Create permanent reports

Author: lmrodriguezr

app/controllers/genomes_controller.rb

@@ -57,16 +57,10 @@ def update_accession
 
   # POST /genomes/1/update_external
   def update_external
-    if @genome.reload_source_json!
-      flash[:notice] = {
-        message: 'External metadata has been updated',
-        report: @genome.ephemeral_report
-      }
+    if @genome.queue_for_external_resources(true) # Force: trust curators
+      flash[:notice] = 'Update has been queued'
     else
-      flash[:alert] = {
-        message: 'Update failed',
-        report: @genome.ephemeral_report
-      }
+      flash[:alert] = 'Update was not queued, something failed'
     end
     redirect_back(fallback_location: @genome)
   end

app/models/application_record.rb

@@ -8,6 +8,7 @@ class ApplicationRecord < ActiveRecord::Base
   has_many(:linked_notifications, class_name: 'Notification',
     as: :linkeable, dependent: :nullify
   )
+  has_many(:reports, as: :linkeable, dependent: :destroy)
 
   def qualified_id
     '%s:%i' % [self.class.to_s, id]

app/models/genome/external_resources.rb

@@ -23,7 +23,7 @@ def reload_source_json!
     case source_database.to_sym
     when :sra
       source_accessions.each do |acc|
-        ephemeral_report << "SRA:#{acc}"
+        ephemeral_report.section "SRA:#{acc}"
         biosample = external_sra_to_biosample(acc)
         ephemeral_resource << "Linked to BioSample#{biosample}"
         data[biosample] ||=
@@ -32,7 +32,7 @@ def reload_source_json!
       end
     when :biosample
       source_accessions.each do |acc|
-        ephemeral_report << "BioSample:#{acc}"
+        ephemeral_report.section "BioSample:#{acc}"
         data[acc] = external_biosample_hash(acc)
         data[acc][:biosample_accessions].each do |acc_alt|
           external_biosample_to_sra(acc_alt)
@@ -42,6 +42,7 @@ def reload_source_json!
 
     self.source_json = { retrieved_at: DateTime.now, samples: data }.to_json
     self.queued_external = nil
+    ephemeral_report.save
     save
   end
 

app/models/report.rb

@@ -0,0 +1,3 @@
+class Report < ApplicationRecord
+  belongs_to :linkeable, polymorphic: true
+end

db/migrate/20251010121257_create_reports.rb

@@ -0,0 +1,11 @@
+class CreateReports < ActiveRecord::Migration[6.1]
+  def change
+    create_table :reports do |t|
+      t.references :linkeable, polymorphic: true, null: false
+      t.text :text
+      t.text :html
+
+      t.timestamps
+    end
+  end
+end

lib/ephemeral_report.rb

@@ -8,11 +8,29 @@ def initialize(obj)
   end
 
   def <<(message)
-    @messages << EphemeralMessage.new(message)
+    @messages << EphemeralMessage.new(message) if message
   end
 
-  def error(message)
-    @messages << EphemeralMessage.new(message, type: :error)
+  %i[info error warn section].each do |type|
+    define_method(type) do |message|
+      @messages << EphemeralMessage.new(message, type: type) if message
+    end
+  end
+
+  def to_s
+    @messages.map(&:to_s).join("\n")
+  end
+
+  def to_html
+    @messages.map(&:to_html).join("\n")
+  end
+
+  def save
+    Report.new(
+      object: obj,
+      text: to_s,
+      html: to_html
+    ).save
   end
 end
 
@@ -28,8 +46,29 @@ def initialize(message, type: :info)
   end
 
   def to_s
-    @message.is_a?(EphemeralMessage) ?
+    @message.is_a?(EphemeralReport) ?
       @message.to_s :
-      '[%s] %s' % [@timestamp.to_s, @message.to_s]
+      '%s: [%s] %s' % [@type.to_s.upcase, @timestamp.to_s, @message.to_s]
+  end
+
+  def to_html
+    @message.is_a?(EphemeralReport) ?
+      @message.to_html :
+      '<div class="%s"><span class="text-muted">[%s]</span> %s</div>' % [
+        html_class, @timestamp.to_s, @message.to_s
+      ]
+  end
+
+  def html_class
+    case type
+    when :error
+      'text-danger'
+    when :warn
+      'text-alert'
+    when :section
+      'text-info'
+    else
+      ''
+    end
   end
 end

test/fixtures/reports.yml

@@ -0,0 +1,13 @@
+# Read about fixtures at https://api.rubyonrails.org/classes/ActiveRecord/FixtureSet.html
+
+one:
+  linkeable: one
+  linkeable_type: Linkeable
+  text: MyText
+  html: MyText
+
+two:
+  linkeable: two
+  linkeable_type: Linkeable
+  text: MyText
+  html: MyText

test/models/report_test.rb

@@ -0,0 +1,7 @@
+require "test_helper"
+
+class ReportTest < ActiveSupport::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end