dms-2024-i4-r4

Gemfile

@@ -15,50 +15,14 @@ gem 'pg', '~> 1.4.6' # All client instance have postgres version >= 9.3
 gem 'puma', '~> 6.0'
 gem 'puma-daemon', require: false
 
-# We have built our own CentOS 7 binaries for various gems
-# (with separate gem files for different ruby versions)
-# Copy these into place if needed
-def add_custom_centos_7_binaries(gem_dir_basename, gem_fnames)
-  gem_dir = if RUBY_PLATFORM == 'x86_64-linux' && File.exist?('/etc/os-release') &&
-               File.readlines('/etc/os-release').grep(/^(ID="centos"|VERSION_ID="7")$/).count == 2
-              "vendor/#{gem_dir_basename}-x86_64-linux-ruby#{RUBY_VERSION.split('.')[0..1].join}"
-            end
-  require 'fileutils'
-  gem_fnames.each do |gem_fname|
-    if gem_dir && Dir.exist?(gem_dir)
-      begin
-        FileUtils.cp "#{gem_dir}/#{gem_fname}", 'vendor/cache/'
-      rescue Errno::EACCES
-        # Deployer account may not have write access to vendor/cache/
-        # (in which case the file in vendor/cache/ is probably already correct)
-      end
-    else
-      FileUtils.rm_f "vendor/cache/#{gem_fname}"
-    end
-  end
-end
-
 # Use SCSS for stylesheets
 gem 'sass-rails'
 # Use CoffeeScript for .coffee assets and views
 gem 'coffee-rails'
 # See https://github.com/rails/execjs#readme for more supported runtimes
 # gem 'therubyracer', platforms: :ruby
 # gem 'mini_racer'
-# Allow mini_racer version to be overridden in a custom Gemfile
-# We need this for mini_racer on Mac OS Monterey, where the old libv8 no longer compiles
-unless defined?(BUNDLER_OVERRIDE_MINI_RACER) && BUNDLER_OVERRIDE_MINI_RACER
-  # We have built our own CentOS 7 binaries for mini_racer
-  # (with separate gem files for Ruby 3.0 and Ruby 3.1)
-  # Copy these into place if needed
-  mini_racer_version = '0.12.0'
-  add_custom_centos_7_binaries('mini_racer',
-                               ["mini_racer-#{mini_racer_version}-x86_64-linux.gem"])
-  gem 'libv8-node', '~> 21.7.2.0'
-  # gem 'mini_racer', '~> 0.12.0'
-  # Lock the gem version: if this changes, we need to rebuild our binaries
-  gem 'mini_racer', mini_racer_version
-end
+gem 'mini_racer', '~> 0.14'
 
 gem 'parser'
 # Turbolinks makes following links in your web application faster. Read more: https://github.com/rails/turbolinks

Gemfile.lock

@@ -83,6 +83,7 @@ GEM
       execjs (~> 2)
     avro (1.11.2)
       multi_json (~> 1.0)
+    base64 (0.2.0)
     bcrypt (3.1.19)
     bindex (0.8.1)
     bio-vcf (0.9.5)
@@ -208,13 +209,14 @@ GEM
     json (2.6.3)
     launchy (2.5.2)
       addressable (~> 2.8)
-    libv8-node (21.7.2.0)
-    libv8-node (21.7.2.0-arm64-darwin)
-    libv8-node (21.7.2.0-x86_64-darwin)
-    libv8-node (21.7.2.0-x86_64-linux)
+    libv8-node (18.19.0.0)
+    libv8-node (18.19.0.0-arm64-darwin)
+    libv8-node (18.19.0.0-x86_64-darwin)
+    libv8-node (18.19.0.0-x86_64-linux)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.1)
     loofah (2.21.3)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -226,10 +228,8 @@ GEM
     method_source (1.0.0)
     mini_mime (1.1.5)
     mini_portile2 (2.8.4)
-    mini_racer (0.12.0)
-      libv8-node (~> 21.7.2.0)
-    mini_racer (0.12.0-x86_64-linux)
-      libv8-node (~> 21.7.2.0)
+    mini_racer (0.14.1)
+      libv8-node (~> 18.19.0.0)
     minitest (5.19.0)
     mocha (2.1.0)
       ruby2_keywords (>= 0.0.5)
@@ -367,7 +367,7 @@ GEM
       pry (>= 0.10.4)
     psych (3.3.2)
     public_suffix (5.0.3)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     puma-daemon (0.3.2)
       puma (>= 5.0)
@@ -451,8 +451,8 @@ GEM
     ruby-ole (1.2.12.2)
     ruby-progressbar (1.13.0)
     ruby-rc4 (0.1.5)
-    ruby-saml (1.14.0)
-      nokogiri (>= 1.10.5)
+    ruby-saml (1.17.0)
+      nokogiri (>= 1.13.10)
       rexml
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
@@ -467,7 +467,9 @@ GEM
       sprockets (> 3.0)
       sprockets-rails
       tilt
-    selenium-webdriver (4.12.0)
+    selenium-webdriver (4.24.0)
+      base64 (~> 0.2)
+      logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -560,10 +562,9 @@ DEPENDENCIES
   highline
   jquery-rails
   jquery-ui-rails!
-  libv8-node (~> 21.7.2.0)
   loofah (>= 2.3.1)
   mail (>= 2.1.1, < 2.8.0)
-  mini_racer (= 0.12.0)
+  mini_racer (~> 0.14)
   minitest
   mocha
   ndr_authenticate (~> 0.3, >= 0.3.3)

app/models/pseudo/death.rb

@@ -35,14 +35,18 @@ def multiple_cause_code(i)
     # and cod10rf_... / cod10r_... fields, to exclusively cod10rf_... / cod10r_... fields.
     def matched_cause_codes(i)
       raise 'Invalid index' unless (1..6).include?(i)
+
       # lineno values are always 1-6
       causes = (1..20).collect do |j|
         cod10r = death_data.send("cod10rf_#{j}") || death_data.send("cod10r_#{j}")
         line = death_data.send("lineno9f_#{j}") || death_data.send("lineno9_#{j}")
         # More recent deaths have inconsistently back-ported lineno values from cod10r values
         line = nil if cod10r && line && death_data.dor.to_i >= 20180206 #  diffs
         # Prefer old lineno9 value, for continuity, and because it's more finegrained
+        raise 'New death cause 1d not yet supported' if cod10r == 'f'
+
         next unless (line || DeathData::COD10R_TO_LINENO9[cod10r]) == i
+
         multiple_cause_code(j)
       end
       causes.compact
@@ -60,7 +64,7 @@ def codt_codfft_extra(i, chunk_size = 75, merge_extra = false)
       codfft = death_data.codfft_1
       return codfft[(i - 1) * chunk_size..(i * chunk_size) - 1] if codfft && codfft.size > 75
 
-      result = death_data["codfft_#{i}"] || (death_data["codt_#{i}"] if i <= 5)
+      result = death_data["codfft_#{i}"] || (death_data["codt_#{i}"] if i <= 6)
       return result unless merge_extra
 
       ([result] + (i + 1..65).collect { |j| death_data["codfft_#{j}"] }).

app/models/pseudo/death_data.rb

@@ -9,7 +9,7 @@ class DeathData < ActiveRecord::Base
     # Numerics from M204
     # lower case letters from LEDR
     #  (-- 0 01 02 03 1` Y 5 6 7 9 41 92 are very rare, and only in older M204 data),
-    COD10R_VALUES = %w[-- 0 01 02 03 1` Y 1 2 3 4 5 6 7 9 10 11 12 41 92 a b c d e].freeze
+    COD10R_VALUES = %w[-- 0 01 02 03 1` Y 1 2 3 4 5 6 7 9 10 11 12 41 92 a b c d e f].freeze
     RETIND_VALUES = %w[1 Y N].freeze # Numeric values from M204, strings from LEDR
 
     # PLOACC10 is supposed to be 1 numerical character (or blank)
@@ -32,7 +32,11 @@ class DeathData < ActiveRecord::Base
     # cod10r c = c = line 10
     # cod10r d = d = line 11
     # cod10r e = e = line 12
-    COD10R_TO_LINENO9 = { 'a' => 1, 'b' => 2, 'c' => 3, 'd' => 4, 'e' => 4,
+    #
+    # From 2024-09-09, an extra cause of death 1d field has been added.
+    # For now, we're mapping this back to cause 1c in LINENO9 terms, to ensure it does not
+    # get lost, but COD10R_TO_LINENO9 should be deprecated, or used the other way around.
+    COD10R_TO_LINENO9 = { 'a' => 1, 'b' => 2, 'c' => 3, 'd' => 4, 'e' => 4, 'f' => 3,
                           '1' => 1, '2' => 2, '3' => 3, '4' => 4, '10' => 4,
                           '11' => 6, '12' => 6 }.freeze
 

config/deploy.rb

@@ -108,11 +108,6 @@
   ruby -e "require 'yaml'; puts YAML.dump('production' => { 'secret_key_base' => 'compile_me' })" > config/secrets.yml
   touch config/special_users.production.yml config/admin_users.yml config/odr_users.yml \
         config/user_yubikeys.yml
-  # Remove mini_racer CentOS 7 shim from Gemfile.lock unless needed
-  if [ -e /etc/os-release ] && \
-     [ 2 -ne $(grep -Ec '^(ID="centos"|VERSION_ID="7")$' /etc/os-release) ]; then
-    sed -i.bak -e '/mini_racer ([0-9.]*-x86_64-linux)/,+1d' Gemfile.lock
-  fi
   printf 'disable-self-update-check true\\nyarn-offline-mirror "./vendor/npm-packages-offline-cache"\\nyarn-offline-mirror-pruning false\\n' > .yarnrc
   RAILS_ENV=production bundle exec rake assets:clobber assets:precompile
   rm config/secrets.yml config/database.yml
@@ -179,14 +174,12 @@
 
 desc 'ensure additional configuration for CentOS deployments'
 task :centos_deployment_specifics do
-  if /\A(3[.]0[.][567]|3[.][123][.])/.match?(fetch(:ruby))
-    # On CentOS 7, we need a newer GCC installation to build gems for new ruby versions
-    # We'd like to do the following, but scl incorrectly handles double quotes in passed commands:
-    # set :default_shell, 'scl enable devtoolset-9 -- sh'
-    set :default_shell, <<~CMD.chomp
-      sh -c 'scl_run() { echo "$@" | scl enable devtoolset-9 -; }; scl_run "$@"'
-    CMD
-  end
+  # On CentOS 7, we need a newer GCC installation to build gems for new ruby versions
+  # We'd like to do the following, but scl incorrectly handles double quotes in passed commands:
+  # set :default_shell, 'scl enable devtoolset-9 -- sh'
+  set :default_shell, <<~CMD.chomp
+    sh -c 'scl_run() { echo "$@" | scl enable devtoolset-9 -; }; scl_run "$@"'
+  CMD
 end
 
 # ==========================================[ DEPLOY ]==========================================

config/mappings/deaths_mapping.yml

@@ -1222,3 +1222,7 @@ columns:
 - column: ward9r
   mappings:
   - field: ward9r
+- column: codt_6
+  mappings:
+  - field: codt_6
+    clean: :itself

db/migrate/20240923153521_add_codt_6_to_pseudo_deathdata.rb

@@ -0,0 +1,29 @@
+# Add column codt_6 to deathdata table
+# New field for cause of death line 1(d)
+# Previously we had:
+# CODT_1 = 1a/a
+# CODT_2 = 1b/b
+# CODT_3 = 1c/c
+# CODT_4 = II/d
+# CODT_5 = II/e
+# now we have:
+# CODT_1 = 1a/a
+# CODT_2 = 1b/b
+# CODT_3 = 1c/c
+# CODT_6 = 1d/d
+# CODT_4 = II/d
+# CODT_5 = II/e
+# Change from 2024-09-09: New field for cause of death  line 1(d) on non-neonatal deaths
+# CODT_6 = 1d/f
+# In the registration it is positioned between CODT_3 and CODT_4
+#
+# "From April 2024 a new MCCD [Medical certificate of cause of death] will
+# replace the existing one to reflect the introduction of medical examiners and
+# bring the new MCCD in line with international standards. These changes will
+# impact how certifying doctors, medical examiners and coroners capture cause
+# of death information on MCCDs/Coroner forms."
+class AddCodt6ToPseudoDeathdata < ActiveRecord::Migration[6.1]
+  def change
+    add_column :death_data, :codt_6, :string
+  end
+end

db/structure.sql

@@ -8332,6 +8332,7 @@ INSERT INTO "schema_migrations" (version) VALUES
 ('20220428152502'),
 ('20220816095442'),
 ('20230525133522'),
-('20240620121939');
+('20240620121939'),
+('20240923153521');
 
 

lib/import/brca/providers/newcastle/newcastle_handler.rb

@@ -25,6 +25,7 @@ def process_fields(record)
             add_organisationcode_testresult(genotype)
             process_test_scope(genotype, record)
             process_test_status(genotype, record)
+            process_test_type(genotype, record)
             final_results = process_variant_records(genotype, record)
             final_results.each { |cur_genotype| @persister.integrate_and_store(cur_genotype) }
           end

lib/import/colorectal/core/genocolorectal.rb

@@ -37,6 +37,9 @@ class Genocolorectal < Import::Germline::Genotype
                            'TP53' => 79,
                            'PALB2' => 3186,
                            'RNF43' => 5019,
+                           'CHEK2' => 865,
+                           'RAD51C' => 3615,
+                           'RAD51D' => 3616,
                            'VHL' => 83,
                            'ATM' => 451 }.freeze
 
@@ -62,6 +65,9 @@ class Genocolorectal < Import::Germline::Genotype
                             (?<tp53>TP53)|
                             (?<palb2>PALB2)|
                             (?<rnf43>RNF43)|
+                            (?<chek2>CHEK2)|
+                            (?<rad51c>RAD51C)|
+                            (?<rad51d>RAD51D)|
                             (?<vhl>VHL) |
                             (?<atm>ATM)/ix # Added by Francesco
 

lib/import/colorectal/providers/leeds/leeds_handler_colorectal.rb

@@ -165,11 +165,17 @@ def process_fullscreen_records(genocolorectal, record, genotypes)
           end
 
           def process_normal_fs(genocolorectal, _record, genotypes)
-            @genes_panel&.each do |gene|
+            if @genes_panel.blank?
               genocolorectal_new = genocolorectal.dup_colo
-              genocolorectal_new.add_gene_colorectal(gene)
               genocolorectal_new.add_status(@teststatus)
               genotypes << genocolorectal_new
+            else
+              @genes_panel&.each do |gene|
+                genocolorectal_new = genocolorectal.dup_colo
+                genocolorectal_new.add_gene_colorectal(gene)
+                genocolorectal_new.add_status(@teststatus)
+                genotypes << genocolorectal_new
+              end
             end
             genotypes
           end
@@ -306,6 +312,10 @@ def allocate_genes
             GENES_PANEL.each do |panel, genes|
               @genes_panel = genes if @genes_hash[panel].include?(@geno)
             end
+
+            return if @genes_panel.present?
+
+            @genes_panel = genes_from_mtype
           end
 
           # Get test status for record based on genotype
@@ -349,6 +359,21 @@ def get_genes_from_report(report)
             genes || []
           end
 
+          def genes_from_mtype
+            case @moleculartestingtype
+            when /r209|diagnostic; lynch/
+              %w[MLH1 MSH2 MSH6 PMS2]
+            when /diagnostic/
+              @indicationcategory == 'fap1&2' ? %w[APC MUTYH] : []
+            when /r210/
+              %w[MLH1 MSH2 MSH6 PMS2 EPCAM]
+            when /r211/
+              %w[APC BMPR1A EPCAM GREM1 MLH1 MSH2 MSH6 MUTYH NTHL1 PMS2 POLD1 POLE PTEN SMAD4 STK11]
+            else
+              []
+            end
+          end
+
           def add_organisationcode_testresult(genocolorectal)
             genocolorectal.attribute_map['organisationcode_testresult'] = '699C0'
           end

lib/import/delimited_file.rb

@@ -20,7 +20,7 @@ class DelimitedFile
       (1..20).collect { |i| "cod10r_#{i}" } +
       (1..20).collect { |i| "cod10rf_#{i}" } +
       (1..65).collect { |i| "codfft_#{i}" } +
-      (1..5).collect { |i| "codt_#{i}" } +
+      (1..6).collect { |i| "codt_#{i}" } +
       %w[corareat corcertt ctrypob ctryr ctydpod ctydr ctypod ctyr dester doddy dodmt dodyr doinqt
          dor emprssdm emprsshf empsecdm empsechf empstdm empsthf esttyped gor9r gorr hautpod hautr
          hropod hror] +

lib/import/helpers/brca/providers/rq3/rq3_constants.rb

@@ -50,6 +50,8 @@ module Rq3Constants
                          [0-9]+[ACGTdelinsup]+)/x
 
             NO_EVIDENCE_REGEX = /no evidence.*?[^cp]\.|no further.*?[^cp]\./i
+            NO_EVIDENCE_EXCEPTION_REGEX = /however\sthe\spreviously\sreported\sheterozygous\svariant\sc.*\sin\sthe\s\S+
+            \sgene\sis\snow\sconsidered\sa\svariant\sof\sunknown\ssignificance/ix
             PROTEIN_REGEX = /p\.\(?(?<impact>.[a-z]+[0-9]+[a-z]+([^[:alnum:]][0-9]+)?|
             [a-z]+[0-9]+[^[:alnum:]])/ix
 

lib/import/helpers/brca/providers/rq3/rq3_helper.rb

@@ -103,14 +103,28 @@ def process_noevidence_records
               true_variant = @testresult.gsub(NO_EVIDENCE_REGEX, '')
               negativegenes = no_evidence.scan(BRCA_REGEX).flatten - true_variant.
                               scan(BRCA_REGEX).flatten
-              process_negative_genes(negativegenes)
-              @genotype.add_gene(unique_brca_genes_from(true_variant).join)
-              process_cdna(true_variant, @genotype)
-              process_protein_impact(true_variant, @genotype)
-              process_exon(true_variant, @genotype)
+              no_evidence_exception= @testresult.scan(NO_EVIDENCE_EXCEPTION_REGEX).join
+              if no_evidence_exception.size.positive?
+                process_no_evidence_exception(no_evidence_exception)
+              else
+                process_negative_genes(negativegenes)
+                @genotype.add_gene(unique_brca_genes_from(true_variant).join)
+                process_cdna(true_variant, @genotype)
+                process_protein_impact(true_variant, @genotype)
+                process_exon(true_variant, @genotype)
+                add_variantpathclass_uv_records(@genotype)
+                @genotypes.append(@genotype)
+              end 
+            end
+
+            def process_no_evidence_exception(testcolumn)
+              @genotype.add_gene(unique_brca_genes_from(testcolumn).join)
+              process_cdna(testcolumn, @genotype)
+              process_protein_impact(testcolumn, @genotype)
+              process_exon(testcolumn, @genotype)
               add_variantpathclass_uv_records(@genotype)
               @genotypes.append(@genotype)
-            end
+            end 
 
             def process_testresult_cdna_variants
               if (@testresult.scan(CDNA_REGEX).size > 1) ||