Via Foundry R SDK

viafoundry is an R package for interacting with the Via Foundry API. It provides functions for user authentication, dynamic endpoint discovery, and executing API calls.

Features

• Authentication: Log in to the Via Foundry API using your credentials.
• Dynamic API Discovery: List all available API endpoints.
• Custom API Calls: Send HTTP requests to any endpoint with parameters or payloads.

Installation

Development Version

You can install the package directly from the source using devtools:

# Install the viafoundry package
install.packages("viafoundry")

# Or

# Install devtools if not already installed
install.packages("devtools")

# Install the viafoundry package
devtools::install_github("viascientific/viafoundry-R-SDK")

Getting Started

Authentication

Before interacting with the API, you need to authenticate and store your credentials. Once authentication is done it will put token into ~/.viaenv file, you don't need to re-authenticate.

Use the authenticate() function:

library(viafoundry)

# Authenticate and save the token
authenticate(
    hostname = "https://your_foundry_server",
    username = "username",
    password = "password",
    config_path = "~/.viaenv",
    overwrite = TRUE
)

or use authenticate() function it will ask the information needed for authentication

library(viafoundry)
authenticate()

Configuration File

The viafoundry package uses a configuration file (~/.viaenv) to store the hostname and token. Example:

{
    "hostname": "http://localhost",
    "token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9..."
}

Listing Available Endpoints

You can list all available API endpoints using the list_endpoints() function:

library(viafoundry)
# Fetch and display available endpoints
endpoints <- discover()
print(endpoints)

Calling an API Endpoint

To interact with a specific API endpoint, use the call_endpoint() function:

library(viafoundry)
# Call an API endpoint
response <- call_endpoint(
    method = "GET",
    endpoint = "/api/v1/process",     # Replace with your desired endpoint
    params = list(key = "value"),   # Optional query parameters
    data = NULL                     # Optional payload for POST/PUT
)

# Print the API response
print(response)

Example workflow

library(viafoundry)

# Step 1: Authenticate
authenticate()

# Step 2: List all available endpoints
endpoints <- discover()
print("Available endpoints:")
print(endpoints)

# Step 3: Call a specific endpoint
response <- call_endpoint(
    method = "GET",
    endpoint = "/api/v1/process"
)
print("API response:")
print(response)

Accessing the reports and load files

You can access any files in the report section using SDK

library(viafoundry)
#get report id from Via Foundry

reportID <- 1 

# Fetch the report 
report <- fetchReportData(reportID)

# Get all processes belong to the report
getProcessNames(report)

# Select the file from a process or a module 
getFileNames(report, "RSEM_module")

# Load a specific file
rsem_data <- loadFile(report, "RSEM_module", "genes_expression_expected_count.tsv")
head(rsem_data)

You can access any files in the report section using SDK

library(viafoundry)
#get report id from Via Foundry

reportID <- 1 

# Fetch the report 
report <- fetchReportData(reportID)

getAllFileNames(report)

# Choose a file from the list, if the extension is not tsv, csv, or txt, the file will be downloaded. you can define download directory

loadFile(report, "DE_module_RSEM", "control_vs_exper_des.Rmd")

This file is automatically created during authentication.

Troubleshooting

Common Issues

1.	Authentication Fails:
-	Verify your `username`, `password`, and `hostname`.
  -	Check if the token in the `~/.viaenv` file is expired.
2.	API Call Fails:
-	Ensure the endpoint exists and you have the necessary permissions.
-	Check the API documentation for the correct method and parameters.
3.	Server Returns HTML Instead of JSON:
-	Ensure the Accept: application/json header is sent with requests. This is handled automatically by the package.

4. If you want to re-authenticate remove the viaenv file (e.g ~/.viaenv)