Feature/fix missing crc sheffield test scopes

lib/import/colorectal/providers/sheffield/sheffield_handler_colorectal.rb

@@ -76,6 +76,11 @@ def process_scope_r209(karyo, genocolorectal, _moleculartestingtype)
           end
 
           def process_scope_r210(karyo, genocolorectal, moleculartestingtype)
+            if karyo.downcase.match(/r240.1\s::\sdiagnostic\sfamilial/)
+              karyo='R240.1 :: Diagnostic familial'
+            elsif karyo.downcase.match(/r242.1\s::\spredictive\stesting/)
+              karyo='R242.1 :: Predictive testing'
+            end
             if R210_PANEL_GENE_MAPPING_FS.keys.include? karyo
               @logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
               genocolorectal.add_test_scope(:full_screen)
@@ -123,6 +128,16 @@ def process_scope_r414(karyo, genocolorectal, moleculartestingtype)
             end
           end
 
+          def process_scope_r216(karyo, genocolorectal, moleculartestingtype)
+            if R216_PANEL_GENE_MAPPING_FS.keys.include? karyo
+              @logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
+              genocolorectal.add_test_scope(:full_screen)
+              @genes_set = R216_PANEL_GENE_MAPPING_FS[karyo]
+            else
+              genocolorectal.add_test_scope(:no_genetictestscope)
+            end
+          end
+
           def process_scope_fap_familial(karyo, genocolorectal, _moleculartestingtype)
             if FAP_FAM_PANEL_GENE_MAPPING_TAR.keys.include? karyo
               @logger.debug "ADDED TARGETED TEST for: #{karyo}"
@@ -183,10 +198,33 @@ def process_scope_colo_ovarian_panel(karyo, genocolorectal, _moleculartestingtyp
           end
 
           def add_test_type(genocolorectal, record)
-            moltestingtype = record.raw_fields['moleculartestingtype']
+            karyo = record.raw_fields['karyotypingmethod'].strip
+            moleculartestingtype = record.raw_fields['moleculartestingtype'].strip.downcase
+
+            test_type = determine_test_type(moleculartestingtype, karyo)
+            genocolorectal.add_molecular_testing_type_strict(test_type) if test_type
+          end
+
+          def determine_test_type(moleculartestingtype, karyo)
+            # First priority: moleculartestingtype
+            return TEST_TYPE_MAPPING_COLO[moleculartestingtype] if TEST_TYPE_MAPPING_COLO.key?(moleculartestingtype)
+            return :predictive if moleculartestingtype.match?(/unaffected/i)
 
-            genocolorectal.add_molecular_testing_type_strict(TEST_TYPE_MAPPING_COLO[moltestingtype.
-              downcase])
+            # Second priority: karyo R-number patterns
+            test_type_from_karyo(karyo)
+          end
+
+          def test_type_from_karyo(karyo)
+            case karyo
+            when /^R(240|205|206|207|208|209|210|211|430|444|216|414|370)/
+              :diagnostic
+            when /^R242/
+              :predictive
+            when /^R(244|246)/
+              :carrier
+            when /^R448/
+              :prenatal
+            end
           end
 
           def process_variants_from_record(genocolorectal, record)
@@ -276,11 +314,10 @@ def process_normal_full_screen(genocolorectal, genocolorectals)
             negative_genes = @genes_set
             if !negative_genes.empty?
               add_other_genes_with_status(negative_genes, genocolorectal, genocolorectals, 1)
-            else 
+            else
               genocolorectals.append(genocolorectal)
             end
-
-
+
             genocolorectals
           end
 

lib/import/helpers/colorectal/providers/rcu/constants.rb

@@ -48,23 +48,25 @@ module Constants
               'r218 :: multiple endocrine neoplasia type 2',
               'r365 :: fumarate hydratase-related tumour syndromes - sdgs',
               'r240 - familial diagnostic testing - hered cancers',
-              'r206 :: inherited breast cancer and ovarian cancer at high familial risk levels',
-              'r216 :: li fraumeni syndrome - sdgs'
+              'r206 :: inherited breast cancer and ovarian cancer at high familial risk levels'
             ].freeze
 
             GENETICTESTSCOPE_METHOD_MAPPING = {
               'colorectal cancer panel' => :process_scope_colorectal_panel,
               'r209 :: inherited colorectal cancer '\
               '(with or without polyposis)' => :process_scope_r209,
               'r210 :: inherited mmr deficiency (lynch syndrome)' => :process_scope_r210,
+              'r210' => :process_scope_r210,
               'r211 :: inherited polyposis - germline test' => :process_scope_r211,
+              'r211'  => :process_scope_r211,
               'fap' => :process_scope_fap,
               'fap familial mutation' => :process_scope_fap_familial,
               'hnpcc' => :process_scope_hnpcc,
               'myh' => :process_scope_myh,
               'breast ovarian & colorectal cancer panel' => :process_scope_colo_ovarian_panel,
               'r211 :: inherited polyposis and early onset colorectal cancer, germline testing'=> :process_scope_r211,
-              'r414 :: apc associated polyposis'=> :process_scope_r414
+              'r414 :: apc associated polyposis'=> :process_scope_r414,
+              'r216 :: li fraumeni syndrome - sdgs' => :process_scope_r216
             }.freeze
 
             COLO_PANEL_GENE_MAPPING_FS = {
@@ -117,18 +119,18 @@ module Constants
               'R210.2 :: Small panel in Leeds' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
               'R210.2 :: Unknown mutation(s) by Small panel' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
               'R210.5 :: Unknown mutation(s) by MLPA or equivalent' => %w[MLH1 MSH2 EPCAM],
-              'R210.1 :: Unknown mutation(s) by Microsatellite instability'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
-              'R210.2 :: Small panel in Leeds - Send DNA'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
+              'R210.1 :: Unknown mutation(s) by Microsatellite instability' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
+              'R210.2 :: Small panel in Leeds - Send DNA' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
+              'R210.2 :: Small panel in Leeds - DNA in Newcastle' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
             }.freeze
 
             R210_PANEL_GENE_MAPPING_TAR = {
               'R240.1 :: Diagnostic familial' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
               'R242.1 :: Predictive MLPA' => %w[MLH1 MSH2 EPCAM],
               'R242.1 :: Predictive testing' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
-              'R242.1 :: Predictive testing - MLPA in Leeds - Send Blood'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
-              'R242.1 :: Predictive testing - MLPA in Leeds - Send DNA'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
-              'R242.1 :: Predictive testing - Seq in Leeds - Send Blood'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
-              'R242.1 :: Predictive testing - Seq in Leeds - Send DNA'=> %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
+              'R240 :: Diagnostic testing for known pathogenic variant(s) - Hereditary Cancers' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
+              'R242 :: Predictive testing for known familial pathogenic variant(s) - Hereditary Cancers' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM],
+              'R448.1 :: Sequence analysis - Sanger in Newcastle' => %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
             }.freeze
 
             R210_PANEL_GENE_MAPPING_MOL = {
@@ -140,7 +142,8 @@ module Constants
               'R211.1 :: Small Panel in Leeds' => %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
               'R211.1 :: Small panel in Leeds - send DNA sample'=> %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
               'R211.1 :: APC and MUTYH genes in Leeds' => %w[APC MUTYH],
-              'R211.2 :: Unknown mutation(s) by MLPA or equivalent' => %w[APC MUTYH]
+              'R211.2 :: Unknown mutation(s) by MLPA or equivalent' => %w[APC MUTYH],
+              'R246.1 :: Small panel Carrier testing of partners at population risk' => %w[]
             }.freeze
 
             R211_PANEL_GENE_MAPPING_TAR = {
@@ -149,14 +152,21 @@ module Constants
               'R242.1 :: Predictive testing' => %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
               'R242.1 :: Predictive testing - Seq in Leeds - Send Blood' => %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
               'R242.1 :: Predictive testing - Seq in Leeds - Analysis only'=> %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
-              'R242.1 :: Predictive testing - Seq in Leeds - Send DNA'=> %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11]
+              'R242.1 :: Predictive testing - Seq in Leeds - Send DNA'=> %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
+              'R242.1 :: Predictive testing - Seq in Leeds' => %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11],
+              'R242 :: Predictive testing for known familial pathogenic variant(s) - Hereditary Cancers' => %w[APC BMPR1A EPCAM MLH1 MSH2 MSH6 MUTYH NTHL1 
+                                                                                                               PMS2 POLD1 POLE PTEN RNF43 SMAD4 STK11]
             }.freeze
 
             R211_PANEL_GENE_MAPPING_MOL = {
               'R387.1 ::  APC and MUTYH analysis only' => %w[APC MUTYH],
               'R244.1 :: Carrier testing' => %w[MUTYH]
             }.freeze
 
+            R216_PANEL_GENE_MAPPING_FS = {
+              'R216.1 :: TP53 NGS in Leeds Analysis only' => %w[TP53]
+          }.freeze
+
             FAP_PANEL_GENE_MAPPING_MOL = {
               'APC gene MLPA' => %w[APC],
               'APC gene sequencing' => %w[APC],
@@ -192,6 +202,7 @@ module Constants
                                  PTEN RAD51C RAD51D STK11 TP53 PMS2]
             }.freeze
 
+
             MOLECULAR_SCOPE_MAPPING = {
               'carrier testing' => :no_genetictestscope,
               'confirmation of familial mutation' => :targeted_mutation,

test/lib/import/colorectal/providers/sheffield/sheffield_handler_colorectal_test.rb

@@ -23,6 +23,22 @@ def setup
     assert_equal 'Targeted Colorectal Lynch or MMR', @genotype.attribute_map['genetictestscope']
   end
 
+  test 'add_test_scope_from_fs_r211' do
+    r211_fs_record = build_raw_record('pseudo_id1' => 'bob')
+    r211_fs_record.raw_fields['genetictestscope'] = 'R211'
+    r211_fs_record.raw_fields['karyotypingmethod'] = 'R211.1 :: Small panel in Leeds - send DNA sample'
+    @handler.add_test_scope_from_geno_karyo(@genotype, r211_fs_record)
+    assert_equal 'Full screen Colorectal Lynch or MMR', @genotype.attribute_map['genetictestscope']
+  end
+
+  test 'add_test_scope_from_fs_r216' do
+    r216_fs_record = build_raw_record('pseudo_id1' => 'bob')
+    r216_fs_record.raw_fields['genetictestscope'] = 'R216 :: Li Fraumeni Syndrome - SDGS'
+    r216_fs_record.raw_fields['karyotypingmethod'] = 'R216.1 :: TP53 NGS in Leeds Analysis only'
+    @handler.add_test_scope_from_geno_karyo(@genotype, r216_fs_record)
+    assert_equal 'Full screen Colorectal Lynch or MMR', @genotype.attribute_map['genetictestscope']
+  end
+
   test 'add_no_scope_from_karyo_targeted' do
     no_scope_record = build_raw_record('pseudo_id1' => 'bob')
     no_scope_record.raw_fields['genetictestscope'] = 'XYZ'
@@ -31,6 +47,44 @@ def setup
     assert_equal 'Unable to assign Colorectal Lynch or MMR genetictestscope', @genotype.attribute_map['genetictestscope']
   end
 
+  test 'add_moltestingtype_from_mapping' do
+    diagnostic_record = build_raw_record('pseudo_id1' => 'bob')
+    diagnostic_record.raw_fields['moleculartestingtype'] = 'Confirmation of Familial Mutation'
+    @handler.add_test_type(@genotype, diagnostic_record)
+    assert_equal 1, @genotype.attribute_map['moleculartestingtype']
+    predictive_record = build_raw_record('pseudo_id1' => 'bob')
+    predictive_record.raw_fields['moleculartestingtype'] = 'Family Studies'
+    @handler.add_test_type(@genotype, predictive_record)
+    assert_equal 2, @genotype.attribute_map['moleculartestingtype']
+  end
+
+  test 'add_moltestingtype_from_karyo' do
+    diagnostic_record = build_raw_record('pseudo_id1' => 'bob')
+    diagnostic_record.raw_fields['moleculartestingtype'] = 'cabbage'
+    diagnostic_record.raw_fields['karyotypingmethod'] = 'R210.2 :: Small panel in Leeds'
+    @handler.add_test_type(@genotype, diagnostic_record)
+    assert_equal 1, @genotype.attribute_map['moleculartestingtype']
+    predictive_record = build_raw_record('pseudo_id1' => 'bob')
+    predictive_record.raw_fields['moleculartestingtype'] = 'cabbage'
+    predictive_record.raw_fields['karyotypingmethod'] = 'R242 :: Predictive testing for known familial pathogenic variant(s) - Hereditary Cancers'
+    @handler.add_test_type(@genotype, predictive_record)
+    assert_equal 2, @genotype.attribute_map['moleculartestingtype']
+    carrier_record = build_raw_record('pseudo_id1' => 'bob')
+    carrier_record.raw_fields['moleculartestingtype'] = 'cabbage'
+    carrier_record.raw_fields['karyotypingmethod'] = 'R246.1 :: Small panel Carrier testing of partners at population risk'
+    @handler.add_test_type(@genotype, carrier_record)
+    assert_equal 3, @genotype.attribute_map['moleculartestingtype']
+  end
+
+  test 'add_moletestingtype_from_mapping_as_priority' do
+    # priority should be given to moleculartestingtype field over karyotypingmethod field
+    diagnostic_record = build_raw_record('pseudo_id1' => 'bob')
+    diagnostic_record.raw_fields['moleculartestingtype'] = 'Diagnostic testing for known mutation'
+    diagnostic_record.raw_fields['karyotypingmethod'] = 'R242 :: Predictive testing for known familial pathogenic variant(s) - Hereditary Cancers'
+    @handler.add_test_type(@genotype, diagnostic_record)
+    assert_equal 1, @genotype.attribute_map['moleculartestingtype']
+  end
+
   test 'add_colorectal_from_raw_test_full_screen' do
     @handler.add_test_scope_from_geno_karyo(@genotype, @record)
     raw_test = @handler.process_variants_from_record(@genotype, @record)
@@ -163,7 +217,7 @@ def setup
     assert_nil genocolorectals[0].attribute_map['gene']
   end
 
-  test 'process_targeted_no_scope_failure' do 
+  test 'process_targeted_no_scope_failure' do
     exon_record = build_raw_record('pseudo_id1' => 'bob')
     exon_record.raw_fields['genetictestscope'] = 'efgh'
     exon_record.raw_fields['karyotypingmethod'] = 'abcd'
@@ -177,7 +231,7 @@ def setup
     assert_equal 9, genocolorectals[0].attribute_map['teststatus']
   end
 
-  test 'process_targeted_no_scope_normal' do 
+  test 'process_targeted_no_scope_normal' do
     exon_record = build_raw_record('pseudo_id1' => 'bob')
     exon_record.raw_fields['genetictestscope'] = 'efgh'
     exon_record.raw_fields['karyotypingmethod'] = 'abcd'
@@ -193,7 +247,7 @@ def setup
     assert_nil genocolorectals[0].attribute_map['gene']
   end
 
-  test 'process_targeted_no_scope_abnormal' do 
+  test 'process_targeted_no_scope_abnormal' do
     exon_record = build_raw_record('pseudo_id1' => 'bob')
     exon_record.raw_fields['genetictestscope'] = 'efgh'
     exon_record.raw_fields['karyotypingmethod'] = 'abcd'
@@ -209,6 +263,42 @@ def setup
     assert_equal 2804, genocolorectals[0].attribute_map['gene']
   end
 
+  test 'process_targeted_diagnostic_familial_r240' do
+    diag_fam_record = build_raw_record('pseudo_id1' => 'bob')
+    diag_fam_record.raw_fields['genetictestscope'] = 'R210'
+    diag_fam_record.raw_fields['karyotypingmethod'] = 'R240.1 :: Diagnostic familial - MLPA in Leeds - Send Blood'
+    diag_fam_record.raw_fields['genotype'] = 'MSH2-c.1234_5678del-p.(Gln321fs)-Heterozygous-UV5'
+    @handler.add_test_scope_from_geno_karyo(@genotype, diag_fam_record)
+    @handler.add_test_type(@genotype, diag_fam_record)
+    genocolorectals = @handler.process_variants_from_record(@genotype, diag_fam_record)
+    assert_equal 1, genocolorectals.size
+    assert_equal 'Targeted Colorectal Lynch or MMR', @genotype.attribute_map['genetictestscope']
+    assert_equal 1, @genotype.attribute_map['moleculartestingtype']
+    assert_equal 2, genocolorectals[0].attribute_map['teststatus']
+    assert_equal 2804, genocolorectals[0].attribute_map['gene']
+    assert_equal 'p.Gln321fs', genocolorectals[0].attribute_map['proteinimpact']
+    assert_equal 'c.1234_5678del', genocolorectals[0].attribute_map['codingdnasequencechange']
+  end
+
+  test 'process_targeted_predictive_testing_r242' do
+    predictive_record = build_raw_record('pseudo_id1' => 'bob')
+    predictive_record.raw_fields['genetictestscope'] = 'R210'
+    predictive_record.raw_fields['karyotypingmethod'] = 'R242 :: Predictive testing for known familial pathogenic variant(s) - Hereditary Cancers'
+    predictive_record.raw_fields['genotype'] = 'MSH2-c.1234_5678del-p.(Gln321fs)-Heterozygous-UV5'
+    predictive_record.raw_fields['moleculartestingtype'] = 'cabbage'
+    @handler.add_test_scope_from_geno_karyo(@genotype, predictive_record)
+    # get moleculartestingtype from karyo (priority 2)
+    @handler.add_test_type(@genotype, predictive_record)
+    genocolorectals = @handler.process_variants_from_record(@genotype, predictive_record)
+    assert_equal 1, genocolorectals.size
+    assert_equal 'Targeted Colorectal Lynch or MMR', @genotype.attribute_map['genetictestscope']
+    assert_equal 2, @genotype.attribute_map['moleculartestingtype']
+    assert_equal 2, genocolorectals[0].attribute_map['teststatus']
+    assert_equal 2804, genocolorectals[0].attribute_map['gene']
+    assert_equal 'p.Gln321fs', genocolorectals[0].attribute_map['proteinimpact']
+    assert_equal 'c.1234_5678del', genocolorectals[0].attribute_map['codingdnasequencechange']
+  end
+
   test 'process_cdna_change' do
     @logger.expects(:debug).with('SUCCESSFUL cdna change parse for: 1653dup')
     @handler.process_cdna_change(@genotype, @record.raw_fields['genotype'])