test_that("expected datasts", { # transpose to 1 col/dataframe synapse_tables_wide <- genieBPC::synapse_tables %>% dplyr::arrange(df) %>% tidyr::pivot_wider(id_cols = c(cohort, version, release_date), names_from = df, values_from = synapse_id, ) # expect only pre-specified names expect_equal(names(synapse_tables_wide), c("cohort", "version", "release_date", "pt_char", "ca_dx_index", "ca_dx_non_index", "ca_drugs", "prissmm_imaging", "prissmm_pathology", "ca_radtx", "prissmm_md", "tumor_marker", "cpt", "mutations_extended", "fusions", "cna", "variable_synopsis")) # expect all data releases to have the following data frames expect_equal(nrow(synapse_tables_wide), nrow(synapse_tables_wide %>% tidyr::drop_na(pt_char, ca_dx_index, ca_dx_non_index, ca_drugs, prissmm_imaging, prissmm_pathology, prissmm_md, cpt, mutations_extended, fusions, cna, variable_synopsis))) # expect only certain cohorts to have tumor marker data synapse_tables_wide_tm_cohorts <- synapse_tables_wide %>% dplyr::filter(stringr::str_to_upper(cohort) %in% c("CRC", "BRCA", "PANC", "PROSTATE")) expect_equal(nrow(synapse_tables_wide_tm_cohorts), nrow(synapse_tables_wide %>% tidyr::drop_na(tumor_marker))) # expect onlycertain cohorts to have radiation data synapse_tables_wide_rt_cohorts <- synapse_tables_wide %>% dplyr::filter(stringr::str_to_upper(cohort) %in% c("PANC", "PROSTATE", "BLADDER")) expect_equal(nrow(synapse_tables_wide_rt_cohorts), nrow(synapse_tables_wide %>% tidyr:: drop_na(ca_radtx))) # cohort, version and release dates always populated" expect_equal(nrow(synapse_tables_wide), nrow(synapse_tables_wide %>% tidyr::drop_na(cohort, version, release_date))) })