From 4f77eb56639e62e53a15f71ed26be567a52f37ed Mon Sep 17 00:00:00 2001
From: jlopez <jimmy.lopez0023@gmail.com>
Date: Wed, 1 Apr 2020 11:36:36 +0200
Subject: [PATCH] Code: Update biocmanager mechanims & add asynchronous request
---
R/helper_functions.R | 7 ++++---
app.R | 16 +++++++++-------
server/opt_home.R | 45 +++++++++++++++++++++++++-------------------
3 files changed, 39 insertions(+), 29 deletions(-)
diff --git a/R/helper_functions.R b/R/helper_functions.R
index dccd82b..b7c2b57 100644
--- a/R/helper_functions.R
+++ b/R/helper_functions.R
@@ -1,3 +1,5 @@
+TOTO <<- 0
+
getPackagesWithTitle <- function() {
contrib.url("https://cran.rstudio.com/", "source")
description <- sprintf("%s/web/packages/packages.rds",
@@ -8,10 +10,9 @@ getPackagesWithTitle <- function() {
url(description, "rb")
}
on.exit(close(con))
+
db <- readRDS(gzcon(con))
- rownames(db) <- NULL
-
- db[, c("Package", "Title", "Version")]
+ db[, c("Package", "Title", "Version")]
}
diff --git a/app.R b/app.R
index 6bebe07..918d465 100644
--- a/app.R
+++ b/app.R
@@ -9,6 +9,11 @@ library(githubinstall)
require(stringi)
library(devtools)
library(yaml)
+library(BiocManager)
+library(promises)
+library(future)
+plan(multiprocess)
+
source("./R/helper_functions.R", local = T)
source("./R/menugauche.R", local = T)
@@ -41,17 +46,14 @@ UI <- dashboardPage(
)
server <- function( input, output, session) {
-
- source("https://bioconductor.org/biocLite.R")
-
+
session$userData <- c()
-
disable("rcranpackagelist")
- #allCRAN <<- as.data.frame(available.packages(repo = "http://cran.us.r-project.org")[, c("Package")])
- allCRAN <<- as.data.frame(getPackagesWithTitle())
- allBIO <<- as.data.frame(available.packages(repo = biocinstallRepos()[1])[, c("Package", "Version")])
+ allCRAN <<- c()
+ allBIO <<- c()
allGITHUB <<- data.frame(Package=character(), Version=character())
+
TMP <<- yaml.load_file("container.yaml")$containers
i = 1
j = 1
diff --git a/server/opt_home.R b/server/opt_home.R
index 8cf2f2c..2c7dc4a 100755
--- a/server/opt_home.R
+++ b/server/opt_home.R
@@ -1,16 +1,22 @@
output$dtrcranpackage <- DT::renderDataTable({
-
-
- result <- allCRAN
-
- return(result)
+ future({
+ cran <- as.data.frame(getPackagesWithTitle())
+ cran
+ }) %...>% (function(result) {
+ allCRAN <<- result
+ return(result)
+ })
}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
output$dtrbioconductorpackage <- DT::renderDataTable({
- result <- allBIO
-
- return(result)
+ future({
+ bioc <- as.data.frame(available.packages(repo = BiocManager::repositories()[1])[, c("Package", "Version")])
+ bioc
+ }) %...>% (function(result) {
+ allBIO <<- result
+ return(result)
+ })
}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
output$dtrgithubpackage <- DT::renderDataTable({
@@ -31,8 +37,6 @@ output$dtbiocontainer <- DT::renderDataTable({
return(result)
}, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
-getWorkflows
-
output$dtWorkflows <- DT::renderDataTable({
result <- data.frame(Workflow=character(),
Author=character(),
@@ -909,16 +913,19 @@ observeEvent(input$findGithub, {
name <- input$inputGithub
if(!stri_isempty(name)) {
- allGITHUB <<- data.frame(Package = gh_suggest(name, keep_title = FALSE), Title = attr(gh_suggest(name, keep_title = TRUE), "title"))
-
- if(length(allGITHUB) >= 1 ) {
- output$dtrgithubpackage <- DT::renderDataTable({
- result <- allGITHUB
- return(result)
- }, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
- }
+ future({
+ github <- data.frame(Package = gh_suggest(name, keep_title = FALSE), Title = attr(gh_suggest(name, keep_title = TRUE), "title"))
+ github
+ }) %...>% (function(result) {
+ allGITHUB <<- result
+ if(length(allGITHUB) >= 1 ) {
+ output$dtrgithubpackage <- DT::renderDataTable({
+ result <- allGITHUB
+ return(result)
+ }, filter='top', escape = FALSE, rownames= FALSE,server = TRUE)
+ }
+ })
}
-
})
--
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