Validate fasta sequence ID before checking for its inclusion in the DB

Author: tadast

lib/sequenceserver/database.rb

@@ -52,6 +52,8 @@ def retrieve(accession, coords = nil)
     # Returns true if the database contains the given sequence id.
     # Returns false otherwise.
     def include?(id)
+      raise ArgumentError, "Invalid sequence id: #{id}" unless id =~ SequenceServer::BLAST::VALID_SEQUENCE_ID
+
       cmd = "blastdbcmd -entry '#{id}' -db #{name}"
       sys(cmd, path: config[:bin]) rescue false
     end

spec/database_spec.rb

@@ -27,8 +27,24 @@ module SequenceServer
       Database[id].first
     end
 
-    it 'knows if a given accession is in the database or not' do
-      solenopsis_protein_database.include?('SI2.2.0_06267').should be_truthy
+    describe '#include?' do
+      it 'knows if a given accession is present in the database' do
+        expect(solenopsis_protein_database).to include('SI2.2.0_06267')
+      end
+
+      it 'knows if a given accession is absent in the database' do
+        expect(solenopsis_protein_database).not_to include('LOL.2.0_404')
+      end
+
+      it 'validates the id' do
+        expect do
+          solenopsis_protein_database.include?("';hi")
+        end.to raise_error(ArgumentError, "Invalid sequence id: ';hi")
+      end
+    end
+
+    describe '#retrieve' do
+
     end
   end
 end