También para incluir automaticamente la fecha.

sqlFunctions.R

@@ -102,7 +102,7 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
   }
 }
 
-sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL){
+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"}
   
@@ -150,10 +150,30 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
       }
       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")) %>% arrange(CODIGO)
+      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$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
+      }
+    }else{cnag.exp<-NULL}
+    if (any(sapply(nhc.table$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<-NULL}
     if (clinics.mod){
       ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
       upd.clinics<-sqlFetch(conn, "CLINICOS")
@@ -168,6 +188,8 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
     writeData(wb, "NHC", merge(data.frame("NHC"=nhcs), 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)
   }
 }