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@ -1,9 +1,16 @@ |
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require(RODBC) |
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sqlDropLast<-function(conn, tablename, droplast=1){ |
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sqlDropLast<-function(conn, tablename, droplast=1,dbtype=NULL){ |
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if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"} |
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if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} |
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table<-sqlFetch(conn, tablename) |
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table<-table[1:(nrow(table)-droplast),] |
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sqlSave(conn, table, tablename = tablename, safer = F) |
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if (dbtype == "OV"){sqlSave(conn, table, tablename = tablename, safer = F)} |
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if (dbtype == "UM"){ |
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sqlDrop(conn, tablename) |
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sqlSave(conn, table, tablename = tablename, safer = F)} |
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} |
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sqlInitialize<-function(){ |
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@ -15,7 +22,10 @@ sqlInitialize<-function(){ |
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source("ruta_database.R", encoding = "UTF-8") |
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} |
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sqlBackUp<-function(dbfile=file,bu.dir){ |
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sqlBackUp<-function(dbfile=file,conn=dta,bu.dir=NULL){ |
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if(sqlTables(conn) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){bu.dir<-"BU_UM"} |
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if(sqlTables(conn) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"BU_OVARIO"} |
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db=strsplit(dbfile, "/")[[1]]%>% tail(n=1) |
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bu_path<-gsub(db,bu.dir,dbfile) |
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if (!dir.exists(bu_path)){ |
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@ -26,7 +36,10 @@ sqlBackUp<-function(dbfile=file,bu.dir){ |
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file.copy(dbfile, cp_bu) |
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} |
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sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype){ |
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sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype=NULL){ |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"} |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} |
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if (dbtype == "OV"){ |
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db<-c("dbtables"="SAMPLES", "dbcode"="OVID", "dbsamples"="samples") |
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query<-paste0("SELECT O.NHC,S.* FROM ",db["dbtables"]," S INNER JOIN ",db["dbcode"]," O ON O.",db["dbcode"],"=S.",db["dbcode"]) |
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@ -47,7 +60,10 @@ sqlShowSamples<-function(conn=dta, nhcs=nhc.test, verb=F, dbtype){ |
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} |
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} |
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sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){ |
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sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype=NULL){ |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"} |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} |
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if (dbtype == "OV"){ |
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db<-c("dbcode"="OVID") |
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} |
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@ -66,7 +82,8 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){ |
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} |
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if(dbtype=="UM"){ |
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dbid<-merge(dbid, newtab, all=T) %>% select(Id,NHC,UMID) %>% arrange(Id) |
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dbid$Id<-rownames(dbid) |
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dbid$Id<-as.numeric(rownames(dbid)) |
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dbid$NHC<-as.numeric(dbid$NHC) |
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} |
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rownames(dbid)<-as.character(1:nrow(dbid)) |
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dbid<-filter(dbid, NHC %in% new.nhc) %>% mutate(NHC=as.character(NHC)) |
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@ -81,100 +98,202 @@ sqlGenOVID<-function(conn=dta, nhcs=nhc.test, verb=T, sinc=F, dbtype){ |
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} |
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} |
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sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T){ |
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upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) |
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if (samples.mod){ |
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## Generar código para las nuevas muestras |
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samples<-sqlFetch(conn, "SAMPLES") |
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if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){ |
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next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1 |
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}else{ |
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next.samp<-1 |
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sqlWriteTemp<-function(conn=dta, nhcs=nhc.test, file="queryOV.xlsx", samples.mod=T, clinics.mod=T, dbtype=NULL){ |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"} |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} |
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if (dbtype=="OV"){ |
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upd.ovid<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) |
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if (samples.mod){ |
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## Generar código para las nuevas muestras |
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samples<-sqlFetch(conn, "SAMPLES") |
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if(sum(grepl(paste0("OV",Sys.time() %>% format("%y")), samples$samples)) > 0){ |
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next.samp<-gsub(paste0("OV",Sys.time() %>% format("%y")),"", samples$samples) %>% as.numeric %>% max(na.rm=T)+1 |
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}else{ |
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next.samp<-1 |
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} |
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last.samp<-next.samp+(length(nhcs)-1) |
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new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) |
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new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp)) |
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samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) |
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} |
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if (clinics.mod){ |
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## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos |
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upd.clinics<-sqlFetch(conn, "CLINICS") |
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ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) |
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upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID") |
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upd.clinics$NHC<-as.character(upd.clinics$NHC) |
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for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} |
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} |
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last.samp<-next.samp+(length(nhcs)-1) |
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new.samp<-sprintf("OV%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) |
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new.samp.df<-merge(sqlFetch(dta,"OVID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "samples"=new.samp)) |
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samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(samples) |
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} |
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if (clinics.mod){ |
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## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos |
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upd.clinics<-sqlFetch(conn, "CLINICS") |
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ovid.new<-sqlFetch(conn, "OVID") %>% filter(NHC %in% nhcs) |
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upd.clinics<-merge(ovid.new,upd.clinics, all.x=T, by="OVID") |
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upd.clinics$NHC<-as.character(upd.clinics$NHC) |
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for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} |
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## Exportar tablas a la plantilla de entrada para su rellenado |
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wb <- loadWorkbook(file) |
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writeData(wb, "NHC", upd.ovid) |
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if (samples.mod){writeData(wb,"samples",samples.exp)} |
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if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)} |
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saveWorkbook(wb,file,overwrite = TRUE) |
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} |
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if (dbtype=="UM"){ |
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upd.umid<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs) |
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if (samples.mod){ |
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## Generar código para las nuevas muestras |
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samples<-sqlFetch(conn, "MUESTRAS") |
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if(sum(grepl(paste0("UM",Sys.time() %>% format("%y")), samples$CODIGO)) > 0){ |
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next.samp<-gsub(paste0("UM",Sys.time() %>% format("%y")),"", samples$CODIGO) %>% as.numeric %>% max(na.rm=T)+1 |
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}else{ |
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next.samp<-1 |
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} |
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last.samp<-next.samp+(length(nhcs)-1) |
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new.samp<-sprintf("UM%s%02d",Sys.time() %>% format("%y"),next.samp:last.samp) |
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new.samp.df<-merge(sqlFetch(dta,"UMID") %>% merge(data.frame("NHC"=nhcs)), data.frame("NHC"=nhcs, "CODIGO"=new.samp)) |
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samples.exp<-merge(samples %>% slice(0), new.samp.df %>% select(-NHC), all=T) %>% select(colnames(samples)) %>% arrange(CODIGO) |
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} |
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if (clinics.mod){ |
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## Importar los datos clínicos de pacientes existentes y generar nueva entrada par los nuevos |
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upd.clinics<-sqlFetch(conn, "CLINICOS") |
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umid.new<-sqlFetch(conn, "UMID") %>% filter(NHC %in% nhcs) |
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upd.clinics<-merge(umid.new,upd.clinics %>% select(-Id), all.x=T, by="UMID") |
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upd.clinics$NHC<-as.character(upd.clinics$NHC) |
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for (i in colnames(upd.clinics)[sapply(upd.clinics, lubridate::is.POSIXct)]){upd.clinics[,i]<-as.Date(upd.clinics[,i])} |
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} |
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## Exportar tablas a la plantilla de entrada para su rellenado |
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wb <- loadWorkbook(file) |
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writeData(wb, "NHC", upd.umid) |
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if (samples.mod){writeData(wb,"samples",samples.exp)} |
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if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)} |
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saveWorkbook(wb,file,overwrite = TRUE) |
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} |
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## Exportar tablas a la plantilla de entrada para su rellenado |
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wb <- loadWorkbook(file) |
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writeData(wb, "NHC", upd.ovid) |
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if (samples.mod){writeData(wb,"samples",samples.exp)} |
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if (clinics.mod){writeData(wb,"CLINICS",upd.clinics)} |
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saveWorkbook(wb,file,overwrite = TRUE) |
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} |
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sqlSincBD<-function(conn=dta, filetemp="QueryOV.xlsx", sinc.samples=F, sinc.clinics=F){ |
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## Añadir código de muestra nueva a la base de datos |
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nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow |
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upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T) |
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if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} |
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sqlSincBD<-function(conn=dta, filetemp="queryOV.xlsx", sinc.samples=F, sinc.clinics=F, dbtype=NULL){ |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "UMID") %>% nrow > 0){dbtype<-"UM"} |
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if(sqlTables(dta) %>% filter(TABLE_NAME == "OVID") %>% nrow > 0){dbtype<-"OV"} |
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if (sinc.samples & nrow(upd.samples) > 0){ |
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upd.samples$IQ_date<-as.Date(upd.samples$IQ_date) |
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upd.samples$TIL_date<-as.Date(upd.samples$TIL_date) |
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### !! Atención, esto cambia la base de datos: |
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sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date")) |
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print("Tabla SAMPLES sincronizada.") |
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## Añadir código de muestra nueva a la base de datos |
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if (dbtype == "OV"){ |
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print("DB OV detectada") |
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nsamples<-sqlFetch(conn, "SAMPLES") %>% nrow |
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upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T) |
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if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} |
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if (sinc.samples & nrow(upd.samples) > 0){ |
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upd.samples$IQ_date<-as.Date(upd.samples$IQ_date) |
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upd.samples$TIL_date<-as.Date(upd.samples$TIL_date) |
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### !! Atención, esto cambia la base de datos: |
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sqlSave(conn, upd.samples, tablename="SAMPLES", append = T, varTypes = c("IQ_date"="date","TIL_date"="date")) |
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print("Tabla SAMPLES sincronizada.") |
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} |
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} |
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if (dbtype == "UM"){ |
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print("DB UM detectada") |
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nsamples<-sqlFetch(conn, "MUESTRAS") %>% nrow |
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upd.samples<-read.xlsx(filetemp, sheet = "samples", detectDates = T) |
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if (nrow(upd.samples) > 0){rownames(upd.samples)<-(nsamples+1):(nsamples+nrow(upd.samples)) %>% as.character} |
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if (sinc.samples & nrow(upd.samples) > 0){ |
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upd.samples$FECHA_RECEPCION<-as.Date(upd.samples$FECHA_RECEPCION) |
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upd.samples$TIPO<-as.character(upd.samples$TIPO) |
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upd.samples$OBS<-as.character(upd.samples$OBS) |
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### !! Atención, esto cambia la base de datos: |
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sqlSave(conn, upd.samples, tablename="MUESTRAS", append = T, varTypes = c("FECHA_RECEPCION"="Date"), rownames = F) |
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print("Tabla MUESTRAS sincronizada.") |
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} |
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} |
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## Añadir datos clínicos modificados a la base de datos |
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upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T) |
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ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))] |
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rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames |
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clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC) |
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rownames(clinics.mod)<-rnames |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))] |
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for (i in fechas){ |
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clinics.mod[,i]<-as.Date(clinics.mod[,i]) |
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if (dbtype == "OV"){ |
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upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T) |
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ovid.mod<-upd.clinics$OVID[upd.clinics$OVID %in% (sqlFetch(dta, "CLINICS") %>% pull(OVID))] |
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rnames<-sqlFetch(conn, "CLINICS") %>% filter(OVID %in% ovid.mod) %>% rownames |
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clinics.mod<-upd.clinics %>% filter(OVID %in% ovid.mod) %>% select(-NHC) |
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rownames(clinics.mod)<-rnames |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.mod)[grepl("DO|date", colnames(clinics.mod))] |
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for (i in fechas){ |
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clinics.mod[,i]<-as.Date(clinics.mod[,i]) |
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} |
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sqlUpdate(conn, clinics.mod,"CLINICS") |
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print("Tabla CLINICS modificada.") |
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} |
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} |
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if (dbtype == "UM"){ |
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upd.clinics<-read.xlsx(filetemp, sheet = "CLINICS",detectDates = T) |
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umid.mod<-upd.clinics$UMID[upd.clinics$UMID %in% (sqlFetch(dta, "CLINICOS") %>% pull(UMID))] |
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rnames<-sqlFetch(conn, "CLINICOS") %>% filter(UMID %in% umid.mod) %>% rownames |
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clinics.mod<-upd.clinics %>% filter(UMID %in% umid.mod) %>% select(-NHC) |
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rownames(clinics.mod)<-rnames |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.mod)[grepl("date|MET_DX|DoB", colnames(clinics.mod), ignore.case = T)] |
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for (i in fechas){ |
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clinics.mod[,i]<-as.Date(clinics.mod[,i]) |
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} |
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sqlUpdate(conn, clinics.mod,"CLINICOS") |
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print("Tabla CLINICOS modificada.") |
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} |
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sqlUpdate(conn, clinics.mod,"CLINICS") |
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print("Tabla CLINICS modificada.") |
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} |
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## Añadir datos clínicos nuevos a la base de datos |
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nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow |
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ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))] |
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clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC) |
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if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))] |
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varTypes<-rep("Date",length(fechas)) |
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names(varTypes)<-fechas |
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for (i in fechas){ |
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clinics.new[,i]<-as.Date(clinics.new[,i]) |
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if (dbtype == "OV"){ |
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nsamples.clin<-sqlFetch(conn, "CLINICS") %>% nrow |
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ovid.new<-upd.clinics$OVID[!upd.clinics$OVID %in% (sqlFetch(conn, "CLINICS") %>% pull(OVID))] |
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clinics.new<-upd.clinics %>% filter(OVID %in% ovid.new) %>% select(-NHC) |
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if (length(ovid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.new)[grepl("DO|date", colnames(clinics.new))] |
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varTypes<-rep("Date",length(fechas)) |
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names(varTypes)<-fechas |
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for (i in fechas){ |
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clinics.new[,i]<-as.Date(clinics.new[,i]) |
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} |
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sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes) |
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print("Tabla CLINICS sincronizada.") |
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} |
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} |
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if (dbtype == "UM"){ |
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nsamples.clin<-sqlFetch(conn, "CLINICOS") %>% nrow |
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umid.new<-upd.clinics$UMID[!upd.clinics$UMID %in% (sqlFetch(conn, "CLINICOS") %>% pull(UMID))] |
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clinics.new<-upd.clinics %>% filter(UMID %in% umid.new) %>% select(-NHC) |
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if (length(umid.new) > 0){rownames(clinics.new)<-(nsamples.clin+1):(nsamples.clin+nrow(clinics.new)) %>% as.character} |
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### !! Atención, esto cambia la base de datos: |
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if (sinc.clinics){ |
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fechas<-colnames(clinics.new)[grepl("date|MET_DX|DoB", colnames(clinics.new), ignore.case = T)] |
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varTypes<-rep("Date",length(fechas)) |
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names(varTypes)<-fechas |
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for (i in fechas){ |
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clinics.new[,i]<-as.Date(clinics.new[,i]) |
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} |
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sqlSave(conn, clinics.new, tablename="CLINICOS", append = T, varTypes = varTypes) |
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print("Tabla CLINICOS sincronizada.") |
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} |
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sqlSave(conn, clinics.new, tablename="CLINICS", append = T, varTypes = varTypes) |
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print("Tabla CLINICS sincronizada.") |
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} |
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} |
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sqlMultiSamples<-function(kbl=F, NHC=F){ |
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query<-sqlQuery(dta, "SELECT M.UMID,U.NHC,M.FECHA_RECEPCION,M.CODIGO,C.CODIGO,R.CODIGO |
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FROM ((MUESTRAS M |
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sqlMultiSamples<-function(kbl=F, NHC=F, full=F){ |
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query<-sqlQuery(dta, "SELECT U.UMID,U.NHC,M.FECHA_RECEPCION,M.TIPO,M.CODIGO,C.CODIGO,R.CODIGO,R.ESTADO |
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FROM ((UMID U |
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LEFT OUTER JOIN MUESTRAS M ON U.UMID=M.UMID) |
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LEFT OUTER JOIN CNAG C ON M.CODIGO=C.CODIGO) |
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LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO) |
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LEFT OUTER JOIN UMID U ON U.UMID=M.UMID") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2") |
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LEFT OUTER JOIN RNADNA R ON M.CODIGO=R.CODIGO") %>% rename("CNAG"="CODIGO.1","RNADNA"="CODIGO.2") |
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if (full==F){query<- query %>% filter(!is.na(CODIGO))} |
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if (NHC==F){query<- query %>% select(-NHC)} |
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|
query<-query %>% mutate( |
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|
CNAG=case_when(!is.na(CNAG)~"X",TRUE~""), |
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RNADNA=case_when(!is.na(RNADNA)~"X",TRUE~"") |
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) |
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|
RNADNA=case_when((!is.na(RNADNA) & (ESTADO=="ENV"))~"X", |
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|
(!is.na(RNADNA) & (is.na(ESTADO)))~".", |
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TRUE~"") |
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|
) %>% select(-ESTADO) |
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if (kbl==T){ |
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|
query %>% kableExtra::kbl() %>% kableExtra::kable_styling(full_width = F, bootstrap_options = c("striped")) |
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|
}else{ |
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