genepixR

genepixR is an R package for calling the Gen-EpiX API. It contains only generic API-client code so RIVM-specific analysis scripts can depend on the package without importing the Gen-EpiX backend repository.

Install

Install the package from the private GitHub repository:

install.packages("remotes")
remotes::install_github("RIVM-bioinformatics/gen-epix-R")

The package uses httr2 for HTTP requests. Install chromote as well when interactive browser login is needed:

install.packages(c("httr2", "chromote"))

Use the CASEDB client

The case type and column identifiers are deliberately supplied by the caller; the package does not contain disease- or organization-specific identifiers.

library(genepixR)

case_type_id <- "case-type-id"
case_db_url <- "https://casedb.example"
login_url <- "https://casedb.example"

access_token <- login_with_chromote(login_url)
query_result <- retrieve_cases_by_query(
    case_db_url,
    access_token,
    case_type_id = case_type_id
)
case_ids <- unlist(query_result$case_ids, use.names = FALSE)
cases <- retrieve_cases_by_id(
    case_db_url,
    access_token,
    case_ids = case_ids,
    case_type_id = case_type_id
)

For non-interactive jobs, provide an access token through the job's secret management and call the client functions directly.

Retrieve all cases from the command line

After installing the package, the generic example script is available in the repository at inst/scripts/retrieve_all_cases.R. It retrieves all visible cases for one case type and stores the result as an RDS file:

export GEN_EPIX_ACCESS_TOKEN="..."
Rscript inst/scripts/retrieve_all_cases.R \
    "https://casedb.example" \
    "case-type-id" \
    "cases.rds"

For interactive authentication, omit GEN_EPIX_ACCESS_TOKEN and set GEN_EPIX_LOGIN_URL to the web application URL. The script will open a Chromote browser window and wait for login.

Tests

Run the unit tests from the repository root:

Rscript tests/test-client.R

The interactive CASEDB test is kept separate and runs only when explicitly enabled:

GEN_EPIX_RUN_E2E=true Rscript tests/test-client-e2e.R