tests/testthat/test-Pubmed_search.R

In bakaburg1/BaySREn: BaySREn. An R package to automatise citation collection and screening in Systematic Reviews. Based on Bayesian active machine learning

query <- "(systematic review) AND ((heart failure) AND (COPD))" # Very strict rule to avoid large result sets
year_query <- "2021"

expected_struct <- c(
  Order = "integer", ID = "character", Title = "character", Abstract = "character",
  DOI = "character", Authors = "character", URL = "character",
  Journal = "character", Journal_short = "character", Article_type = "character",
  Mesh = "character", Author_keywords = "character", Published = "character",
  Source = "character", Source_type = "character", Creation_date = "POSIXct"
)

test_that("PUBMED can be searched without an API key", {
  results <- try(suppressWarnings(search_pubmed(query, year_query, api_key = NULL, record_limit = 100)), silent = TRUE)

  test_search_result(results, expected_struct)
})

test_that("PUBMED can be searched using an API key", {
  skip_if(is.null(getOption("baysren.ncbi_api_key")), "PUBMED API key required")

  results <- try(search_pubmed(query, year_query, api_key = getOption("baysren.ncbi_api_key"), record_limit = 100), silent = TRUE)

  test_search_result(results, expected_struct)
})

rm(query, year_query)