Add c14 issues #260

The low-hanging fruit: MISSING_C14_AGE, VERY_OLD_C14, MISSING_C14_ERROR,
MISSING_D13C, MISSING_D13C_ERROR, MISSING_C14_METHOD,
MISSING_C14_LAB_ID, and MISSING_C14_LAB

app/controllers/issues/c14s_controller.rb

@@ -0,0 +1,24 @@
+class Issues::C14sController < IssuesController
+  load_and_authorize_resource
+
+  # GET /issues/c14s/:issue
+  def index
+    if params[:issue].present?
+      @c14s = C14.send(params[:issue])
+    else
+      @c14s = C14.all
+    end
+
+    if params.has_key?(:c14s_order_by)
+      order = { params[:c14s_order_by] => params.fetch(:c14s_order, "asc") }
+    else
+      order = :id
+    end
+    @c14s = @c14s.reorder(order)
+
+    respond_to do |format|
+      format.html { @pagy, @c14s = pagy(@c14s) }
+    end
+  end
+
+end

app/helpers/issues_helper.rb

@@ -1,19 +1,35 @@
 module IssuesHelper
   def issue_label(issue)
-    case issue
-    when :missing_taxon
-      "MISSING_TAXON"
-    when :unknown_taxon
-      "UNKNOWN_TAXON"
-    end
+    issue.to_s.upcase
   end
 
   def issue_description(issue)
     case issue
+    # C14s
+    when :missing_c14_age
+      "Radiocarbon date with no age value"
+    when :very_old_c14
+      "Radiocarbon date with an age greater than 50000 uncal BP"
+    when :missing_c14_error
+      "Radiocarbon date with no error associated with age value"
+    when :missing_d13c
+      "Radiocarbon date with no δ13C value"
+    when :missing_d13c_error
+      "Radiocarbon date with no error associated with δ13C value"
+    when :missing_c14_method
+      "Method used to obtain radiocarbon measurement (e.g. conventional, AMS) is not recorded"
+    when :missing_c14_lab_id
+      "No laboratory identifier recorded for radiocarbon date"
+    when :missing_c14_lab
+      "No radiocarbon laboratory associated with radiocarbon date"
+    # Samples
     when :missing_taxon
       "Taxonomic classification of the sample material is unknown"
+    # Taxons
     when :unknown_taxon
       "Taxon not matched to the GBIF Backbone Taxonomy"
+    else
+      ""
     end
   end
 

app/models/c14.rb

@@ -26,32 +26,37 @@
 #  index_c14s_on_superseded_by   (superseded_by)
 #
 class C14 < ApplicationRecord
-  include DataHelper
-
-  include PgSearch::Model
-  pg_search_scope :search, 
-    against: :lab_identifier, 
-    using: { tsearch: { prefix: true } } # match partial words
-  multisearchable against: :lab_identifier
-
-  acts_as_copy_target # enable CSV exports
-  has_paper_trail
-
-  validates :bp, :std, presence: true
 
   belongs_to :sample
   accepts_nested_attributes_for :sample, reject_if: :all_blank
-  validates_associated :sample
-
-  delegate :context, to: :sample
-  delegate :site, to: :sample
 
   belongs_to :c14_lab, optional: true
   belongs_to :source_database, optional: true
 
   has_many :citations, as: :citing
   has_many :references, :through => :citations
 
+  delegate :context, to: :sample
+  delegate :site, to: :sample
+
+  validates :bp, :std, presence: true
+  validates_associated :sample
+
+  include Versioned
+
+  include HasIssues
+  @issues = [ :missing_c14_age, :very_old_c14, :missing_c14_error, 
+              :missing_d13c, :missing_d13c_error, :missing_c14_method, 
+              :missing_c14_lab_id, :missing_c14_lab ]
+
+  include PgSearch::Model
+  pg_search_scope :search, 
+    against: :lab_identifier, 
+    using: { tsearch: { prefix: true } } # match partial words
+  multisearchable against: :lab_identifier
+
+  acts_as_copy_target # enable CSV exports
+
   def self.label
     "radiocarbon date"
   end
@@ -75,6 +80,49 @@ def cal_age
       nil
     end
   end
+
+  # Issues
+
+  scope :missing_c14_age, -> { where(bp: nil) }
+  def missing_c14_age?
+    bp.blank?
+  end
+
+  scope :very_old_c14, -> { where("bp > 50000") }
+  def very_old_c14?
+    return nil if bp.blank?
+    bp > 50000
+  end
+
+  scope :missing_c14_error, -> { where(std: nil) }
+  def missing_c14_error?
+    std.blank?
+  end
+
+  scope :missing_d13c, -> { where(delta_c13: nil) }
+  def missing_d13c?
+    delta_c13.blank?
+  end
+
+  scope :missing_d13c_error, -> { where(delta_c13_std: nil) }
+  def missing_d13c_error?
+    delta_c13_std.blank?
+  end
+
+  scope :missing_c14_method, -> { where(method: nil) }
+  def missing_c14_method?
+    method.blank?
+  end
+
+  scope :missing_c14_lab_id, -> { where(lab_identifier: nil) }
+  def missing_c14_lab_id?
+    lab_identifier.blank?
+  end
+
+  scope :missing_c14_lab, -> { where(c14_lab_id: nil) }
+  def missing_c14_lab?
+    c14_lab_id.blank?
+  end
 
 end
 

app/models/taxon.rb

@@ -29,10 +29,6 @@ class Taxon < ApplicationRecord
   include HasIssues
   @issues = [ :unknown_taxon ]
 
-  scope :unknown_taxon, -> { where(gbif_id: nil) }
-  def unknown_taxon?
-    not gbif_id?
-  end
 
   include PgSearch::Model
   pg_search_scope :search, 
@@ -113,4 +109,11 @@ def self.label
     "taxon"
   end
 
+  # Issues
+
+  scope :unknown_taxon, -> { where(gbif_id: nil) }
+  def unknown_taxon?
+    not gbif_id?
+  end
+
 end

app/views/curate/index.html.erb

@@ -68,6 +68,12 @@
         </tr>
       </thead>
       <tbody>
+        <% C14.issues.each do |issue| %>
+          <tr>
+            <td class="small"><%= issue_label(issue) %></td>
+            <td class="text-end font-monospace"><%= link_to C14.send(issue).count, issues_c14s_path + "/" + issue.to_s %></td>
+          </tr>
+        <% end %>
         <% Sample.issues.each do |issue| %>
           <tr>
             <td class="small"><%= issue_label(issue) %></td>

app/views/issues/_nav.html.erb

@@ -15,7 +15,8 @@
         <% issue_path = base_path + "/" + issue.to_s %>
         <a href="<%= issue_path %>" 
            class="nav-link <%= active_class(issue_path) %>"
-           <%= active_aria(issue_path) %>>
+           <%= active_aria(issue_path) %>
+           title="<%= issue_description(issue) %>">
            <%= issue_label(issue) %>
            <span class="badge text-bg-info"><%= model.send(issue).count %></span>
         </a>

app/views/issues/c14s/_table.html.erb

@@ -0,0 +1,50 @@
+<table class="table table-hover">
+  <thead>
+    <tr>
+      <th scope="col">
+        <%= link_to_order_by "ID", :id %>
+        <% if ordered_by?(:id) %>
+          <span class="text-muted"><%= order_indicator %></span>
+        <% end %>
+      </th>
+      <th scope="col">
+        <%= link_to_order_by "Lab ID", :lab_identifier %>
+        <% if ordered_by?(:lab_identifier) %>
+          <span class="text-muted"><%= order_indicator %></span>
+        <% end %>
+      </th>
+      <th scope="col">
+        <%= link_to_order_by "C14 Lab", :c14_lab_id %>
+        <% if ordered_by?(:c14_lab_id) %>
+          <span class="text-muted"><%= order_indicator %></span>
+        <% end %>
+      </th>
+      <th scope="col">Method</th>
+      <th scope="col">Age</th>
+      <th scope="col">Error</th>
+      <th scope="col">δ13C</th>
+      <th scope="col">δ13C error</th>
+      <th scope="col">Issues</th>
+    </tr>
+  </thead>
+
+  <tbody>
+    <% c14s.each do |c14| %>
+      <tr>
+        <td class="text-muted"><%= link_to c14.id, c14 %></td>
+        <td><%= c14.lab_identifier %></td>
+        <td><%= c14.c14_lab_id %></td>
+        <td><%= c14.method %></td>
+        <td><%= c14.bp %></td>
+        <td><%= c14.std %></td>
+        <td><%= c14.delta_c13 %></td>
+        <td><%= c14.delta_c13_std %></td>
+        <td><% c14.issues.each do |issue| %>
+          <%= issue_badge(issue) %>
+        <% end %></td>
+      </tr>
+
+    </tr>
+  <% end %>
+  </tbody>
+</table>

app/views/issues/c14s/index.html.erb

@@ -0,0 +1,12 @@
+<% content_for :title, "Issues – Radiocarbon dates" %>
+<% content_for :help do %>
+<% end %>
+
+<h2 class="border-bottom">Radiocarbon dates</h2>
+
+<%= render "issues/nav", model: C14, base_path: issues_c14s_path %>
+
+<turbo-frame id="issues-c14s-table">
+  <%= render "table", c14s: @c14s %>
+  <%== pagy_bootstrap_nav(@pagy) %>
+</turbo-frame>

config/routes.rb

@@ -87,6 +87,7 @@
     end
   end
   namespace :issues do 
+    resources :c14s, only: :index, concerns: :has_issues
     resources :samples, only: :index, concerns: :has_issues
     resources :taxons, only: :index, concerns: :has_issues
   end