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

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Costa
2022-03-01 14:26:15 +01:00
parent e948b086ed
commit f4f4e6a350
1 changed files with 24 additions and 2 deletions
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sqlFunctions.R
+24 -2
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@@ -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 == "UMID") %>% nrow > 0){dbtype<-"UM"}
if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} 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) last.samp<-next.samp+(length(nhcs)-1)
new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) 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) 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){ if (clinics.mod){
## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos ## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos
upd.clinics<-sqlFetch(conn, "CLINICOS") 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)) writeData(wb, "NHC", merge(data.frame("NHC"=nhcs), upd.umid, sort = F))
if (samples.mod){writeData(wb,"samples",samples.exp)} if (samples.mod){writeData(wb,"samples",samples.exp)}
if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)} if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)}
writeData(wb,"CNAG",cnag.exp)
writeData(wb,"RNADNA",rna.exp)
saveWorkbook(wb,file,overwrite = TRUE) saveWorkbook(wb,file,overwrite = TRUE)
} }
} }