Add resources

Accessing additional resources inside a Viash component.

If a script needs access to an external file, it needs to be added as a resource in the config.

First, create a file called my_file.txt.

echo 'Here are the contents of my_file.txt' > my_file.txt

echo 'Here are the contents of my_file.txt' > my_file.txt

echo 'Here are the contents of my_file.txt' > my_file.txt

echo 'Here are the contents of my_file.txt' > my_file.txt

echo 'Here are the contents of my_file.txt' > my_file.txt

echo 'Here are the contents of my_file.txt' > my_file.txt

Next, the file needs to be added to the config as a resource. This will let Viash know to copy the new file inside a component’s resource directory.

functionality:
  name: example_bash
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: bash_script
      path: script.sh
    - path: my_file.txt
platforms:
  - type: docker
    image: bash:4.0
  - type: native
  - type: nextflow

functionality:
  name: example_csharp
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: csharp_script
      path: script.csx
    - path: my_file.txt
platforms:
  - type: docker
    image: ghcr.io/data-intuitive/dotnet-script:1.3.1
  - type: native
  - type: nextflow

functionality:
  name: example_js
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: javascript_script
      path: script.js
    - path: my_file.txt
platforms:
  - type: docker
    image: node:19-bullseye-slim
  - type: native
  - type: nextflow

functionality:
  name: example_python
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: python_script
      path: script.py
    - path: my_file.txt
platforms:
  - type: docker
    image: python:3.10-slim
  - type: native
  - type: nextflow

functionality:
  name: example_r
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: r_script
      path: script.R
    - path: my_file.txt
platforms:
  - type: docker
    image: eddelbuettel/r2u:22.04
  - type: native
  - type: nextflow

functionality:
  name: example_scala
  description: A minimal example component.
  arguments:
    - type: file
      name: --input
      example: file.txt
      required: true
    - type: file
      name: --output
      direction: output
      example: output.txt
      required: true
  resources:
    - type: scala_script
      path: script.scala
    - path: my_file.txt
platforms:
  - type: docker
    image: sbtscala/scala-sbt:eclipse-temurin-19_36_1.7.2_2.13.10
  - type: native
  - type: nextflow

Lastly, to access a resource from within the script, use the resources_dir meta-variable:

#!/bin/bash

## VIASH START
par_input=path/to/file.txt
par_output=output.txt
## VIASH END

# view resource file
cat "$meta_resources_dir/my_file.txt"

# copy file
echo "Copying '$par_input' to '$par_output'."
cp -r "$par_input" "$par_output"

using System.IO;

// VIASH START
var par = new {
  input = "path/to/file.txt",
  output = "output.txt"
};
// VIASH END

// view resource file
string myFile = $"{meta.resources_dir}/my_file.txt";
string text = File.ReadAllText(myFile);
Console.WriteLine(text);

// copy file
Console.WriteLine($"Copying '{par.input}' to '{par.output}'.");
File.Copy(par.input, par.output, true);

const fs = require('fs');

// VIASH START
let par = {
  'input': 'path/to/file.txt',
  'output': 'output.txt'
};
// VIASH END

// view resource file
const my_file = `${meta['resources_dir']}/my_file.txt`
fs.readFile(my_file, 'utf8', (err, data) => {
  if (err) throw err;
  console.log(data);
});

// copy file
console.log(`Copying '${par['input']}' to '${par['output']}'`)
fs.copyFile(par['input'], par['output'], (err) => {
  if (err) throw err;
});

import shutil

## VIASH START
par = {
  'input': 'file.txt',
  'output': 'output.txt'
}
## VIASH END

# view resource file
my_file = f"{meta['resources_dir']}/my_file.txt"
with open(my_file, "r") as f:
  print(f.read())

# copy file
print(f"Copying '{par['input']}' to '{par['output']}'.")
shutil.copyfile(par['input'], par['output'])

## VIASH START
par <- list(
  "input" = 'file.txt',
  "output" = 'output.txt'
)
## VIASH END

# view resource file
lines <- readLines(paste0(meta$resources_dir, "/my_file.txt"))
cat(lines, sep = "\n")

# copy file
cat("Copying '", par$input, "' to '", par$output, "'.\n", sep = "")
file.copy(par$input, par$output)

import java.nio.file.StandardCopyOption.REPLACE_EXISTING
import java.nio.file.Files
import java.nio.file.Paths

// VIASH START
case class ViashPar(input: String, output: String)
val par = ViashPar(
  "path/to/file.txt",
  "output.txt"
)
// VIASH END

// view resource file
val myFile = s"${meta.resources_dir}/my_file.txt"
val src = scala.io.Source.fromFile(myFile)
src.getLines.foreach(println)

// copy file
println(s"Copying '${par.input}' to '${par.output}'.")
val fileIn = Paths.get(par.input)
val fileOut = Paths.get(par.output)
Files.copy(fileIn, fileOut, REPLACE_EXISTING)

Now we can run the component as follows:

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_bash:latest'
[warning] Could not pull from 'example_bash:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_bash:latest' with Dockerfile
Here are the contents of my_file.txt
Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/bash/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/bash/foo.txt'.

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_csharp:latest'
[warning] Could not pull from 'example_csharp:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_csharp:latest' with Dockerfile
Here are the contents of my_file.txt

Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/csharp/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/csharp/foo.txt'.

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_js:latest'
[warning] Could not pull from 'example_js:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_js:latest' with Dockerfile
Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/js/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/js/foo.txt'
Here are the contents of my_file.txt

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_python:latest'
[warning] Could not pull from 'example_python:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_python:latest' with Dockerfile
Here are the contents of my_file.txt

Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/python/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/python/foo.txt'.

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_r:latest'
[warning] Could not pull from 'example_r:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_r:latest' with Dockerfile
Here are the contents of my_file.txt
Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/r/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/r/foo.txt'.
[1] TRUE

viash run config.vsh.yaml -- --input config.vsh.yaml --output foo.txt

[notice] Checking if Docker image is available at 'example_scala:latest'
[warning] Could not pull from 'example_scala:latest'. Docker image doesn't exist or is not accessible.
[notice] Building container 'example_scala:latest' with Dockerfile
warning: 1 deprecation
warning: 1 deprecation (since 2.13.3)
warning: 2 deprecations in total; re-run with -deprecation for details
Here are the contents of my_file.txt
Copying '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/scala/config.vsh.yaml' to '/viash_automount/tmp/Rtmpe4UVQx/add-dependencies743e4e38486f/scala/foo.txt'.