From 42f252558e7e0379446e0b759efbe3bf178fc584 Mon Sep 17 00:00:00 2001
From: Stephen Turner <vustephen@gmail.com>
Date: Sun, 18 Aug 2024 13:31:18 -0400
Subject: [PATCH] add tests

---
 R/biorecap.R                   | 10 ++++++----
 man/biorecap_report.Rd         |  5 ++++-
 tests/testthat/test-biorecap.R | 21 +++++++++++++++++++++
 3 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/R/biorecap.R b/R/biorecap.R
index 71a0d18..d392a71 100644
--- a/R/biorecap.R
+++ b/R/biorecap.R
@@ -81,7 +81,7 @@ get_preprints <- function(subject="all", baseurl="https://connect.biorxiv.org/bi
     dplyr::bind_rows(.id="subject") |>
     dplyr::select("subject", title="item_title", url="item_link", abstract="item_description") |>
     dplyr::mutate(dplyr::across(dplyr::everything(), trimws))
-  if (nrow(preprints)<1L) stop("Something went wrong. No papers found for subject ", subject)
+  if (nrow(preprints)<1L) stop("Something went wrong. No papers found for subject ", subject) #nocov
 
   if (clean) {
     preprints <-
@@ -229,6 +229,7 @@ tt_preprints <- function(preprints, cols=c("title", "summary"), width=c(1,3)) {
 #' @param nsentences Number of sentences to summarize each paper in.
 #' @param model The model to use for generating summaries. See [ollamar::list_models()].
 #' @param use_example_preprints Use the example preprints data included with the package instead of fetching new data from bioRxiv. For diagnostic/testing purposes only.
+#' @param ... Other arguments passed to [rmarkdown::render()].
 #'
 #' @return Nothing; called for its side effects to produce a report.
 #' @export
@@ -240,15 +241,16 @@ tt_preprints <- function(preprints, cols=c("title", "summary"), width=c(1,3)) {
 #' biorecap_report(subject=c("bioinformatics", "genomics", "synthetic_biology"),
 #'                 output_dir=output_dir)
 #' }
-biorecap_report <- function(output_dir=".", subject=NULL, nsentences=2L, model="llama3.1", use_example_preprints=FALSE) {
+biorecap_report <- function(output_dir=".", subject=NULL, nsentences=2L, model="llama3.1", use_example_preprints=FALSE, ...) {
   skeleton <- system.file("rmarkdown/templates/biorecap/skeleton/skeleton.Rmd", package="biorecap", mustWork = TRUE)
   output_dir <- normalizePath(output_dir)
   output_file <- paste0("biorecap-report-", format(Sys.time(), "%Y-%m-%d-%H%M%S"), ".html")
   output_csv <- file.path(output_dir, sub("\\.html$", ".csv", output_file))
   if (!use_example_preprints && is.null(subject)) stop("You must provide a subject. See ?subjects.")
-  if (tools::file_ext(output_file) != "html") stop("Output file must have an .html extension.")
+  if (tools::file_ext(output_file) != "html") stop("Output file must have an .html extension.") #nocov
   rmarkdown::render(input=skeleton,
                     output_file=output_file,
                     output_dir=output_dir,
-                    params=list(subject=subject, nsentences=nsentences, model=model, use_example_preprints=use_example_preprints, output_csv=output_csv))
+                    params=list(subject=subject, nsentences=nsentences, model=model, use_example_preprints=use_example_preprints, output_csv=output_csv),
+                    ...)
 }
diff --git a/man/biorecap_report.Rd b/man/biorecap_report.Rd
index 14c349c..4934d67 100644
--- a/man/biorecap_report.Rd
+++ b/man/biorecap_report.Rd
@@ -9,7 +9,8 @@ biorecap_report(
   subject = NULL,
   nsentences = 2L,
   model = "llama3.1",
-  use_example_preprints = FALSE
+  use_example_preprints = FALSE,
+  ...
 )
 }
 \arguments{
@@ -22,6 +23,8 @@ biorecap_report(
 \item{model}{The model to use for generating summaries. See \code{\link[ollamar:list_models]{ollamar::list_models()}}.}
 
 \item{use_example_preprints}{Use the example preprints data included with the package instead of fetching new data from bioRxiv. For diagnostic/testing purposes only.}
+
+\item{...}{Other arguments passed to \code{\link[rmarkdown:render]{rmarkdown::render()}}.}
 }
 \value{
 Nothing; called for its side effects to produce a report.
diff --git a/tests/testthat/test-biorecap.R b/tests/testthat/test-biorecap.R
index 9ef0da4..d3b7ac6 100644
--- a/tests/testthat/test-biorecap.R
+++ b/tests/testthat/test-biorecap.R
@@ -18,5 +18,26 @@ test_that("add_prompt", {
   expect_true(inherits(res, "tbl"))
   expect_error(expect_warning(add_prompt(iris)))
   expect_error(add_prompt("invalid"))
+  expect_warning(add_prompt(data.frame(title=character(), abstract=character())))
+  expect_error(add_prompt(data.frame(title=character())))
+  expect_error(add_prompt(data.frame(abstract=character())))
 })
 
+test_that("add_summary", {
+  expect_error(expect_warning(add_summary(data.frame())))
+  expect_warning(add_summary(data.frame(prompt=character())))
+  expect_silent(add_summary(structure(data.frame(prompt=character()), class=c("preprints_prompt", "data.frame"))))
+})
+
+test_that("tt_preprints", {
+  expect_silent(res <- tt_preprints(example_preprints[1:2,]))
+  expect_true(inherits(res, "tinytable"))
+})
+
+test_that("tt_preprints", {
+  output_dir <- tempdir()
+  expect_silent(biorecap_report(use_example_preprints=TRUE, output_dir=output_dir, quiet=TRUE))
+  expect_error(biorecap_report(use_example_preprints=FALSE, output_dir=output_dir))
+})
+
+