Fake list inputs with baclava.

If a workflow has any ports of depth > 0 then the inputs are converted to
baclava format and uploaded as a single document. This includes local files but
remote files can not be handled this way.

Tests have been updated to include checks for mixed input depth workflows.

Rakefile

@@ -67,6 +67,7 @@ spec = Gem::Specification.new do |s|
   s.add_development_dependency('libxml-ruby', '>= 1.1.4')
   s.add_development_dependency('nokogiri', '>= 1.5.0')
   s.add_development_dependency('rdoc', '>= 3.9.4')
+  s.add_runtime_dependency('taverna-baclava', '~> 1.0.0')
   s.add_runtime_dependency('hirb', '>= 0.4.0')
 end
 

lib/t2-server/run.rb

@@ -32,6 +32,8 @@
 
 require 'base64'
 require 'time'
+require 'rubygems'
+require 'taverna-baclava'
 
 module T2Server
 
@@ -328,7 +330,7 @@ def start
       raise RunStateError.new(state, :initialized) if state != :initialized
 
       # set all the inputs
-      _set_all_inputs unless baclava_input?
+      _check_and_set_inputs unless baclava_input?
 
       @server.set_run_attribute(@identifier, @links[:status],
         state_to_text(:running), "text/plain", @credentials)
@@ -877,6 +879,20 @@ def download_output_data(path, range = nil)
 
     private
 
+    # Check each input to see if it requires a list input and call the
+    # requisite upload method for the entire set of inputs.
+    def _check_and_set_inputs
+      lists = false
+      input_ports.each_value do |port|
+        if port.depth > 0
+          lists = true
+          break
+        end
+      end
+
+      lists ? _fake_lists : _set_all_inputs
+    end
+
     # Set all the inputs on the server. The inputs must have been set prior to
     # this call using the InputPort API.
     def _set_all_inputs
@@ -906,6 +922,33 @@ def _set_all_inputs
       end
     end
 
+    # Fake being able to handle lists as inputs by converting everything into
+    # one big baclava document and uploading that. This has to be done for all
+    # inputs or none at all. The inputs must have been set prior to this call
+    # using the InputPort API.
+    def _fake_lists
+      data_map = {}
+
+      input_ports.each_value do |port|
+        next unless port.set?
+
+        if port.file?
+          unless port.remote_file?
+            file = File.read(port.file)
+            data_map[port.name] = Taverna::Baclava::Node.new(file)
+          end
+        else
+          data_map[port.name] = Taverna::Baclava::Node.new(port.value)
+        end
+      end
+
+      # Create and upload the baclava data.
+      baclava = Taverna::Baclava::Writer.write(data_map)
+      upload_data(baclava, "in.baclava")
+      @server.set_run_attribute(@identifier, @links[:baclava], "in.baclava",
+        "text/plain", @credentials)
+    end
+
     # Check that the uri passed in is suitable for credential use:
     #  * rserve uris must not have a path.
     #  * http(s) uris must have at least "/" as their path.

test/tc_run.rb

@@ -79,6 +79,41 @@ def test_status_codes
     end
   end
 
+  # Test run with list inputs
+  def test_run_list_input
+    T2Server::Run.create($uri, $wkf_lists, $creds, $conn_params) do |run|
+      many = [[["boo"]], [["", "Hello"]], [], [[], ["test"], []]]
+      single = [1, 2, 3, 4, 5]
+      single_out = single.map { |v| v.to_s } # Taverna outputs strings!
+
+      run.input_port("SINGLE_IN").value = single
+      run.input_port("MANY_IN").value = many
+      assert_nothing_raised { run.start }
+      assert(run.running?)
+      run.wait
+
+      assert_equal(run.output_port("MANY").value, many)
+      assert_equal(run.output_port("SINGLE").value, single_out)
+    end
+  end
+
+  # Test run with a list and file input
+  def test_run_list_and_file
+    T2Server::Run.create($uri, $wkf_l_v, $creds, $conn_params) do |run|
+      list = ["one", 2, :three]
+      list_out = list.map { |v| v.to_s }
+
+      run.input_port("list_in").value = list
+      run.input_port("singleton_in").file = $file_input
+      assert_nothing_raised { run.start }
+      assert(run.running?)
+      run.wait
+
+      assert_equal(run.output_port("list_out").value, list_out)
+      assert_equal(run.output_port("singleton_out").value, "Hello, World!")
+    end
+  end
+
   # Test run with xml input
   def test_run_xml_input
     T2Server::Run.create($uri, $wkf_xml, $creds, $conn_params) do |run|

test/ts_t2server.rb

@@ -77,6 +77,7 @@
 
   $wkf_pass   = File.read("test/workflows/pass_through.t2flow")
   $wkf_lists  = File.read("test/workflows/empty_list.t2flow")
+  $wkf_l_v    = File.read("test/workflows/list_and_value.t2flow")
   $wkf_xml    = File.read("test/workflows/xml_xpath.t2flow")
   $wkf_fail   = File.read("test/workflows/always_fail.t2flow")
   $wkf_errors = File.read("test/workflows/list_with_errors.t2flow")

test/workflows/list_and_value.t2flow

@@ -0,0 +1,12 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="2d5f4961-acc0-43c4-989d-c0249e9695a6" role="top"><name>Workflow3</name><inputPorts><port><name>singleton_in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>list_in</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>list_out</name><annotations /></port><port><name>singleton_out</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>list_out</port></sink><source type="dataflow"><port>list_in</port></source></datalink><datalink><sink type="dataflow"><port>singleton_out</port></sink><source type="dataflow"><port>singleton_in</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>2d5f4961-acc0-43c4-989d-c0249e9695a6</identification>
+      </annotationBean>
+      <date>2012-03-13 17:05:40.688 GMT</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>