Corregir carga librerías para merge

BDAccess/app.R

@@ -1,9 +1,13 @@
 library(shiny)
 library(rhandsontable)
+<<<<<<< HEAD
 library(tidyverse)
 library(reshape2)
 library(Matrix)
 library(CitFuns)
+=======
+library(BDCIT)
+>>>>>>> main
 
 print(getwd())
 source("../sqlFunctions.R", encoding = "UTF-8")
@@ -57,6 +61,7 @@ ui <- fluidPage(
                              choices = list("NHC" = 1, "UMID/OVID" = 2, "UM/OV"=3), 
                              selected = 2),
                 textInput("id", label = "ID", value = ""),
+                actionButton("nitrosync", "Actualiza Nitrógeno")
             ),
             mainPanel(
                 htmlOutput("report"),
@@ -696,6 +701,92 @@ server <- function(input, output) {
         nitro
     })
     
+    observeEvent(input$nitrosync, {
+        
+        if (input$dbtype == "UM"){
+            ## Copia de backup
+            
+            if (!dir.exists(NitroRoute)){
+                dir.create(NitroRoute)
+                print(paste0("Back Up directory ", NitroRoute, " created"))
+            }
+            
+            write.xlsx(
+                sqlFetch(dta, "NITROGEN"),
+                file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","UM-Nitrogen.xlsx")
+            )
+            
+            table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
+            
+            table.um<-table %>% filter( grepl("UM|MU", Nombre) | grepl("Met|Prim|hep|Enn",Nombre, ignore.case = T) |
+                                            Nombre == "TILs f. 21/09/20" | Nombre == "TILS DISG f. 03/07/20")
+            
+            table.um<-add_column(table.um,.before=1, "CODIGO"=str_extract(table.um$Nombre, "UM[0-9]{4}"))
+            
+            table.samp<-sqlQuery(dta, "SELECT U.NHC,M.* FROM MUESTRAS M INNER JOIN UMID U ON M.UMID=U.UMID")
+            table.samp$FECHA_RECEPCION<-table.samp$FECHA_RECEPCION+24*60*60
+            
+            
+            table.um<-add_column(table.um, .after=1,
+                                 "FECHA"=str_extract(table.um$Nombre, "[0-9]{2}[\\./][0-9]{2}[\\./][0-9]{2}") %>% gsub("\\.","/",.))
+            table.um$FECHA<-as.POSIXct(table.um$FECHA, format="%d/%m/%y")
+            
+            table.um<-merge(table.um, table.samp %>% select(CODIGO,FECHA_RECEPCION), by.x="FECHA", by.y="FECHA_RECEPCION", all.x=T)
+            table.um<-table.um %>% mutate(CODIGO=case_when(is.na(CODIGO.x)~CODIGO.y, TRUE~CODIGO.x), .before=1) %>% select(-CODIGO.x,-CODIGO.y)
+            
+            table.um[table.um$Nombre == "MU Met f. 10/02/20","CODIGO"]<-"UM0009"
+            table.um[table.um$Nombre == "TILs Diss Met","CODIGO"]<-"UM0020"
+            table.um[table.um$Nombre == "UM Met","CODIGO"]<-"UM0020"
+            table.um[table.um$Nombre == "UM MET NHC 11489341","CODIGO"]<-"UM0044"
+            table.um[table.um$Nombre == "UM Primary 20278822","CODIGO"]<-"UM0029"
+            table.um[table.um$Nombre == "Hip Nod Hep NHC11489341","CODIGO"]<-"UM0044"
+            
+            ## Actualización
+            
+            sqlDrop(dta, "NITROGEN")
+            sqlSave(dta, table.um %>% select(-FECHA) %>% filter(!is.na(CODIGO)), tablename="NITROGEN", rownames=F)
+        }
+        if (input$dbtype == "OV"){
+            ## Copia de backup
+
+            if (!dir.exists(NitroRoute)){
+                dir.create(NitroRoute)
+                print(paste0("Back Up directory ", NitroRoute, " created"))
+            }
+            
+            write.xlsx(
+                sqlFetch(dta, "NITROGEN"),
+                file=paste0(NitroRoute, format(Sys.time(), format="%Y%m%d"),"-","OV-Nitrogen.xlsx")
+            )
+            
+            ## Lectura del excel
+            table<-read.xlsx(paste0(gsub("/BU_NITRO/", "", NitroRoute),"/Nitrogen_ICO.xlsx"))
+            
+            table.ov<-table %>% filter(grepl("OV",Nombre))
+            table.ov<-filter(table.ov, !grepl("OVA",Nombre))
+            
+            table.ov<-add_column(table.ov,.before=1, "CODIGO"=str_extract(table.ov$Nombre, "OV[0-9]{4}"))
+            table.ov[table.ov$Nombre == "Ascitis OV","CODIGO"]<-"OV2105"
+            
+            table.ov<-table.ov %>% add_column(SampType=NA, .after=1)
+            table.ov[grepl("TIL",table.ov$Nombre, ignore.case = T),"SampType"]<-"TILs"
+            table.ov[grepl("frag",table.ov$Nombre, ignore.case = T)|grepl("frag",table.ov$Observaciones, ignore.case = T),"SampType"]<-"FRAG"
+            table.ov[grepl("slide",table.ov$Nombre, ignore.case = T)|grepl("slide",table.ov$Observaciones, ignore.case = T),"SampType"]<-"SLIDE"
+            table.ov[(is.na(table.ov$SampType) | !(table.ov$SampType == "TILs")) & 
+                         (grepl("disg|diss",table.ov$Nombre, ignore.case = T)|
+                              grepl("disg|diss",table.ov$Observaciones, ignore.case = T)),"SampType"]<-"DISG"
+            table.ov[table.ov$Nombre == "Ascitis OV", "SampType"]<-"ASC"
+            table.ov[20:25,"SampType"]<-"DISG"
+            table.ov[63:68,"SampType"]<-"DISG"
+            
+            ## Actualización
+            
+            sqlDrop(dta, "NITROGEN")
+            sqlSave(dta, table.ov, tablename="NITROGEN", rownames=F)
+        }
+
+    })
+    
     ## scRNAseq
     
     output$PATID = renderUI({