---
title: "Download test  IMC data - steinbock"
author: "Nils Eling"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

This script downloads the steinbock output of a small test dataset.
The Github repository containing this data can be accessed [here](https://github.com/BodenmillerGroup/TestData).

More specifically, we will use the `210308_ImcTestData` dataset.

## Download the steinbock output

Here, we will first download the output of the [steinbock](https://github.com/BodenmillerGroup/steinbock).
For this, we an use the automatically generated Github assets.

```{r download-cpout}
cur_url <- "https://github.com/BodenmillerGroup/TestData/releases/download/v1.0.7/210308_ImcTestData_steinbock.tar.gz"

download.file(cur_url, "210308_ImcTestData_steinbock.tar.gz")
untar("210308_ImcTestData_steinbock.tar.gz")
unlink("210308_ImcTestData_steinbock.tar.gz")
```

## Only copy the needed files

For reading in the single-cell features, we will only need to copy the .csv files and the folders containing the individual measurements.

```{r copy-files, message=FALSE}
files_of_interest <- c("cells.csv", "panel.csv", "steinbock.sh", "images.csv")

folders_of_interest <- c("neighbors", "intensities", "regionprops")

lapply(folders_of_interest, function(x){
    dir.create(paste0("../extdata/mockData/steinbock/", x))
    file.copy(list.files(paste0("datasets/210308_ImcTestData/steinbock/", x), 
                         full.names = TRUE),
          paste0("../extdata/mockData/steinbock/", x), 
          overwrite = TRUE)
})

file.copy(paste0("datasets/210308_ImcTestData/steinbock/", files_of_interest),
          "../extdata/mockData/steinbock/", 
          overwrite = TRUE)
unlink("datasets/", recursive = TRUE)
```



