|
|
| |
|
|
| a <- tempdir() |
| sql_path <- file.path(a, |
| "idbac_tests", |
| "sqlite", fsep = "/") |
| dir.create(sql_path) |
| sql_path <- normalizePath(sql_path, |
| "/") |
|
|
| test_that("idbac_create() gives path", { |
| expect_equal(idbac_create("testdb", |
| sql_path), |
| file.path(sql_path, |
| "testdb.sqlite") |
| ) |
| }) |
|
|
|
|
| pool <- idbac_connect("testdb", |
| sql_path) |
|
|
|
|
| test_that("idbac_create gives example db connection", { |
| expect_equal(length(pool), 1) |
| expect_true(inherits(pool[[1]], "Pool")) |
| expect_equal(labels(pool), "testdb") |
| }) |
|
|
| pool <- pool[[1]] |
|
|
|
|
|
|
| mzml_path <- file.path(a, |
| "idbac_tests", |
| "mzml", |
| fsep = "/") |
| mzml_path <- normalizePath(mzml_path, |
| "/") |
| mzml_path <- list.files(mzml_path, full.names = T) |
|
|
|
|
| test_that("db_from_mzml gives messages", { |
| expect_message( |
| suppressWarnings({ |
| db_from_mzml(mzFilePaths = mzml_path, |
| sampleIds = LETTERS[1:4], |
| idbacPool = pool, |
| acquisitionInfo = NULL, |
| halfWindowSize = 2) |
| }) |
| ) |
| }) |
|
|
|
|
| mass_hashes <- pool::poolWithTransaction(pool, |
| function(conn){ |
| statement <- glue::glue( |
| "SELECT spectrum_mass_hash |
| FROM spectra" |
| ) |
| query <- DBI::dbSendStatement(statement = statement, |
| con = conn) |
| selectedMeta <- DBI::dbFetch(query) |
| DBI::dbClearResult(query) |
| return(selectedMeta) |
| |
| }) |
|
|
| test_that("expected masses are present", { |
| expect_equal(sort(unique(unlist(mass_hashes))), |
| c("08caa9e63bcce83c", "90d91118298abb99")) |
| }) |
|
|
