From 8c2d46dc6f82ae26725784e356b9d793890167c7 Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Wed, 30 Oct 2024 09:35:54 +0200 Subject: [PATCH 1/2] Downgrade missing metadata file when checking model output submission to check failure and remove early return. Resolves #138 --- R/check_submission_metadata_file_exists.R | 2 +- R/validate_model_file.R | 3 - .../check_submission_metadata_file_exists.md | 2 +- tests/testthat/_snaps/validate_pr.md | 867 ++++++++++++++---- tests/testthat/test-validate_pr.R | 8 + 5 files changed, 711 insertions(+), 171 deletions(-) diff --git a/R/check_submission_metadata_file_exists.R b/R/check_submission_metadata_file_exists.R index 22aee264..d0a98149 100644 --- a/R/check_submission_metadata_file_exists.R +++ b/R/check_submission_metadata_file_exists.R @@ -38,6 +38,6 @@ check_submission_metadata_file_exists <- function(file_path, hub_path = ".") { msg_subject = "Metadata file", msg_attribute = msg_attribute, msg_verbs = c("exists", "does not exist"), - error = TRUE + error = FALSE ) } diff --git a/R/validate_model_file.R b/R/validate_model_file.R index 532f9ade..6a5a1917 100644 --- a/R/validate_model_file.R +++ b/R/validate_model_file.R @@ -91,9 +91,6 @@ validate_model_file <- function(hub_path, file_path, file_path = file_path ), file_path ) - if (is_any_error(checks$metadata_exists)) { - return(checks) - } custom_checks <- execute_custom_checks(validations_cfg_path = validations_cfg_path) checks <- combine(checks, custom_checks) diff --git a/tests/testthat/_snaps/check_submission_metadata_file_exists.md b/tests/testthat/_snaps/check_submission_metadata_file_exists.md index bc85bed9..70078663 100644 --- a/tests/testthat/_snaps/check_submission_metadata_file_exists.md +++ b/tests/testthat/_snaps/check_submission_metadata_file_exists.md @@ -12,7 +12,7 @@ Code check_submission_metadata_file_exists(hub_path = hub_path, file_path = "random-model/2022-10-01-random-model.csv") Output - + Error: ! Metadata file does not exist at path 'model-metadata/random-model.yml' or 'model-metadata/random-model.yaml'. diff --git a/tests/testthat/_snaps/validate_pr.md b/tests/testthat/_snaps/validate_pr.md index 9ae58713..04a0a142 100644 --- a/tests/testthat/_snaps/validate_pr.md +++ b/tests/testthat/_snaps/validate_pr.md @@ -240,14 +240,14 @@ Code str(mod_checks_error) Output - Classes 'hub_validations', 'list' hidden list of 32 - $ valid_config :List of 4 + List of 48 + $ valid_config :List of 4 ..$ message : chr "All hub config files are valid. \n " ..$ where : chr "mod_del_hub" ..$ call : chr "check_config_hub_valid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ model_output_mod :List of 6 + $ model_output_mod :List of 6 ..$ message : chr "Previously submitted model output files must not be modified. \n 'model-output/hub-baseline/2022-10-08-hub-base"| __truncated__ ..$ trace : NULL ..$ parent : NULL @@ -255,7 +255,7 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... - $ model_output_mod_1 :List of 6 + $ model_output_mod_1 :List of 6 ..$ message : chr "Previously submitted model output files must not be removed. \n 'model-output/team1-goodmodel/2022-10-15-team1-"| __truncated__ ..$ trace : NULL ..$ parent : NULL @@ -263,7 +263,7 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... - $ model_metadata_mod :List of 6 + $ model_metadata_mod :List of 6 ..$ message : chr "Previously submitted model metadata files must not be removed. \n 'model-metadata/team1-goodmodel.yaml' removed." ..$ trace : NULL ..$ parent : NULL @@ -271,92 +271,92 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... - $ file_exists :List of 4 + $ file_exists :List of 4 ..$ message : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name :List of 4 + $ file_name :List of 4 ..$ message : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location :List of 4 + $ file_location :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid :List of 4 + $ round_id_valid :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format :List of 4 + $ file_format :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists :List of 4 + $ metadata_exists :List of 4 ..$ message : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_read :List of 4 + $ file_read :List of 4 ..$ message : chr "File could be read successfully. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_read" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_round_id_col :List of 4 + $ valid_round_id_col :List of 4 ..$ message : chr "`round_id_col` name is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ unique_round_id :List of 4 + $ unique_round_id :List of 4 ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_unique_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ match_round_id :List of 4 + $ match_round_id :List of 4 ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_match_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ colnames :List of 4 + $ colnames :List of 4 ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_colnames" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ col_types :List of 4 + $ col_types :List of 4 ..$ message : chr "Column data types match hub schema. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_col_types" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_vals :List of 5 + $ valid_vals :List of 5 ..$ message : chr "`tbl` contains valid values/value combinations. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_values" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ rows_unique :List of 4 + $ rows_unique :List of 4 ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_rows_unique" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ req_vals :List of 5 + $ req_vals :List of 5 ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ missing : tibble [0 x 6] (S3: tbl_df/tbl/data.frame) @@ -369,101 +369,208 @@ ..$ call : chr "check_tbl_values_required" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_valid :List of 4 + $ value_col_valid :List of 4 ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_non_desc :List of 5 + $ value_col_non_desc :List of 5 ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_value_col_ascending" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_sum1 :List of 4 + $ value_col_sum1 :List of 4 ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col_sum1" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_taskid_set:List of 4 + $ spl_compound_taskid_set :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_taskid_set" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_tid :List of 4 + $ spl_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_non_compound_tid :List of 4 + $ spl_non_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_non_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_n :List of 4 + $ spl_n :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_n" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists_1 :List of 4 + $ file_exists_1 :List of 4 ..$ message : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name_1 :List of 4 + $ file_name_1 :List of 4 ..$ message : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location_1 :List of 4 + $ file_location_1 :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid_1 :List of 4 + $ round_id_valid_1 :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format_1 :List of 4 + $ file_format_1 :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists_1 :List of 6 + $ metadata_exists_1 :List of 6 ..$ message : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n "| __truncated__ ..$ trace : NULL ..$ parent : NULL ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE - ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... + ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... + $ file_read_1 :List of 4 + ..$ message : chr "File could be read successfully. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_file_read" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_round_id_col_1 :List of 4 + ..$ message : chr "`round_id_col` name is valid. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_valid_round_id_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ unique_round_id_1 :List of 4 + ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_unique_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ match_round_id_1 :List of 4 + ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_match_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ colnames_1 :List of 4 + ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_colnames" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ col_types_1 :List of 4 + ..$ message : chr "Column data types match hub schema. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_col_types" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_vals_1 :List of 5 + ..$ message : chr "`tbl` contains valid values/value combinations. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_values" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ rows_unique_1 :List of 4 + ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_rows_unique" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ req_vals_1 :List of 5 + ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ missing : tibble [0 x 7] (S3: tbl_df/tbl/data.frame) + .. ..$ origin_date : chr(0) + .. ..$ target : chr(0) + .. ..$ horizon : chr(0) + .. ..$ location : chr(0) + .. ..$ age_group : chr(0) + .. ..$ output_type : chr(0) + .. ..$ output_type_id: chr(0) + ..$ call : chr "check_tbl_values_required" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_valid_1 :List of 4 + ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_non_desc_1 :List of 5 + ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_value_col_ascending" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_sum1_1 :List of 4 + ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col_sum1" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_taskid_set_1:List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_taskid_set" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_non_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_non_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_n_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_n" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + - attr(*, "class")= chr [1:2] "hub_validations" "list" --- Code str(mod_checks_warn) Output - Classes 'hub_validations', 'list' hidden list of 32 - $ valid_config :List of 4 + List of 48 + $ valid_config :List of 4 ..$ message : chr "All hub config files are valid. \n " ..$ where : chr "mod_del_hub" ..$ call : chr "check_config_hub_valid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ model_output_mod :List of 6 + $ model_output_mod :List of 6 ..$ message : chr "Previously submitted model output files must not be modified. \n 'model-output/hub-baseline/2022-10-08-hub-base"| __truncated__ ..$ trace : NULL ..$ parent : NULL @@ -471,7 +578,7 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... - $ model_output_mod_1 :List of 6 + $ model_output_mod_1 :List of 6 ..$ message : chr "Previously submitted model output files must not be removed. \n 'model-output/team1-goodmodel/2022-10-15-team1-"| __truncated__ ..$ trace : NULL ..$ parent : NULL @@ -479,7 +586,7 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... - $ model_metadata_mod :List of 6 + $ model_metadata_mod :List of 6 ..$ message : chr "Previously submitted model metadata files must not be removed. \n 'model-metadata/team1-goodmodel.yaml' removed." ..$ trace : NULL ..$ parent : NULL @@ -487,92 +594,92 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... - $ file_exists :List of 4 + $ file_exists :List of 4 ..$ message : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name :List of 4 + $ file_name :List of 4 ..$ message : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location :List of 4 + $ file_location :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid :List of 4 + $ round_id_valid :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format :List of 4 + $ file_format :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists :List of 4 + $ metadata_exists :List of 4 ..$ message : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_read :List of 4 + $ file_read :List of 4 ..$ message : chr "File could be read successfully. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_read" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_round_id_col :List of 4 + $ valid_round_id_col :List of 4 ..$ message : chr "`round_id_col` name is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ unique_round_id :List of 4 + $ unique_round_id :List of 4 ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_unique_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ match_round_id :List of 4 + $ match_round_id :List of 4 ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_match_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ colnames :List of 4 + $ colnames :List of 4 ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_colnames" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ col_types :List of 4 + $ col_types :List of 4 ..$ message : chr "Column data types match hub schema. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_col_types" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_vals :List of 5 + $ valid_vals :List of 5 ..$ message : chr "`tbl` contains valid values/value combinations. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_values" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ rows_unique :List of 4 + $ rows_unique :List of 4 ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_rows_unique" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ req_vals :List of 5 + $ req_vals :List of 5 ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ missing : tibble [0 x 6] (S3: tbl_df/tbl/data.frame) @@ -585,204 +692,311 @@ ..$ call : chr "check_tbl_values_required" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_valid :List of 4 + $ value_col_valid :List of 4 ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_non_desc :List of 5 + $ value_col_non_desc :List of 5 ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_value_col_ascending" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_sum1 :List of 4 + $ value_col_sum1 :List of 4 ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col_sum1" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_taskid_set:List of 4 + $ spl_compound_taskid_set :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_taskid_set" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_tid :List of 4 + $ spl_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_non_compound_tid :List of 4 + $ spl_non_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_non_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_n :List of 4 + $ spl_n :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_n" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists_1 :List of 4 + $ file_exists_1 :List of 4 ..$ message : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name_1 :List of 4 + $ file_name_1 :List of 4 ..$ message : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location_1 :List of 4 + $ file_location_1 :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid_1 :List of 4 + $ round_id_valid_1 :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format_1 :List of 4 + $ file_format_1 :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists_1 :List of 6 + $ metadata_exists_1 :List of 6 ..$ message : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n "| __truncated__ ..$ trace : NULL ..$ parent : NULL ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE - ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... + ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... + $ file_read_1 :List of 4 + ..$ message : chr "File could be read successfully. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_file_read" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_round_id_col_1 :List of 4 + ..$ message : chr "`round_id_col` name is valid. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_valid_round_id_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ unique_round_id_1 :List of 4 + ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_unique_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ match_round_id_1 :List of 4 + ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_match_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ colnames_1 :List of 4 + ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_colnames" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ col_types_1 :List of 4 + ..$ message : chr "Column data types match hub schema. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_col_types" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_vals_1 :List of 5 + ..$ message : chr "`tbl` contains valid values/value combinations. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_values" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ rows_unique_1 :List of 4 + ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_rows_unique" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ req_vals_1 :List of 5 + ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ missing : tibble [0 x 7] (S3: tbl_df/tbl/data.frame) + .. ..$ origin_date : chr(0) + .. ..$ target : chr(0) + .. ..$ horizon : chr(0) + .. ..$ location : chr(0) + .. ..$ age_group : chr(0) + .. ..$ output_type : chr(0) + .. ..$ output_type_id: chr(0) + ..$ call : chr "check_tbl_values_required" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_valid_1 :List of 4 + ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_non_desc_1 :List of 5 + ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_value_col_ascending" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_sum1_1 :List of 4 + ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col_sum1" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_taskid_set_1:List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_taskid_set" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_non_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_non_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_n_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_n" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + - attr(*, "class")= chr [1:2] "hub_validations" "list" --- Code str(mod_checks_message) Output - Classes 'hub_validations', 'list' hidden list of 32 - $ valid_config :List of 4 + List of 48 + $ valid_config :List of 4 ..$ message : chr "All hub config files are valid. \n " ..$ where : chr "mod_del_hub" ..$ call : chr "check_config_hub_valid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ model_output_mod :List of 4 + $ model_output_mod :List of 4 ..$ message : chr "Previously submitted model output file\n 'model-output/hub-baseline/2022-10-08-hub-baseline.csv' modified." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ model_output_mod_1 :List of 4 + $ model_output_mod_1 :List of 4 ..$ message : chr "Previously submitted model output file\n 'model-output/team1-goodmodel/2022-10-15-team1-goodmodel.csv' removed." ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-15-team1-goodmodel.csv" ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ model_metadata_mod :List of 4 + $ model_metadata_mod :List of 4 ..$ message : chr "Previously submitted model metadata file\n 'model-metadata/team1-goodmodel.yaml' removed." ..$ where : 'fs_path' chr "team1-goodmodel.yaml" ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists :List of 4 + $ file_exists :List of 4 ..$ message : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name :List of 4 + $ file_name :List of 4 ..$ message : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location :List of 4 + $ file_location :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid :List of 4 + $ round_id_valid :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format :List of 4 + $ file_format :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists :List of 4 + $ metadata_exists :List of 4 ..$ message : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_read :List of 4 + $ file_read :List of 4 ..$ message : chr "File could be read successfully. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_read" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_round_id_col :List of 4 + $ valid_round_id_col :List of 4 ..$ message : chr "`round_id_col` name is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ unique_round_id :List of 4 + $ unique_round_id :List of 4 ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_unique_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ match_round_id :List of 4 + $ match_round_id :List of 4 ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_match_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ colnames :List of 4 + $ colnames :List of 4 ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_colnames" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ col_types :List of 4 + $ col_types :List of 4 ..$ message : chr "Column data types match hub schema. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_col_types" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_vals :List of 5 + $ valid_vals :List of 5 ..$ message : chr "`tbl` contains valid values/value combinations. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_values" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ rows_unique :List of 4 + $ rows_unique :List of 4 ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_rows_unique" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ req_vals :List of 5 + $ req_vals :List of 5 ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ missing : tibble [0 x 6] (S3: tbl_df/tbl/data.frame) @@ -795,186 +1009,293 @@ ..$ call : chr "check_tbl_values_required" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_valid :List of 4 + $ value_col_valid :List of 4 ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_non_desc :List of 5 + $ value_col_non_desc :List of 5 ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_value_col_ascending" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_sum1 :List of 4 + $ value_col_sum1 :List of 4 ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col_sum1" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_taskid_set:List of 4 + $ spl_compound_taskid_set :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_taskid_set" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_tid :List of 4 + $ spl_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_non_compound_tid :List of 4 + $ spl_non_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_non_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_n :List of 4 + $ spl_n :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_n" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists_1 :List of 4 + $ file_exists_1 :List of 4 ..$ message : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name_1 :List of 4 + $ file_name_1 :List of 4 ..$ message : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location_1 :List of 4 + $ file_location_1 :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid_1 :List of 4 + $ round_id_valid_1 :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format_1 :List of 4 + $ file_format_1 :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists_1 :List of 6 + $ metadata_exists_1 :List of 6 ..$ message : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n "| __truncated__ ..$ trace : NULL ..$ parent : NULL ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE - ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... + ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... + $ file_read_1 :List of 4 + ..$ message : chr "File could be read successfully. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_file_read" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_round_id_col_1 :List of 4 + ..$ message : chr "`round_id_col` name is valid. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_valid_round_id_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ unique_round_id_1 :List of 4 + ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_unique_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ match_round_id_1 :List of 4 + ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_match_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ colnames_1 :List of 4 + ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_colnames" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ col_types_1 :List of 4 + ..$ message : chr "Column data types match hub schema. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_col_types" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_vals_1 :List of 5 + ..$ message : chr "`tbl` contains valid values/value combinations. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_values" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ rows_unique_1 :List of 4 + ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_rows_unique" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ req_vals_1 :List of 5 + ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ missing : tibble [0 x 7] (S3: tbl_df/tbl/data.frame) + .. ..$ origin_date : chr(0) + .. ..$ target : chr(0) + .. ..$ horizon : chr(0) + .. ..$ location : chr(0) + .. ..$ age_group : chr(0) + .. ..$ output_type : chr(0) + .. ..$ output_type_id: chr(0) + ..$ call : chr "check_tbl_values_required" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_valid_1 :List of 4 + ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_non_desc_1 :List of 5 + ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_value_col_ascending" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_sum1_1 :List of 4 + ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col_sum1" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_taskid_set_1:List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_taskid_set" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_non_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_non_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_n_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_n" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + - attr(*, "class")= chr [1:2] "hub_validations" "list" --- Code str(mod_checks_none) Output - Classes 'hub_validations', 'list' hidden list of 29 - $ valid_config :List of 4 + List of 45 + $ valid_config :List of 4 ..$ message : chr "All hub config files are valid. \n " ..$ where : chr "mod_del_hub" ..$ call : chr "check_config_hub_valid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_exists :List of 4 + $ file_exists :List of 4 ..$ message : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name :List of 4 + $ file_name :List of 4 ..$ message : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location :List of 4 + $ file_location :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid :List of 4 + $ round_id_valid :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format :List of 4 + $ file_format :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists :List of 4 + $ metadata_exists :List of 4 ..$ message : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_read :List of 4 + $ file_read :List of 4 ..$ message : chr "File could be read successfully. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_read" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_round_id_col :List of 4 + $ valid_round_id_col :List of 4 ..$ message : chr "`round_id_col` name is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ unique_round_id :List of 4 + $ unique_round_id :List of 4 ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_unique_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ match_round_id :List of 4 + $ match_round_id :List of 4 ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_match_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ colnames :List of 4 + $ colnames :List of 4 ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_colnames" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ col_types :List of 4 + $ col_types :List of 4 ..$ message : chr "Column data types match hub schema. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_col_types" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_vals :List of 5 + $ valid_vals :List of 5 ..$ message : chr "`tbl` contains valid values/value combinations. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_values" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ rows_unique :List of 4 + $ rows_unique :List of 4 ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_rows_unique" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ req_vals :List of 5 + $ req_vals :List of 5 ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ missing : tibble [0 x 6] (S3: tbl_df/tbl/data.frame) @@ -987,101 +1308,208 @@ ..$ call : chr "check_tbl_values_required" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_valid :List of 4 + $ value_col_valid :List of 4 ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_non_desc :List of 5 + $ value_col_non_desc :List of 5 ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_value_col_ascending" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_sum1 :List of 4 + $ value_col_sum1 :List of 4 ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col_sum1" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_taskid_set:List of 4 + $ spl_compound_taskid_set :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_taskid_set" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_tid :List of 4 + $ spl_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_non_compound_tid :List of 4 + $ spl_non_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_non_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_n :List of 4 + $ spl_n :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_n" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists_1 :List of 4 + $ file_exists_1 :List of 4 ..$ message : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name_1 :List of 4 + $ file_name_1 :List of 4 ..$ message : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location_1 :List of 4 + $ file_location_1 :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid_1 :List of 4 + $ round_id_valid_1 :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format_1 :List of 4 + $ file_format_1 :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists_1 :List of 6 + $ metadata_exists_1 :List of 6 ..$ message : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n "| __truncated__ ..$ trace : NULL ..$ parent : NULL ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE - ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... + ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... + $ file_read_1 :List of 4 + ..$ message : chr "File could be read successfully. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_file_read" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_round_id_col_1 :List of 4 + ..$ message : chr "`round_id_col` name is valid. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_valid_round_id_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ unique_round_id_1 :List of 4 + ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_unique_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ match_round_id_1 :List of 4 + ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_match_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ colnames_1 :List of 4 + ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_colnames" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ col_types_1 :List of 4 + ..$ message : chr "Column data types match hub schema. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_col_types" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_vals_1 :List of 5 + ..$ message : chr "`tbl` contains valid values/value combinations. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_values" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ rows_unique_1 :List of 4 + ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_rows_unique" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ req_vals_1 :List of 5 + ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ missing : tibble [0 x 7] (S3: tbl_df/tbl/data.frame) + .. ..$ origin_date : chr(0) + .. ..$ target : chr(0) + .. ..$ horizon : chr(0) + .. ..$ location : chr(0) + .. ..$ age_group : chr(0) + .. ..$ output_type : chr(0) + .. ..$ output_type_id: chr(0) + ..$ call : chr "check_tbl_values_required" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_valid_1 :List of 4 + ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_non_desc_1 :List of 5 + ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_value_col_ascending" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_sum1_1 :List of 4 + ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col_sum1" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_taskid_set_1:List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_taskid_set" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_non_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_non_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_n_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_n" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + - attr(*, "class")= chr [1:2] "hub_validations" "list" --- Code str(mod_checks_in_window) Output - Classes 'hub_validations', 'list' hidden list of 31 - $ valid_config :List of 4 + List of 47 + $ valid_config :List of 4 ..$ message : chr "All hub config files are valid. \n " ..$ where : chr "mod_del_hub" ..$ call : chr "check_config_hub_valid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ model_output_mod :List of 6 + $ model_output_mod :List of 6 ..$ message : chr "Previously submitted model output files must not be removed. \n 'model-output/team1-goodmodel/2022-10-15-team1-"| __truncated__ ..$ trace : NULL ..$ parent : NULL @@ -1089,7 +1517,7 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... - $ model_metadata_mod :List of 6 + $ model_metadata_mod :List of 6 ..$ message : chr "Previously submitted model metadata files must not be removed. \n 'model-metadata/team1-goodmodel.yaml' removed." ..$ trace : NULL ..$ parent : NULL @@ -1097,92 +1525,92 @@ ..$ call : chr "check_pr_modf_del_file" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... - $ file_exists :List of 4 + $ file_exists :List of 4 ..$ message : chr "File exists at path 'model-output/hub-baseline/2022-10-08-hub-baseline.csv'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name :List of 4 + $ file_name :List of 4 ..$ message : chr "File name \"2022-10-08-hub-baseline.csv\" is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location :List of 4 + $ file_location :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid :List of 4 + $ round_id_valid :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format :List of 4 + $ file_format :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists :List of 4 + $ metadata_exists :List of 4 ..$ message : chr "Metadata file exists at path 'model-metadata/hub-baseline.yml'. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_read :List of 4 + $ file_read :List of 4 ..$ message : chr "File could be read successfully. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_file_read" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_round_id_col :List of 4 + $ valid_round_id_col :List of 4 ..$ message : chr "`round_id_col` name is valid. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_valid_round_id_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ unique_round_id :List of 4 + $ unique_round_id :List of 4 ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_unique_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ match_round_id :List of 4 + $ match_round_id :List of 4 ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_match_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ colnames :List of 4 + $ colnames :List of 4 ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_colnames" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ col_types :List of 4 + $ col_types :List of 4 ..$ message : chr "Column data types match hub schema. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_col_types" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ valid_vals :List of 5 + $ valid_vals :List of 5 ..$ message : chr "`tbl` contains valid values/value combinations. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_values" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ rows_unique :List of 4 + $ rows_unique :List of 4 ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_rows_unique" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ req_vals :List of 5 + $ req_vals :List of 5 ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ missing : tibble [0 x 6] (S3: tbl_df/tbl/data.frame) @@ -1195,87 +1623,194 @@ ..$ call : chr "check_tbl_values_required" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_valid :List of 4 + $ value_col_valid :List of 4 ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_non_desc :List of 5 + $ value_col_non_desc :List of 5 ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ error_tbl : NULL ..$ call : chr "check_tbl_value_col_ascending" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ value_col_sum1 :List of 4 + $ value_col_sum1 :List of 4 ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_value_col_sum1" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_taskid_set:List of 4 + $ spl_compound_taskid_set :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_taskid_set" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_compound_tid :List of 4 + $ spl_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_non_compound_tid :List of 4 + $ spl_non_compound_tid :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_non_compound_tid" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ spl_n :List of 4 + $ spl_n :List of 4 ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." ..$ where : 'fs_path' chr "hub-baseline/2022-10-08-hub-baseline.csv" ..$ call : chr "check_tbl_spl_n" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... - $ file_exists_1 :List of 4 + $ file_exists_1 :List of 4 ..$ message : chr "File exists at path 'model-output/team1-goodmodel/2022-10-22-team1-goodmodel.csv'. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_exists" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_name_1 :List of 4 + $ file_name_1 :List of 4 ..$ message : chr "File name \"2022-10-22-team1-goodmodel.csv\" is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_name" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_location_1 :List of 4 + $ file_location_1 :List of 4 ..$ message : chr "File directory name matches `model_id`\n metadata in file name. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_location" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ round_id_valid_1 :List of 4 + $ round_id_valid_1 :List of 4 ..$ message : chr "`round_id` is valid. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_valid_round_id" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ file_format_1 :List of 4 + $ file_format_1 :List of 4 ..$ message : chr "File is accepted hub format. \n " ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_file_format" ..$ use_cli_format: logi TRUE ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... - $ metadata_exists_1 :List of 6 + $ metadata_exists_1 :List of 6 ..$ message : chr "Metadata file does not exist at path 'model-metadata/team1-goodmodel.yml' or\n "| __truncated__ ..$ trace : NULL ..$ parent : NULL ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" ..$ call : chr "check_submission_metadata_file_exists" ..$ use_cli_format: logi TRUE - ..- attr(*, "class")= chr [1:5] "check_error" "hub_check" "rlang_error" "error" ... + ..- attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_error" "error" ... + $ file_read_1 :List of 4 + ..$ message : chr "File could be read successfully. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_file_read" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_round_id_col_1 :List of 4 + ..$ message : chr "`round_id_col` name is valid. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_valid_round_id_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ unique_round_id_1 :List of 4 + ..$ message : chr "`round_id` column \"origin_date\" contains a single, unique round ID value. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_unique_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ match_round_id_1 :List of 4 + ..$ message : chr "All `round_id_col` \"origin_date\" values match submission `round_id` from file name. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_match_round_id" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ colnames_1 :List of 4 + ..$ message : chr "Column names are consistent with expected round task IDs and std column names. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_colnames" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ col_types_1 :List of 4 + ..$ message : chr "Column data types match hub schema. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_col_types" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ valid_vals_1 :List of 5 + ..$ message : chr "`tbl` contains valid values/value combinations. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_values" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ rows_unique_1 :List of 4 + ..$ message : chr "All combinations of task ID column/`output_type`/`output_type_id` values are unique. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_rows_unique" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ req_vals_1 :List of 5 + ..$ message : chr "Required task ID/output type/output type ID combinations all present. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ missing : tibble [0 x 7] (S3: tbl_df/tbl/data.frame) + .. ..$ origin_date : chr(0) + .. ..$ target : chr(0) + .. ..$ horizon : chr(0) + .. ..$ location : chr(0) + .. ..$ age_group : chr(0) + .. ..$ output_type : chr(0) + .. ..$ output_type_id: chr(0) + ..$ call : chr "check_tbl_values_required" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_valid_1 :List of 4 + ..$ message : chr "Values in column `value` all valid with respect to modeling task config. \n " + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_non_desc_1 :List of 5 + ..$ message : chr "Values in `value` column are non-decreasing as output_type_ids increase for all unique task ID\n value/outpu"| __truncated__ + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ error_tbl : NULL + ..$ call : chr "check_tbl_value_col_ascending" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_success" "hub_check" "rlang_message" "message" ... + $ value_col_sum1_1 :List of 4 + ..$ message : chr "No pmf output types to check for sum of 1. Check skipped." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_value_col_sum1" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_taskid_set_1:List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_taskid_set` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_taskid_set" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_non_compound_tid_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_non_compound_tid` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_non_compound_tid" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + $ spl_n_1 :List of 4 + ..$ message : chr "No v3 samples found in model output data to check. Skipping `check_tbl_spl_n` check." + ..$ where : 'fs_path' chr "team1-goodmodel/2022-10-22-team1-goodmodel.csv" + ..$ call : chr "check_tbl_spl_n" + ..$ use_cli_format: logi TRUE + ..- attr(*, "class")= chr [1:5] "check_info" "hub_check" "rlang_message" "message" ... + - attr(*, "class")= chr [1:2] "hub_validations" "list" # validate_pr handles errors in determining submission window & file renaming diff --git a/tests/testthat/test-validate_pr.R b/tests/testthat/test-validate_pr.R index 51763425..02d325c1 100644 --- a/tests/testthat/test-validate_pr.R +++ b/tests/testthat/test-validate_pr.R @@ -63,6 +63,10 @@ test_that("validate_pr flags modifications and deletions in PR", { branch = "test-mod-del" ) + # This checks that removed metadata and model-output files are detected and + # flagged as check errors. + # It also checks that missing metadata files do not cause early return + # of submission validation of model output file. mod_checks_error <- suppressMessages( validate_pr( hub_path = temp_hub, @@ -90,6 +94,10 @@ test_that("validate_pr flags modifications and deletions in PR", { ) ) + # This checks that removed metadata and model-output files are detected and + # flagged as check failure. + # It also checks that missing metadata files do not cause early return + # of submission validation of model output file. mod_checks_warn <- suppressMessages( validate_pr( hub_path = temp_hub, From 2f94d148a27e88c12e948b0f67214f3417f8a34a Mon Sep 17 00:00:00 2001 From: Anna Krystalli Date: Wed, 30 Oct 2024 11:01:03 +0200 Subject: [PATCH 2/2] Update check_table.csv --- inst/check_table.csv | 2 +- man/validate_model_file.Rd | 4 ++-- man/validate_pr.Rd | 4 ++-- man/validate_submission.Rd | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/inst/check_table.csv b/inst/check_table.csv index ff1da59a..fffb51c8 100644 --- a/inst/check_table.csv +++ b/inst/check_table.csv @@ -6,7 +6,7 @@ file_name,File name valid,TRUE,check_error,validate_model_file,check_file_name,, file_location,File located in correct team directory,FALSE,check_failure,validate_model_file,check_file_location,,FALSE round_id_valid,File round ID is valid hub round IDs,TRUE,check_error,validate_model_file,check_valid_round_id,,FALSE file_format,File format is accepted hub/round format,TRUE,check_error,validate_model_file,check_file_format,,FALSE -metadata_exists,Model metadata file exists in expected location,TRUE,check_error,validate_model_file,check_submission_metadata_file_exists,,FALSE +metadata_exists,Model metadata file exists in expected location,FALSE,check_failure,validate_model_file,check_submission_metadata_file_exists,,FALSE file_read,File can be read without errors,TRUE,check_error,validate_model_data,check_file_read,,FALSE valid_round_id_col,Round ID var from config exists in data column names. Skipped if `round_id_from_var` is FALSE in config.,FALSE,check_failure,validate_model_data,check_valid_round_id_col,,FALSE unique_round_id,Round ID column contains a single unique round ID. Skipped if `round_id_from_var` is FALSE in config.,TRUE,check_error,validate_model_data,check_tbl_unique_round_id,,FALSE diff --git a/man/validate_model_file.Rd b/man/validate_model_file.Rd index c2d8be99..8ddd3f28 100644 --- a/man/validate_model_file.Rd +++ b/man/validate_model_file.Rd @@ -85,8 +85,8 @@ Details of checks performed by \code{validate_model_file()}\if{html}{\out{ - - + + diff --git a/man/validate_pr.Rd b/man/validate_pr.Rd index 306fda4d..c5c2a0cc 100644 --- a/man/validate_pr.Rd +++ b/man/validate_pr.Rd @@ -184,8 +184,8 @@ Details of checks performed by \code{validate_submission()}\if{html}{\out{
metadata_exists Model metadata file exists in expected location TRUE check_error FALSE check_failure
- - + + diff --git a/man/validate_submission.Rd b/man/validate_submission.Rd index fe6cae0d..cc3b0702 100644 --- a/man/validate_submission.Rd +++ b/man/validate_submission.Rd @@ -148,8 +148,8 @@ Details of checks performed by \code{validate_submission()}\if{html}{\out{
metadata_exists Model metadata file exists in expected location TRUE check_error FALSE check_failure
- - + +
metadata_exists Model metadata file exists in expected location TRUE check_error FALSE check_failure