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Merge pull request #716 from molgenis/test/omics
test: xenon-omics
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| library(dsOmicsClient) | ||
| library(purrr) | ||
| library(tibble) | ||
| gwas_prepare_data <- function() { | ||
| lapply(1:2, function(x) { | ||
| ds.GenotypeData( | ||
| x = paste0("chr", x), covars = "pheno_object", | ||
| columnId = "subject_id", sexId = "sex", | ||
| male_encoding = "male", female_encoding = "female", | ||
| case_control_column = "diabetes_diagnosed_doctor", | ||
| case = "Yes", control = "No", | ||
| newobj.name = paste0("gds.Data", x), datasources = conns | ||
| ) | ||
| }) | ||
| } | ||
|
|
||
| verify_meta_gwas <- function(gwas_results) { | ||
| gwas_dim <- dim(gwas_results) | ||
| verify_output( | ||
| function_name = "ds.metaGWAS", object = gwas_dim, | ||
| expected = as.integer(c(144785, 10)), | ||
| fail_msg = xenon_fail_msg$clt_dim | ||
| ) | ||
| } | ||
|
|
||
| omics_ref <- tribble( | ||
| ~file_name, ~path, ~url, ~object_name, ~format, | ||
| "chr1.gds", file.path(test_config$test_file_path, "chr1.gds"), "https://github.com/isglobal-brge/brge_data_large/blob/master/inst/extdata/GWAS_example/chr1_maf_filtered_small.vcf.gz?raw=true", "chr1", "VCF2GDS", | ||
| "chr2.gds", file.path(test_config$test_file_path, "chr2.gds"), "https://github.com/isglobal-brge/brge_data_large/blob/master/inst/extdata/GWAS_example/chr2_maf_filtered_small.vcf.gz?raw=true", "chr2", "VCF2GDS", | ||
| "ega_phenotypes.tsv", file.path(test_config$test_file_path, "ega_phenotypes.tsv"), "https://github.com/isglobal-brge/brge_data_large/blob/master/inst/extdata/GWAS_example/ega_synthetic_data_phenotypes_treated_with_nas.tsv?raw=true", "ega_phenotypes", "tsv" | ||
| ) | ||
|
|
||
| run_omics_tests <- function(project, url, token, auth_type, ADMIN_MODE, profile, profile_info, ref, | ||
| skip_tests, user, admin_pwd, interactive, update_auto) { | ||
| test_name <- "xenon-omics" | ||
| if (do_skip_test(test_name, skip_tests)) { | ||
| return() | ||
| } | ||
| if (ADMIN_MODE) { | ||
| cli_alert_warning("Cannot test working with resources as basic authenticated admin") | ||
| } else if (!"resourcer" %in% profile_info$packageWhitelist) { | ||
| cli_alert_warning(sprintf("Resourcer not available for profile: %s, skipping testing using resources.", profile)) | ||
| } else { | ||
| set_dm_permissions(user = user, admin_pwd = admin_pwd, required_projects = list(project), interactive = interactive, update_auto = update_auto, url = url) | ||
|
|
||
| download_many_sources(ref = omics_ref, skip_tests = NULL) | ||
|
|
||
| upload_many_sources( | ||
| project = project, ref = omics_ref, folder = "omics", url = url, | ||
| token = token, auth_type = auth_type, skip_tests = NULL | ||
| ) | ||
|
|
||
| omics_resources <- create_many_resources( | ||
| ref = omics_ref, project = project, | ||
| folder = "omics", url = url, skip_tests = NULL | ||
| ) | ||
|
|
||
| upload_many_resources( | ||
| project = project, folder = "omics", resource = omics_resources, | ||
| ref = omics_ref | ||
| ) | ||
|
|
||
| assign_many_resources(project = project, folder = "omics", ref = omics_ref) | ||
|
|
||
| map(c("chr1", "chr2"), ~ DSI::datashield.assign.expr( | ||
| conns = conns, symbol = .x, expr = as.symbol(paste0("as.resource.object(", .x, ")")) | ||
| )) | ||
|
|
||
| DSI::datashield.assign.expr(conns = conns, symbol = "pheno_object", expr = quote(as.resource.data.frame(ega_phenotypes))) | ||
|
|
||
| gwas_prepare_data() | ||
| gwas_results <- ds.metaGWAS( | ||
| genoData = paste0("gds.Data", 1:2), | ||
| model = diabetes_diagnosed_doctor ~ sex + hdl_cholesterol | ||
| )[[1]] | ||
| verify_meta_gwas(gwas_results) | ||
| } | ||
| cli_alert_success(sprintf("%s passed!", test_name)) | ||
| } |