Commit in cytometry.

ruta_database.R

@@ -1 +1,4 @@
-file<-"C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/OVARIO.accdb"
+# file<-"C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/MELANOMA UVEAL CIT.accdb"
+# file<-"C:/Users/47926492N/OneDrive - IDIBELL - Institut d'Investigació Biomèdica de Bellvitge/RATG-PIULATS/OVARIO.accdb"
+UMfile<-file<-"C:/Users/47926492N/Documents/Test/MELANOMA UVEAL CIT.accdb"
+OVfile<-file<-"C:/Users/47926492N/Documents/Test/OVARIO.accdb"

sqlFunctions.R

@@ -13,13 +13,14 @@ sqlLastDrop<-function(conn, tablename, droplast=1,dbtype=NULL){
     sqlSave(conn, table, tablename = tablename, safer = F)}
 }
 
-sqlInitialize<-function(){
+
+sqlInitialize<-function(ruta="ruta_database.R"){
   library(tidyverse)
   library(RODBC)
   library(openxlsx)
   
   ## Conexión a la base de datos
-  source("ruta_database.R", encoding = "UTF-8")
+  source(ruta, encoding = "UTF-8")
 }
 
 sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){
@@ -61,23 +62,29 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL){
 }
 
 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(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"}
-  if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
+  if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"}
   
   if (dbtype == "OV"){
-    db<-c("dbcode"="OVID")
+    db<-c("dbcode"="OVID", "dbpref"="OVID")
   }
   if (dbtype == "UM"){
-    db<-c("dbcode"="UMID")
+    db<-c("dbcode"="UMID","dbpref"="UMID")
+  }
+  if (dbtype == "CC"){
+    db<-c("dbcode"="PATID", "dbpref"="CCID")
   }
   
   dbid<-sqlFetch(conn,db["dbcode"])
-  
   new.nhc<-nhcs[!nhcs %in% dbid$NHC] %>% unique()
+
   if(length(new.nhc) > 0){
+    if (nrow(dbid) == 0){next.num<-1}else{
     next.num<-gsub(db["dbcode"],"",dbid[,db["dbcode"]]) %>% as.numeric %>% max(na.rm=T)+1
+    }
+    print(next.num)
     last.num<-next.num+(length(new.nhc)-1)
-    newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbcode"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
+    newtab<-data.frame("NHC"=new.nhc, "ID"=sprintf("%s%04d",db["dbpref"],next.num:last.num)) %>% rename(!!db["dbcode"]:="ID")
     if(dbtype=="OV"){
       dbid<-rbind(dbid,newtab)
     }
@@ -86,6 +93,10 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){
       # dbid$Id<-as.numeric(rownames(dbid))
       dbid$NHC<-as.numeric(dbid$NHC)
     }
+    if (dbtype=="CC"){
+      dbid<-merge(dbid, newtab, all=T) %>% select(NHC,PATID) %>% arrange(PATID)
+      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))
     
@@ -167,13 +178,13 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
       if (today==TRUE){
         cnag.exp$FECHA_ENVIO<-format(Sys.Date(), "%d/%m/%y")
       }
-    }else{cnag.exp<-NULL}
+    }else{cnag.exp<-sqlFetch(dta, "CNAG") %>% slice(0)}
     if (any(sapply(nhc.table$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<-NULL}
+    }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")
@@ -184,7 +195,12 @@ sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod
     }
     
     ## Exportar tablas a la plantilla de entrada para su rellenado
-    wb <- loadWorkbook(file)
+    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)}