Merge pull request #603 from Sage-Bionetworks/FDS-2087-error-handling

Fds 2087 error handling
Sage-Bionetworks · Jul 9, 2024 · 7af8e11 · 7af8e11
2 parents fa669e9 + f1521b4
commit 7af8e11
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Showing 3 changed files with 304 additions and 2 deletions.
diff --git a/R/read_dca_config.R b/R/read_dca_config.R
@@ -0,0 +1,148 @@
+#' @title Read the DCA config file and report issues
+#' @param config URL or filepath to a DCA JSON config file
+read_dca_config <- function(config) {
+  conf <- jsonlite::fromJSON(config)
+
+  name_check <- function(req, prov) {
+    if (!all(req %in% prov)) {
+      which_miss <- req[which(!req %in% prov)]
+      stop(sprintf("DCA config missing %s", which_miss))
+    }
+  }
+
+  lvl_1_props_req <- list(
+    "dcc" = list(),
+    "dca" = list(),
+    "schematic" = list()
+  )
+  lvl_1_props_ops <- list() # Placeholder for optional properties
+  lvl_1_props_conf <- names(conf)
+  name_check(names(lvl_1_props_req), lvl_1_props_conf)
+
+  dca_props_req <- list() # Placeholder for required DCA properties
+  dca_props_ops <- list(
+    "use_compliance_dashboard" = FALSE,
+    "primary_col" = "#2a668d",
+    "secondary_col" = "#184e71",
+    "sidebar_col" = "#191919"
+  )
+  dca_props_conf <- names(conf$dca)
+  name_check(names(dca_props_req), dca_props_conf)
+
+  if (!"use_compliance_dashboard" %in% dca_props_conf) {
+    conf$dca$use_compliance_dashboard <- FALSE
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$primary_col <- "#2a668d"
+  }
+  if (!"secondary_col" %in% dca_props_conf) {
+    conf$dca$secondary_col <- "#184e71"
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$sidebar_col <- "#191919"
+  }
+
+  dcc_props_req <- list(
+    "name" = list(),
+    "synapse_asset_view" = list(),
+    "data_model_url" = list(),
+    "template_menu_config_file" = list()
+  )
+  dcc_props_ops <- list(
+    "data_model_info" = NA_character_,
+    "logo_location" = "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/demo/sage_logo_mark_only.png",
+    "logo_link" = "https://synapse.org",
+    "dcc_help_link" = NA_character_,
+    "portal_help_link" = NA_character_
+  )
+  dcc_props_conf <- names(conf$dcc)
+  name_check(names(dcc_props_req), dcc_props_conf)
+
+  if (!"logo_location" %in% dcc_props_conf) {
+    conf$dcc$logo_location <- dcc_props_ops$logo_location
+  }
+  if (!"logo_link" %in% dcc_props_conf) {
+    conf$dcc$logo_link <- dcc_props_ops$logo_link
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  schematic_props_req <- list(
+    "manifest_generate" = list(),
+    "model_validate" = list(),
+    "model_submit" = list()
+  )
+  schematic_props_ops <- list(
+    "global" = list()
+  )
+  schematic_props_conf <- names(conf$schematic)
+  name_check(names(schematic_props_req), schematic_props_conf)
+
+  if (!"global" %in% schematic_props_conf) {
+    conf$schematic$global <- list()
+  }
+
+  global_ops <- list(
+    "data_model_labels" = "class_label"
+  )
+  global_conf <- names(conf$schematic$global)
+  if (!"data_model_labels" %in% global_conf) {
+    conf$schematic$global$data_model_labels <- "class_label"
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mg_props_req <- list(
+    "output_format" = "excel",
+    "use_annotations" = TRUE
+  )
+  mg_props_ops <- list()
+  mg_props_conf <- names(conf$schematic$manifest_generate)
+  name_check(names(mg_props_req), mg_props_conf)
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mv_props_req <- list(
+    "restrict_rules" = FALSE
+  )
+  mv_props_ops <- list(
+    "cross_manifest_validation" = FALSE
+  )
+  mv_props_conf <- names(conf$schematic$model_validate)
+  name_check(names(mv_props_req), mv_props_conf)
+
+  if (!"cross_manifest_validation" %in% mv_props_conf) {
+    conf$schematic$model_validate$cross_manifest_validation <- FALSE
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  ms_props_req <- list(
+    "table_manipulation" = "replace",
+    "manifest_record_type" = "file_only"
+  )
+  ms_props_ops <- list(
+    "table_column_names" = "class_label",
+    "annotation_keys" = "class_label",
+    "file_annotations_upload" = TRUE,
+    "hide_blanks" = FALSE
+  )
+  ms_props_conf <- names(conf$schematic$model_submit)
+  name_check(names(ms_props_req), ms_props_conf)
+
+  if (!"table_column_names" %in% ms_props_conf) {
+    conf$schematic$model_submit$table_column_names <- "class_label"
+  }
+  if (!"annotation_keys" %in% ms_props_conf) {
+    conf$schematic$model_submit$annotation_keys <- "class_label"
+  }
+  if (!"file_annotations_upload" %in% ms_props_conf) {
+    conf$schematic$model_submit$file_annotations_upload <- TRUE
+  }
+  if (!"hide_blanks" %in% ms_props_conf) {
+    conf$schematic$model_submit$hide_blanks <- FALSE
+  }
+
+  conf
+
+}
diff --git a/functions/read_dca_config.R b/functions/read_dca_config.R
@@ -0,0 +1,148 @@
+#' @title Read the DCA config file and report issues
+#' @param config URL or filepath to a DCA JSON config file
+read_dca_config <- function(config) {
+  conf <- jsonlite::fromJSON(config)
+
+  name_check <- function(req, prov) {
+    if (!all(req %in% prov)) {
+      which_miss <- req[which(!req %in% prov)]
+      stop(sprintf("DCA config missing %s", which_miss))
+    }
+  }
+
+  lvl_1_props_req <- list(
+    "dcc" = list(),
+    "dca" = list(),
+    "schematic" = list()
+  )
+  lvl_1_props_ops <- list() # Placeholder for optional properties
+  lvl_1_props_conf <- names(conf)
+  name_check(names(lvl_1_props_req), lvl_1_props_conf)
+
+  dca_props_req <- list() # Placeholder for required DCA properties
+  dca_props_ops <- list(
+    "use_compliance_dashboard" = FALSE,
+    "primary_col" = "#2a668d",
+    "secondary_col" = "#184e71",
+    "sidebar_col" = "#191919"
+  )
+  dca_props_conf <- names(conf$dca)
+  name_check(names(dca_props_req), dca_props_conf)
+
+  if (!"use_compliance_dashboard" %in% dca_props_conf) {
+    conf$dca$use_compliance_dashboard <- FALSE
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$primary_col <- "#2a668d"
+  }
+  if (!"secondary_col" %in% dca_props_conf) {
+    conf$dca$secondary_col <- "#184e71"
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$sidebar_col <- "#191919"
+  }
+
+  dcc_props_req <- list(
+    "name" = list(),
+    "synapse_asset_view" = list(),
+    "data_model_url" = list(),
+    "template_menu_config_file" = list()
+  )
+  dcc_props_ops <- list(
+    "data_model_info" = NA_character_,
+    "logo_location" = "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/demo/sage_logo_mark_only.png",
+    "logo_link" = "https://synapse.org",
+    "dcc_help_link" = NA_character_,
+    "portal_help_link" = NA_character_
+  )
+  dcc_props_conf <- names(conf$dcc)
+  name_check(names(dcc_props_req), dcc_props_conf)
+
+  if (!"logo_location" %in% dcc_props_conf) {
+    conf$dcc$logo_location <- dcc_props_ops$logo_location
+  }
+  if (!"logo_link" %in% dcc_props_conf) {
+    conf$dcc$logo_link <- dcc_props_ops$logo_link
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  schematic_props_req <- list(
+    "manifest_generate" = list(),
+    "model_validate" = list(),
+    "model_submit" = list()
+  )
+  schematic_props_ops <- list(
+    "global" = list()
+  )
+  schematic_props_conf <- names(conf$schematic)
+  name_check(names(schematic_props_req), schematic_props_conf)
+
+  if (!"global" %in% schematic_props_conf) {
+    conf$schematic$global <- list()
+  }
+
+  global_ops <- list(
+    "data_model_labels" = "class_label"
+  )
+  global_conf <- names(conf$schematic$global)
+  if (!"data_model_labels" %in% global_conf) {
+    conf$schematic$global$data_model_labels <- "class_label"
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mg_props_req <- list(
+    "output_format" = "excel",
+    "use_annotations" = TRUE
+  )
+  mg_props_ops <- list()
+  mg_props_conf <- names(conf$schematic$manifest_generate)
+  name_check(names(mg_props_req), mg_props_conf)
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mv_props_req <- list(
+    "restrict_rules" = FALSE
+  )
+  mv_props_ops <- list(
+    "cross_manifest_validation" = FALSE
+  )
+  mv_props_conf <- names(conf$schematic$model_validate)
+  name_check(names(mv_props_req), mv_props_conf)
+
+  if (!"cross_manifest_validation" %in% mv_props_conf) {
+    conf$schematic$model_validate$cross_manifest_validation <- FALSE
+  }
+
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  ms_props_req <- list(
+    "table_manipulation" = "replace",
+    "manifest_record_type" = "file_only"
+  )
+  ms_props_ops <- list(
+    "table_column_names" = "class_label",
+    "annotation_keys" = "class_label",
+    "file_annotations_upload" = TRUE,
+    "hide_blanks" = FALSE
+  )
+  ms_props_conf <- names(conf$schematic$model_submit)
+  name_check(names(ms_props_req), ms_props_conf)
+
+  if (!"table_column_names" %in% ms_props_conf) {
+    conf$schematic$model_submit$table_column_names <- "class_label"
+  }
+  if (!"annotation_keys" %in% ms_props_conf) {
+    conf$schematic$model_submit$annotation_keys <- "class_label"
+  }
+  if (!"file_annotations_upload" %in% ms_props_conf) {
+    conf$schematic$model_submit$file_annotations_upload <- TRUE
+  }
+  if (!"hide_blanks" %in% ms_props_conf) {
+    conf$schematic$model_submit$hide_blanks <- FALSE
+  }
+
+  conf
+
+}
diff --git a/server.R b/server.R
@@ -141,7 +141,13 @@ shinyServer(function(input, output, session) {
       }, 1L)
       asset_views(all_asset_views[has_access == 1])
 
-      if (length(asset_views) == 0) stop("You do not have DOWNLOAD access to any supported Asset Views.")
+      if (length(asset_views) == 0) {
+        nx_report_error(
+          title = "You do not have DOWNLOAD access to any supported Asset Views",
+          message = "Contact your DCC admin for access"
+        )
+        hide(selector = "#NXReportButton") # hide OK button so users can't continue
+      }
       updateSelectInput(session, "dropdown_asset_view",
                         choices = asset_views()
       )
@@ -178,7 +184,7 @@ shinyServer(function(input, output, session) {
     tenant_config_react(tenants_config[tenants_config$synapse_asset_view == selected$master_asset_view(), ])
     if (dca_schematic_api == "offline") tenant_config_react(tenants_config[tenants_config$name == "DCA Demo", ])
 
-    dcc_config_react(read_json(
+    dcc_config_react(read_dca_config(
       file.path(config_dir, tenant_config_react()$config_location)
     ))