t2-server 0.9.1 → 0.9.2

data/t2-server.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "t2-server"
-  s.version = "0.9.1"
+  s.version = "0.9.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Robert Haines"]

data/test/tc_admin.rb

@@ -37,14 +37,17 @@ class TestAdmin < Test::Unit::TestCase
   def test_admin
     T2Server::Server.new($uri, $conn_params) do |server|
 
-      # unauthorized
+      # Test for a user that we know isn't configured on the server.
       assert_raise(T2Server::AuthorizationError) do
         server.administrator(T2Server::HttpBasic.new("u", "p"))
       end
 
+      # Test for a user that is in the system but may or may not be a
+      # superuser. If the user is not a superuser then don't perform any more
+      # tests on the admin resource.
       begin
         server.administrator($creds)
-      rescue T2Server::T2ServerError => e
+      rescue T2Server::AccessForbiddenError => e
         # ignore, just don't run more tests
         return
       end

data/test/tc_run.rb

@@ -79,6 +79,17 @@ class TestRun < Test::Unit::TestCase
     end
   end
 
+  # Test run with no input or output
+  def test_run_no_ports
+    T2Server::Run.create($uri, $wkf_no_io, $creds, $conn_params) do |run|
+      assert_nothing_raised { run.input_ports }
+      assert_nothing_raised { run.start }
+      assert(run.running?)
+      run.wait
+      assert_nothing_raised { run.output_ports }
+    end
+  end
+
   # Test run with list inputs
   def test_run_list_input
     T2Server::Run.create($uri, $wkf_lists, $creds, $conn_params) do |run|

data/test/tc_server.rb

@@ -40,11 +40,11 @@ class TestServer < Test::Unit::TestCase
     end
   end
 
-  def test_run_creation_deletion
+  def test_run_creation
     T2Server::Server.new($uri, $conn_params) do |server|
       assert_nothing_raised(T2Server::T2ServerError) do
         run = server.create_run($wkf_pass, $creds)
-        server.delete_run(run, $creds)
+        run.delete
       end
     end
   end

data/test/tc_util.rb

@@ -72,3 +72,47 @@ class TestUriStripping < Test::Unit::TestCase
     assert_equal(username, r_creds.username)
   end
 end
+
+class TestUriPathAppending < Test::Unit::TestCase
+  def test_append
+    original = URI.parse("http://www.example.com:8080/old")
+    original_copy = URI.parse("http://www.example.com:8080/old")
+    extra_path = "new/bit"
+    blank_path = ""
+    appended = URI.parse("http://www.example.com:8080/old/new/bit")
+
+    # Prove it works.
+    assert_equal(appended, T2Server::Util.append_to_uri_path(original, extra_path))
+    assert_equal(original, T2Server::Util.append_to_uri_path(original, blank_path))
+
+    # Make sure the original is not changed!
+    assert_equal(original, original_copy)
+  end
+end
+
+class TestUriPathReplacement < Test::Unit::TestCase
+  def test_replace
+    original = URI.parse("http://www.example.com:8080/old/path")
+    original_copy = URI.parse("http://www.example.com:8080/old/path")
+    new_path = "/new/path"
+    replaced = URI.parse("http://www.example.com:8080/new/path")
+
+    # Prove it works.
+    assert_equal(replaced, T2Server::Util.replace_uri_path(original, new_path))
+
+    # Make sure the original is not changed!
+    assert_equal(original, original_copy)
+  end
+end
+
+class TestGetUriPathLeaf < Test::Unit::TestCase
+  def test_get_leaf
+    uri1 = URI.parse("http://www.example.com:8080/old/path")
+    uri2 = URI.parse("http://www.example.com:8080/")
+    uri3 = URI.parse("http://www.example.com:8080")
+
+    assert_equal("path", T2Server::Util.get_path_leaf_from_uri(uri1))
+    assert_equal("", T2Server::Util.get_path_leaf_from_uri(uri2))
+    assert_equal("", T2Server::Util.get_path_leaf_from_uri(uri3))
+  end
+end

data/test/ts_t2server.rb

@@ -84,6 +84,7 @@ if address != ""
   $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")
+  $wkf_no_io  = File.read("test/workflows/no-ports.t2flow")
   $list_input = "test/workflows/empty_list_input.baclava"
   $file_input = "test/workflows/in.txt"
   $file_strs  = "test/workflows/strings.txt"

data/test/workflows/no-ports.t2flow

@@ -0,0 +1,76 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="e304f436-2871-4ca7-b03d-bf4aaaddf81e" role="top"><name>Workflow1</name><inputPorts /><outputPorts /><processors><processor><name>Concatenate_two_strings</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</name><depth>0</depth></port></inputPorts><outputPorts /><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
+  <inputs>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+      <name>string1</name>
+      <depth>0</depth>
+      <mimeTypes>
+        <string>'text/plain'</string>
+      </mimeTypes>
+      <handledReferenceSchemes />
+      <translatedElementType>java.lang.String</translatedElementType>
+      <allowsLiteralValues>true</allowsLiteralValues>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+      <name>string2</name>
+      <depth>0</depth>
+      <mimeTypes>
+        <string>'text/plain'</string>
+      </mimeTypes>
+      <handledReferenceSchemes />
+      <translatedElementType>java.lang.String</translatedElementType>
+      <allowsLiteralValues>true</allowsLiteralValues>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
+  </inputs>
+  <outputs>
+    <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+      <name>output</name>
+      <depth>0</depth>
+      <mimeTypes>
+        <string>'text/plain'</string>
+      </mimeTypes>
+      <granularDepth>0</granularDepth>
+    </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
+  </outputs>
+  <classLoaderSharing>workflow</classLoaderSharing>
+  <localDependencies />
+  <artifactDependencies />
+  <script>output = string1 + string2;</script>
+  <dependencies />
+  <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>
+</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>1.4</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>1.4</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>1.4</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>1.4</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>1.4</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="string1" depth="0" /><port name="string2" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Text_constant</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+  <value>Test</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>string2_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
+  <value>silly</value>
+</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string1</port></sink><source type="processor"><processor>Text_constant</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Concatenate_two_strings</processor><port>string2</port></sink><source type="processor"><processor>string2_value</processor><port>value</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>e304f436-2871-4ca7-b03d-bf4aaaddf81e</identification>
+      </annotationBean>
+      <date>2012-09-12 09:11:13.768 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

data/version.yml

@@ -1,4 +1,4 @@
 ---
   :major: 0
   :minor: 9
-  :patch: 1
+  :patch: 2

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: t2-server
 version: !ruby/object:Gem::Version
-  version: 0.9.1
+  version: 0.9.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-30 00:00:00.000000000 Z
+date: 2012-10-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -195,6 +195,7 @@ files:
 - test/workflows/in.txt
 - test/workflows/list_and_value.t2flow
 - test/workflows/list_with_errors.t2flow
+- test/workflows/no-ports.t2flow
 - test/workflows/pass_through.t2flow
 - test/workflows/secure/basic-http.t2flow
 - test/workflows/secure/basic-https.t2flow