tests/testthat/test-publication.R

In lifs-tools/rmzTab-m: R Package Client for mzTab-M Reference Implementation and Validation API

# Automatically generated by openapi-generator (https://openapi-generator.tech)
# Please update as you see appropriate

context("Test Publication")

model.instance <- Publication$new()

ref.json <- '{
      "id" : 1,
      "publicationItems" : [ {
        "type" : "pubmed",
        "accession" : "29039908"
      }, {
        "type" : "doi",
        "accession" : "10.1021/acs.analchem.7b03576"
      } ]
    }'

test_that("publication", {
  
  model.instance <- model.instance$fromJSONString(ref.json)
  expect_equal(model.instance$`id`, 1)
  expect_equal(length(model.instance$`publicationItems`), 2)
  expect_equal(model.instance$`publicationItems`[[1]]$`type`, "pubmed")
  expect_equal(model.instance$`publicationItems`[[1]]$`accession`, "29039908")
  expect_equal(model.instance$`publicationItems`[[2]]$`type`, "doi")
  expect_equal(model.instance$`publicationItems`[[2]]$`accession`, "10.1021/acs.analchem.7b03576")
}
)

test_that("publication$toDataFrame() works", {
  model.instance <- model.instance$fromJSONString(ref.json)
  df <- model.instance$toDataFrame()
  expect_equal(model.instance$`id`, 1)
  expect_equal(length(model.instance$`publicationItems`), 2)
  expect_equal(model.instance$`publicationItems`[[1]]$`type`, "pubmed")
  expect_equal(model.instance$`publicationItems`[[1]]$`accession`, "29039908")
  expect_equal(model.instance$`publicationItems`[[2]]$`type`, "doi")
  expect_equal(model.instance$`publicationItems`[[2]]$`accession`, "10.1021/acs.analchem.7b03576")
}
)

test_that("publication$fromDataFrame() works", {
  
  publicationMtd <- 
'
MTD\tpublication[1]\tpubmed:29039908|doi:10.1021/acs.analchem.7b03576																			
MTD\tpublication[2]\tpubmed:21063943|doi:10.1007/978-1-60761-987-1_6																			
'
  mzTabTable <- readMzTabString(publicationMtd)
  metadataTable <- extractMetadata(mzTabTable)
  idElements <- extractIdElements(metadataTable, "publication", "name")
  expect_equal(length(idElements), 2)
  model.instance <- Publication$new()
  model.instance$fromDataFrame(idElements[[1]])
  
  expect_equal(model.instance$`id`, 1)
  expect_equal(length(model.instance$`publicationItems`), 2)
  expect_equal(model.instance$`publicationItems`[[1]]$`type`, "pubmed")
  expect_equal(model.instance$`publicationItems`[[1]]$`accession`, "29039908")
  expect_equal(model.instance$`publicationItems`[[2]]$`type`, "doi")
  expect_equal(model.instance$`publicationItems`[[2]]$`accession`, "10.1021/acs.analchem.7b03576")
}
)