Update tests documentation and break down into smaller components

Author: villegar

tests/testthat/test-audit_safe_people.R

@@ -22,6 +22,9 @@ test_that("rocrate method validates RO-Crate object", {
   expect_no_error(
     audit_safe_people(crate)
   )
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("rocrate method fails for invalid object", {
@@ -44,6 +47,9 @@ test_that("opal method returns RO-Crate with expected attributes", {
 
   expect_equal(attr(crate, "audit_type"), "Safe People")
   expect_true("project" %in% names(attributes(crate)))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("opal method works with specific project", {
@@ -61,6 +67,12 @@ test_that("opal method works with specific project", {
 
   expect_s3_class(crate, "rocrate")
   expect_equal(attr(crate, "project"), attr(opal_con, "PROJECT"))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("opal method errors for unknown project", {
@@ -92,4 +104,7 @@ test_that("path argument is stored as attribute", {
   )
 
   expect_equal(attr(crate, "path"), tempdir())
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })

tests/testthat/test-audit_safe_project.R

@@ -40,6 +40,9 @@ test_that("opal method returns RO-Crate with expected attributes", {
 
   expect_equal(attr(crate, "audit_type"), "Safe Project")
   expect_true("project" %in% names(attributes(crate)))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("opal method works with specific project", {
@@ -56,6 +59,9 @@ test_that("opal method works with specific project", {
 
   expect_s3_class(crate, "rocrate")
   expect_equal(attr(crate, "project"), attr(opal_con, "PROJECT"))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("opal method errors for unknown project", {
@@ -67,6 +73,9 @@ test_that("opal method errors for unknown project", {
     "No data details were found",
     fixed = TRUE
   )
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("path argument is stored as attribute", {
@@ -82,4 +91,7 @@ test_that("path argument is stored as attribute", {
   )
 
   expect_equal(attr(crate, "path"), tempdir())
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })

tests/testthat/test-audit_study.R

@@ -33,6 +33,9 @@ test_that("list method returns list with expected attributes", {
   expect_equal(attr(crate, "audit_type"), "Study")
   expect_true("demo" %in% names(crate))
   expect_true(length(crate) == 1)
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("list method works with specific project", {
@@ -48,6 +51,9 @@ test_that("list method works with specific project", {
   )
 
   expect_equal(attr(crate, "project"), attr(opal_con, "PROJECT"))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("list method errors for unknown project", {
@@ -59,6 +65,9 @@ test_that("list method errors for unknown project", {
     "No data details were found",
     fixed = TRUE
   )
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("path argument is stored as attribute", {
@@ -74,4 +83,7 @@ test_that("path argument is stored as attribute", {
   )
 
   expect_equal(attr(crate, "path"), tempdir())
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })

tests/testthat/test-dsROCrate.R

@@ -13,6 +13,9 @@ test_that("init() dispatches to init.opal() with real Opal connection", {
 
   expect_s3_class(res, "rocrate")
   expect_identical(attr(res, "connection"), opal_con)
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("init.opal() attaches metadata using demo Opal server", {
@@ -34,6 +37,9 @@ test_that("init.opal() attaches metadata using demo Opal server", {
   expect_identical(attr(res, "tables"), attr(opal_con, "TABLES"))
   expect_identical(attr(res, "user"), attr(opal_con, "PEOPLE"))
   expect_true(dir.exists(attr(res, "path")))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("init.rocrate() reuses stored attributes with demo Opal server", {
@@ -54,6 +60,9 @@ test_that("init.rocrate() reuses stored attributes with demo Opal server", {
   expect_identical(attr(res, "tables"), attr(opal_con, "TABLES"))
   expect_identical(attr(res, "user"), attr(opal_con, "PEOPLE"))
   expect_identical(attr(res, "path"), attr(crate, "path"))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("init.opal() errors on invalid connection object", {

tests/testthat/test-rocrate_report.R

@@ -295,6 +295,9 @@ test_that("rocrate_report works end-to-end with real dsROCrate audit outputs", {
   expect_true("safe_people" %in% names(result))
   expect_true("safe_project" %in% names(result))
   expect_true("safe_data" %in% names(result))
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("rocrate_report.character loads crate from disk", {
@@ -331,6 +334,9 @@ test_that("rocrate_report.character loads crate from disk", {
   # ---- assertions ----
   expect_true(file.exists(out_file))
   expect_type(result, "list")
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("rocrate_report.list aggregates outputs from a study audit", {
@@ -365,6 +371,9 @@ test_that("rocrate_report.list aggregates outputs from a study audit", {
   # ---- assertions ----
   expect_true(file.exists(out_file))
   expect_type(result, "list")
+
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
 })
 
 test_that("rocrate_report.list handles missing outputs from a study audit", {

tests/testthat/test-safe-data.R

@@ -1,50 +1,96 @@
-test_that("safe_data works", {
-  # open connection to OBiBa's Opal demo server
-  opal_con <- opal_demo_con()
-
-  basic_rocrate <- rocrateR::rocrate_5s()
-
-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
-  # - - - - - - - - - - - - - - - - - ERRORS - - - - - - - - - - - - - - - - - #
-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
-  # attempt calling function with invalid class
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+# - - - - - - - - - - - - - - - - - ERRORS - - - - - - - - - - - - - - - - - #
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+test_that("safe_data fails when attempt calling function with invalid class", {
   expect_error(
     dsROCrate::safe_data(structure(list(), class = "InvalidClass"))
   )
+})
+
+test_that("safe_data fails when attempt calling with invalid connection", {
+  # setup
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
 
-  # attempt calling with invalid connection
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_data(connection = NULL)
   )
+})
+
+test_that("safe_data fails when attempt adding invalid project", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
 
-  # attempt adding invalid project
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_data(project = "Invalid Project", connection = opal_con)
   )
 
-  # attempt calling without a project
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+test_that("safe_data fails when attempt calling without a project", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_data(connection = opal_con)
   )
 
-  # attempt calling with project = NULL
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+test_that("safe_data fails when attempt calling with project = NULL", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_data(connection = opal_con, project = NULL)
   )
 
-  # attempt calling with multiple projects
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+test_that("safe_data fails when attempt calling with multiple projects", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_data(connection = opal_con, project = c("A", "B"))
   )
 
-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
-  # - - - - - - - - - - - - - - - - - VALID  - - - - - - - - - - - - - - - - - #
-  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+# - - - - - - - - - - - - - - - - - VALID  - - - - - - - - - - - - - - - - - #
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+test_that("safe_data works", {
+  # open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   # add all datasets for a valid project
   basic_rocrate_2 <- basic_rocrate |>
     dsROCrate::safe_data(

tests/testthat/test-safe-people.R

@@ -1,15 +1,19 @@
-test_that("safe_people works", {
-  # open connection to OBiBa's Opal demo server
-  opal_con <- opal_demo_con()
-
-  basic_rocrate <- rocrateR::rocrate_5s()
-
-  # attempt calling function with invalid class
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+# - - - - - - - - - - - - - - - - - ERRORS - - - - - - - - - - - - - - - - - #
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+test_that("safe_people fails when attempt calling function with invalid class", {
   expect_error(
     dsROCrate::safe_people(structure(list(), class = "InvalidClass"))
   )
+})
+
+test_that("safe_people fails when attempt adding user to RO-Crate without project entity, `@type = 'Project`", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
 
-  # attempt adding user to RO-Crate without project entity, `@type = 'Project`
   expect_warning(
     basic_rocrate_1 <- opal_con |>
       dsROCrate::safe_people(
@@ -18,12 +22,36 @@ test_that("safe_people works", {
       )
   )
 
-  # attempt calling with invalid connection
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+test_that("safe_people fails when attempt calling with invalid connection", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   expect_error(
     basic_rocrate |>
       dsROCrate::safe_people(user = attr(opal_con, "PEOPLE"), connection = NULL)
   )
 
+  # close connection to OBiBa's Opal demo server
+  opalr::opal.logout(opal_con)
+})
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+# - - - - - - - - - - - - - - - - - VALID  - - - - - - - - - - - - - - - - - #
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#
+test_that("safe_people works", {
+  # setup
+  ## open connection to OBiBa's Opal demo server
+  opal_con <- opal_demo_con()
+  ## create basic RO-Crate
+  basic_rocrate <- rocrateR::rocrate_5s()
+
   # add project entity to the RO-Crate
   basic_rocrate_2 <- basic_rocrate |>
     rocrateR::add_entity(rocrateR::entity("Fake Project", type = "Project"))