Merge pull request #30 from nationalparkservice/congruence-checks

Add ability to run metadata-only checks

R/tabular_data_congruence.R

@@ -667,6 +667,7 @@ test_date_range <- function(directory = here::here(), metadata = load_metadata(d
 
 #' Run all congruence checks
 #'
+#' @param check_metadata_only Only run checks on the metadata and skip anything involving data files.
 #' @inheritParams load_data
 #' @inheritParams test_metadata_version
 #'
@@ -677,12 +678,17 @@ test_date_range <- function(directory = here::here(), metadata = load_metadata(d
 #' dir <- DPchecker_example("BICY_veg")
 #' run_congruence_checks(dir)
 #'
-run_congruence_checks <- function(directory = here::here(), metadata = load_metadata(directory)) {
+run_congruence_checks <- function(directory = here::here(), metadata = load_metadata(directory), check_metadata_only = FALSE) {
+
   err_count <- 0
   warn_count <- 0
   total_count <- 10  # Don't forget to update this number when adding more checks!
 
-  cli::cli_h1("Running all congruence checks")
+  if (check_metadata_only) {
+    cli::cli_h1("Running metadata-only checks (skipping checks against data files)")
+  } else {
+    cli::cli_h1("Running all congruence checks")
+  }
   cli::cli_h2("Checking metadata compliance")
   tryCatch(test_validate_schema(metadata),
            error = function(e) {
@@ -739,45 +745,48 @@ run_congruence_checks <- function(directory = here::here(), metadata = load_meta
              cli::cli_bullets(c(e$message, e$body))
            })
 
-  cli::cli_h2("Checking that metadata is consistent with data file(s)")
-  tryCatch(test_file_name_match(directory, metadata),
-           error = function(e) {
-             err_count <<- err_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-             cli::cli_abort(c("x" = "You must correct the above error before the rest of the congruence checks can run."))
+  if (!check_metadata_only) {
+    cli::cli_h2("Checking that metadata is consistent with data file(s)")
+    tryCatch(test_file_name_match(directory, metadata),
+             error = function(e) {
+               err_count <<- err_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+               cli::cli_abort(c("x" = "You must correct the above error before the rest of the congruence checks can run."))
              },
-           warning = function(w) {
-             warn_count <<- warn_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-           })
-  tryCatch(test_fields_match(directory, metadata),
-           error = function(e) {
-             err_count <<- err_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-             cli::cli_abort(c("x" = "You must correct the above error before the rest of the congruence checks can run."))
+             warning = function(w) {
+               warn_count <<- warn_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+             })
+    tryCatch(test_fields_match(directory, metadata),
+             error = function(e) {
+               err_count <<- err_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+               cli::cli_abort(c("x" = "You must correct the above error before the rest of the congruence checks can run."))
              },
-           warning = function(w) {
-             warn_count <<- warn_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-           })
-  tryCatch(test_numeric_fields(directory, metadata),
-           error = function(e) {
-             err_count <<- err_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-           },
-           warning = function(w) {
-             warn_count <<- warn_count + 1
-             cli::cli_bullets(c(w$message, w$body))
-           })
-  tryCatch(test_date_range(directory, metadata),
-           error = function(e) {
-             err_count <<- err_count + 1
-             cli::cli_bullets(c(e$message, e$body))
-           },
-           warning = function(w) {
-             warn_count <<- warn_count + 1
-             cli::cli_bullets(c(w$message, w$body))
-           })
+             warning = function(w) {
+               warn_count <<- warn_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+             })
+    tryCatch(test_numeric_fields(directory, metadata),
+             error = function(e) {
+               err_count <<- err_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+             },
+             warning = function(w) {
+               warn_count <<- warn_count + 1
+               cli::cli_bullets(c(w$message, w$body))
+             })
+    tryCatch(test_date_range(directory, metadata),
+             error = function(e) {
+               err_count <<- err_count + 1
+               cli::cli_bullets(c(e$message, e$body))
+             },
+             warning = function(w) {
+               warn_count <<- warn_count + 1
+               cli::cli_bullets(c(w$message, w$body))
+             })
+  }
+
   cli::cli_h2("Summary")
   if (err_count > 0) {
     cli::cli_alert_danger("{err_count} errors to address")
@@ -786,7 +795,12 @@ run_congruence_checks <- function(directory = here::here(), metadata = load_meta
     cli::cli_alert_warning("{warn_count} warnings to look into")
   }
   if (warn_count + err_count == 0) {
-    cli::cli_alert_success("Success! All congruence checks passed.")
+    check_type <- if (check_metadata_only) {
+      "metadata"
+    } else {
+      "congruence"
+    }
+    cli::cli_alert_success("Success! All {check_type} checks passed.")
   }
 
   return(invisible(c("errors" = err_count, "warnings" = warn_count)))

tests/testthat/_snaps/tabular_data_congruence.md

@@ -30,3 +30,26 @@
       
       v Success! All congruence checks passed.
 
+---
+
+    Code
+      run_congruence_checks(here::here(good_dir, "BICY_good"), check_metadata_only = TRUE)
+    Message <cliMessage>
+      
+      -- Running metadata-only checks (skipping checks against data files) -----------
+      
+      -- Checking metadata compliance --
+      
+    Message <rlang_message>
+      v Your metadata is schema valid.
+      v Each data file name is used exactly once in the metadata file.
+      v Your EML version is supported.
+      v Metadata indicates that each data file contains a field delimiter that is a single character
+      v Metadata indicates that each data file contains exactly one header row.
+      v Metadata indicates data files do not have footers.
+    Message <cliMessage>
+      
+      -- Summary --
+      
+      v Success! All metadata checks passed.
+

tests/testthat/test-tabular_data_congruence.R

@@ -42,6 +42,7 @@ cli::test_that_cli("run_congruence_checks works", configs = "plain", {
   expect_error(run_congruence_checks(here::here(bad_dir, "data_metadata_mismatch", "BICY_files")),
                "You must correct the above error")
   expect_snapshot(run_congruence_checks(here::here(good_dir, "BICY_good")))
+  expect_snapshot(run_congruence_checks(here::here(good_dir, "BICY_good"), check_metadata_only = TRUE))
 })
 
 # ---- test_metadata_version ----