Development

.github/workflows/check-standard-real-requests.yaml

@@ -7,6 +7,7 @@ on:
     branches: main
   schedule:
     - cron: '23 3 23 * *'
+  workflow_dispatch:
 
 name: R-CMD-check-real-requests
 
@@ -33,6 +34,7 @@ jobs:
       EDI_USER: ${{ secrets.EDI_USER }}
       EDI_PASS: ${{ secrets.EDI_PASS }}
       EDI_API_KEY: ${{ secrets.EDI_API_KEY }}
+      EDI_TEST_THROTTLE_DELAY: 2
       RUN_ALL_TESTS: true
       VCR_TURN_OFF: true
 
@@ -75,6 +77,7 @@ jobs:
       EDI_USER: ${{ secrets.EDI_USER }}
       EDI_PASS: ${{ secrets.EDI_PASS }}
       EDI_API_KEY: ${{ secrets.EDI_API_KEY }}
+      EDI_TEST_THROTTLE_DELAY: 2
       RUN_ALL_TESTS: true
       VCR_TURN_OFF: true
 

.github/workflows/check-standard.yaml

@@ -5,6 +5,7 @@ on:
     branches: development
   pull_request:
     branches: development
+  workflow_dispatch:
 
 name: R-CMD-check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: EDIutils
 Title: An API Client for the Environmental Data Initiative Repository
-Version: 3.0.0
+Version: 3.0.1
 Authors@R: 
     c(person("Colin", "Smith", email = "colin.smith@wisc.edu", role = c("aut", "cre"), comment = "0000-0003-2261-9931"),
     person("Corinna", "Gries", role = "ctb", comment = "0000-0002-9091-6543"),

NEWS.md

@@ -1,3 +1,16 @@
+EDIutils 3.0.1 (2026-08-18)
+===========================
+
+### MINOR IMPROVEMENTS
+
+  * Migrated the test suite and VCR cassette fixtures to the PASTA staging environment (`https://pasta-s.lternet.edu`), preventing test pollution on the production repository.
+  * Enhanced entity and descendant tests to dynamically resolve entity IDs and derived package identifiers at runtime.
+  * Added configurable request throttling (`EDI_TEST_THROTTLE_DELAY`, default 2s in CI) for live HTTP test requests to prevent HTTP 429 rate limit errors.
+  * Configured VCR cassette mocks for `read_data_package_archive()`.
+  * Refactored test-only helper functions into `tests/testthat/helper-test-package.R` to keep package runtime namespace clean and modular.
+  * Updated GitHub Actions CI workflows with sequential execution (`max-parallel: 1`), request throttling, and `workflow_dispatch` manual triggers.
+
+
 EDIutils 3.0.0 (2026-07-27)
 ===========================
 

R/read_data_package_from_doi.R

@@ -4,6 +4,7 @@
 #' format "shoulder/pasta/md5"
 #' @param ore (logical) Return an OAI-ORE compliant resource map in RDF-XML
 #' format
+#' @inheritParams read_metadata
 #'
 #' @return (character or xml_document) A resource map with reference URLs to
 #' each of the metadata, data, and quality report resources that comprise the
@@ -43,8 +44,8 @@
 #' #> [7] <rdf:Description rdf:about="http://www.openarchives.org/ore/terms ...
 #' #> [8] <rdf:Description rdf:about="http://www.openarchives.org/ore/terms ...
 #' }
-read_data_package_from_doi <- function(doi, ore = FALSE) {
-  url <- paste0(base_url("production"), "/package/doi/", doi)
+read_data_package_from_doi <- function(doi, ore = FALSE, env = "production") {
+  url <- paste0(base_url(env), "/package/doi/", doi)
   if (ore) {
     url <- paste0(url, "?ore")
   }

R/utilities.R

@@ -92,97 +92,6 @@ base_url_portal <- function(env) {
 
 
 
-#' Set environment variables for testing data package evaluation and upload
-#'
-#' @description Testing data package evaluation and upload requires a web
-#' accessible data entity, EML metadata describing the data entity, and an EDI
-#' repository user account. Use of this function presupposes the data entity
-#' has been stashed
-#'
-#' @param userId (character) EDI repository userId
-#' @param url (character) URL from which the EDI repository can download the
-#' test data.txt entity. This URL cannot contain any redirects.
-#'
-#' @return Environmental variables \code{EDI_USERID = userId} and
-#' \code{EDI_TEST_URL = url}
-#'
-#' @details The results of this function are used to create a test EML file for
-#' create, update, and delete tests.
-#'
-#' @noRd
-#'
-config_test_eml <- function(userId, url) {
-  Sys.setenv(EDI_USERID = userId)
-  Sys.setenv(EDI_TEST_URL = url)
-}
-
-
-
-
-
-
-
-
-#' Create an EML file for testing create, update, delete operations
-#'
-#' @param path (character) Path to directory in which the test EML will be
-#' written to file
-#' @param packageId (character) Package identifier, of the form
-#' "scope.identifier.revision", for the new EML file
-#' @param edi_id (character) The EDI ID of the user creating the test EML.
-#' An EDI ID can be obtained from the EDI Identity and Access 
-#' Manager (\url{https://auth.edirepository.org/auth/ui/signin}).
-#'
-#' @return (character) Full path to EML file written by this function to
-#' \code{path}. Should be \code{tempdir()} if executed in a testthat context.
-#'
-#' @details Copies "eml.xml" at /inst/extdata, adds the userId, packageId, and
-#' URL, then writes to \code{paste0(path, "/", packageId, ".xml)}
-#'
-#' @noRd
-#'
-create_test_eml <- function(path, packageId, edi_id) {
-  # Read EML template
-  eml <- system.file("extdata", "eml.xml", package = "EDIutils")
-  eml <- xml2::read_xml(eml)
-  # Add packageId
-  xml2::xml_attr(eml, "packageId") <- packageId
-  # Add principal
-  principal <- xml2::xml_find_first(eml, ".//principal")
-  xml2::xml_text(principal) <- edi_id
-  # Add URL
-  url <- xml2::xml_find_first(eml, ".//online/url")
-  xml2::xml_text(url) <- Sys.getenv("EDI_TEST_URL")
-  # Write file
-  xml2::write_xml(eml, paste0(path, "/", packageId, ".xml"))
-  dest <- paste0(path, "/", packageId, ".xml")
-  return(dest)
-}
-
-
-
-
-
-
-
-
-#' Get the first data package in the staging environment for testing
-#'
-#' @return (character) Data package ID of the form "scope.identifier.revision".
-#'
-#' @noRd
-#'
-get_test_package <- function() {
-  user_data_packages <- list_user_data_packages("EDI-0c385786add7d657afe19ddf52858a6a7226ba32", env = "staging")
-  return(user_data_packages[1])
-}
-
-
-
-
-
-
-
 #' Parse package ID into scope, identifier, and revision
 #'
 #' @param package.id (character) Data packageId
@@ -363,7 +272,7 @@ is_vcr_replaying <- function() {
   if (requireNamespace("vcr", quietly = TRUE)) {
     cass <- vcr::current_cassette()
     if (!is.null(cass)) {
-      return(cass$record %in% c("none", "once"))
+      return(cass$replaying())
     }
   }
   return(FALSE)
@@ -430,61 +339,6 @@ api_delete <- function(url, ...) {
 
 
 
-#' Skip tests when logged out
-#'
-#' @details Facilitates testing of functions requiring authentication
-#'
-#' @noRd
-#'
-skip_if_logged_out <- function() {
-  has_token <- (Sys.getenv("EDI_TOKEN") != "") && (Sys.getenv("EDI_TOKEN") != "foobar")
-  has_key <- (Sys.getenv("EDI_API_KEY") != "") && (Sys.getenv("EDI_API_KEY") != "foobar")
-
-  if (has_key && tolower(Sys.getenv("RUN_ALL_TESTS")) != "true") {
-    testthat::skip("Skipping computationally heavy authenticated test. Set RUN_ALL_TESTS='true' to run.")
-  }
-
-  if (has_token || has_key) {
-    return(invisible(TRUE))
-  }
-  testthat::skip("Not run when logged out. Login with 'login()'.")
-}
-
-
-
-
-
-
-
-
-#' Skip tests when EML configuration is missing
-#'
-#' @details Facilitates testing create, update, and delete for a test data
-#' package
-#'
-#' @noRd
-#'
-skip_if_missing_eml_config <- function() {
-  has_userid <- Sys.getenv("EDI_USERID") != ""
-  has_url <- Sys.getenv("EDI_TEST_URL") != ""
-  if (has_userid & has_url) {
-    return(invisible(TRUE))
-  }
-  msg <- paste0(
-    "Not run when test EML config is missing. Set config with ",
-    "'config_test_eml()'."
-  )
-  testthat::skip(msg)
-}
-
-
-
-
-
-
-
-
-
 #' Convert newline separated text to character vector
 #'
 #' @param txt (character) New line separated character string returned from

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/ropensci/EDIutils",
   "issueTracker": "https://github.com/ropensci/EDIutils/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "3.0.0",
+  "version": "3.0.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -174,7 +174,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "790.455KB",
+  "fileSize": "837.79KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

cran-comments.md

@@ -1,18 +1,20 @@
 ## Release Summary
-This EDIutils release, version 3.0.0, transitions all API wrapper functions to 
-support mandatory authenticated access using EDI API keys. To minimize the 
-impact on downstream workflows, authentication requires minimal updates: users 
-simply need to set their API key as an environment variable or pass it directly 
-into the login() function.
+This is a minor release (v3.0.1) updating test infrastructure and test isolation:
+* Migrated test suite and VCR mock fixtures to the PASTA staging environment to 
+  prevent test pollution on the production repository.
+* Dynamically resolve test entity and descendant identifiers.
+* Added request throttling for live HTTP test requests to prevent HTTP 429 rate 
+  limiting.
+* Modularized internal test helper utilities.
 
 
 ## Test environments
 * aarch64-apple-darwin20, (local machine), R 4.6.0
 * aarch64-apple-darwin20 (R-hub), R Under development (unstable) (2026-06-24 r90190)
-* x86_64-w64-mingw32 (R-hub), R Under development (unstable) (2026-07-26 r90304 ucrt)
+* x86_64-w64-mingw32 (R-hub), R Under development (unstable) (2026-08-17 r90424 ucrt)
 * x86_64-w64-mingw32 (R-hub), R version 4.6.1 (2026-06-24 ucrt)
 * x86_64-w64-mingw32 (R-hub), R version 4.5.3 (2026-03-11 ucrt)
-* x86_64-pc-linux-gnu Ubuntu (R-hub), R development (unstable) (2026-07-26 r90304)
+* x86_64-pc-linux-gnu Ubuntu (R-hub), R Under development (unstable) (2026-08-17 r90423)
 * x86_64-pc-linux-gnu Ubuntu (R-hub), R version 4.6.1 RC (2026-06-18 r90185)
 * x86_64-pc-linux-gnu Ubuntu (R-hub), R version 4.6.1 (2026-06-24)
 

tests/fixtures/create_data_package_archive.yml

@@ -1,7 +1,7 @@
 http_interactions:
 - request:
     method: post
-    uri: https://pasta.lternet.edu/package/archive/eml/knb-lter-sev/31999/1
+    uri: https://pasta-s.lternet.edu/package/archive/eml/edi/1923/1
     body:
       encoding: ''
       string: ''

tests/fixtures/get_audit_count.yml

@@ -1,7 +1,7 @@
 http_interactions:
 - request:
     method: get
-    uri: https://pasta.lternet.edu/audit/count?category=warn&fromTime=2021-12-01&toTime=2021-12-05
+    uri: https://pasta-s.lternet.edu/audit/count?category=warn&fromTime=2021-12-01&toTime=2021-12-05
     body:
       encoding: ''
       string: ''

tests/fixtures/get_docid_reads.yml

@@ -1,7 +1,7 @@
 http_interactions:
 - request:
     method: get
-    uri: https://pasta.lternet.edu/audit/reads/knb-lter-sgs/817
+    uri: https://pasta-s.lternet.edu/audit/reads/edi/1923
     body:
       encoding: ''
       string: ''
@@ -28,7 +28,7 @@ http_interactions:
         <?xml version="1.0" encoding="UTF-8"?>
         <resourceReads>
             <resource>
-                <resourceId>https://pasta.lternet.edu/package/metadata/eml/knb-lter-sgs/817/17</resourceId>
+                <resourceId>https://pasta-s.lternet.edu/package/metadata/eml/knb-lter-sgs/817/17</resourceId>
                 <resourceType>metadata</resourceType>
                 <scope>knb-lter-sgs</scope>
                 <identifier>817</identifier>
@@ -37,7 +37,7 @@ http_interactions:
                 <nonRobotReads>518</nonRobotReads>
             </resource>
             <resource>
-                <resourceId>https://pasta.lternet.edu/package/eml/knb-lter-sgs/817/17</resourceId>
+                <resourceId>https://pasta-s.lternet.edu/package/eml/knb-lter-sgs/817/17</resourceId>
                 <resourceType>dataPackage</resourceType>
                 <scope>knb-lter-sgs</scope>
                 <identifier>817</identifier>
@@ -46,7 +46,7 @@ http_interactions:
                 <nonRobotReads>394</nonRobotReads>
             </resource>
             <resource>
-                <resourceId>https://pasta.lternet.edu/package/report/eml/knb-lter-sgs/817/17</resourceId>
+                <resourceId>https://pasta-s.lternet.edu/package/report/eml/knb-lter-sgs/817/17</resourceId>
                 <resourceType>report</resourceType>
                 <scope>knb-lter-sgs</scope>
                 <identifier>817</identifier>
@@ -55,7 +55,7 @@ http_interactions:
                 <nonRobotReads>11</nonRobotReads>
             </resource>
             <resource>
-                <resourceId>https://pasta.lternet.edu/package/data/eml/knb-lter-sgs/817/17/7c1ee60c37b60b35f05c94475c070750</resourceId>
+                <resourceId>https://pasta-s.lternet.edu/package/data/eml/knb-lter-sgs/817/17/7c1ee60c37b60b35f05c94475c070750</resourceId>
                 <resourceType>data</resourceType>
                 <scope>knb-lter-sgs</scope>
                 <identifier>817</identifier>