add more high level tests for xml and json output

unipept · Jun 21, 2015 · 85f7a96 · 85f7a96
1 parent 9868271
commit 85f7a96
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diff --git a/test/commands/unipept/test_pept2lca.rb b/test/commands/unipept/test_pept2lca.rb
@@ -61,5 +61,30 @@ def test_run_with_fasta_multiple_batches
       assert(lines.next.start_with? '>tost,AALTER,1,root,no rank')
       assert_raises(StopIteration) { lines.next }
     end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format json >test AALTER AALER >tost AALTER))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2lca --host http://api.unipept.ugent.be --batch 2 --format xml >test AALTER AALER >tost AALTER))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end
diff --git a/test/commands/unipept/test_pept2prot.rb b/test/commands/unipept/test_pept2prot.rb
@@ -47,5 +47,30 @@ def test_run_with_fasta_multiple_batches
       assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
       assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
     end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be --batch 2 --format json >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2prot --host http://api.unipept.ugent.be --batch 2 --format xml >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end
diff --git a/test/commands/unipept/test_pept2taxa.rb b/test/commands/unipept/test_pept2taxa.rb
@@ -47,5 +47,30 @@ def test_run_with_fasta_multiple_batches
       assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
       assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
     end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be --batch 2 --format json >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(pept2taxa --host http://api.unipept.ugent.be --batch 2 --format xml >test EGGAGSSTGQR ENFVYIAK >tost EGGAGSSTGQR))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end
diff --git a/test/commands/unipept/test_taxa2lca.rb b/test/commands/unipept/test_taxa2lca.rb
@@ -35,5 +35,29 @@ def test_run
       assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
       assert(lines.next.start_with? '1678,Bifidobacterium,genus')
     end
+
+    def test_run_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxa2lca --host http://api.unipept.ugent.be --format xml 216816 1680))
+      end
+      lines = out.each_line
+      output = lines.to_a.join('').chomp
+      assert_equal('', err)
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+    end
+
+    def test_run_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxa2lca --host http://api.unipept.ugent.be --format json 216816 1680))
+      end
+      lines = out.each_line
+      output = lines.to_a.join('').chomp
+      assert_equal('', err)
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(!output.include?(']['))
+    end
   end
 end
diff --git a/test/commands/unipept/test_taxonomy.rb b/test/commands/unipept/test_taxonomy.rb
@@ -45,5 +45,30 @@ def test_run_with_fasta_multiple_batches
       assert(lines.select { |line| line.start_with? '>test,216816,' }.size >= 1)
       assert(lines.select { |line| line.start_with? '>tost,1,' }.size >= 1)
     end
+
+    def test_run_with_fasta_multiple_batches_json
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxonomy --host http://api.unipept.ugent.be --batch 2 --format json >test 1 216816 >tost 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '[')
+      assert(output.end_with? ']')
+      assert(!output.include?('}{'))
+      assert(output.include? 'fasta_header')
+    end
+
+    def test_run_with_fasta_multiple_batches_xml
+      out, err = capture_io_while do
+        Commands::Unipept.run(%w(taxonomy --host http://api.unipept.ugent.be --batch 2 --format xml >test 1 216816 >tost 1))
+      end
+      lines = out.each_line
+      assert_equal('', err)
+      output = lines.to_a.join('').chomp
+      assert(output.start_with? '<results>')
+      assert(output.end_with? '</results>')
+      assert(output.include? '<fasta_header>')
+    end
   end
 end