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bfabricShiny R package

Demonstration

Enables connecting R and bfabric using REST

bfabricPy-read-R

Command line triggered analytics

The animated gif below illustrates the interaction between an application (performing quality control on mass spectrometric measurements using rawDiag) and the B-Fabric platform on the command line level using the R console.

code_snippet_demo

The R code as used in the animated gif.

## R --no-save < code_snippet.R
## devtools::install_github("fgcz/bfabricShiny")
## devtools::install_github("fgcz/rawDiag")
stopifnot(R.Version()['major'] >= '4',
    require('rawDiag'),
    require('bfabricShiny'))

## Define B-Fabric input workunit
workunitid <- 165473

## Query metadata from B-Fabric
Q <- bfabricShiny::read(login, webservicepassword,
  endpoint = 'resource',
  query = list('workunitid' = workunitid), as_data_frame=FALSE)

## setting root directory
rawfilenames <- Q$res |>
    sapply(function(x)file.path('/srv/www/htdocs/', x$relativepath))

## Extract MS data from BLOBs using the rawDiag R package
## That requires storage access via SSH, NFS, or SAMBA
RAW <- rawfilenames |>
    parallel::mclapply(rawDiag::read.raw, mc.cores = 12) |>
    base::Reduce(f = rbind)

## Print a summary
RAW |> rawDiag::summary.rawDiag()

## Have fun with visualization https://doi.org/10.1021/acs.jproteome.8b00173
## (a)
RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25)
## (b)
RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25) +
  ggplot2::facet_wrap(~ filename)
## (c)
RAW |> rawDiag::PlotTicBasepeak(method = 'overlay')
## (d)
RAW |> rawDiag::PlotInjectionTime(method = 'overlay')

INSTALL

## Debian 12
apt-get install r-base libcurl4-openssl-dev lcmaps-openssl-interface -y

use source code from GitHub

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

if (!requireNamespace("PKI", quietly = TRUE))
    install.packages('PKI')

devtools::install_github("cpanse/shinyStore")
devtools::install_github('fgcz/bfabricShiny', build_vignettes = FALSE,
  quiet = FALSE)

Use cases

Run shiny based queue generator application

pkgs <- c('devtools', 'tidyverse', 'shiny', 'affy', 'limma')
pkgs[!pkgs %in% installed.packages()] |> 
  BiocManager::install()

devtools::install_github('protViz/SRMService', build_vignettes = FALSE,
  quiet = FALSE)

system.file("shiny", "queue_generator10", package = "bfabricShiny") |>
  shiny::runApp(display.mode = "normal")

JSON - SOAP proxy using python

  • run
python3 bfabric_flask.py

If a certified key is available, Flask will use SSL certificate and run on port 5001. Otherwise it will run using http and port 5000. Note that the port configuration can be changed in the bfabric_flask.py script.

# code snippet from bfabric_flask.py:
if exists('/etc/ssl/fgcz-host.pem') and exists('/etc/ssl/private/fgcz-host_key.pem'):    
    app.run(debug=False, host="0.0.0.0", port=5001, ssl_context=('/etc/ssl/fgcz-host.pem', '/etc/ssl/private/fgcz-host_key.pem'))
else:
   app.run(debug=False, host="127.0.0.1", port=5000)

See bfabric_flask.py on GitHub for more details.

  • simple tests
curl http://127.0.0.1:5000/sample/1

# R
rv <- httr::POST("https://host:5001/read", body = jsonlite::toJSON(list(login = "login", webservicepassword = "webservicepassword", endpoint = "user", query = list("login" = "cpanse"))), encode = "json")
httr::content(rv)

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

## generate public pem key file
ssh-keygen -f $PWD/bfabricShiny.key.pub -e -m PEM > bfabricShiny.key.pub.pem

## test
R -q -e "PKI::PKI.load.key(file = 'bfabricShiny.key.pub.pem')"

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')
    }
  })