Safer linking from SRA to BioSample

A strange issue with NCBI was causing the wrong BioSamples to be linked. This has been resolved now.
seq-code · Nov 4, 2024 · cc7b358 · cc7b358
1 parent ec1fe75
commit cc7b358
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Showing 3 changed files with 33 additions and 9 deletions.
diff --git a/app/models/genome/external_resources.rb b/app/models/genome/external_resources.rb
@@ -55,10 +55,27 @@ def external_sra_to_biosamples(acc)
           'XREF_LINK[DB[text() = "ENA-SAMPLE"]]/ID'
       ).map(&:text)
     elsif ng.xpath('//EXPERIMENT_SET').present?
-      ng.xpath(
-        '//EXPERIMENT_SET/EXPERIMENT/DESIGN/SAMPLE_DESCRIPTOR/' \
-          'IDENTIFIERS/PRIMARY_ID'
-      ).map(&:text)
+      # Unfortunately, we should prefer external IDs over primary IDs because
+      # NCBI E-Utils has a strange tendency to return the wrong biosample when
+      # using SRS... accessions. For example, see:
+      # 
+      # - https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample
+      #   &id=SRS22988103&rettype=xml&retmode=text
+      # - https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample
+      #   &id=SAMN13193749&rettype=xml&retmode=text
+      # 
+      # The first is using the accession SRS22988103 but it (wrongly) retrieves
+      # data for SAMN22988103 (= SRS11001113). Apparently the backend code
+      # simply strips off the alphabetic prefix and uses the numeric part
+      # without checking
+      sample_id =
+        ng.xpath(
+          '//EXPERIMENT_SET/EXPERIMENT/DESIGN/SAMPLE_DESCRIPTOR/IDENTIFIERS'
+        )
+      biosample_id =
+        sample_id.xpath('EXTERNAL_ID[@namespace="BioSample"]').map(&:text)
+      biosample_id.present? ? biosample_id :
+        sample_id.xpath('PRIMARY_ID').map(&:text)
     else
       [] # Unknown XML specification
     end
@@ -82,7 +99,7 @@ def external_biosample_hash_ebi(acc)
 
     ng = Nokogiri::XML(body)
     {}.tap do |hash|
-      h = {}
+      h = { api: 'EBI' }
       h[:title] = ng.xpath('//SAMPLE_SET/SAMPLE/TITLE').text
       h[:description] = ng.xpath('//SAMPLE_SET/SAMPLE/DESCRIPTION').text
       h[:attributes] = Hash[
@@ -103,7 +120,7 @@ def external_biosample_hash_ncbi(acc)
 
     ng = Nokogiri::XML(body)
     {}.tap do |hash|
-      h = {}
+      h = { api: 'NCBI' }
       h[:title] = ng.xpath('//BioSampleSet/BioSample/Description/Title').text
       h[:description] =
         ng.xpath('//BioSampleSet/BioSample/Description/Comment/Paragraph').text

diff --git a/app/views/genomes/_samples.html.erb b/app/views/genomes/_samples.html.erb
@@ -108,9 +108,16 @@
         <ul>
           <% @genome.source_hash[:samples].each do |acc, sample| %>
             <% id = modal(acc, size: 'lg') do %>
-              <% if sample[:from_sra] %>
+              <% if sample[:from_sra] || sample[:api] %>
                 <div class="alert alert-info">
-                  Retrieved via <%= to_sentence(sample[:from_sra]) %>
+                  Metadata retrieved
+                  <% if sample[:api] %>
+                    using the <%= sample[:api] %> API
+                  <% end %>
+                  <% if sample[:from_sra] %>
+                    via <%= to_sentence(sample[:from_sra]) %>
+                    (linked through the EBI API)
+                  <% end %>
                 </div>
               <% end %>
               <p class="lead mx-2">

diff --git a/config/environments/development.rb b/config/environments/development.rb
@@ -62,7 +62,7 @@
   config.file_watcher = ActiveSupport::EventedFileUpdateChecker
 
   # Turn off API checks for external services
-  config.bypass_external_apis = true
+  config.bypass_external_apis = !ENV['ALLOW_EXTERNAL_APIS'].present?
 
   # DataCite access
   config.datacite = {