Updated documentation

NAMESPACE

@@ -8,6 +8,7 @@ export(MNR.DB.Geometries)
 export(MNR.DB.Organisations)
 export(MNR.DB.Users)
 export(MNR.GeoPlot)
+export(attachResourcePaths)
 export(resourcePrefix)
 export(use_mnr_ui)
 import(dplyr)

R/db.R

@@ -1,8 +1,13 @@
+#' MNR database queries base class
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB <- R6::R6Class(
   "MNR.DB",
   public = list(
+    #' @description Initialises the instance with a database client
+    #'    \link[AVSDevR.DBClient]{DBClient}
+    #' @param db_client <\link[AVSDevR.DBClient]{DBClient}> A DBClient instance
     initialize = function(db_client) {
       if (is.null(db_client) || !inherits(db_client, "DBClient")) {
         rlang::abort(
@@ -11,6 +16,10 @@ MNR.DB <- R6::R6Class(
       }
       private$db_client <- db_client
     },
+
+    #' @description Returns the current DBClient instance in use
+    #' @returns <\link[AVSDevR.DBClient]{DBClient}> The DBClient instance used
+    #'    by the class instance
     getDBClient = function() {
       private$db_client
     }

R/db_actuals.R

@@ -1,9 +1,14 @@
+#' MNR database queries for Actuals
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB.Actuals <- R6::R6Class(
   "MNR.DB.Actuals",
   inherit = MNR.DB,
   public = list(
+    #' @description Select the actuals for `refs`
+    #' @param refs <character> The MNR application noise source references
+    #' @returns A tibble of Actuals for `refs`
     selectActuals = function(refs) {
       cat("Actuals:\n")
       private$db_client$table("actual_activities") %>%
@@ -25,6 +30,11 @@ MNR.DB.Actuals <- R6::R6Class(
         dplyr::collect() %>%
         dplyr::glimpse()
     },
+
+    #' @description Returns the current actuals for a application or builds a
+    #'     default actuals list from the proposed locations if there are none
+    #' @param refs <character> The MNR application noise source references
+    #' @returns A tibble of the proposed actuals
     selectProposedActuals = function(refs) {
       partA <- private$db_client$table("proposed_activities") %>%
         dplyr::filter(is.null(deleted_at), is.null(cancelled_at)) %>%
@@ -91,9 +101,12 @@ MNR.DB.Actuals <- R6::R6Class(
       dplyr::bind_rows(partA, partB) %>%
         dplyr::glimpse()
     },
-    upsertActuals = function(actuals.sf, geometries) {
+
+    #' @description Upserts the actuals in the actuals.sf into the database
+    #' @param actuals.sf <sf> An sf table containing the new actuals
+    upsertActuals = function(actuals.sf) {
       if (length(actuals.sf) == 0 || (nrow(actuals.sf) == 0)) {
-        return(TRUE)
+        return(invisible(NULL))
       }
 
       self$deleteActuals(unique(actuals.sf$ref))
@@ -115,7 +128,7 @@ MNR.DB.Actuals <- R6::R6Class(
 
       if (nrow(actuals) == 0) {
         cat("## No actuals to insert\n")
-        return(TRUE)
+        return(invisible(NULL))
       }
 
       cat("## Inserting locations for actuals\n")
@@ -171,8 +184,11 @@ MNR.DB.Actuals <- R6::R6Class(
         "location_conservation_area_distances", sac_distance_rows
       )
 
-      TRUE
+      invisible(NULL)
     },
+
+    #' @description Deletes actuals for `refs`
+    #' @param refs <character> The MNR application noise source references
     deleteActuals = function(refs) {
       cat("## Deleting old actuals for", paste(refs, collapse = ","), "\n")
       old_references <- private$db_client$table("actual_activities") %>%
@@ -199,6 +215,8 @@ MNR.DB.Actuals <- R6::R6Class(
           "locations", old_locations %>% dplyr::rename(id = location_id)
         )
       }
+
+      invisible(NULL)
     }
   )
 )

R/db_applications.R

@@ -1,15 +1,26 @@
+#' MNR database queries for Applications
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB.Applications <- R6::R6Class(
   "MNR.DB.Applications",
   inherit = MNR.DB,
   public = list(
+    #' @description Initialises the instance with a database client from
+    #'    \link[AVSDevR.DBClient]{DBClient}
+    #' @param db_client <\link[AVSDevR.DBClient]{DBClient}> A DBClient instance
     initialize = function(db_client) {
       super$initialize(db_client)
       private$db_users <- MNR.DB.Users$new(db_client)
       private$db_orgs <- MNR.DB.Organisations$new(db_client)
     },
 
+    #' @description Fetch application details from a permissions query
+    #' @param perm_query A permissions_query object
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query details object (collect = FALSE) or a collected tibble
+    #'     of application details
     collectFromPermissions = function(perm_query, collect = TRUE) {
       # nolint end
       if (getOption("debug", FALSE)) {
@@ -22,6 +33,15 @@ MNR.DB.Applications <- R6::R6Class(
         private$db_client$collectOrReturn()
     },
 
+    #' @description Fetch applications details from the database without any
+    #'     filtering applied
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     getUnfilteredApplications = function(
       as_permissions = FALSE, collect = TRUE
     ) {
@@ -42,6 +62,16 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetch application details from the database with filtering
+    #'     for administration rights applied (assuming the user has the role)
+    #' @param user_id <integer> The user to check
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     getAdminApplications = function(
       user_id = -1, as_permissions = FALSE, collect = TRUE
     ) {
@@ -61,6 +91,16 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetch application details from the database filtered to
+    #'     those that are publicly available (ie. not draft or what-if)
+    #' @param user_id <integer> The user to check
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     getPublicOnlyApplications = function(
       user_id = -1, as_permissions = FALSE, collect = TRUE
     ) {
@@ -80,6 +120,17 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetch application details from the database filtered to
+    #'     those that are related to a user (via submitter, organisation or
+    #'     agent/recipient)
+    #' @param user_id <integer> The user to check
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     getRelatedApplications = function(
       user_id, as_permissions = FALSE, collect = TRUE
     ) {
@@ -102,6 +153,16 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetch application details from the database filtered to
+    #'     those that are related to a user's organisation
+    #' @param user_id <integer> The user to check
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     # nolint next: object_length_linter. Descriptive function name
     getUserOrganisationApplications = function(
       user_id, as_permissions = FALSE, collect = TRUE
@@ -123,6 +184,15 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetch a list of applications belonging to a user
+    #' @param user_id <integer> The user to check
+    #' @param as_permissions <logical> Returns a permissions_query if TRUE else
+    #'     the applications if FALSE
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A permissions_query object (as_permissions = TRUE,
+    #'     collect = FALSE) or query details object (as_permissions = FALSE,
+    #'     collect = FALSE) or a collected tibble of application details
     getUserApplications = function(
       user_id, as_permissions = FALSE, collect = TRUE
     ) {
@@ -145,6 +215,11 @@ MNR.DB.Applications <- R6::R6Class(
       self$collectFromPermissions(perm_qry, collect)
     },
 
+    #' @description Fetches the state of an application from the database
+    #' @param application_id <integer> The id of the application to check
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A list containing the state flags of an application
     getApplicationState = function(application_id, collect = TRUE) {
       if (length(application_id) == 0) {
         application_id <- -1

R/db_geometries.R

@@ -1,9 +1,17 @@
+#' MNR database queries for Gemoetries
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB.Geometries <- R6::R6Class(
   "MNR.DB.Geometries",
   inherit = MNR.DB,
   public = list(
+    #' @description Fetches the Oil & Gas block information from the database
+    #' @param with_geometries <logical> Also fetch the block geometries
+    #' @param ordered <logical> Sort the blocks (has an overhead)
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object or a collected sf of the blocks
     getBlocks = function(
       with_geometries = TRUE, ordered = FALSE, collect = TRUE
     ) {
@@ -45,6 +53,11 @@ MNR.DB.Geometries <- R6::R6Class(
       qry
     },
 
+    #' @description Retrieves the Conservation Areas from the database
+    #' @param with_geometries <logical> Also fetch the geometries
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object or a collected sf of the conservation areas
     getConservationAreas = function(with_geometries = TRUE, collect = TRUE) {
       qry <- private$db_client$table("conservation_areas")
 
@@ -60,6 +73,11 @@ MNR.DB.Geometries <- R6::R6Class(
       qry
     },
 
+    #' @description Retrieves the Marine Regions from the database
+    #' @param with_geometries <logical> Also fetch the geometries
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object or a collected sf of the marine regions
     getMarineRegions = function(with_geometries = TRUE, collect = TRUE) {
       qry <- private$db_client$table("marine_regions")
 
@@ -75,11 +93,22 @@ MNR.DB.Geometries <- R6::R6Class(
       qry
     },
 
+    #' @description Retrieves the block marine region map table from the
+    #'    database
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object or collected query of the block marine regions
     getBlockMarineRegions = function(collect = TRUE) {
       qry <- private$db_client$table("block_marine_regions")
       private$db_client$collectOrReturn(qry)
     },
 
+    #' @description Retrieves the block conservation areas map table from the
+    #'    database
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object or collected query of the block conservation
+    #'     areas
     # nolint next: object_length_linter. Descriptive function name required
     getBlockConservationAreaDistances = function(collect = TRUE) {
       qry <- private$db_client$table("block_conservation_area_distances")

R/db_organisations.R

@@ -1,9 +1,17 @@
+#' MNR database queries for Organsiations
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB.Organisations <- R6::R6Class(
   "MNR.DB.Organisations",
   inherit = MNR.DB,
   public = list(
+    #' @description Fetch the details of an organisation from the database
+    #' @param org_id <integer> The id of the organisation to fetch
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A query object for an organsation (collect = FALSE) or a
+    #'     tibble with the organisation details
     getOrganisation = function(org_id, collect = TRUE) {
       private$db_client$table("organisations") %>%
         dplyr::filter(flag_approved == TRUE) %>%
@@ -11,6 +19,14 @@ MNR.DB.Organisations <- R6::R6Class(
         private$db_client$collectOrReturn()
     },
 
+    #' @description Fetch the details of all organisations from the database
+    #' @param as_int <logical> Return only the ids (TRUE)
+    #' @param name_only <logical> Return only the name (TRUE)
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns The organisation ids if as_int is TRUE, the organisation names
+    #'    if as_int is FALSE and name_only is TRUE, else the organisations or an
+    #'    uncollected query object
     getAllOrganisations = function(
       as_int = FALSE, name_only = TRUE, collect = TRUE
     ) {
@@ -29,6 +45,9 @@ MNR.DB.Organisations <- R6::R6Class(
       }
     },
 
+    #' @description Check if an organisation is a regulator
+    #' @param org_id <integer> The id of the organisation to check
+    #' @returns TRUE if the organisation is a regulator
     isRegulator = function(org_id) {
       private$db_client$table("organisations") %>%
         dplyr::filter(flag_approved == TRUE) %>%
@@ -39,6 +58,14 @@ MNR.DB.Organisations <- R6::R6Class(
         magrittr::is_greater_than(0)
     },
 
+    #' @description Fetch the details of all the regulators from the database
+    #' @param as_int <logical> Return only the ids (TRUE)
+    #' @param name_only <logical> Return only the name (TRUE)
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns The regulator ids if as_int is TRUE, the regulator names if
+    #'    as_int is FALSE and name_only is TRUE, else the regulator or an
+    #'    uncollected query object
     getRegulators = function(as_int = FALSE, name_only = TRUE, collect = TRUE) {
       qry <- private$db_client$table("organisations") %>%
         dplyr::filter(flag_approved == TRUE) %>%
@@ -56,6 +83,12 @@ MNR.DB.Organisations <- R6::R6Class(
       }
     },
 
+    #' @description Fetch the members of an organisation
+    #' @param org_name <character> The name of the organisation to check
+    #' @param org_id <integer> The id of the organisation to check
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns A tibble of the organisation members or an uncollected query
     getOrganisationMembers = function(
       org_name = "", org_id = -1, collect = TRUE
     ) {
@@ -80,45 +113,25 @@ MNR.DB.Organisations <- R6::R6Class(
         private$db_client$collectOrReturn()
     },
 
-    #' @depricated
+    #' @description Check if user's organisation is an agent for another
-    getUsersFromOrg = function(org_name = "", org_id = -1, collect = TRUE) {
+    #'    organisation
-      .Deprecated(new = "getOrganisationMembers")
+    #' @param org_id <integer> The id of the organisation to check
-
+    #' @returns TRUE if the user's organisation is an agent
-      private$db_client$table("users") %>%
+    isAgent = function(org_id) {
-        dplyr::filter(flag_enabled == TRUE) %>%
+      private$db_client$table("organisation_agents") %>%
-        dplyr::filter(flag_verified == TRUE) %>%
-        dplyr::mutate(known_as = paste(first_name, last_name)) %>%
-        dplyr::left_join(
-          private$db_client$table("organisation_members") %>%
-            dplyr::filter(flag_approved == TRUE) %>%
-            dplyr::select(user_id, organisation_id),
-          by = c(id = "user_id")
-        ) %>%
-        dplyr::inner_join(
-          private$db_client$table("organisations") %>%
-            dplyr::filter(flag_approved == TRUE) %>%
-            dplyr::filter((id == !!org_id) | (name == !!org_name)) %>%
-            dplyr::select(id),
-          by = c(organisation_id = "id")
-        ) %>%
-        dplyr::select(-organisation_id) %>%
-        private$db_client$collectOrReturn()
-    },
-
-    isAgent = function(user_id) {
-      private$db_client$table("organisation_members") %>%
         dplyr::filter(flag_approved == TRUE) %>%
-        dplyr::filter(user_id == !!user_id) %>%
+        dplyr::filter(agent_id == !!org_id) %>%
-        dplyr::inner_join(
-          private$db_client$table("organisation_agents") %>%
-            dplyr::filter(flag_approved == TRUE),
-          by = c(organisation_id = "agent_id")
-        ) %>%
         dplyr::count() %>%
         dplyr::pull() %>%
         magrittr::is_greater_than(0)
     },
 
+    #' @description Fetch the agents of an organisation
+    #' @param org_id <integer> The id of the organisation to check
+    #' @param as_int <logical> Return only the id (TRUE)
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns An uncollected query object or a tibble of agents
     getOrganisationAgents = function(org_id, as_int = FALSE, collect = TRUE) {
       qry <- private$db_client$table("organisation_agents") %>%
         dplyr::filter(flag_approved == TRUE) %>%
@@ -140,6 +153,12 @@ MNR.DB.Organisations <- R6::R6Class(
       }
     },
 
+    #' @description Fetch the recipients of an organisation
+    #' @param agent_id <integer> The id of the organisation (agent) to check
+    #' @param as_int <logical> Return only the id (TRUE)
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns An uncollected query object or a tibble of recipients
     getAgentRecipients = function(agent_id, as_int = FALSE, collect = TRUE) {
       qry <- private$db_client$table("organisation_agents") %>%
         dplyr::filter(flag_approved == TRUE) %>%
@@ -161,94 +180,15 @@ MNR.DB.Organisations <- R6::R6Class(
       }
     },
 
-    #' @depricated
+    #' @description Fetch the organisation of a user
-    getAgentForOrganisations = function(
+    #' @param user_id <integer> The id of the user to fetch the organisation of
-      org_ids, as_int = FALSE, name_only = TRUE, collect = TRUE
+    #' @param as_int <logical> Return only the id (TRUE)
-    ) {
+    #' @param name_only <logical> Return only the name (TRUE)
-      .Deprecated(new = "getOrganisationAgents")
+    #' @param collect <logical> Collect the query before returning (TRUE) or
-
+    #'     return the built query object (FALSE)
-      qry <- private$db_client$table("organisations") %>%
+    #' @returns The organisation id if as_int is TRUE, the organisation name if
-        dplyr::filter(flag_approved == TRUE) %>%
+    #'    as_int is FALSE and name_only is TRUE, else the organisation or an
-        dplyr::inner_join(
+    #'    uncollected query object
-          private$db_client$table("organisation_agents") %>%
-            dplyr::filter(flag_approved == TRUE) %>%
-            dplyr::filter(organisation_id %in% !!org_ids) %>%
-            dplyr::select(agent_id) %>%
-            dplyr::collapse(),
-          by = c(id = "agent_id")
-        ) %>%
-        dplyr::distinct()
-
-      if (as_int) {
-        qry %>%
-          dplyr::pull(id)
-      } else if (name_only) {
-        qry %>%
-          dplyr::pull(name)
-      } else {
-        qry %>%
-          private$db_client$collectOrReturn()
-      }
-    },
-
-    #' @depricated
-    getRecipientOrganisations = function(
-      org_id, as_int = FALSE, name_only = TRUE, collect = TRUE
-    ) {
-      .Deprecated(new = "getAgentRecipients")
-
-      qry <- private$db_client$table("organisations") %>%
-        dplyr::filter(flag_approved == TRUE) %>%
-        dplyr::inner_join(
-          private$db_client$table("organisation_agents") %>%
-            dplyr::filter(flag_approved == TRUE) %>%
-            dplyr::filter(agent_id %in% !!org_id) %>%
-            dplyr::select(organisation_id) %>%
-            dplyr::collapse(),
-          by = c(id = "organisation_id")
-        ) %>%
-        dplyr::distinct()
-
-      if (as_int) {
-        qry %>%
-          dplyr::pull(id)
-      } else if (name_only) {
-        qry %>%
-          dplyr::pull(name)
-      } else {
-        qry %>%
-          private$db_client$collectOrReturn()
-      }
-    },
-
-    #' @depricated
-    getUserOrgs = function(
-      user_id, as_int = TRUE, name_only = TRUE, collect = TRUE
-    ) {
-      .Deprecated(new = "getUserOrganisation")
-
-      qry <- private$db_client$table("organisations") %>%
-        dplyr::filter(flag_approved == TRUE) %>%
-        dplyr::left_join(
-          private$db_client$table("organisation_members") %>%
-            dplyr::filter(flag_approved == TRUE) %>%
-            dplyr::select(user_id, organisation_id),
-          by = c(id = "organisation_id")
-        ) %>%
-        dplyr::filter(user_id == !!user_id)
-
-      if (as_int) {
-        qry %>%
-          dplyr::pull(id)
-      } else if (name_only) {
-        qry %>%
-          dplyr::pull(name)
-      } else {
-        qry %>%
-          private$db_client$collectOrReturn()
-      }
-    },
-
     getUserOrganisation = function(
       user_id, as_int = TRUE, name_only = TRUE, collect = TRUE
     ) {

R/db_users.R

@@ -1,9 +1,17 @@
+#' MNR database queries for Users
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.DB.Users <- R6::R6Class(
   "MNR.DB.Users",
   inherit = MNR.DB,
   public = list(
+    #' @description Initialises the instance with a database client from
+    #'    \link[AVSDevR.DBClient]{DBClient}
+    #' @param db_client <\link[AVSDevR.DBClient]{DBClient}> A DBClient instance
+    #' @param admin_role_slug <character> The slug of the application
+    #'    administrator role within UserFrosting
+    #'    (Defaults to: "application-admin")
     initialize = function(db_client, admin_role_slug = NULL) {
       super$initialize(db_client)
       private$db_uf <- AVSDevR.UserFrosting::UFDatabase$new(db_client)
@@ -13,16 +21,34 @@ MNR.DB.Users <- R6::R6Class(
       }
     },
 
+    #' @description Get user information from the database
+    #' @param user_id <integer> The user id to fetch
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns <list> Details of the user denoted by user_id
     getUser = function(user_id, collect = TRUE) {
       private$db_uf$getUser(user_id, collect)
     },
+
+    #' @description Get user name from the database
+    #' @param user_id <integer> The user id to fetch
+    #' @returns <character> The user's name
     getUserName = function(user_id) {
       private$db_uf$getUserName(user_id)
     },
+
+    #' @description Get user roles from the database
+    #' @param user_id <integer> The user id to fetch
+    #' @param collect <logical> Collect the query before returning (TRUE) or
+    #'     return the built query object (FALSE)
+    #' @returns <character> A list of user roles
     getUserRoles = function(user_id, collect = TRUE) {
       private$db_uf$getUserRoles(user_id, collect)
     },
 
+    #' @description Check if a user is an application administrator
+    #' @param user_id <integer> The user id to fetch
+    #' @returns <logical> TRUE if the user is an administrator
     isApplicationsAdmin = function(user_id) {
       self$getUserRoles(user_id, collect = FALSE) %>%
         dplyr::filter(slug == !!private$admin_role_slug) %>%

R/geoPlot.R

@@ -1,14 +1,32 @@
+mnr_geoplot_env <- new.env()
+
+#' MNR GIS plot base map generator
+#'
+#' Base layers are loaded and cached on first call to each of the boot methods.
+#'
 #' @export
 # nolint next: object_name_linter. R6Class
 MNR.GeoPlot <- R6::R6Class(
   "MNR.GeoPlot",
   public = list(
+    #' @description Initialises the object by building the grid lines
     initialize = function() {
       private$bootGridLines()
     },
 
+    #' @description Loads the JNCC layers required from file for the base map
     bootLayers = function() {
-      private$boundaryIoM <- sf::st_read(
+      if (exists("layers_loaded", envir = mnr_geoplot_env)) {
+        private$boundaryIoM <- get("boundaryIoM", envir = mnr_geoplot_env)
+        private$boundaryMSFD <- get("boundaryMSFD", envir = mnr_geoplot_env)
+        private$boundaryUKCS <- get("boundaryUKCS", envir = mnr_geoplot_env)
+        private$boundaryUKTerritorial <- get(
+          "boundaryUKTerritorial", envir = mnr_geoplot_env
+        )
+        return(invisible(NULL))
+      }
+
+      boundaryIoM <- sf::st_read(
         file.path(
           system.file(package = "AVSDevR.MarineNoiseRegistry"),
           "layers",
@@ -16,7 +34,7 @@ MNR.GeoPlot <- R6::R6Class(
         ),
         quiet = TRUE
       )
-      private$boundaryMSFD <- sf::st_read(
+      boundaryMSFD <- sf::st_read(
         file.path(
           system.file(package = "AVSDevR.MarineNoiseRegistry"),
           "layers",
@@ -24,7 +42,7 @@ MNR.GeoPlot <- R6::R6Class(
         ),
         quiet = TRUE
       )
-      private$boundaryUKCS <- sf::st_read(
+      boundaryUKCS <- sf::st_read(
         file.path(
           system.file(package = "AVSDevR.MarineNoiseRegistry"),
           "layers",
@@ -32,7 +50,7 @@ MNR.GeoPlot <- R6::R6Class(
         ),
         quiet = TRUE
       )
-      private$boundaryUKTerritorial <- sf::st_read(
+      boundaryUKTerritorial <- sf::st_read(
         file.path(
           system.file(package = "AVSDevR.MarineNoiseRegistry"),
           "layers",
@@ -40,15 +58,34 @@ MNR.GeoPlot <- R6::R6Class(
         ),
         quiet = TRUE
       )
+
+      assign("boundaryIoM", boundaryIoM, envir = mnr_geoplot_env)
+      assign("boundaryMSFD", boundaryMSFD, envir = mnr_geoplot_env)
+      assign("boundaryUKCS", boundaryUKCS, envir = mnr_geoplot_env)
+      assign(
+        "boundaryUKTerritorial", boundaryUKTerritorial, envir = mnr_geoplot_env
+      )
+      assign("layers_loaded", TRUE, envir = mnr_geoplot_env)
+
+      invisible(self$bootLayers())
     },
 
+    #' @description Loads the Oil & Gas quadrants from file for the base map
     bootQuadrants = function() {
+      if (exists("quadrants_loaded", envir = mnr_geoplot_env)) {
+        private$quadrants <- get("quadrants", envir = mnr_geoplot_env)
+        private$quadrant_annotations <- get(
+          "quadrant_annotations", envir = mnr_geoplot_env
+        )
+        return(invisible(NULL))
+      }
+
       old_opts <- options(sf_use_s2 = FALSE)
       on.exit({
         options(old_opts)
       })
 
-      private$quadrants <- sf::st_read(
+      quadrants <- sf::st_read(
         file.path(
           system.file(package = "AVSDevR.MarineNoiseRegistry"),
           "layers",
@@ -56,26 +93,47 @@ MNR.GeoPlot <- R6::R6Class(
         ),
         quiet = TRUE
       )
-      private$quadrant_annotations <- suppressWarnings({
+      quadrant_annotations <- suppressWarnings({
-        private$quadrants %>%
+        quadrants %>%
           dplyr::select(quadrnt) %>%
           sf::st_centroid()
       })
+
+      assign("quadrants", quadrants, envir = mnr_geoplot_env)
+      assign(
+        "quadrant_annotations", quadrant_annotations, envir = mnr_geoplot_env
+      )
+      assign("quadrants_loaded", TRUE, envir = mnr_geoplot_env)
+
+      invisible(self$bootQuadrants())
     },
 
+    #' @description Loads the Conservation Areas from the database for the base
+    #'    map.
+    #' @param db_client <\link[AVSDevR.DBClient]{DBClient}> A DBClient instance
     bootConservationAreas = function(db_client) {
+      if (exists("conservation_areas_loaded", envir = mnr_geoplot_env)) {
+        private$conservation_areas <- get(
+          "conservation_areas", envir = mnr_geoplot_env
+        )
+        private$conservation_area_colours <- get(
+          "conservation_area_colours", envir = mnr_geoplot_env
+        )
+        return(invisible(NULL))
+      }
+
       old_opts <- options(sf_use_s2 = FALSE)
       on.exit({
         options(old_opts)
       })
 
-      private$conservation_areas <- db_client$table("conservation_areas") %>%
+      conservation_areas <- db_client$table("conservation_areas") %>%
         dplyr::select(name, season, geom) %>%
         db_client$collectGeometries() %>%
         sf::st_sf() %>%
         sf::st_cast("MULTIPOLYGON")
 
-      colour_palette <- private$conservation_areas %>%
+      colour_palette <- conservation_areas %>%
         dplyr::mutate(
           colour = sapply(season, function(s) {
             switch(
@@ -88,13 +146,31 @@ MNR.GeoPlot <- R6::R6Class(
         ) %>%
         dplyr::pull(colour)
 
-      private$conservation_area_colours <- private$conservation_areas %>%
+      conservation_area_colours <- conservation_areas %>%
         sf::st_coordinates() %>%
         tibble::as_tibble() %>%
         dplyr::mutate(colour = colour_palette[L3]) %>%
         dplyr::pull(colour)
+
+      assign("conservation_areas", conservation_areas, envir = mnr_geoplot_env)
+      assign(
+        "conservation_area_colours", conservation_area_colours,
+        envir = mnr_geoplot_env
+      )
+      assign("conservation_areas", TRUE, envir = mnr_geoplot_env)
+
+      invisible(self$bootConservationAreas())
     },
 
+    #' @description Generates a base plotly map with optional layers included
+    #' @param ... Options to call plotly::plot_ly with
+    #' @param with_jncc_layers <logical> Includes the JNCC base layers if TRUE
+    #'    (call obj$bootLayers() first)
+    #' @param with_quadrants <logical> Includes the Oil & Gas Quadrants if TRUE
+    #'    (call obj$bootQuadrants() first)
+    #' @param with_conservation_areas <logical> Includes the Conservation Areas
+    #'     if TRUE (call obj$bootConservationAreas() first)
+    #' @returns A plolty object base map
     makeBasePlot = function(
       ..., with_jncc_layers = TRUE, with_quadrants = FALSE,
       with_conservation_areas = FALSE
@@ -151,6 +227,16 @@ MNR.GeoPlot <- R6::R6Class(
         )
     },
 
+    #' @description Bounds a mapbox map to a specific area and zoom
+    #' @param p A plotly mapbox map object
+    #' @param c_lat <numeric> Center latitude
+    #' @param c_lon <numeric> Center longitude
+    #' @param zoom <numeric> A mapbox zoom level
+    #' @param xmin <numeric> Minimum longitude to bound with
+    #' @param ymin <numeric> Minimum latitude to bound with
+    #' @param xmax <numeric> Maximum longitude to bound with
+    #' @param ymax <numeric> Maximum latitude to bound with
+    #' @returns The plotly object
     boundMap = function(
       p, c_lat = 56, c_lon = -5.5, zoom = 3.5, xmin = -25, ymin = 45, xmax = 5,
       ymax = 65
@@ -186,6 +272,13 @@ MNR.GeoPlot <- R6::R6Class(
 
 
     bootGridLines = function() {
+      if (exists("gridlines_loaded", envir = mnr_geoplot_env)) {
+        private$major_lines <- get("major_lines", envir = mnr_geoplot_env)
+        private$minor_lines <- get("minor_lines", envir = mnr_geoplot_env)
+        private$zero_lines <- get("zero_lines", envir = mnr_geoplot_env)
+        return(invisible(NULL))
+      }
+
       old_opts <- options(sf_use_s2 = FALSE)
       on.exit({
         options(old_opts)
@@ -215,25 +308,31 @@ MNR.GeoPlot <- R6::R6Class(
           )
       }
       suppressMessages({
-        private$major_lines <- points %>%
+        major_lines <- points %>%
-          dplyr::filter(is_major) %>%
+            dplyr::filter(is_major) %>%
-          sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
+            sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
-          dplyr::group_by(grp) %>%
+            dplyr::group_by(grp) %>%
-          dplyr::summarise() %>%
+            dplyr::summarise() %>%
-          sf::st_cast("LINESTRING")
+            sf::st_cast("LINESTRING")
-        private$minor_lines <- points %>%
+        minor_lines <- points %>%
-          dplyr::filter(!is_major) %>%
+            dplyr::filter(!is_major) %>%
-          sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
+            sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
-          dplyr::group_by(grp) %>%
+            dplyr::group_by(grp) %>%
-          dplyr::summarise() %>%
+            dplyr::summarise() %>%
-          sf::st_cast("LINESTRING")
+            sf::st_cast("LINESTRING")
-        private$zero_lines <- points %>%
+        zero_lines <- points %>%
-          dplyr::filter((lat == 0) | (lon == 0)) %>%
+            dplyr::filter((lat == 0) | (lon == 0)) %>%
-          sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
+            sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) %>%
-          dplyr::group_by(grp) %>%
+            dplyr::group_by(grp) %>%
-          dplyr::summarise() %>%
+            dplyr::summarise() %>%
-          sf::st_cast("LINESTRING")
+            sf::st_cast("LINESTRING")
+        assign("major_lines", major_lines, envir = mnr_geoplot_env)
+        assign("minor_lines", minor_lines, envir = mnr_geoplot_env)
+        assign("zero_lines", zero_lines, envir = mnr_geoplot_env)
       })
+
+      assign("gridlines_loaded", TRUE, envir = mnr_geoplot_env)
+      private$bootGridLines()
     },
 
     addGridLines = function(p) {

R/use_mnr_ui.R

@@ -1,3 +1,5 @@
+#' Attaches the MNR stylesheets and scripts to the UI
+#'
 #' @export
 use_mnr_ui <- function() {
   attachResourcePaths()
@@ -21,11 +23,16 @@ use_mnr_ui <- function() {
   )
 }
 
+#' Provides the resource path for MNR specific files
+#'
 #' @export
 resourcePrefix <- function() {
   paste0("avsdev_mnr_", utils::packageVersion("AVSDevR.MarineNoiseRegistry"))
 }
 
+#' Attaches the MNR resource path to Shiny if not already attached
+#'
+#' @export
 attachResourcePaths <- function() {
   if (!(resourcePrefix() %in% names(shiny::resourcePaths()))) {
     shiny::addResourcePath(
@@ -33,4 +40,5 @@ attachResourcePaths <- function() {
       system.file("www", package = "AVSDevR.MarineNoiseRegistry")
     )
   }
+  invisible(NULL)
 }

man/MNR.DB.Actuals.Rd

@@ -0,0 +1,123 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db_actuals.R
+\name{MNR.DB.Actuals}
+\alias{MNR.DB.Actuals}
+\title{MNR database queries for Actuals}
+\value{
+A tibble of Actuals for \code{refs}
+
+A tibble of the proposed actuals
+}
+\description{
+MNR database queries for Actuals
+
+MNR database queries for Actuals
+}
+\section{Super class}{
+\code{\link[AVSDevR.MarineNoiseRegistry:MNR.DB]{AVSDevR.MarineNoiseRegistry::MNR.DB}} -> \code{MNR.DB.Actuals}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB.Actuals-selectActuals}{\code{MNR.DB.Actuals$selectActuals()}}
+\item \href{#method-MNR.DB.Actuals-selectProposedActuals}{\code{MNR.DB.Actuals$selectProposedActuals()}}
+\item \href{#method-MNR.DB.Actuals-upsertActuals}{\code{MNR.DB.Actuals$upsertActuals()}}
+\item \href{#method-MNR.DB.Actuals-deleteActuals}{\code{MNR.DB.Actuals$deleteActuals()}}
+\item \href{#method-MNR.DB.Actuals-clone}{\code{MNR.DB.Actuals$clone()}}
+}
+}
+\if{html}{\out{
+<details open><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="getDBClient"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-getDBClient'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$getDBClient()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="initialize"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-initialize'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$initialize()</code></a></span></li>
+</ul>
+</details>
+}}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Actuals-selectActuals"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Actuals-selectActuals}{}}}
+\subsection{Method \code{selectActuals()}}{
+Select the actuals for \code{refs}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Actuals$selectActuals(refs)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{refs}}{\if{html}{\out{<character>}} The MNR application noise source references}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Actuals-selectProposedActuals"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Actuals-selectProposedActuals}{}}}
+\subsection{Method \code{selectProposedActuals()}}{
+Returns the current actuals for a application or builds a
+default actuals list from the proposed locations if there are none
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Actuals$selectProposedActuals(refs)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{refs}}{\if{html}{\out{<character>}} The MNR application noise source references}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Actuals-upsertActuals"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Actuals-upsertActuals}{}}}
+\subsection{Method \code{upsertActuals()}}{
+Upserts the actuals in the actuals.sf into the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Actuals$upsertActuals(actuals.sf)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{actuals.sf}}{\if{html}{\out{<sf>}} An sf table containing the new actuals}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Actuals-deleteActuals"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Actuals-deleteActuals}{}}}
+\subsection{Method \code{deleteActuals()}}{
+Deletes actuals for \code{refs}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Actuals$deleteActuals(refs)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{refs}}{\if{html}{\out{<character>}} The MNR application noise source references}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Actuals-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Actuals-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Actuals$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.DB.Applications.Rd

@@ -0,0 +1,306 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db_applications.R
+\name{MNR.DB.Applications}
+\alias{MNR.DB.Applications}
+\title{MNR database queries for Applications}
+\value{
+A query details object (collect = FALSE) or a collected tibble
+of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A permissions_query object (as_permissions = TRUE,
+collect = FALSE) or query details object (as_permissions = FALSE,
+collect = FALSE) or a collected tibble of application details
+
+A list containing the state flags of an application
+}
+\description{
+MNR database queries for Applications
+
+MNR database queries for Applications
+}
+\section{Super class}{
+\code{\link[AVSDevR.MarineNoiseRegistry:MNR.DB]{AVSDevR.MarineNoiseRegistry::MNR.DB}} -> \code{MNR.DB.Applications}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB.Applications-new}{\code{MNR.DB.Applications$new()}}
+\item \href{#method-MNR.DB.Applications-collectFromPermissions}{\code{MNR.DB.Applications$collectFromPermissions()}}
+\item \href{#method-MNR.DB.Applications-getUnfilteredApplications}{\code{MNR.DB.Applications$getUnfilteredApplications()}}
+\item \href{#method-MNR.DB.Applications-getAdminApplications}{\code{MNR.DB.Applications$getAdminApplications()}}
+\item \href{#method-MNR.DB.Applications-getPublicOnlyApplications}{\code{MNR.DB.Applications$getPublicOnlyApplications()}}
+\item \href{#method-MNR.DB.Applications-getRelatedApplications}{\code{MNR.DB.Applications$getRelatedApplications()}}
+\item \href{#method-MNR.DB.Applications-getUserOrganisationApplications}{\code{MNR.DB.Applications$getUserOrganisationApplications()}}
+\item \href{#method-MNR.DB.Applications-getUserApplications}{\code{MNR.DB.Applications$getUserApplications()}}
+\item \href{#method-MNR.DB.Applications-getApplicationState}{\code{MNR.DB.Applications$getApplicationState()}}
+\item \href{#method-MNR.DB.Applications-clone}{\code{MNR.DB.Applications$clone()}}
+}
+}
+\if{html}{\out{
+<details open><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="getDBClient"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-getDBClient'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$getDBClient()</code></a></span></li>
+</ul>
+</details>
+}}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-new"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-new}{}}}
+\subsection{Method \code{new()}}{
+Initialises the instance with a database client from
+\link[AVSDevR.DBClient]{DBClient}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$new(db_client)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{db_client}}{<\link[AVSDevR.DBClient]{DBClient}> A DBClient instance}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-collectFromPermissions"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-collectFromPermissions}{}}}
+\subsection{Method \code{collectFromPermissions()}}{
+Fetch application details from a permissions query
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$collectFromPermissions(perm_query, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{perm_query}}{A permissions_query object}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getUnfilteredApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getUnfilteredApplications}{}}}
+\subsection{Method \code{getUnfilteredApplications()}}{
+Fetch applications details from the database without any
+filtering applied
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getUnfilteredApplications(
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getAdminApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getAdminApplications}{}}}
+\subsection{Method \code{getAdminApplications()}}{
+Fetch application details from the database with filtering
+for administration rights applied (assuming the user has the role)
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getAdminApplications(
+  user_id = -1,
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user to check}
+
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getPublicOnlyApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getPublicOnlyApplications}{}}}
+\subsection{Method \code{getPublicOnlyApplications()}}{
+Fetch application details from the database filtered to
+those that are publicly available (ie. not draft or what-if)
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getPublicOnlyApplications(
+  user_id = -1,
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user to check}
+
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getRelatedApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getRelatedApplications}{}}}
+\subsection{Method \code{getRelatedApplications()}}{
+Fetch application details from the database filtered to
+those that are related to a user (via submitter, organisation or
+agent/recipient)
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getRelatedApplications(
+  user_id,
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user to check}
+
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getUserOrganisationApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getUserOrganisationApplications}{}}}
+\subsection{Method \code{getUserOrganisationApplications()}}{
+Fetch application details from the database filtered to
+those that are related to a user's organisation
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getUserOrganisationApplications(
+  user_id,
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user to check}
+
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getUserApplications"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getUserApplications}{}}}
+\subsection{Method \code{getUserApplications()}}{
+Fetch a list of applications belonging to a user
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getUserApplications(
+  user_id,
+  as_permissions = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user to check}
+
+\item{\code{as_permissions}}{\if{html}{\out{<logical>}} Returns a permissions_query if TRUE else
+the applications if FALSE}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-getApplicationState"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-getApplicationState}{}}}
+\subsection{Method \code{getApplicationState()}}{
+Fetches the state of an application from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$getApplicationState(application_id, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{application_id}}{\if{html}{\out{<integer>}} The id of the application to check}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Applications-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Applications-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Applications$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.DB.Geometries.Rd

@@ -0,0 +1,166 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db_geometries.R
+\name{MNR.DB.Geometries}
+\alias{MNR.DB.Geometries}
+\title{MNR database queries for Gemoetries}
+\value{
+A query object or a collected sf of the blocks
+
+A query object or a collected sf of the conservation areas
+
+A query object or a collected sf of the marine regions
+
+A query object or collected query of the block marine regions
+
+A query object or collected query of the block conservation
+areas
+}
+\description{
+MNR database queries for Gemoetries
+
+MNR database queries for Gemoetries
+}
+\section{Super class}{
+\code{\link[AVSDevR.MarineNoiseRegistry:MNR.DB]{AVSDevR.MarineNoiseRegistry::MNR.DB}} -> \code{MNR.DB.Geometries}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB.Geometries-getBlocks}{\code{MNR.DB.Geometries$getBlocks()}}
+\item \href{#method-MNR.DB.Geometries-getConservationAreas}{\code{MNR.DB.Geometries$getConservationAreas()}}
+\item \href{#method-MNR.DB.Geometries-getMarineRegions}{\code{MNR.DB.Geometries$getMarineRegions()}}
+\item \href{#method-MNR.DB.Geometries-getBlockMarineRegions}{\code{MNR.DB.Geometries$getBlockMarineRegions()}}
+\item \href{#method-MNR.DB.Geometries-getBlockConservationAreaDistances}{\code{MNR.DB.Geometries$getBlockConservationAreaDistances()}}
+\item \href{#method-MNR.DB.Geometries-clone}{\code{MNR.DB.Geometries$clone()}}
+}
+}
+\if{html}{\out{
+<details open><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="getDBClient"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-getDBClient'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$getDBClient()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="initialize"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-initialize'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$initialize()</code></a></span></li>
+</ul>
+</details>
+}}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-getBlocks"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-getBlocks}{}}}
+\subsection{Method \code{getBlocks()}}{
+Fetches the Oil & Gas block information from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$getBlocks(
+  with_geometries = TRUE,
+  ordered = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{with_geometries}}{\if{html}{\out{<logical>}} Also fetch the block geometries}
+
+\item{\code{ordered}}{\if{html}{\out{<logical>}} Sort the blocks (has an overhead)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-getConservationAreas"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-getConservationAreas}{}}}
+\subsection{Method \code{getConservationAreas()}}{
+Retrieves the Conservation Areas from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$getConservationAreas(with_geometries = TRUE, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{with_geometries}}{\if{html}{\out{<logical>}} Also fetch the geometries}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-getMarineRegions"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-getMarineRegions}{}}}
+\subsection{Method \code{getMarineRegions()}}{
+Retrieves the Marine Regions from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$getMarineRegions(with_geometries = TRUE, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{with_geometries}}{\if{html}{\out{<logical>}} Also fetch the geometries}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-getBlockMarineRegions"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-getBlockMarineRegions}{}}}
+\subsection{Method \code{getBlockMarineRegions()}}{
+Retrieves the block marine region map table from the
+database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$getBlockMarineRegions(collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-getBlockConservationAreaDistances"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-getBlockConservationAreaDistances}{}}}
+\subsection{Method \code{getBlockConservationAreaDistances()}}{
+Retrieves the block conservation areas map table from the
+database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$getBlockConservationAreaDistances(collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Geometries-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Geometries-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Geometries$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.DB.Organisations.Rd

@@ -0,0 +1,294 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db_organisations.R
+\name{MNR.DB.Organisations}
+\alias{MNR.DB.Organisations}
+\title{MNR database queries for Organsiations}
+\value{
+A query object for an organsation (collect = FALSE) or a
+tibble with the organisation details
+
+The organisation ids if as_int is TRUE, the organisation names
+if as_int is FALSE and name_only is TRUE, else the organisations or an
+uncollected query object
+
+TRUE if the organisation is a regulator
+
+The regulator ids if as_int is TRUE, the regulator names if
+as_int is FALSE and name_only is TRUE, else the regulator or an
+uncollected query object
+
+A tibble of the organisation members or an uncollected query
+
+TRUE if the user's organisation is an agent
+
+An uncollected query object or a tibble of agents
+
+An uncollected query object or a tibble of recipients
+
+The organisation id if as_int is TRUE, the organisation name if
+as_int is FALSE and name_only is TRUE, else the organisation or an
+uncollected query object
+}
+\description{
+MNR database queries for Organsiations
+
+MNR database queries for Organsiations
+}
+\section{Super class}{
+\code{\link[AVSDevR.MarineNoiseRegistry:MNR.DB]{AVSDevR.MarineNoiseRegistry::MNR.DB}} -> \code{MNR.DB.Organisations}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB.Organisations-getOrganisation}{\code{MNR.DB.Organisations$getOrganisation()}}
+\item \href{#method-MNR.DB.Organisations-getAllOrganisations}{\code{MNR.DB.Organisations$getAllOrganisations()}}
+\item \href{#method-MNR.DB.Organisations-isRegulator}{\code{MNR.DB.Organisations$isRegulator()}}
+\item \href{#method-MNR.DB.Organisations-getRegulators}{\code{MNR.DB.Organisations$getRegulators()}}
+\item \href{#method-MNR.DB.Organisations-getOrganisationMembers}{\code{MNR.DB.Organisations$getOrganisationMembers()}}
+\item \href{#method-MNR.DB.Organisations-isAgent}{\code{MNR.DB.Organisations$isAgent()}}
+\item \href{#method-MNR.DB.Organisations-getOrganisationAgents}{\code{MNR.DB.Organisations$getOrganisationAgents()}}
+\item \href{#method-MNR.DB.Organisations-getAgentRecipients}{\code{MNR.DB.Organisations$getAgentRecipients()}}
+\item \href{#method-MNR.DB.Organisations-getUserOrganisation}{\code{MNR.DB.Organisations$getUserOrganisation()}}
+\item \href{#method-MNR.DB.Organisations-clone}{\code{MNR.DB.Organisations$clone()}}
+}
+}
+\if{html}{\out{
+<details open><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="getDBClient"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-getDBClient'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$getDBClient()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="initialize"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-initialize'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$initialize()</code></a></span></li>
+</ul>
+</details>
+}}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getOrganisation"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getOrganisation}{}}}
+\subsection{Method \code{getOrganisation()}}{
+Fetch the details of an organisation from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getOrganisation(org_id, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{org_id}}{\if{html}{\out{<integer>}} The id of the organisation to fetch}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getAllOrganisations"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getAllOrganisations}{}}}
+\subsection{Method \code{getAllOrganisations()}}{
+Fetch the details of all organisations from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getAllOrganisations(
+  as_int = FALSE,
+  name_only = TRUE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{as_int}}{\if{html}{\out{<logical>}} Return only the ids (TRUE)}
+
+\item{\code{name_only}}{\if{html}{\out{<logical>}} Return only the name (TRUE)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-isRegulator"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-isRegulator}{}}}
+\subsection{Method \code{isRegulator()}}{
+Check if an organisation is a regulator
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$isRegulator(org_id)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{org_id}}{\if{html}{\out{<integer>}} The id of the organisation to check}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getRegulators"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getRegulators}{}}}
+\subsection{Method \code{getRegulators()}}{
+Fetch the details of all the regulators from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getRegulators(
+  as_int = FALSE,
+  name_only = TRUE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{as_int}}{\if{html}{\out{<logical>}} Return only the ids (TRUE)}
+
+\item{\code{name_only}}{\if{html}{\out{<logical>}} Return only the name (TRUE)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getOrganisationMembers"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getOrganisationMembers}{}}}
+\subsection{Method \code{getOrganisationMembers()}}{
+Fetch the members of an organisation
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getOrganisationMembers(
+  org_name = "",
+  org_id = -1,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{org_name}}{\if{html}{\out{<character>}} The name of the organisation to check}
+
+\item{\code{org_id}}{\if{html}{\out{<integer>}} The id of the organisation to check}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-isAgent"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-isAgent}{}}}
+\subsection{Method \code{isAgent()}}{
+Check if user's organisation is an agent for another
+organisation
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$isAgent(org_id)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{org_id}}{\if{html}{\out{<integer>}} The id of the organisation to check}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getOrganisationAgents"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getOrganisationAgents}{}}}
+\subsection{Method \code{getOrganisationAgents()}}{
+Fetch the agents of an organisation
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getOrganisationAgents(
+  org_id,
+  as_int = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{org_id}}{\if{html}{\out{<integer>}} The id of the organisation to check}
+
+\item{\code{as_int}}{\if{html}{\out{<logical>}} Return only the id (TRUE)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getAgentRecipients"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getAgentRecipients}{}}}
+\subsection{Method \code{getAgentRecipients()}}{
+Fetch the recipients of an organisation
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getAgentRecipients(
+  agent_id,
+  as_int = FALSE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{agent_id}}{\if{html}{\out{<integer>}} The id of the organisation (agent) to check}
+
+\item{\code{as_int}}{\if{html}{\out{<logical>}} Return only the id (TRUE)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-getUserOrganisation"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-getUserOrganisation}{}}}
+\subsection{Method \code{getUserOrganisation()}}{
+Fetch the organisation of a user
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$getUserOrganisation(
+  user_id,
+  as_int = TRUE,
+  name_only = TRUE,
+  collect = TRUE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The id of the user to fetch the organisation of}
+
+\item{\code{as_int}}{\if{html}{\out{<logical>}} Return only the id (TRUE)}
+
+\item{\code{name_only}}{\if{html}{\out{<logical>}} Return only the name (TRUE)}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Organisations-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Organisations-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Organisations$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.DB.Rd

@@ -0,0 +1,68 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db.R
+\name{MNR.DB}
+\alias{MNR.DB}
+\title{MNR database queries base class}
+\value{
+<\link[AVSDevR.DBClient]{DBClient}> The DBClient instance used
+by the class instance
+}
+\description{
+MNR database queries base class
+
+MNR database queries base class
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB-new}{\code{MNR.DB$new()}}
+\item \href{#method-MNR.DB-getDBClient}{\code{MNR.DB$getDBClient()}}
+\item \href{#method-MNR.DB-clone}{\code{MNR.DB$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB-new"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB-new}{}}}
+\subsection{Method \code{new()}}{
+Initialises the instance with a database client
+\link[AVSDevR.DBClient]{DBClient}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB$new(db_client)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{db_client}}{<\link[AVSDevR.DBClient]{DBClient}> A DBClient instance}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB-getDBClient"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB-getDBClient}{}}}
+\subsection{Method \code{getDBClient()}}{
+Returns the current DBClient instance in use
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB$getDBClient()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.DB.Users.Rd

@@ -0,0 +1,154 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/db_users.R
+\name{MNR.DB.Users}
+\alias{MNR.DB.Users}
+\title{MNR database queries for Users}
+\value{
+\if{html}{\out{<list>}} Details of the user denoted by user_id
+
+\if{html}{\out{<character>}} The user's name
+
+\if{html}{\out{<character>}} A list of user roles
+
+\if{html}{\out{<logical>}} TRUE if the user is an administrator
+}
+\description{
+MNR database queries for Users
+
+MNR database queries for Users
+}
+\section{Super class}{
+\code{\link[AVSDevR.MarineNoiseRegistry:MNR.DB]{AVSDevR.MarineNoiseRegistry::MNR.DB}} -> \code{MNR.DB.Users}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.DB.Users-new}{\code{MNR.DB.Users$new()}}
+\item \href{#method-MNR.DB.Users-getUser}{\code{MNR.DB.Users$getUser()}}
+\item \href{#method-MNR.DB.Users-getUserName}{\code{MNR.DB.Users$getUserName()}}
+\item \href{#method-MNR.DB.Users-getUserRoles}{\code{MNR.DB.Users$getUserRoles()}}
+\item \href{#method-MNR.DB.Users-isApplicationsAdmin}{\code{MNR.DB.Users$isApplicationsAdmin()}}
+\item \href{#method-MNR.DB.Users-clone}{\code{MNR.DB.Users$clone()}}
+}
+}
+\if{html}{\out{
+<details open><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="AVSDevR.MarineNoiseRegistry" data-topic="MNR.DB" data-id="getDBClient"><a href='../../AVSDevR.MarineNoiseRegistry/html/MNR.DB.html#method-MNR.DB-getDBClient'><code>AVSDevR.MarineNoiseRegistry::MNR.DB$getDBClient()</code></a></span></li>
+</ul>
+</details>
+}}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-new"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-new}{}}}
+\subsection{Method \code{new()}}{
+Initialises the instance with a database client from
+\link[AVSDevR.DBClient]{DBClient}
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$new(db_client, admin_role_slug = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{db_client}}{<\link[AVSDevR.DBClient]{DBClient}> A DBClient instance}
+
+\item{\code{admin_role_slug}}{\if{html}{\out{<character>}} The slug of the application
+administrator role within UserFrosting
+(Defaults to: "application-admin")}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-getUser"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-getUser}{}}}
+\subsection{Method \code{getUser()}}{
+Get user information from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$getUser(user_id, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user id to fetch}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-getUserName"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-getUserName}{}}}
+\subsection{Method \code{getUserName()}}{
+Get user name from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$getUserName(user_id)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user id to fetch}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-getUserRoles"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-getUserRoles}{}}}
+\subsection{Method \code{getUserRoles()}}{
+Get user roles from the database
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$getUserRoles(user_id, collect = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user id to fetch}
+
+\item{\code{collect}}{\if{html}{\out{<logical>}} Collect the query before returning (TRUE) or
+return the built query object (FALSE)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-isApplicationsAdmin"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-isApplicationsAdmin}{}}}
+\subsection{Method \code{isApplicationsAdmin()}}{
+Check if a user is an application administrator
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$isApplicationsAdmin(user_id)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user_id}}{\if{html}{\out{<integer>}} The user id to fetch}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.DB.Users-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.DB.Users-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.DB.Users$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/MNR.GeoPlot.Rd

@@ -0,0 +1,167 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/geoPlot.R
+\name{MNR.GeoPlot}
+\alias{MNR.GeoPlot}
+\title{MNR GIS plot base map generator}
+\value{
+A plolty object base map
+
+The plotly object
+}
+\description{
+MNR GIS plot base map generator
+
+MNR GIS plot base map generator
+}
+\details{
+Base layers are loaded and cached on first call to each of the boot methods.
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-MNR.GeoPlot-new}{\code{MNR.GeoPlot$new()}}
+\item \href{#method-MNR.GeoPlot-bootLayers}{\code{MNR.GeoPlot$bootLayers()}}
+\item \href{#method-MNR.GeoPlot-bootQuadrants}{\code{MNR.GeoPlot$bootQuadrants()}}
+\item \href{#method-MNR.GeoPlot-bootConservationAreas}{\code{MNR.GeoPlot$bootConservationAreas()}}
+\item \href{#method-MNR.GeoPlot-makeBasePlot}{\code{MNR.GeoPlot$makeBasePlot()}}
+\item \href{#method-MNR.GeoPlot-boundMap}{\code{MNR.GeoPlot$boundMap()}}
+\item \href{#method-MNR.GeoPlot-clone}{\code{MNR.GeoPlot$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-new"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-new}{}}}
+\subsection{Method \code{new()}}{
+Initialises the object by building the grid lines
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$new()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-bootLayers"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-bootLayers}{}}}
+\subsection{Method \code{bootLayers()}}{
+Loads the JNCC layers required from file for the base map
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$bootLayers()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-bootQuadrants"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-bootQuadrants}{}}}
+\subsection{Method \code{bootQuadrants()}}{
+Loads the Oil & Gas quadrants from file for the base map
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$bootQuadrants()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-bootConservationAreas"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-bootConservationAreas}{}}}
+\subsection{Method \code{bootConservationAreas()}}{
+Loads the Conservation Areas from the database for the base
+map.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$bootConservationAreas(db_client)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{db_client}}{<\link[AVSDevR.DBClient]{DBClient}> A DBClient instance}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-makeBasePlot"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-makeBasePlot}{}}}
+\subsection{Method \code{makeBasePlot()}}{
+Generates a base plotly map with optional layers included
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$makeBasePlot(
+  ...,
+  with_jncc_layers = TRUE,
+  with_quadrants = FALSE,
+  with_conservation_areas = FALSE
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{...}}{Options to call plotly::plot_ly with}
+
+\item{\code{with_jncc_layers}}{\if{html}{\out{<logical>}} Includes the JNCC base layers if TRUE
+(call obj$bootLayers() first)}
+
+\item{\code{with_quadrants}}{\if{html}{\out{<logical>}} Includes the Oil & Gas Quadrants if TRUE
+(call obj$bootQuadrants() first)}
+
+\item{\code{with_conservation_areas}}{\if{html}{\out{<logical>}} Includes the Conservation Areas
+if TRUE (call obj$bootConservationAreas() first)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-boundMap"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-boundMap}{}}}
+\subsection{Method \code{boundMap()}}{
+Bounds a mapbox map to a specific area and zoom
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$boundMap(
+  p,
+  c_lat = 56,
+  c_lon = -5.5,
+  zoom = 3.5,
+  xmin = -25,
+  ymin = 45,
+  xmax = 5,
+  ymax = 65
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{p}}{A plotly mapbox map object}
+
+\item{\code{c_lat}}{\if{html}{\out{<numeric>}} Center latitude}
+
+\item{\code{c_lon}}{\if{html}{\out{<numeric>}} Center longitude}
+
+\item{\code{zoom}}{\if{html}{\out{<numeric>}} A mapbox zoom level}
+
+\item{\code{xmin}}{\if{html}{\out{<numeric>}} Minimum longitude to bound with}
+
+\item{\code{ymin}}{\if{html}{\out{<numeric>}} Minimum latitude to bound with}
+
+\item{\code{xmax}}{\if{html}{\out{<numeric>}} Maximum longitude to bound with}
+
+\item{\code{ymax}}{\if{html}{\out{<numeric>}} Maximum latitude to bound with}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-MNR.GeoPlot-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-MNR.GeoPlot-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{MNR.GeoPlot$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}

man/attachResourcePaths.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/use_mnr_ui.R
+\name{attachResourcePaths}
+\alias{attachResourcePaths}
+\title{Attaches the MNR resource path to Shiny if not already attached}
+\usage{
+attachResourcePaths()
+}
+\description{
+Attaches the MNR resource path to Shiny if not already attached
+}

man/resourcePrefix.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/use_mnr_ui.R
+\name{resourcePrefix}
+\alias{resourcePrefix}
+\title{Provides the resource path for MNR specific files}
+\usage{
+resourcePrefix()
+}
+\description{
+Provides the resource path for MNR specific files
+}

man/use_mnr_ui.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/use_mnr_ui.R
+\name{use_mnr_ui}
+\alias{use_mnr_ui}
+\title{Attaches the MNR stylesheets and scripts to the UI}
+\usage{
+use_mnr_ui()
+}
+\description{
+Attaches the MNR stylesheets and scripts to the UI
+}