Tests Requiring Authentication

Some tests require authentication and a minimal data package for evaluation and upload. This vignette demonstrates how to create and run these tests with testthat.

Get an EDI User Account

Request accounts via info@edirepository.org

Use the “staging” Environment!

The EDI repository “staging” environment is a sandbox for testing data package rendering, etc. Do not use the “production” environment for testing. The “production” environment is where publication quality data are released.

Create Tests

Requiring Authentication

The first line of any test requiring authentication should include skip_if_logged_out(). This is an internal use only function located in R/utilities.R. Tests including this line will be skipped unless the R environment variable EDI_API_KEY is set, or the legacy EDI_TOKEN and AUTH_TOKEN variables are set. Authenticate by passing login(key = "your_key") or by defining the environment variable EDI_API_KEY.

Note that computationally heavy tests are skipped when using an API key unless the environment variable RUN_ALL_TESTS is set to "true".

Example:

context("Create journal citation")

testthat::test_that("Test attributes of returned object", {
  skip_if_logged_out()
  journalCitationId <- create_journal_citation(
    packageId = get_test_package(), 
    articleDoi = "10.1890/11-1026.1",
    articleUrl = "https://doi.org/10.1890/11-1026.1",
    articleTitle = "Corridors promote fire via connectivity and edge effects",
    journalTitle = "Ecological Applications",
    relationType = "IsCitedBy",
    env = "staging")
  expect_type(journalCitationId, "double")
  res <- delete_journal_citation(journalCitationId, env = "staging")
  expect_true(res)
})

Requiring Data Package Evaluation or Upload

If evaluation or upload of a data package is required by the test, then include a second line skip_if_missing_eml_config(). Tests including this line will be skipped unless the R environment variables EDI_USERID and EDI_TEST_URL are set. Use config_test_eml() to set these variables.

To set up the minimal test data package:

Copy the test data object at inst/extdata/data.txt to a web accessible location. The EDI repository will download this data object by it’s URL. The URL cannot present any redirects or else the EDI repository will not have access.
Add create_test_eml() to create an EML metadata file within the context of the test. Data packages require unique identifiers that often change from test to test.

Example:

context("Evaluate data package")

testthat::test_that("Test attributes of returned object", {
  skip_if_logged_out()
  skip_if_missing_eml_config()
  # Create data package for evaluation
  identifier <- create_reservation(scope = "edi", env = "staging")
  packageId <- paste0("edi.", identifier, ".1")
  eml <- create_test_eml(
    path = tempdir(), 
    packageId = packageId,
    edi_id = "EDI-543afa80c859825d35d37d9111c24a4a65a0ff3e")
  on.exit(file.remove(eml), add = TRUE, after = FALSE)
  # Evaluate
  transaction <- evaluate_data_package(eml, env = "staging")
  res <- check_status_evaluate(transaction, env = "staging")
  expect_true(res)
  # Read evaluation report
  report <- read_evaluate_report(transaction, env = "staging")
  expect_true("xml_document" %in% class(report))
  delete_reservation("edi", identifier, env = "staging")
})

Run Tests

Standard Mock Tests (Fast / Offline)

By default, the test suite uses vcr cassettes for fast, offline testing:

Run the test suite:
```
devtools::test()
```

Live HTTP Tests Against Staging

To run tests against the live PASTA staging environment instead of recorded VCR cassettes:

Set your staging API key:

Sys.setenv("EDI_API_KEY" = "your_staging_api_key")

(Optional) Configure test data package if running package lifecycle tests:
```
config_test_eml()
```
Enable all authenticated tests:
```
Sys.setenv("RUN_ALL_TESTS" = "true")
```
Bypass VCR cassette playback:
```
Sys.setenv("VCR_TURN_OFF" = "true")
```
Request Throttling: When running real HTTP requests, the test suite automatically introduces a delay between requests (default 1 second) via httr response callbacks to avoid PASTA rate limits (HTTP 429). You can customize or disable this delay via the EDI_TEST_THROTTLE_DELAY environment variable:
```
# Set custom delay in seconds (e.g. 2s or 0s)
Sys.setenv("EDI_TEST_THROTTLE_DELAY" = "1")
```
Run the test suite:
```
devtools::test()
```