t2-server 0.6.0 → 0.6.1

data/CHANGES.rdoc

@@ -1,5 +1,11 @@
 = Changes log for the T2 Ruby Gem
 
+== Version 0.6.1
+
+* Store server addresses internally as URI objects.
+* t2-run-workflow: Add a no-wait option.
+* Fix input value escaping to allow XML in inputs.
+
 == Version 0.6.0
 
 * Add a new API call Run#get_output_ports

data/LICENCE.rdoc

@@ -1,4 +1,4 @@
-Copyright (c) 2010, The University of Manchester, UK.
+Copyright (c) 2010, 2011 The University of Manchester, UK.
 
 All rights reserved.
 

data/README.rdoc

@@ -1,12 +1,12 @@
 = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
 
 Authors::     Robert Haines
-Gem Version:: 0.6.0
+Gem Version:: 0.6.1
 API Version:: 2.2a1
 Contact::     mailto:rhaines@manchester.ac.uk
 URL::         http://taverna.sourceforge.net/
 Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
-Copyright::   (c) 2010 The University of Manchester, UK
+Copyright::   (c) 2010, 2011 The University of Manchester, UK
 
 
 == Synopsis

data/bin/t2-delete-runs

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/bin/t2-run-workflow

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -42,6 +42,7 @@ wkf_file = ""
 output_refs = false
 baclava_out = ""
 delete_run = false
+no_wait = false
 opts = OptionParser.new do |opt|
   opt.banner = "Usage: t2-run-workflow [options] server-address"
   opt.separator ""
@@ -72,6 +73,10 @@ opts = OptionParser.new do |opt|
       baclava_out = "out.xml"
     end
   end
+  opt.on("-n", "--no-wait", "Do not wait for workflow to finish, return " +
+    "once it has started running") do |val|
+      no_wait = true
+  end
   opt.on("-r", "--output-refs", "Return URIs that point to the data items " +
     "of the output rather than the data items themselves.") do |val|
     output_refs = val
@@ -142,6 +147,11 @@ run.set_baclava_output(baclava_out) unless baclava_out == ""
 # start run and wait until it is finished
 run.start
 puts "Started at #{run.start_time}"
+
+# bail out if user doesn't want to wait
+exit 0 if no_wait
+
+# otherwise wait
 print "Running"
 run.wait(:progress => true)
 puts "Finished at #{run.finish_time}"

data/bin/t2-server-info

@@ -1,5 +1,5 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/lib/t2-server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -43,7 +43,7 @@ require 't2-server/run'
 #   Taverna 2 Server instance.
 module T2Server
   # The version of this library
-  GEM_VERSION = "0.6.0"
+  GEM_VERSION = "0.6.1"
   # The version of the Taverna 2 Server API that this library can interface with
   API_VERSION = "2.2a1"
 end

data/lib/t2-server/exceptions.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/lib/t2-server/run.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/lib/t2-server/server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -45,7 +45,7 @@ module T2Server
 
     private_class_method :new
 
-    # The URI of this server instance as a String.
+    # The URI of this server instance.
     attr_reader :uri
     
     # The maximum number of runs that this server will allow at any one time.
@@ -59,12 +59,11 @@ module T2Server
     # :stopdoc:
     # New is private but rdoc does not get it right! Hence :stopdoc: section.
     def initialize(uri, username, password)
-      @uri = uri.strip_path
-      uri = URI.parse(@uri)
-      @host = uri.host
-      @port = uri.port
-      @base_path = uri.path
-      @rest_path = uri.path + "/rest"
+      @uri = uri
+      @host = @uri.host
+      @port = @uri.port
+      @base_path = @uri.path
+      @rest_path = @uri.path + "/rest"
 
       # set up http connection
       @http = Net::HTTP.new(@host, @port)
@@ -72,8 +71,8 @@ module T2Server
       # use ssl?
       @ssl = uri.scheme == "https"
       if ssl?
-        @username = uri.user || username
-        @password = uri.password || password
+        @username = username
+        @password = password
         
         @http.use_ssl = true
         @http.verify_mode = OpenSSL::SSL::VERIFY_NONE
@@ -102,12 +101,23 @@ module T2Server
     # The username and password can also be passed in separately.
     # A Server instance is returned that represents the connection.
     def Server.connect(uri, username="", password="")
+      # we want to use URIs here but strings can be passed in
+      if !uri.instance_of? URI
+        uri = URI.parse(uri.strip_path);
+      end
+      
+      # strip username and password from the URI if present
+      username = uri.user || username
+      password = uri.password || password
+      new_uri = URI::HTTP.new(uri.scheme, nil, uri.host, uri.port, nil,
+        uri.path, nil, nil, nil);
+      
       # see if we've already got this server
-      server = @@servers.find {|s| s.uri == uri}
+      server = @@servers.find {|s| s.uri == new_uri}
 
       if !server
         # no, so create new one and return it
-        server = new(uri, username, password)
+        server = new(new_uri, username, password)
         @@servers << server
       end
       
@@ -235,8 +245,9 @@ module T2Server
         run = run(run)
       end
 
+      xml_value = XML::Node.new_text(value)
       path = "#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}"
-      set_attribute(path, Fragments::RUNINPUTVALUE % value, "application/xml")
+      set_attribute(path, Fragments::RUNINPUTVALUE % xml_value, "application/xml")
     rescue AttributeNotFoundError => e
       if get_runs.has_key? run.uuid
         raise e
@@ -256,8 +267,9 @@ module T2Server
         run = run(run)
       end
 
+      xml_value = XML::Node.new_text(filename)
       path = "#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}"
-      set_attribute(path, Fragments::RUNINPUTFILE % filename, "application/xml")
+      set_attribute(path, Fragments::RUNINPUTFILE % xml_value, "application/xml")
     rescue AttributeNotFoundError => e
       if get_runs.has_key? run.uuid
         raise e

data/lib/t2-server/xml.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/lib/t2server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/test/tc_paths.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/test/tc_run.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -68,6 +68,14 @@ class TestRun < Test::Unit::TestCase
     # deletion
     assert(@run.delete)
 
+    # run with xml input
+    @run = T2Server::Run.create($address, $wkf_xml)
+    @run.set_input("xml","<hello><yes>hello</yes><no>everybody</no><yes>world</yes></hello>")
+    @run.set_input("xpath","//yes")
+    @run.start
+    @run.wait
+    assert_equal(@run.get_output("nodes"), ["hello", "world"])
+
     # run with file input
     @run = T2Server::Run.create($address, $wkf_pass)
 

data/test/tc_server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #

data/test/ts_t2server.rb

@@ -1,4 +1,4 @@
-# Copyright (c) 2010, The University of Manchester, UK.
+# Copyright (c) 2010, 2011 The University of Manchester, UK.
 #
 # All rights reserved.
 #
@@ -57,6 +57,7 @@ require 'tc_paths'
 if $address != ""
   $wkf_pass   = File.read("test/workflows/pass_through.t2flow")
   $wkf_lists  = File.read("test/workflows/empty_list.t2flow")
+  $wkf_xml    = File.read("test/workflows/xml_xpath.t2flow")
   $list_input = "test/workflows/empty_list_input.baclava"
   $file_input = "test/workflows/in.txt"
 

data/test/workflows/xml_xpath.t2flow

@@ -0,0 +1,137 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="bac27078-6e26-48b0-a127-56146f1eff2b" role="top"><name>Workflow1</name><inputPorts><port><name>xml</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>xpath</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>nodes</name><annotations /></port><port><name>xml_nodes</name><annotations /></port></outputPorts><processors><processor><name>get_element</name><inputPorts><port><name>xml-text</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>nodelistAsXML</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelistAsXML" to="nodelistAsXML" /><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+  <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker</localworkerName>
+  <script>import org.dom4j.Document;
+import org.dom4j.Node;
+import org.dom4j.io.SAXReader;
+
+SAXReader reader = new SAXReader(false);
+reader.setIncludeInternalDTDDeclarations(false);
+reader.setIncludeExternalDTDDeclarations(false);
+
+Document document = reader.read(new StringReader(xmltext));
+List nodelist = document.selectNodes(xpath);
+
+// Process the elements in the nodelist
+ArrayList outputList = new ArrayList();
+ArrayList outputXmlList = new ArrayList();
+
+String val = null;
+String xmlVal = null;
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
+	Node element = (Node) iter.next();
+	xmlVal = element.asXML();
+	val = element.getStringValue();
+	if (val != null &amp;&amp; !val.equals("")) {
+		outputList.add(val);
+		outputXmlList.add(xmlVal);
+	}
+
+}
+
+List nodelist=outputList;
+List nodelistAsXML=outputXmlList;</script>
+  <dependencies>
+    <string>dom4j:dom4j:1.6</string>
+  </dependencies>
+  <classLoaderSharing>workflow</classLoaderSharing>
+  <localDependencies />
+  <artifactDependencies>
+    <net.sf.taverna.raven.repository.BasicArtifact>
+      <groupId>dom4j</groupId>
+      <artifactId>dom4j</artifactId>
+      <version>1.6</version>
+      <hashCode>716010169</hashCode>
+    </net.sf.taverna.raven.repository.BasicArtifact>
+  </artifactDependencies>
+  <inputs>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+      <handledReferenceSchemes />
+      <translatedElementType>java.lang.String</translatedElementType>
+      <allowsLiteralValues>true</allowsLiteralValues>
+      <name>xpath</name>
+      <depth>0</depth>
+      <mimeTypes>
+        <string>'text/plain'</string>
+      </mimeTypes>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+      <handledReferenceSchemes />
+      <translatedElementType>java.lang.String</translatedElementType>
+      <allowsLiteralValues>true</allowsLiteralValues>
+      <name>xml-text</name>
+      <depth>0</depth>
+      <mimeTypes>
+        <string>'text/xml'</string>
+      </mimeTypes>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+  </inputs>
+  <outputs>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+      <granularDepth>1</granularDepth>
+      <name>nodelist</name>
+      <depth>1</depth>
+      <mimeTypes>
+        <string>l('text/plain')</string>
+      </mimeTypes>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+      <granularDepth>1</granularDepth>
+      <name>nodelistAsXML</name>
+      <depth>1</depth>
+      <mimeTypes>
+        <string>l('text/plain')</string>
+      </mimeTypes>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+  </outputs>
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+  <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+  <backoffFactor>1.0</backoffFactor>
+  <initialDelay>1000</initialDelay>
+  <maxDelay>5000</maxDelay>
+  <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="xml-text" depth="0" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>get_element</processor><port>xml-text</port></sink><source type="dataflow"><port>xml</port></source></datalink><datalink><sink type="processor"><processor>get_element</processor><port>xpath</port></sink><source type="dataflow"><port>xpath</port></source></datalink><datalink><sink type="dataflow"><port>nodes</port></sink><source type="processor"><processor>get_element</processor><port>nodelist</port></source></datalink><datalink><sink type="dataflow"><port>xml_nodes</port></sink><source type="processor"><processor>get_element</processor><port>nodelistAsXML</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>bac27078-6e26-48b0-a127-56146f1eff2b</identification>
+      </annotationBean>
+      <date>2011-05-13 10:10:44.677 BST</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>221474df-64d5-4da5-bd27-244625a8bcfa</identification>
+      </annotationBean>
+      <date>2011-05-13 10:04:40.297 BST</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>00e06598-e7fa-4509-8276-4fbee7d8e525</identification>
+      </annotationBean>
+      <date>2011-05-13 10:01:30.899 BST</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>082e06b0-6bfa-4287-a109-0163fa81fd9b</identification>
+      </annotationBean>
+      <date>2011-05-13 09:54:10.765 BST</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: t2-server
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 5
   prerelease: false
   segments: 
   - 0
   - 6
-  - 0
-  version: 0.6.0
+  - 1
+  version: 0.6.1
 platform: ruby
 authors: 
 - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-10 00:00:00 +00:00
+date: 2011-05-13 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -94,6 +94,7 @@ files:
 - test/workflows/pass_through.t2flow
 - test/workflows/empty_list_input.baclava
 - test/workflows/empty_list.t2flow
+- test/workflows/xml_xpath.t2flow
 - test/workflows/in.txt
 - test/ts_t2server.rb
 - README.rdoc