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bfabricShiny

enables connecting R and bfabric using REST

bfabricPy-read-R

INSTALL

apt-get install r-base libcurl4-openssl-dev

use source code from github

#  install.packages('devtools')
library(devtools)
install_github("trestletech/shinyStore")
install_github('cpanse/bfabricShiny', build_vignettes = FALSE, quiet = FALSE)

Demonstration

JSON - SOAP proxy using python

  • run
python3 bfabric_flask.py
  • simple json test
curl http://127.0.0.1:5000/sample/1

Sample Query

R> (Q <- query(login, webservicepassword, 
   endpoint = 'resource',
   query = list('filechecksum' = "65518d3ccc6b4f3c83c132dae147fc0e")))
$res
$res[[1]]
$res[[1]]$`_id`
[1] 1301179

$res[[1]]$created
[1] "Thu, 11 Jul 2019 07:00:11 GMT"

$res[[1]]$createdby
[1] "pfeeder"

$res[[1]]$description
[1] "```{r}\r\nR> library(bfabricShiny)\r\nR> (Q <- query(login, webservicepassword, endpoint = 'resource', query = list('filechecksum' = \"65518d3ccc6b4f3c83c132dae147fc0e\")))\r\n$res\r\n$res[[1]]\r\n$res[[1]]$`_id`\r\n[1] 1301179\r\n\r\n$res[[1]]$created\r\n[1] \"Thu, 11 Jul 2019 07:00:11 GMT\"\r\n\r\n$res[[1]]$createdby\r\n[1] \"pfeeder\"\r\n\r\n$res[[1]]$filechecksum\r\n[1] \"65518d3ccc6b4f3c83c132dae147fc0e\"\r\n\r\n$res[[1]]$junk\r\n[1] FALSE\r\n\r\n$res[[1]]$modified\r\n[1] \"Thu, 11 Jul 2019 07:00:11 GMT\"\r\n\r\n$res[[1]]$modifiedby\r\n[1] \"pfeeder\"\r\n\r\n$res[[1]]$name\r\n[1] \"20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$project\r\n$res[[1]]$project$`_id`\r\n[1] 3181\r\n\r\n$res[[1]]$relativepath\r\n[1] \"p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$sample\r\n$res[[1]]$sample$`_id`\r\n[1] 200295\r\n\r\n$res[[1]]$size\r\n[1] 235625610\r\n\r\n$res[[1]]$status\r\n[1] \"available\"\r\n\r\n$res[[1]]$storage\r\n$res[[1]]$storage$`_id`\r\n[1] 2\r\n\r\n$res[[1]]$uris\r\n$res[[1]]$uris[[1]]\r\n[1] \"http://fgcz-proteomics.uzh.ch/dm/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$uris[[2]]\r\n[1] \"http://fgcz-proteomics.uzh.ch/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$uris[[3]]\r\n[1] \"scp://fgcz-ms.uzh.ch/srv/www/htdocs/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$uris[[4]]\r\n[1] \"scp://fgcz-r-021.uzh.ch/export/lv_iduzh01/projects/,/export/lv_iduzh02/projects/,/export/lv_iduzh03/projects/,/export/lv_iduzh04/projects/,/export/lv_iduzh05/PAS/p65/RawData_Archive/,/export/lv_iduzh06/projects/,/export/lv_iduzh07/projects/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$url\r\n[1] \"scp://fgcz-ms.uzh.ch/srv/www/htdocs/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw\"\r\n\r\n$res[[1]]$workunit\r\n$res[[1]]$workunit$`_id`\r\n[1] 200896\r\n\r\nR> \r\n\r\nR> table(sapply((Q <- query(login, webservicepassword, endpoint = 'resource', query = list('name' = \"%autoQC4L%\")))[[1]], function(x){x$project$`_id`}))\r\n\r\n  65 1000 1147 1352 1654 1687 1875 1876 1951 2059 2069 2135 2175 2192 \r\n  13   74   12    6    3    1    2   16    2    1    2    3    1    1 \r\n2193 2211 2213 2272 2310 2342 2433 2447 2479 2501 2558 2621 2631 2687 \r\n   5    1    1    2    1    2    1    1    1    1    1    4    2    2 \r\n2692 2695 2702 2748 2749 2760 2799 2830 2858 2882 2885 2889 2898 2901 \r\n   1    2    2    2    5    2    2    2    1    1    8    2    3    1 \r\n2915 2916 2928 2933 2946 2954 2960 2961 2993 2995 2997 3000 3024 3025 \r\n   4    5    7    3    1    4    2    1    8    2    1   87    1    5 \r\n3026 3036 3047 3053 3061 3067 3075 3086 3101 3106 3127 3134 3144 3146 \r\n  12    1    3    1    3    1    1    4    2    5    1    6    4    3 \r\n3147 3165 3175 3180 3181 \r\n   1    1    2    2    1 \r\nR> \r\n\r\n```"

$res[[1]]$filechecksum
[1] "65518d3ccc6b4f3c83c132dae147fc0e"

$res[[1]]$junk
[1] FALSE

$res[[1]]$modified
[1] "Tue, 23 Jul 2019 14:27:57 GMT"

$res[[1]]$modifiedby
[1] "cpanse"

$res[[1]]$name
[1] "20190710_005_autoQC4L.raw"

$res[[1]]$project
$res[[1]]$project$`_id`
[1] 3181


$res[[1]]$relativepath
[1] "p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"

$res[[1]]$sample
$res[[1]]$sample$`_id`
[1] 200295


$res[[1]]$size
[1] 235625610

$res[[1]]$status
[1] "available"

$res[[1]]$storage
$res[[1]]$storage$`_id`
[1] 2


$res[[1]]$uris
$res[[1]]$uris[[1]]
[1] "http://fgcz-proteomics.uzh.ch/dm/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"

$res[[1]]$uris[[2]]
[1] "http://fgcz-proteomics.uzh.ch/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"

$res[[1]]$uris[[3]]
[1] "scp://fgcz-ms.uzh.ch/srv/www/htdocs/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"

$res[[1]]$uris[[4]]
[1] "scp://fgcz-r-021.uzh.ch/export/lv_iduzh01/projects/,/export/lv_iduzh02/projects/,/export/lv_iduzh03/projects/,/export/lv_iduzh04/projects/,/export/lv_iduzh05/PAS/p65/RawData_Archive/,/export/lv_iduzh06/projects/,/export/lv_iduzh07/projects/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"


$res[[1]]$url
[1] "scp://fgcz-ms.uzh.ch/srv/www/htdocs/p3181/Proteomics/QEXACTIVEHFX_1/tobiasko_20190710/20190710_005_autoQC4L.raw"

$res[[1]]$workunit
$res[[1]]$workunit$`_id`
[1] 200896




R> 


R> table(sapply((Q <- query(login, webservicepassword,
   endpoint = 'resource',
   query = list('name' = "%autoQC4L%")))[[1]], function(x){x$project$`_id`}))

  65 1000 1147 1352 1654 1687 1875 1876 1951 2059 2069 2135 2175 2192 
  13   74   12    6    3    1    2   16    2    1    2    3    1    1 
2193 2211 2213 2272 2310 2342 2433 2447 2479 2501 2558 2621 2631 2687 
   5    1    1    2    1    2    1    1    1    1    1    4    2    2 
2692 2695 2702 2748 2749 2760 2799 2830 2858 2882 2885 2889 2898 2901 
   1    2    2    2    5    2    2    2    1    1    8    2    3    1 
2915 2916 2928 2933 2946 2954 2960 2961 2993 2995 2997 3000 3024 3025 
   4    5    7    3    1    4    2    1    8    2    1   87    1    5 
3026 3036 3047 3053 3061 3067 3075 3086 3101 3106 3127 3134 3144 3146 
  12    1    3    1    3    1    1    4    2    5    1    6    4    3 
3147 3165 3175 3180 3181 
   1    1    2    2    1 
R>

restart the shiny server

service shiny-server stop && service shiny-server start

Shiny

queue generator application

qgs <- system.file("shiny", "queue_generator", package = "bfabricShiny")
shiny::runApp(qgs, display.mode = "normal")

bfabric authentification

bfabricauth <- system.file("shiny", "simple_auth", package = "bfabricShiny")
shiny::runApp(bfabricauth, display.mode = "normal", port=8080)

On howto generate keys?

cd bfabricShiny/inst/keys &&  ssh-keygen -f $PWD/bfabricShiny.key -t rsa

PTM-MarkerFinder

ptmmf <- system.file("shiny", "PTM_MarkerFinder", package = "bfabricShiny")
shiny::runApp(ptmmf, display.mode = "normal", port=8080)

SOP create your own application

The idea is to fetch a RData file stored in bfabric.

Setup

  • install the python package https://github.com/cpanse/bfabricPy
  • install install_github("https://github.com/cpanse/bfabricShiny")
  • run the SOAP-REST proxy python3 bfabric_flask.py
  • manage the key thing for housing the bfabric login/webpassword
  • run RStudio - create a new shiny app
  • in the shiny ui.R change
   mainPanel(
      tabsetPanel(
        tabPanel("bfabric", bfabricInput("bfabric8")),
        tabPanel("plot", plotOutput("distPlot"))
      )

  • on the shiny server.R

    • library(bfabricShiny)
    • add to shiny server function bf <- callModule(bfabric, "bfabric8", applicationid = c(155))

  • run the shiny application; check input$relativepath

Data staging

  • on the shiny server.R - define the way you are going to ``stage'' the data
.ssh_load_RData <- function(host = 'fgcz-r-021.uzh.ch', user = 'cpanse', file = NULL){
  e <- new.env()

  cmd <- paste('cat ',  file)

  ssh_cmd <- paste("ssh ", user, "@", host, " '", cmd, "'", sep="")
  message(ssh_cmd)

  S <- load(pipe(ssh_cmd))

  for (x in S){
    assign(x, get(x), e)
  }
  e
}

.load_RData <- function(file = NULL){
  e <- new.env()

  S <- load(file)

  for (x in S){
    assign(x, get(x), e)
  }
  e
}

  # returns an env
  getRDataEnv <- eventReactive(input$load, {
    # this is the ``output'' of the bfabric shiny module
    message(input$relativepath)

    filename <- file.path('/srv/www/htdocs/', input$relativepath)

    if (file.exists(filename)){
      .load_RData(file=filename)
    }else{
      .ssh_load_RData(file = filename, host = 'fgcz-r-021.uzh.ch')
    }
  })