tests/testthat/test-batch-cite.R

In matriz: Literature Matrix Synthesis Tools for Epidemiology and Health Science Research

# Mock file creation for testing
create_mock_bib_file <- function(content, file_name = tempfile(fileext = ".bib")) {
  writeLines(content, file_name)
  return(file_name)
}

# Tests for parse_citation
test_that("parse_citation correctly parses a single BibTeX entry", {
  mock_file <- create_mock_bib_file("@article{key1, author= {Smith J}, title= {Example}, year= {2024} }")
  parsed <- parse_citation(mock_file)
  expect_type(parsed, "character")
  expect_match(parsed, "@article")
  expect_match(parsed, "author = \\{Smith J\\}")
})

# Tests for parse_batch_citation
test_that("parse_batch_citation correctly parses multiple BibTeX entries", {
  mock_file <- create_mock_bib_file(
  "@article{key1,
    author= {Smith J},
    title= {Example One},
    year= {2024}
  }

  @book{key2,
    author= {Jones K},
    title= {Example Two},
    publisher= {Publisher},
    year= {2023}
  }
  "
  )
  parsed <- parse_batch_citation(mock_file)
  expect_type(parsed, "character")
  expect_length(parsed, 2)
  expect_match(parsed[1], "@article")
  expect_match(parsed[2], "@book")
})

test_that("parse_batch_citation returns NULL for empty files", {
  mock_file <- create_mock_bib_file("")
  expect_warning(result <- parse_batch_citation(mock_file), "No citations found")
  expect_null(result)
})

test_that("parse_batch_citation warns for unmatched braces", {
  mock_file <- create_mock_bib_file(
    "@article{key1,
    author= {Smith J,
    title= {Example One},
    year= {2024}
  ")
  expect_warning(parse_batch_citation(mock_file), "Unmatched braces")
})

# Tests for format_batch_ama_citation
test_that("format_batch_ama_citation formats article citations correctly", {
  entries <- c(
    "@article{key1,
    author= {Smith J},
    title= {Example Article},
    journal= {Journal One},
    year= {2024},
    volume= {10},
    pages= {100-110},
    doi= {10.1234/example}
  }")

  parsed <- format_batch_ama_citation(entries)
  expect_type(parsed, "list")
  expect_match(parsed$citation, "J Smith. Example Article. Journal One. 2024;10:100-110. doi:10.1234/example")
})

test_that("format_batch_ama_citation formats book citations correctly", {
  entries <- c(
    "@book{key2,
    author= {Jones K},
    title= {Example Book},
    publisher= {Publisher},
    year= {2023},
    edition= {2nd}
  }
  ")
  parsed <- format_batch_ama_citation(entries)
  expect_type(parsed, "list")
  expect_match(parsed$citation, "K Jones. Example Book. 2nd ed. Publisher; 2023")
})

test_that("format_batch_ama_citation handles missing fields gracefully", {
  entries <- c(
    "@article{key3,
    author= {Brown L},
    title= {No Journal Name},
    year= {2022}
  }
  ")
  parsed <- format_batch_ama_citation(entries)
  expect_type(parsed, "list")
  expect_match(parsed$citation, "L Brown. No Journal Name. 2022")
})

test_data <- data.frame(
  year = 2025,
  citation = " ",
  keywords = " ",
  profession = "underwater basket weaver",
  electronic = "YES",
  purpose = "To investigate the depth of the oceans and retireve weaving materials",
  study_design = "ethnography",
  outcome_var = "perceived attitudes towards basket weaving",
  predictor_var = NA,
  sample = "a small school of clown fish",
  setting = "Italy",
  drop_rate = 0.13,
  inclusion_criteria = "clow fish in Adriatic Sea",
  ehtnicity = "oceanic",
  age = "0 - 1 year",
  sex = "both",
  income = " ",
  education = "none",
  measures = "perceived attitudes",
  analysis = "qualitative",
  results = "no significant differences",
  limitations = "small sample size",
  implications = "clow fish don't like humans taking their homes for their own basket weaving endeavors",
  ethical_concerns = "no informed consent given to school of clown fish",
  biases = "clownfish always try to be funny. Lack of seriounness",
  notes = "more research needed",
  stringsAsFactors = FALSE
)

test_citations <- c("test1.bib", "test2.bib")

test_that("function throws error for invalid input types", {
  expect_error(process_batch_citation(list(), test_citations), "is.data.frame")
  expect_error(process_batch_citation(test_data, 123), "is.character")
})

test_that("function throws error for non-existent citation files", {
  non_existent_files <- c("non_existent1.bib", "non_existent2.bib")
  expect_error(process_batch_citation(test_data, non_existent_files), "file.exists")
})

test_that("parse_batch_citation correctly parses multiple BibTeX entries", {
  mock_file <- create_mock_bib_file(
    "@article{key1,
  author= {Smith J},
  title= {Example One},
  year= {2024}
}

@book{key2,
  author= {Jones K},
  title= {Example Two},
  publisher= {Publisher},
  year= {2023}
}"
  )

  parsed <- parse_batch_citation(mock_file)

  # Expect the output to be a character vector
  expect_type(parsed, "character")

  # Expect two entries in the parsed result
  expect_length(parsed, 2)

  # Validate that the first entry appears to be an article
  expect_match(parsed[1], "@article")

  # Validate that the second entry appears to be a book
  expect_match(parsed[2], "@book")
})


# Test: A file with a single BibTeX entry is parsed correctly
test_that("parse_batch_citation correctly parses a single BibTeX entry", {
  mock_file <- create_mock_bib_file(
    "@inproceedings{key_single,
  author= {Doe J},
  title= {Single Entry Example},
  year= {2025}
}"
  )
  parsed <- parse_batch_citation(mock_file)

  expect_type(parsed, "character")
  expect_length(parsed, 1)
  expect_match(parsed[1], "@inproceedings")
  expect_match(parsed[1], "author\\s*=\\s*\\{Doe J\\}")
  expect_match(parsed[1], "year\\s*=\\s*\\{2025\\}")
})

# Test: Non-existent file causes an error
test_that("parse_batch_citation throws an error for non-existent files", {
  fake_file <- tempfile(fileext = ".bib")
  # Ensure the file does not exist
  if (file.exists(fake_file)) unlink(fake_file)

  expect_error(parse_batch_citation(fake_file), "cannot open")
})