Strain parsing

- Improve strain parsing
- See also #28
- Implement check for Recommendation 19

app/helpers/names_helper.rb

@@ -1,37 +1,17 @@
 module NamesHelper
-  def strain_html(str, opts = {})
+  def strain_html(name, opts = {})
     opts[:ext] = true if opts[:ext].nil?
-
-    ext  = opts[:ext] ? '<sup class="fas fa-external-link-alt "> </sup>' : ''
-    collections = {
-      DSM:  'https://www.dsmz.de/collection/catalogue/details/culture/DSM-',
-      JCM:  'https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=',
-      KCTC: 'https://kctc.kribb.re.kr/collection/view?sn=',
-      ATCC: 'https://www.atcc.org/products/',
-      BCRC: 'https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=',
-      LMG:  'https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=',
-      NBRC: 'https://www.nite.go.jp/nbrc/catalogue/' \
-            'NBRCCatalogueDetailServlet?ID=IFO&CAT=',
-      IFO:  'https://www.nite.go.jp/nbrc/catalogue/' \
-            'NBRCCatalogueDetailServlet?ID=IFO&CAT=',
-      NCTC: 'https://www.culturecollections.org.uk/products/bacteria/' \
-            'detail.jsp?collection=nctc&refId=NCTC+',
-      CIP:  'https://catalogue-crbip.pasteur.fr/' \
-            'fiche_catalogue.xhtml?crbip=CIP%20',
-      PCC:  'https://catalogue-crbip.pasteur.fr/' \
-            'fiche_catalogue.xhtml?crbip=PCC%20',
-      CCUG: 'https://www.ccug.se/strain?id=',
-      NRRL: 'https://nrrl.ncaur.usda.gov/cgi-bin/usda/prokaryote/' \
-            'report.html?nrrlcodes='
-    }
-    o = sanitize(str).gsub(/\s*=\s*/, ' = ')
-    collections.each do |k, v|
-      o = o.gsub(
-        /(?<=Strain: | = |^)(#{k})[ -]([\d\-A-Za-z]+)(?= = |$)/,
-        "<a href='#{v}\\2' target='_blank'>\\1 \\2 #{ext}</a>"
-      )
-    end
-    o.html_safe
+    ext = opts[:ext] ? '<sup class="fas fa-external-link-alt "> </sup>' : ''
+    parsed = name.type_is_strain? ? :type_strain_parsed : :genome_strain_parsed
+    name.send(parsed).map do |str|
+      if str.is_a? Hash
+        '<a href="%s" target="_blank">%s %s</a>' % [
+          str[:url], sanitize(str[:accession]), ext
+        ]
+      else
+        str
+      end
+    end.join(' = ').html_safe
   end
 
   def link_to_name_type(name)
@@ -51,7 +31,7 @@ def link_to_name_type(name)
           fa_icon('external-link-alt', class: 'ml-1')
       end
     elsif name.type_is_strain?
-      strain_html(name.type_text)
+      content_tag(:span, 'Strain: ') + strain_html(name)
     else
       name.type_text
     end

app/models/name.rb

@@ -234,6 +234,30 @@ def type_material_hash
     def type_material_name(type)
       type_material_hash[type.to_sym]&.[](:name)
     end
+
+    def culture_collections
+      {
+        DSM:  'https://www.dsmz.de/collection/catalogue/details/culture/DSM-%s',
+        JCM:  'https://www.jcm.riken.jp/cgi-bin/jcm/jcm_number?JCM=%s',
+        KCTC: 'https://kctc.kribb.re.kr/collection/view?sn=%s',
+        ATCC: 'https://www.atcc.org/products/%s',
+        BCRC: 'https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=%s',
+        LMG:  'https://bccm.belspo.be/catalogues/lmg-strain-details?NUM=%s',
+        NBRC: 'https://www.nite.go.jp/nbrc/catalogue/' \
+              'NBRCCatalogueDetailServlet?ID=IFO&CAT=%s',
+        IFO:  'https://www.nite.go.jp/nbrc/catalogue/' \
+              'NBRCCatalogueDetailServlet?ID=IFO&CAT=%s',
+        NCTC: 'https://www.culturecollections.org.uk/products/bacteria/' \
+              'detail.jsp?collection=nctc&refId=NCTC+%s',
+        CIP:  'https://catalogue-crbip.pasteur.fr/' \
+              'fiche_catalogue.xhtml?crbip=CIP%%20%s',
+        PCC:  'https://catalogue-crbip.pasteur.fr/' \
+              'fiche_catalogue.xhtml?crbip=PCC%%20%s',
+        CCUG: 'https://www.ccug.se/strain?id=%s',
+        NRRL: 'https://nrrl.ncaur.usda.gov/cgi-bin/usda/prokaryote/' \
+              'report.html?nrrlcodes=%s'
+      }
+    end
   end
 
   # ============ --- STATUS --- ============
@@ -663,6 +687,41 @@ def type_genome
     end
   end
 
+  def type_strain_parsed
+    return {} unless type_is_strain?
+    strain_parsed(type_accession)
+  end
+
+  def genome_strain_parsed
+    return {} unless genome_strain?
+    strain_parsed(genome_strain)
+  end
+
+  def strain_parsed(strain)
+    strain.split(/ *= */).map do |str|
+      parts = str.split(/[ -]+/, 2)
+      coll = parts.count == 2 ? parts[0].upcase.to_sym : nil
+
+      if url_base = self.class.culture_collections[coll]
+        {
+          collection: coll,
+          accession: parts.join(' '),
+          url: url_base % parts[1]
+        }
+      else
+        str
+      end
+    end
+  end
+
+  def genome_strain_collections
+    return unless genome_strain?
+
+    genome_strain_parsed
+      .map { |i| i.is_a?(Hash) ? i[:collection] : nil }
+      .compact.uniq.count
+  end
+
   def expected_type_rank
     return nil if !rank? || %w[species subspecies domain].include?(rank)
     return 'species' if rank == 'genus'

app/models/name/quality_checks.rb

@@ -360,7 +360,12 @@ class QcWarning
       # - Rule 18c requires the implementation of neotype designations
       #   [TODO: issue #12] no checks are to be implemented
       # - Rule 19 is implied by the SeqCode Registry structure
-      # - Recommendation 19 [TODO: Checklist, TODO: issue #28]:
+      # - Recommendation 19:
+      unavailable_reference_strain: {
+        message: 'If isolated, reference strains should be submitted to two ' \
+                 'culture collections',
+        recommendations: %w[19]
+      }.merge(@@link_to_edit_type),
       #   When a strain belonging to a taxon named under the SeqCode is
       #   isolated, a reference strain should be designated and submitted to two
       #   culture collections in different countries. Reference strains have no
@@ -772,6 +777,9 @@ def qc_warnings
 
     if type_is_genome?
       @qc_warnings.add(:ambiguous_type_genome) # check
+      if genome_strain? && genome_strain_collections < 2
+        @qc_warnings.add(:unavailable_reference_strain)
+      end
       @qc_warnings.add(:missing_genome_kind) unless type_genome.kind.present?
       @qc_warnings.add(:sequence_not_found) if type_genome.auto_failed.present?
 

app/views/names/_name_pdf.html.erb

@@ -39,7 +39,7 @@
       <div class="avoid-page-break">
         <dt>Reference Strain</dt>
         <dd>
-          <%= strain_html(name.genome_strain, ext: false) %>
+          <%= strain_html(name, ext: false) %>
         </dd>
       </div>
     <% end %>

app/views/names/_nomenclature.html.erb

@@ -76,13 +76,13 @@
     <dt>
       <%= fa_icon('flask') %> Reference strain
       <%= help_message('Reference Strain') do %>
-        This strain indicates the source of the genome used as type
-        material. However, the strain itself is not considered
-        type material and does not have standing in nomenclature.
+        This cultured strain indicates the source of the genome used as type
+        material. However, the strain itself is not considered type material and
+        does not have standing in nomenclature.
       <% end %>
     </dt>
     <dd>
-      <%= strain_html(@name.genome_strain) %>
+      <%= strain_html(@name) %>
     </dd>
   <% end %>
 

app/views/names/edit_type.html.erb

@@ -34,7 +34,7 @@
     <div id="name_genome_strain_container">
       <%=
         f.input(
-          :genome_strain, label: 'Genome strain (an isolate)',
+          :genome_strain, label: 'Genome strain (an isolate or other culture)',
           hint: 'Strain associated to the type genome. ' \
                 'Use "=" to separate multiple equivalent strain accessions.'
         )