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

@@ -13,6 +13,7 @@ sqlLastDrop<-function(conn, tablename, droplast=1,dbtype=NULL){
     sqlSave(conn, table, tablename = tablename, safer = F)}
 }
 
+
 sqlInitialize<-function(ruta="ruta_database.R"){
   library(tidyverse)
   library(RODBC)
@@ -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))