Added test for process_lineage_variants_data.

app/models/organism.rb

@@ -42,13 +42,18 @@ def lineage_variants_data(data_server, organism_slug)
       return { data_fetched: false }
     end
 
-    primer_sets = JSON.parse(tracks_req.body)
+    process_lineage_variants_data tracks_req.body, defaults_req.body, lineages_req.body
+  end
+
+  def process_lineage_variants_data(tracks_json, defaults_json, lineages_json)
+
+    primer_sets = JSON.parse(tracks_json)
 
-    defaults_parsed = JSON.parse(defaults_req.body)
+    defaults_parsed = JSON.parse(defaults_json)
     default_tracks = defaults_parsed['tracks']
     default_lineage = defaults_parsed['lineage']
 
-    lineage_sets = JSON.parse(lineages_req.body)
+    lineage_sets = JSON.parse(lineages_json)
 
     { data_fetched: true, primer_sets:, default_tracks:, lineage_sets:,
       default_lineage: }

app/models/organism_taxon.rb

@@ -2,4 +2,5 @@
 
 class OrganismTaxon < ApplicationRecord
   belongs_to :lineage_caller
+  belongs_to :organism
 end

test/fixtures/lineage_callers.yml

@@ -0,0 +1,5 @@
+default:
+    name: "default"
+    version_specifiers: ""
+    pending_version_specifiers: ""
+    script_name: "default"

test/fixtures/organism_taxa.yml

@@ -0,0 +1,6 @@
+sars_cov_2_taxon:
+    name: "SARS-CoV-2"
+    organism: sars_cov_2
+    reference_accession: "NC_045512.2"
+    ncbi_taxon_id: 2697049
+    lineage_caller: default

test/fixtures/organisms.yml

@@ -1,3 +1,4 @@
 sars_cov_2:
-  name: SARS-CoV-2
-  ncbi_taxon_id: 1
+  name: "SARS-CoV-2"
+  slug: "sars-cov-2"
+  public: true

test/models/organism_test.rb

@@ -3,7 +3,49 @@
 require 'test_helper'
 
 class OrganismTest < ActiveSupport::TestCase
+  setup do
+    @organism = Organism.new
+  end
+
   test 'instantiation' do
-    assert_not_nil Organism.new
+    assert_not_nil @organism
+  end
+
+  test 'process_lineage_variants_data returns correct data structure on valid JSON' do
+    tracks_json = '{"track1": "value1"}'
+    defaults_json = '{"tracks": "default_tracks", "lineage": "default_lineage"}'
+    lineages_json = '{"lineage1": "value1"}'
+
+    expected = {
+      data_fetched: true,
+      primer_sets: {'track1' => 'value1'},
+      default_tracks: 'default_tracks',
+      lineage_sets: {'lineage1' => 'value1'},
+      default_lineage: 'default_lineage'
+    }
+
+    assert_equal expected, @organism.process_lineage_variants_data(tracks_json, defaults_json, lineages_json)
+  end
+
+  test 'process_lineage_variants_data handles JSON parsing errors gracefully' do
+    invalid_json = 'invalid_json'
+
+    assert_raises(JSON::ParserError) do
+      @organism.process_lineage_variants_data(invalid_json, invalid_json, invalid_json)
+    end
+  end
+
+  test 'process_lineage_variants_data returns empty hashes for empty JSON strings' do
+    empty_json = '{}'
+
+    expected = {
+      data_fetched: true,
+      primer_sets: {},
+      default_tracks: nil,
+      lineage_sets: {},
+      default_lineage: nil
+    }
+
+    assert_equal expected, @organism.process_lineage_variants_data(empty_json, empty_json, empty_json)
   end
 end

test/test_helper.rb

@@ -4,6 +4,8 @@
 require_relative '../config/environment'
 require 'rails/test_help'
 
+require 'mocha/minitest'
+
 module ActiveSupport
   class TestCase
     # Run tests in parallel with specified workers