tests/testthat/test-readPedigrees.R

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

test_that("readGedcom reads and parses a GEDCOM file correctly", {
  # Create a temporary GEDCOM file for testing
  gedcom_content <- c(
    "0 HEAD",
    "1 GEDC",
    "2 VERS 5.5",
    "2 FORM LINEAGE-LINKED",
    "1 CHAR UTF-8",
    "1 LANG English",
    "0 @I1@ INDI",
    "1 NAME John /Doe/",
    "1 SEX M",
    "1 BIRT",
    "2 DATE 1 JAN 1900",
    "2 PLAC Someplace",
    "0 @I2@ INDI",
    "1 NAME Jane /Smith/",
    "1 SEX F",
    "1 BIRT",
    "2 DATE 2 FEB 1910",
    "2 PLAC Anotherplace"
  )
  temp_file <- tempfile(fileext = ".ged")
  writeLines(gedcom_content, temp_file)

  # Call readGedcom
  df <- readGedcom(temp_file, verbose = TRUE, skinny = FALSE)
  # note to self, the code is not reading in the 2nd person. and is also not reading in the birth date and place
  # Check that the data frame has the expected structure
  expect_true("id" %in% colnames(df))
  expect_true("name_given" %in% colnames(df))
  expect_true("name_surn" %in% colnames(df))
  expect_true("sex" %in% colnames(df))
  expect_true("birth_date" %in% colnames(df))
  expect_true("birth_place" %in% colnames(df))

  # Check the contents of the data frame
  expect_equal(nrow(df), 2)
  expect_equal(df$name_given[1], "John")
  expect_equal(df$name_surn[1], "Doe")
  expect_equal(df$sex[1], "M")
  expect_equal(df$birth_date[1], "1 JAN 1900")
  expect_equal(df$birth_place[1], "Someplace")
  expect_equal(df$name_given[2], "Jane")
  expect_equal(df$name_surn[2], "Smith")
  expect_equal(df$sex[2], "F")
  expect_equal(df$birth_date[2], "2 FEB 1910")
  expect_equal(df$birth_place[2], "Anotherplace")

  # Clean up temporary file
  unlink(temp_file)
})

test_that("readGedcom combines duplicate columns correctly", {
  # Create a temporary GEDCOM file for testing
  gedcom_content <- c(
    "0 @I1@ INDI",
    "1 NAME John /Doe/",
    "1 GIVN John",
    "1 SEX M",
    "0 @I2@ INDI",
    "1 NAME Jane /Smith/",
    "1 GIVN Jane",
    "1 SEX F"
  )
  temp_file <- tempfile(fileext = ".ged")
  writeLines(gedcom_content, temp_file)

  # Call readGedcom with combine_cols = TRUE
  df <- readGedcom(temp_file, verbose = TRUE, combine_cols = TRUE)

  # Check that the data frame has the expected structure
  expect_true("name_given" %in% colnames(df))
  expect_false("name_given_pieces" %in% colnames(df))

  # Check the contents of the data frame
  expect_equal(nrow(df), 2)
  expect_equal(df$name_given[1], "John")
  expect_equal(df$name_given[2], "Jane")

  # Clean up temporary file
  unlink(temp_file)
})

test_that("readGedcom removes empty columns correctly", {
  # Create a temporary GEDCOM file for testing
  gedcom_content <- c(
    "0 @I1@ INDI",
    "1 NAME John /Doe/",
    "1 SEX M"
  )
  temp_file <- tempfile(fileext = ".ged")
  writeLines(gedcom_content, temp_file)

  # Call readGedcom with remove_empty_cols = TRUE
  df <- readGedcom(temp_file, verbose = TRUE, remove_empty_cols = TRUE)

  # Check that empty columns are removed
  expect_false("birth_date" %in% colnames(df))
  expect_false("birth_place" %in% colnames(df))

  # Clean up temporary file
  unlink(temp_file)
})

test_that("readGedcom handles skinny option correctly", {
  # Create a temporary GEDCOM file for testing
  gedcom_content <- c(
    "0 @I1@ INDI",
    "1 NAME John /Doe/",
    "1 SEX M",
    "1 FAMC @F1@",
    "1 FAMS @F2@"
  )
  temp_file <- tempfile(fileext = ".ged")
  writeLines(gedcom_content, temp_file)

  # Call readGedcom with skinny = TRUE
  df <- readGedcom(temp_file, verbose = TRUE, skinny = TRUE)

  # Check that FAMC and FAMS columns are removed
  expect_false("FAMC" %in% colnames(df))
  expect_false("FAMS" %in% colnames(df))

  # Clean up temporary file
  unlink(temp_file)
})

test_that("processParents adds momID and dadID correctly", {
  # Create a data frame for testing
  df_temp <- data.frame(
    id = c("I1", "I2", "I3"),
    sex = c("M", "F", "M"),
    FAMS = c("@F1@", "@F1@", NA),
    FAMC = c(NA, NA, "@F1@"),
    stringsAsFactors = FALSE
  )

  # Call processParents
  df_temp <- processParents(df_temp, datasource = "gedcom")

  # Check the structure of the data frame
  expect_true("momID" %in% colnames(df_temp))
  expect_true("dadID" %in% colnames(df_temp))

  # Check the contents of the data frame
  expect_equal(df_temp$momID[1], NA_character_)
  expect_equal(df_temp$dadID[1], NA_character_)
  expect_equal(df_temp$momID[2], NA_character_)
  expect_equal(df_temp$dadID[2], NA_character_)
  expect_equal(df_temp$momID[3], "I2")
  expect_equal(df_temp$dadID[3], "I1")

  # Create a more complex data frame for testing
  df_temp <- data.frame(
    id = c("I1", "I2", "I3", "I4", "I5"),
    sex = c("M", "F", "M", "F", "M"),
    FAMS = c("@F1@", "@F1@", "@F2@", "@F2@", "@F3@"),
    FAMC = c(NA, NA, "@F1@", "@F1@", "@F2@"),
    stringsAsFactors = FALSE
  )

  # Call processParents
  df_temp <- processParents(df_temp, datasource = "gedcom")

  # Check the contents of the data frame
  expect_equal(df_temp$momID[3], "I2")
  expect_equal(df_temp$dadID[3], "I1")
  expect_equal(df_temp$momID[4], "I2")
  expect_equal(df_temp$dadID[4], "I1")
  expect_equal(df_temp$momID[5], "I4")
  expect_equal(df_temp$dadID[5], "I3")
})

test_that("if file does not exist, readGedcom throws an error", {
  # Call readGedcom with a non-existent file
  expect_error(readGedcom("nonexistent.ged"))
})



# readWikifamilytree

test_that("readWikifamilytree reads a simple file correctly", {
  # Create a temporary WikiFamilyTree file for testing
  # Example usage
  family_tree_text <- "{{familytree/start |summary=I have a brother Joe and a little sister: my mom married my dad, and my dad's parents were Grandma and Grandpa; they had another child, Aunt Daisy.}}
{{familytree | | | | GMa |~|y|~| GPa | | GMa=Gladys|GPa=Sydney}}
{{familytree | | | | | | | |)|-|-|-|.| }}
{{familytree | | | MOM |y| DAD | |DAISY| MOM=Mom|DAD=Dad|DAISY=[[Daisy Duke]]}}
{{familytree | |,|-|-|-|+|-|-|-|.| | | }}
{{familytree | JOE | | ME  | | SIS | | | JOE=My brother Joe|ME='''Me!'''|SIS=My little sister}}
{{familytree/end}}"

  result <- readWikifamilytree(family_tree_text)

  # list(
  #  summary = summary_text,
  #  members = members_df,
  #  structure = tree_long,
  #  relationships = relationships_df
  # )
  expect_equal(
    result$summary,
    "I have a brother Joe and a little sister: my mom married my dad, and my dad's parents were Grandma and Grandpa; they had another child, Aunt Daisy."
  )
})