RubyGems - t2-server - Versions diffs - 0.5.2 → 0.5.3 - Mend

t2-server 0.5.2 → 0.5.3

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Files changed (8) hide show

data/CHANGES.rdoc +4 -0
data/README.rdoc +1 -1
data/lib/t2-server.rb +1 -1
data/lib/t2-server/run.rb +16 -12
data/test/tc_run.rb +3 -2
data/test/workflows/empty_list.t2flow +22 -11
data/test/workflows/empty_list_input.baclava +86 -77
metadata +4 -4

data/CHANGES.rdoc CHANGED Viewed

@@ -1,5 +1,9 @@
 = Changes log for the T2 Ruby Gem
+== Version 0.5.3
+* Fix an issue with singleton value/empty list confusion for output ports.
 == Version 0.5.2
 * Fix two issues with the retrieving of workflow outputs.

data/README.rdoc CHANGED Viewed

@@ -1,7 +1,7 @@
 = Taverna[http://www.taverna.org.uk/] 2 Server Interaction Gem
 Authors::     Robert Haines
-Gem Version:: 0.5.2
+Gem Version:: 0.5.3
 API Version:: 2.2a1
 Contact::     mailto:rhaines@manchester.ac.uk
 URL::         http://taverna.sourceforge.net/

data/lib/t2-server.rb CHANGED Viewed

@@ -43,7 +43,7 @@ require 't2-server/run'
 #   Taverna 2 Server instance.
 module T2Server
   # The version of this library
-  GEM_VERSION = "0.5.2"
+  GEM_VERSION = "0.5.3"
   # The version of the Taverna 2 Server API that this library can interface with
   API_VERSION = "2.2a1"
 end

data/lib/t2-server/run.rb CHANGED Viewed

@@ -452,22 +452,26 @@ module T2Server
     private
     def _get_output(output, refs=false, top=true)
       output.strip_path!
-      result = []
-      # look at the contents of the output port
-      lists, items = ls("out/#{output}")
-      # if lists and items are empty then it's an empty list
-      # although it could be a single value if we're at the top level
-      if top and lists == [] and items == []
-        # as we are at the top level, just return the single value
-        if refs
-          return "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
-        else
-          return @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
+      # if at the top level we need to check if the port represents a list
+      # or a singleton value
+      if top
+        lists, items = ls("out")
+        if items.include? output
+          if refs
+            return "#{@server.uri}/rest/runs/#{@uuid}/#{@links[:wdir]}/out/#{output}"
+          else
+            return @server.get_run_attribute(@uuid, "#{@links[:wdir]}/out/#{output}")
+          end
         end
       end
+      # we're not at the top level so look at the contents of the output port
+      lists, items = ls("out/#{output}")
+      # build up lists of results
+      result = []
       # for each list recurse into it and add the items to the result
       lists.each {|list| result << _get_output("#{output}/#{list}", refs, false)}

data/test/tc_run.rb CHANGED Viewed

@@ -90,8 +90,9 @@ class TestRun < Test::Unit::TestCase
     assert_nothing_raised(T2Server::RunStateError) do
       @run.wait
     end
-    assert_equal(@run.get_output("OUT"), [[["boo"]], [["", "hello"]],
-      [], [[], ["test"], []]])
+    assert_equal(@run.get_output("SINGLE"), [])
+    assert_equal(@run.get_output("MANY"), [[], [["Hello", ""]], [[], ["test"],
+      []], [["boo"]]])
     # run with baclava output
     @run = T2Server::Run.create($address, $wkf_hello)

data/test/workflows/empty_list.t2flow CHANGED Viewed

@@ -1,12 +1,23 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="536f469a-fd80-4efa-8d76-6cb2514123ec" role="top"><name>Workflow1</name><inputPorts><port><name>IN</name><depth>2</depth><granularDepth>2</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>OUT</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>OUT</port></sink><source type="dataflow"><port>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>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
-      </annotationBean>
-      <date>2010-11-04 18:00:12.867 GMT</date>
-      <creators />
-      <curationEventList />
-    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
-  </annotationAssertions>
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.2.0"><dataflow id="373bb615-7dd3-46b4-9e3c-ee38e7460403" role="top"><name>Workflow1</name><inputPorts><port><name>MANY_IN</name><depth>3</depth><granularDepth>3</granularDepth><annotations /></port><port><name>SINGLE_IN</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>MANY</name><annotations /></port><port><name>SINGLE</name><annotations /></port></outputPorts><processors /><conditions /><datalinks><datalink><sink type="dataflow"><port>MANY</port></sink><source type="dataflow"><port>MANY_IN</port></source></datalink><datalink><sink type="dataflow"><port>SINGLE</port></sink><source type="dataflow"><port>SINGLE_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>536f469a-fd80-4efa-8d76-6cb2514123ec</identification>
+      </annotationBean>
+      <date>2010-11-04 18:00:12.867 GMT</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>373bb615-7dd3-46b4-9e3c-ee38e7460403</identification>
+      </annotationBean>
+      <date>2010-11-09 13:50:13.127 GMT</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
 </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

data/test/workflows/empty_list_input.baclava CHANGED Viewed

@@ -1,77 +1,86 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
-  <b:dataThing key="IN">
-    <b:myGridDataDocument lsid="" syntactictype="l(l('null'))">
-      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
-      <b:partialOrder lsid="" type="list">
-        <b:relationList>
-          <b:relation parent="0" child="1" />
-          <b:relation parent="1" child="2" />
-          <b:relation parent="2" child="3" />
-        </b:relationList>
-        <b:itemList>
-          <b:partialOrder lsid="" type="list" index="0">
-            <b:relationList>
-              <b:relation parent="0" child="1" />
-              <b:relation parent="1" child="2" />
-            </b:relationList>
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList />
-                <b:itemList />
-              </b:partialOrder>
-              <b:partialOrder lsid="" type="list" index="1">
-                <b:relationList />
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData>dGVzdA==</b:dataElementData>
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-              <b:partialOrder lsid="" type="list" index="2">
-                <b:relationList />
-                <b:itemList />
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="1">
-            <b:relationList />
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList>
-                  <b:relation parent="0" child="1" />
-                </b:relationList>
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData>aGVsbG8=</b:dataElementData>
-                  </b:dataElement>
-                  <b:dataElement lsid="" index="1">
-                    <b:dataElementData />
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="2">
-            <b:relationList />
-            <b:itemList>
-              <b:partialOrder lsid="" type="list" index="0">
-                <b:relationList />
-                <b:itemList>
-                  <b:dataElement lsid="" index="0">
-                    <b:dataElementData>Ym9v</b:dataElementData>
-                  </b:dataElement>
-                </b:itemList>
-              </b:partialOrder>
-            </b:itemList>
-          </b:partialOrder>
-          <b:partialOrder lsid="" type="list" index="3">
-            <b:relationList />
-            <b:itemList />
-          </b:partialOrder>
-        </b:itemList>
-      </b:partialOrder>
-    </b:myGridDataDocument>
-  </b:dataThing>
-</b:dataThingMap>
+<?xml version="1.0" encoding="UTF-8"?>
+<b:dataThingMap xmlns:b="http://org.embl.ebi.escience/baclava/0.1alpha">
+  <b:dataThing key="MANY_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l(l(l('null')))">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList>
+          <b:relation parent="0" child="1" />
+          <b:relation parent="1" child="2" />
+          <b:relation parent="2" child="3" />
+        </b:relationList>
+        <b:itemList>
+          <b:partialOrder lsid="" type="list" index="0">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>Ym9v</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="1">
+            <b:relationList />
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList>
+                  <b:relation parent="0" child="1" />
+                </b:relationList>
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData />
+                  </b:dataElement>
+                  <b:dataElement lsid="" index="1">
+                    <b:dataElementData>SGVsbG8=</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="2">
+            <b:relationList />
+            <b:itemList />
+          </b:partialOrder>
+          <b:partialOrder lsid="" type="list" index="3">
+            <b:relationList>
+              <b:relation parent="0" child="1" />
+              <b:relation parent="1" child="2" />
+            </b:relationList>
+            <b:itemList>
+              <b:partialOrder lsid="" type="list" index="0">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="1">
+                <b:relationList />
+                <b:itemList>
+                  <b:dataElement lsid="" index="0">
+                    <b:dataElementData>dGVzdA==</b:dataElementData>
+                  </b:dataElement>
+                </b:itemList>
+              </b:partialOrder>
+              <b:partialOrder lsid="" type="list" index="2">
+                <b:relationList />
+                <b:itemList />
+              </b:partialOrder>
+            </b:itemList>
+          </b:partialOrder>
+        </b:itemList>
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+  <b:dataThing key="SINGLE_IN">
+    <b:myGridDataDocument lsid="" syntactictype="l('null')">
+      <s:metadata xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha" />
+      <b:partialOrder lsid="" type="list">
+        <b:relationList />
+        <b:itemList />
+      </b:partialOrder>
+    </b:myGridDataDocument>
+  </b:dataThing>
+</b:dataThingMap>

metadata CHANGED Viewed

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: t2-server
 version: !ruby/object:Gem::Version
-  hash: 15
+  hash: 13
   prerelease: false
   segments:
   - 0
   - 5
-  - 2
-  version: 0.5.2
+  - 3
+  version: 0.5.3
 platform: ruby
 authors:
 - Robert Haines
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
-date: 2010-11-05 00:00:00 +00:00
+date: 2010-11-09 00:00:00 +00:00
 default_executable:
 dependencies:
 - !ruby/object:Gem::Dependency