stopadforms

stopadforms is an R package and Shiny application to allow reviewers to view and score submissions to the STOP-AD Compound Submission Portal.

The application is hosted at https://sagebio.shinyapps.io/stopadforms/. To use it, you must be a member of the STOP-AD_Reviewers Synapse team and be logged in to Synapse. To save reviews, you must be a Certified User on Synapse.

Installation 

#install latest dccvalidator
install.packages("dccvalidator")
#install app from package
devtools::install_github("Sage-Bionetworks/stopadforms")

Calculating scores for a submission

Below is an example of how to calculate scores for a submission outside of the Shiny app (i.e. in an R script). This example uses sample data included in the package.

library("stopadforms")

## Create a list with the form data id as the name, and the path to the included
## JSON file as the value
sample_sub <- list(
  "242" = system.file("extdata", "testdata.json", package = "stopadforms")
)

## Load the JSON data and convert to a data frame
dat <- process_submissions(sample_sub, lookup_table = lookup_table)

## Append clinical multiplier used in calculations
submission <- append_clinical_to_submission(dat)

## Load weighted scores. The contents of this file correspond to the output of
## the `pull_reviews_table()` function.
scores <- read.csv(
  system.file("extdata", "weighted_scores.csv", package = "stopadforms"),
  stringsAsFactors = FALSE
)

## Calculate overall score
calculate_submission_score(submission, scores)
#> [1] 0.2631988

See vignette("scoring", package = "stopadforms") for a detailed description of the scoring process and an example of how to score real submissions that are stored in Synapse.

Running the application locally

Set localDevelopment variable to “TRUE” in “app.R” file of main directory. Populate the config.yml file in the parent directory with secrets from lastpass for the “testing” profile. Contact IT if you need access.

app.R

localDevelopment = TRUE

config.yml

testing:
  app_url: http://127.0.0.1:8100
  client_id: ***
  client_secret: ***
  client_name: "local"

default:
  app_url: https://sagebio.shinyapps.io/stopadforms/
  client_id: ***
  client_secret: ***
  client_name: "stopadforms"

With the app.R file selected in R Studio, run the shiny app by clicking the button in R Studio.

Scores entered while running the application locally will persist on Synapse.

See vignette("deploying-stopadforms", package = "stopadforms") for information on how we deploy the app on the Sage Bionetworks Shiny Pro server.

Setting up github actions to deploy

  • Enable workflows in the GitHub repository
  • Under secrets click ‘New repository secret’
  • Enter secrets for RSCONNECT_USER, RSCONNECT_TOKEN, and RSCONNECT_SECRET, the values for which are saved in Sage’s LastPass.
  • Enter secrets for OAUTH_CLIENT_ID, and OAUTH_CLIENT_SECRET for a Synapse OAuth client configured for this application.
  • Trigger the GitHub action.
  • Check out the app here: https://sagebio.shinyapps.io/stopadforms-staging.
  • After verifying correctness, create a Git branch named release*, e.g., release-1.0.
  • The app’ will become available at https://sagebio.shinyapps.io/stopadforms

Please note that the stopadforms project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.