Fix biocontainer

R/helper_functions.R

@@ -37,14 +37,14 @@ getBioconductorPackage <- function() {
   i=1
   for (tools in data) {
     
-    if(length(tools$install) > 0) {
+    #if(length(tools$install) > 0) {
     
     Tool[i] = tools$name
     Version[i] = tools$version
     Description[i] = tools$description
     Link[i] = paste0("<a href='", tools$documentation, "'>documentation</a>")
     i = i + 1
-    }
+    #}
   }
   
   # Link = c("<a href='https://github.com/r78v10a07/DiffExpIR'>documentation</a>",
@@ -70,10 +70,16 @@ getInstallToolPackageBioContainer <- function(tool) {
   intalls <- ""
   
   for (tools in data) {
-      if(tools$name == tool) {
-        res <- paste0("\t", tools$install, collapse='\n' )
-        return(res)
-      } 
+      splitB <- strsplit(tool, "%")  
+      name <- splitB[[1]][1]
+      version <- splitB[[1]][2]
+      
+      if(tools$name == name) {
+        if(tools$version == version) {
+          res <- paste0("\t", tools$install, collapse='\n' )
+          return(res)
+        }
+      }
   }
 
   return("\t")

app.R

@@ -33,8 +33,6 @@ UI <- dashboardPage(
   )
 )
 
-
-
 server <- function( input, output, session) {
   
   source("https://bioconductor.org/biocLite.R")
@@ -47,6 +45,7 @@ server <- function( input, output, session) {
   allCRAN <<- as.data.frame(getPackagesWithTitle())
   allBIO <<- as.data.frame(available.packages(repo = biocinstallRepos()[1])[, c("Package", "Version")])
   allGITHUB <<- data.frame(Package=character(), Version=character())
+  allBIOCONTAINER <<- yaml.load_file("container.yaml")$containers
   
   hide("downloadContainerFile")
 

pages/pages_def_home.R

@@ -48,6 +48,8 @@ tabHome = fluidPage(align="left",
                                             br(), br(),
                                             DT::dataTableOutput('dtrgithubpackage')),
                                           tabPanel('BioContainer tools',
+                                                   div(id = "formContainer",
+                                                   selectizeInput('selectedBiocontainer', 'Biocontainer tools selected:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000))),
                                                    DT::dataTableOutput('dtbiocontainer')
                                                    )
                              )

server/opt_home.R

@@ -218,12 +218,20 @@ createContentFile <- function() {
   } #END R
 
   
-  if(!is.null(input$dtbiocontainer_rows_all)) {
+  print(input$selectedBiocontainer)
+
+  if(!is.null(input$selectedBiocontainer)) {
+    
+
+
+    
+
+  #if(!is.null(input$dtbiocontainer_rows_all)) {
     
-    biotools = getBioconductorPackage() 
+    #biotools = getBioconductorPackage() 
     
-    selectBioTool<- biotools[input$dtbiocontainer_rows_all,]
-    selectBioTool <- selectBioTool[,"BioContainer_Tool"]
+    #selectBioTool <- biotools[input$dtbiocontainer_rows_all,]
+    selectBioTool <- input$selectedBiocontainer
     
     #result <- paste(result, "\tmv /etc/apt/sources.list /etc/apt/sources.list.bkp && \\",
     #                "\techo -e \"deb mirror://mirrors.ubuntu.com/mirrors.txt xenial main restricted universe multiverse\\n\\ ",
@@ -273,6 +281,8 @@ createContentFile <- function() {
     result <- paste0(result, "\n")
     
     for (tool in selectBioTool){
+      
+      
         
       result <- paste(result, getInstallToolPackageBioContainer(tool), sep="\n\n")
       
@@ -310,6 +320,22 @@ output$downloadContainerFile <- downloadHandler(
   }
 )
 
+observe({
+  
+  if(is.null(input$dtbiocontainer_rows_selected)) {
+    shinyjs::reset("formContainer")
+  } else {
+    i = 1
+    selectBiocontainer <- list()
+    for(x in input$dtbiocontainer_rows_selected) {
+      selectBiocontainer[i] = paste(allBIOCONTAINER[[x]]$name, allBIOCONTAINER[[x]]$version, sep = "%")
+      i = i + 1
+    }
+    selectBiocontainer <- c(unlist(selectBiocontainer))
+    updateSelectizeInput(session,"selectedBiocontainer", choices = selectBiocontainer, selected = selectBiocontainer, options = list())
+  }
+})
+
 observeEvent(input$dtrgithubpackage_rows_selected, {