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.
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")
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()
The viafoundry package uses a configuration file (~/.viaenv)
to store the hostname
and token. Example:
{
"hostname": "http://localhost",
"token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9..."
}
You can list all available API endpoints using the list_endpoints() function:
library(viafoundry)
# Fetch and display available endpoints
endpoints <- discover()
print(endpoints)
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)
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)
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")
You can first get the available directories in report and upload the files to those directories. After
creating new plots(e.g png
, pdf
) or would like to upload some analysis code to organize the data within the
report section you can use this method.
library(viafoundry)
#get report id from Via Foundry
reportID <- 1
getReportDirs(1) # [1] "summary" "multiqc" "multiqc" etc.
response <- uploadReportFile(1, "FILE_LOCATION", dir="summary") # Change the file location
print(response)
List All Processes
- Fetches all existing processes from the API.
- Example:
R
processes <- listProcesses()
print(processes)
Get Process Details
- Retrieves details for a specific process.
- Example:
R
process_details <- getProcess("12345")
print(process_details)
Create a New Process
- Creates a new process using provided data. Make sure add all necessary parameters to create a process.
- Example:
R
new_process <- createProcess(list(name = "New Process", description = "Example Process"))
print(new_process)
Update an Existing Process
- Updates a process with given data.
- Example:
R
updated_process <- updateProcess("12345", list(name = "Updated Process"))
print(updated_process)
Delete a Process
- Deletes a process by its ID.
- Example:
R
deleteProcess("12345")
Duplicate a Process
- Duplicates an existing process.
- Example:
R
duplicated_process <- duplicateProcess("12345")
print(duplicated_process)
Get Process Revisions
- Fetches all revisions for a given process.
- Example:
R
revisions <- getProcessRevisions("12345")
print(revisions)
Check Process Usage
- Checks if a process is used in pipelines or runs.
- Example:
R
usage <- checkProcessUsage("12345")
print(usage)
Create a Menu Group
- Creates a new menu group.
- Example:
R
new_menu_group <- createMenuGroup("New Menu Group")
print(new_menu_group)
List Menu Groups
- Lists all menu groups.
- Example:
R
menu_groups <- listMenuGroups()
print(menu_groups)
Update a Menu Group
- Updates a menu group name.
- Example:
R
updated_menu_group <- updateMenuGroup("123", "Updated Menu Name")
print(updated_menu_group)
List Parameters
- Fetches all parameters.
- Example:
R
parameters <- listParameters()
print(parameters)
Create a New Parameter
- Creates a new parameter.
- Example:
R
new_parameter <- createParameter(list(name = "New Param", type = "string"))
print(new_parameter)
Update a Parameter
- Updates an existing parameter.
- Example:
R
updated_parameter <- updateParameter("123", list(name = "Updated Param"))
print(updated_parameter)
Delete a Parameter
- Deletes a parameter by its ID.
- Example:
R
deleteParameter("123")
Get Pipeline Parameters
- Retrieves parameter list for a pipeline.
- Example:
R
pipeline_params <- getPipelineParameters("pipeline123")
print(pipeline_params)
The ViaFoundry SDK
for R allows you to save your session history while working in R. This is particularly useful for maintaining reproducibility and tracking the commands you execute.
To save your session history to a file with a timestamp, you can use the prepareSessionHistory
function:
# Save session history
history_file <- prepareSessionHistory()
print(paste("Session history saved to:", history_file))
You can also upload your session history to the server.
response <- uploadSessionHistory(report_id = "12345", dir = "session_logs")
print("Session History Upload Response:", response)
This functionality ensures that your session history is automatically saved and uploaded for reproducibility.
username
, password
, and hostname
.~/.viaenv
file is expired.application/json
header is sent with requests. This is handled automatically by the package.viaenv
file (e.g ~/.viaenv
) Any scripts or data that you put into this service are public.
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