From afa036c4a8086f130b9e2e1fadbdc3171bf5646f Mon Sep 17 00:00:00 2001
From: Scott Chamberlain <sachamber@fredhutch.org>
Date: Fri, 26 Jan 2024 01:24:41 -0800
Subject: [PATCH] fix #5 add tests mocking requests, add suggest pkgs jsonlite
 and webmockr

---
 DESCRIPTION                              |  2 +
 tests/testthat/helper-proofr.R           |  1 +
 tests/testthat/helper-stubs.R            | 59 ++++++++++++++++++++++++
 tests/testthat/test-proof_authenticate.R | 41 ++++++++++++++++
 tests/testthat/test-proof_cancel.R       | 43 +++++++++++++++++
 tests/testthat/test-proof_header.R       |  4 +-
 tests/testthat/test-proof_start.R        | 41 ++++++++++++++++
 tests/testthat/test-proof_status.R       | 55 ++++++++++++++++++++++
 8 files changed, 244 insertions(+), 2 deletions(-)
 create mode 100644 tests/testthat/helper-proofr.R
 create mode 100644 tests/testthat/helper-stubs.R
 create mode 100644 tests/testthat/test-proof_authenticate.R
 create mode 100644 tests/testthat/test-proof_cancel.R
 create mode 100644 tests/testthat/test-proof_start.R
 create mode 100644 tests/testthat/test-proof_status.R

diff --git a/DESCRIPTION b/DESCRIPTION
index d33baa9..59f9a40 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,9 +15,11 @@ Imports:
     glue,
     httr
 Suggests: 
+    jsonlite,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
+    webmockr,
     withr
 Config/testthat/edition: 3
 VignetteBuilder: knitr
diff --git a/tests/testthat/helper-proofr.R b/tests/testthat/helper-proofr.R
new file mode 100644
index 0000000..4e437d4
--- /dev/null
+++ b/tests/testthat/helper-proofr.R
@@ -0,0 +1 @@
+library(webmockr)
diff --git a/tests/testthat/helper-stubs.R b/tests/testthat/helper-stubs.R
new file mode 100644
index 0000000..e5162ca
--- /dev/null
+++ b/tests/testthat/helper-stubs.R
@@ -0,0 +1,59 @@
+response_status_running <- list(
+  canJobStart = FALSE,
+  jobStatus = "RUNNING",
+  cromwellUrl = "https://some.url",
+  jobInfo = list(
+    WORKFLOWLOGDIR = "/some/path",
+    SCRATCHDIR = "/some/path",
+    SLURM_JOB_ID = "someid",
+    CROMWELL_DIR = "/some/path",
+    SERVERLOGDIR = "/some/path",
+    SINGULARITY_CACHEDIR = "/some/path",
+    SERVERTIME = "1-0",
+    USE_AWS = FALSE,
+    SLURM_JOB_ACCOUNT = "/some/path"
+  )
+)
+
+response_status_not_running <- list(
+  canJobStart = TRUE,
+  jobStatus = NULL,
+  cromwellUrl = NULL,
+  jobInfo = list(
+    WORKFLOWLOGDIR = NULL,
+    SCRATCHDIR = NULL,
+    SLURM_JOB_ID = NULL,
+    CROMWELL_DIR = NULL,
+    SERVERLOGDIR = NULL,
+    SINGULARITY_CACHEDIR = NULL,
+    SERVERTIME = NULL,
+    USE_AWS = NULL,
+    SLURM_JOB_ACCOUNT = NULL
+  )
+)
+
+response_start_success <- list(
+  job_id = "12345678",
+  info = "Job submitted successfully. Some message"
+)
+
+response_start_conflict <- list(
+  message = "Job is already running"
+)
+
+response_cancel_success <- list(
+  message = "Proof/cromwell job for user xxxxx has been cancelled"
+)
+
+response_cancel_conflict <- list(
+  message = "Job is not running, nothing to delete"
+)
+
+response_authenticate_success <- list(
+  username = "jane",
+  token = "somerandomstring",
+  server_url = NULL,
+  proxy_url = NULL,
+  job_id = NULL,
+  token_creation_date = NULL
+)
diff --git a/tests/testthat/test-proof_authenticate.R b/tests/testthat/test-proof_authenticate.R
new file mode 100644
index 0000000..a8a3a6e
--- /dev/null
+++ b/tests/testthat/test-proof_authenticate.R
@@ -0,0 +1,41 @@
+test_that("proof_authenticate - error behavior", {
+  # errors if no username supplied
+  expect_error(proof_authenticate(),
+    '"username" is missing')
+
+  # errors if no password supplied
+  expect_error(proof_authenticate(username = "apple"),
+    '"password" is missing')
+
+  # username should be character
+  expect_error(proof_authenticate(5),
+    'username must be of class character')
+
+  # password should be character
+  expect_error(proof_authenticate(username = "apple", password = 5),
+    'password must be of class character')
+})
+
+test_that("proof_start - success", {
+  stub_registry_clear()
+  stub_request("post", make_url("authenticate")) %>%
+    to_return(
+      body = jsonlite::toJSON(
+        response_authenticate_success, auto_unbox = TRUE),
+      status = 200L,
+      headers = list('Content-type' = "application/json")
+    )
+  stub_registry()
+
+  enable(quiet = TRUE)
+
+  auth_res <- proof_authenticate("jane", "faketoken")
+
+  expect_type(auth_res, "character")
+  expect_equal(auth_res, "somerandomstring")
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+  Sys.unsetenv("PROOF_TOKEN")
+})
diff --git a/tests/testthat/test-proof_cancel.R b/tests/testthat/test-proof_cancel.R
new file mode 100644
index 0000000..481d900
--- /dev/null
+++ b/tests/testthat/test-proof_cancel.R
@@ -0,0 +1,43 @@
+test_that("proof_cancel - success", {
+  stub_registry_clear()
+  stub_request("delete", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(response_cancel_success, auto_unbox = TRUE),
+      status = 200L,
+      headers = list('Content-type' = "application/json")
+    )
+  stub_registry()
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    cancel_res <- proof_cancel()
+  })
+
+  expect_type(cancel_res, "list")
+  expect_type(cancel_res$message, "character")
+  expect_match(cancel_res$message, "cancelled")
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})
+
+test_that("proof_cancel - not running, can not cancel", {
+  stub_request("delete", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(response_cancel_conflict, auto_unbox = TRUE),
+      status = 409L,
+      headers = list('Content-type' = "application/json")
+    )
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    expect_error(proof_cancel(), "Job is not running, nothing to delete")
+  })
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})
diff --git a/tests/testthat/test-proof_header.R b/tests/testthat/test-proof_header.R
index 40a4cf1..26f812c 100644
--- a/tests/testthat/test-proof_header.R
+++ b/tests/testthat/test-proof_header.R
@@ -8,7 +8,7 @@ test_that("proof_header", {
   expect_match(proof_header("adf")$headers[[1]], "adf")
 
   # If PROOF_TOKEN env var set, fxn can find it
-  withr::with_envvar(c("PROOF_TOKEN" = "world"), {
-    expect_match(proof_header()$headers[[1]], "world")
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    expect_match(proof_header()$headers[[1]], "notarealtoken")
   })
 })
diff --git a/tests/testthat/test-proof_start.R b/tests/testthat/test-proof_start.R
new file mode 100644
index 0000000..7319ebe
--- /dev/null
+++ b/tests/testthat/test-proof_start.R
@@ -0,0 +1,41 @@
+test_that("proof_start - success", {
+  stub_request("post", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(response_start_success, auto_unbox = TRUE),
+      status = 200L,
+      headers = list('Content-type' = "application/json")
+    )
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    start_res <- proof_start()
+  })
+
+  expect_type(start_res, "list")
+  expect_type(start_res$job_id, "character")
+  expect_type(start_res$info, "character")
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})
+
+test_that("proof_start - already running", {
+  stub_request("post", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(response_start_conflict, auto_unbox = TRUE),
+      status = 409L,
+      headers = list('Content-type' = "application/json")
+    )
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    expect_error(proof_start(), "Job is already running")
+  })
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})
diff --git a/tests/testthat/test-proof_status.R b/tests/testthat/test-proof_status.R
new file mode 100644
index 0000000..a081b09
--- /dev/null
+++ b/tests/testthat/test-proof_status.R
@@ -0,0 +1,55 @@
+test_that("proof_status - server IS running", {
+  stub_request("get", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(
+        response_status_running, auto_unbox = TRUE, null = "null"),
+      status = 200L,
+      headers = list('Content-type' = "application/json")
+    )
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    status_res <- proof_status()
+  })
+
+  expect_type(status_res, "list")
+  expect_type(status_res$canJobStart, "logical")
+  expect_type(status_res$jobStatus, "character")
+  expect_type(status_res$cromwellUrl, "character")
+  expect_type(status_res$jobInfo, "list")
+  for (item in status_res$jobInfo) {
+    expect_true(inherits(item, c("character", "logical")))
+  }
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})
+
+test_that("proof_status - server IS NOT running", {
+  stub_request("get", make_url("cromwell-server")) %>%
+    to_return(
+      body = jsonlite::toJSON(
+        response_status_not_running, auto_unbox = TRUE, null = "null"),
+      status = 200L,
+      headers = list('Content-type' = "application/json")
+    )
+
+  enable(quiet = TRUE)
+
+  withr::with_envvar(c("PROOF_TOKEN" = "notarealtoken"), {
+    status_res <- proof_status()
+  })
+
+  expect_type(status_res, "list")
+  expect_type(status_res$canJobStart, "logical")
+  expect_null(status_res$jobStatus)
+  expect_null(status_res$cromwellUrl)
+  expect_type(status_res$jobInfo, "list")
+  for (item in status_res$jobInfo) expect_null(item)
+
+
+  stub_registry_clear()
+  disable(quiet = TRUE)
+})