First Release
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giancarlo
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# Dockerfile
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#
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# version: 1.0
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# author: Giancarlo Panichi
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# date: 2020/10/09
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# R images
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# see for more image:
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# https://hub.docker.com/u/rocker/
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#
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# Version-stable build of R, rstudio, and R packages ~2.48GB
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# FROM rocker/tidyverse:latest
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#
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# In this case I will use the r-base image by adding some debian packages
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# necessary for the correct build of the image.
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# In this case I will obtain an image of ~1.2GB.
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# Better ad-hoc solutions can be found to reduce the image size.
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#
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# Base Version ~824MB
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FROM rocker/r-base:latest
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RUN apt-get update -qq && apt-get -y --no-install-recommends install \
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libssl-dev \
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libxml2-dev \
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libcairo2-dev \
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libssh2-1-dev \
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libsasl2-dev \
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libcurl4-openssl-dev
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## create directories
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RUN mkdir -p /code
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WORKDIR /code
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RUN mkdir -p src
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## copy files
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COPY /src/* src/
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COPY sortapp .
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RUN chmod +x sortapp
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## install R-packages
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RUN Rscript src/install_packages.R
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## create a link
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WORKDIR /
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RUN ln -sf /code/sortapp /usr/bin/sortapp
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# RUN Script
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# CMD sortapp
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# SortAppR
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SortAppR is a simple example that allows you to sort a file in input.
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Starting from this example, you can first create an simple script R and then a docker image in which it is installed the created script.
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This example declare the sortapp command as entrypoint.
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So once you can use this command at command line to run the example:
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```
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sortapp <token> <file-item-id> <temp-dir-item-id>
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```
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The image created in this way can be executed in a container with the following command:
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```
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docker run -i -t --rm --name sortappr-cont sortappr sortapp <token> <file-item-id> <temp-dir-item-id>
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```
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To be able to create an image from this application you need to have Docker and Docker-Compose installed on your machine and the relative python packages, see:
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[Docker](https://docs.docker.com/engine/),
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[Docker-Compose](https://docs.docker.com/compose/install/) and
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[Docker Package for Python](https://pypi.org/project/docker/).
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## Useful Commands
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### Create Docker Image
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```
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docker build -t sortappr .
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```
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### Save Docker Image in file
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```
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docker save sortappr | gzip > sortappr.tar.gz
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```
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### Publish Docker Image on DockerHub
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Re-tagging an existing local image:
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```
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docker tag sortappr <hub-user>/<repo-name>[:<tag>]
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```
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Login in DockerHub(use your Docker ID):
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```
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docker login
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```
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Now you can push this repository to the registry designated by its name or tag:
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```
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docker push <hub-user>/<repo-name>:<tag>
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```
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Then logout for security:
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```
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docker logout
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```
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#!/bin/bash
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#
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# SortApp
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#
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# version: 1.0
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# author: Giancarlo Panichi
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# date: 2020/10/09
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#
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echo "Run Rscript"
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echo "Token: " $1
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echo "FileItemId: " $2
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echo "TempFolderItemId" $3
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Rscript /code/src/sortapp.R $1 $2 $3
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#
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# StorageHubCL.R
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#
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# version: 1.0
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# author: Giancarlo Panichi
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# date: 2020/10/09
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# GoogleVIS is very verbose
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#suppressPackageStartupMessages(library(googleVis))
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library(XML)
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require(XML)
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library(jsonlite)
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library(stringr)
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library(httr)
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require("httr")
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discoverStorageHub<-function(){
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urlString = paste("http://registry.d4science.org/icproxy/gcube/service/GCoreEndpoint/DataAccess/StorageHub?gcube-token=",token,sep="")
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got<-GET(urlString, timeout(1*3600))
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xmlfile <- xmlTreeParse(got)
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class(xmlfile)
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xmltop = xmlRoot(xmlfile)
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listxpath = xpathSApply(xmltop, "//Results/Result")
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print(listxpath)
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listx<-(rapply(listxpath, function(x) head(x, 1)))
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if (length(listx)>0){
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storagehubEP<<-as.character(listx[which(listx=="Endpoint")[[1]]+3])
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}else{
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cat("Found no storage ub endpoint\n")
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}
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}
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downloadSH<-function(itemid,filename){
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cat("About to download",itemid,"\n")
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cat("Downloading...\n")
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reqDownload<<-paste(sep="",storagehubEP,"/items/",itemid,"/download?exclude=hl:accounting&gcube-token=",token);
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download.file(url = reqDownload, destfile = filename, method="wget", quiet = T, mode = "w",cacheOK = FALSE)
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cat("All done.\n")
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}
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uploadSH<-function(folderitemid,localfilename,filename, descr){
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cat("About to upload: [folder=",folderitemid,", filename=",filename,"\n")
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cat("Uploading...\n")
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reqUpload<<-paste(storagehubEP,"/items/",folderitemid,"/create/FILE?gcube-token=",token,sep="");
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print(reqUpload)
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res<-POST(reqUpload,
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body=list(name=filename, description=descr, file=upload_file(localfilename)),
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add_headers("Content-Type" = "multipart/form-data"),
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verbose())
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print(res)
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cat("All done.\n")
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}
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@ -0,0 +1,13 @@
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# Install Packages
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#
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# Uncomment and add necessary packages
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#
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#install.packages("devtools", repos = "http://cran.rstudio.com/",dependencies=TRUE)
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#install.packages("dplyr", dependencies=TRUE)
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#install.packages("ggplot2", dependencies=TRUE)
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#install.packages("forcats", dependencies=TRUE)
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install.packages("XML", dependencies=TRUE)
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install.packages("jsonline", dependencies=TRUE)
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install.packages("stringr", dependencies=TRUE)
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install.packages("httr", dependencies=TRUE)
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@ -0,0 +1,46 @@
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#
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# SortAppr.R
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#
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# version: 1.0
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# author: Giancarlo Panichi
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# date: 2020/10/09
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print("Start SortApp.R")
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args <- commandArgs(trailingOnly = TRUE)
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print(args)
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print(paste("current dir: ",getwd()),sep="")
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setwd("/code/src")
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print(paste("working dir: ",getwd()),sep="")
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source("StorageHubCL.R")
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token<-args[1]
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itemid<-args[2]
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tempfolderitemid<-args[3]
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filename<-"sortableelements.txt"
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discoverStorageHub()
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downloadSH(itemid,filename)
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print("Read from SH...")
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print("Read data from file...")
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df <- read.table("sortableelements.txt",header = FALSE)
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print("Sort data...")
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df <- df[order(df[,1]),]
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print(df)
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print("Write data to file...")
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write.table(df, "result.txt", append = FALSE, sep = " ", dec = ".",
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row.names = FALSE, col.names = FALSE)
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print("Save on SH...")
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uploadSH(tempfolderitemid,"result.txt","result.txt","SortApp result")
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print("SortApp.R done")
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