Docker

shiny_app/server.R

@@ -97,30 +97,33 @@ shinyServer(function(input, output, session) {
         # print(SWCpaths[i])
         #Xvfb :100 -ac &
         #export DISPLAY=:100.0
-        log0 <- system('export DISPLAY=:8469; Xvfb :8469 -auth /dev/null  > xvfblog.txt 2>&1 &', intern=T)
-        output$console <- renderPrint({
-          return(print(log0))
-        })
+        #log0 <- system('export DISPLAY=:8469; Xvfb :8469 -auth /dev/null  > xvfblog.txt 2>&1 &', intern=T)
+        #output$console <- renderPrint({
+        #  return(print(log0))
+        #})
         # log0 <- system('xhost local:allencenter', intern=T)
         # output$console <- renderPrint({
         #   return(print(log0))
         # })
-        log0 <- system('ls', intern=T)
-        output$console <- renderPrint({
-          return(print(log0))
-        })
-        log <- system(paste0('Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o "',SWCpaths[i],'"_prep.swc #l 3 #s 2 #r 1"'),
-                      intern=T)
-        output$console <- renderPrint({
-          return(print(log))
-        })
-        pathswc <- data.frame(file=paste0("SWCFILE=",SWCpaths[i],"_prep.swc"))
-        write.table(pathswc,file="mydatabase.ano",col.names=F,row.names=F,quote=F)
-        log2 <- system('Vaa3D/vaa3d -x blastneuron -f batch_compute -p \"#i mydatabase.ano #o features.csv"',
-                      intern=T)
-        output$console <- renderPrint({
-          return(print(log2))
-        })
+        #log0 <- system('ls', intern=T)
+        #output$console <- renderPrint({
+        #  return(print(log0))
+        #})
+        #log <- system(paste0('Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o "',SWCpaths[i],'"_prep.swc #l 3 #s 2 #r 1"'),
+        #              intern=T)
+        #output$console <- renderPrint({
+        #  return(print(log))
+        #})
+        #pathswc <- data.frame(file=paste0("SWCFILE=",SWCpaths[i],"_prep.swc"))
+        #write.table(pathswc,file="mydatabase.ano",col.names=F,row.names=F,quote=F)
+        #log2 <- system('Vaa3D/vaa3d -x blastneuron -f batch_compute -p \"#i mydatabase.ano #o features.csv"',
+        #             intern=T)
+        #output$console <- renderPrint({
+        #  return(print(log2))
+        #})
+        # zx merge all call system to one call
+        # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2'))
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]
@@ -129,10 +132,12 @@ shinyServer(function(input, output, session) {
         # })
 
         # Add distance metrics
-        gspath <- Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")) 
-        log3 <- system(paste0('Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',gspath,' ',SWCpaths[i],' -p 2 -o dists/',i,'.txt'),
-                       intern=T)
-        dataFile <- readLines(paste0("dists/",i,".txt"))
+        #gspath <- Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")) 
+        #log3 <- system(paste0('Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',gspath,' ',SWCpaths[i],' -p 2 -o dists/',i,'.txt'),
+        #              intern=T)
+        #dataFile <- readLines(paste0("dists/",i,".txt"))
+        #zx change path to i._dists_tmp.txt
+        dataFile <- readLines(paste0(i,"_dists_tmp.txt"))
 
         dfdist <- data.frame(esa1t2=NA,esa2t1=NA,ab_esa=NA,dsa=NA,pds1t2=NA,pds2t1=NA,a_pds=NA)
         dfdist$esa1t2 <- as.numeric(strsplit(dataFile[3],'=')[[1]][2])
@@ -145,6 +150,7 @@ shinyServer(function(input, output, session) {
 
         # Add image metrics
         # which(ids=="5") this is index for data to get image metrics
+
         dfim <- data[which(ids==strsplit(SWCnames[i],"[.]")[[1]][1])[1],c(29:54)]
 
         IQ <- read.csv(paste0(IQpaths[i]),header=T)
@@ -172,13 +178,16 @@ shinyServer(function(input, output, session) {
         data <- rbind(data,idata)
         # print("Rbind done")
 
+        #zx remove vaa3d plugins output files
+        system("rm *_dists_tmp.txt features.csv mydatabase.ano") 
+
         # Remove remote files
-        system("rm dists/*",
-               intern=T)
-        system("rm features.csv",
-               intern=T)
-        system("rm mydatabase.ano",
-               intern=T)
+        # system("rm dists/*",
+        #        intern=T)
+        # system("rm features.csv",
+        #        intern=T)
+        # system("rm mydatabase.ano",
+        #        intern=T)
       }
 
     }

shiny_app/ui.R

@@ -136,7 +136,9 @@ shinyUI(fluidPage(
           # Input: Select a file ----
           fileInput("file1", "Choose SWC and their associated IQ files",
               multiple = TRUE,
-              accept = c(".swc",".eswc",".txt"))),
+              #accept = c(".swc",".eswc",".txt"))),
+              #zx add .csv
+              accept = c(".swc",".eswc",".txt",".csv"))),
 
           # # Input: Checkbox 
           # checkboxGroupInput("variableinpdat", "Choose images of uploaded reconstructions","",selected="variableinpdat",inline=TRUE),