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Corregir carga librerías para merge

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Costa 2 years ago
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commit
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1 changed files with 91 additions and 0 deletions
  1. +91
    -0
      BDAccess/app.R

+ 91
- 0
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({

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