Merge pull request #82 from jmchilton/output_action_testing

More functional tests of output actions.

test/api/test_tools.py

@@ -539,6 +539,59 @@ class ToolsTestCase( api.ApiTestCase ):
         }
         self._run_and_check_simple_collection_mapping( history_id, inputs )
 
+    @skip_without_tool( "output_action_change_format" )
+    def test_map_over_with_output_format_actions( self ):
+        for use_action in ["do", "dont"]:
+            history_id = self.dataset_populator.new_history()
+            hdca_id = self.__build_pair( history_id, [ "123", "456" ] )
+            inputs = {
+                "input_cond|dispatch": use_action,
+                "input_cond|input": { 'batch': True, 'values': [ { 'src': 'hdca', 'id': hdca_id } ] },
+            }
+            create = self._run( 'output_action_change_format', history_id, inputs ).json()
+            outputs = create[ 'outputs' ]
+            jobs = create[ 'jobs' ]
+            implicit_collections = create[ 'implicit_collections' ]
+            self.assertEquals( len( jobs ), 2 )
+            self.assertEquals( len( outputs ), 2 )
+            self.assertEquals( len( implicit_collections ), 1 )
+            output1 = outputs[ 0 ]
+            output2 = outputs[ 1 ]
+            output1_details = self.dataset_populator.get_history_dataset_details( history_id, dataset=output1 )
+            output2_details = self.dataset_populator.get_history_dataset_details( history_id, dataset=output2 )
+            assert output1_details[ "file_ext" ] == "txt" if (use_action == "do") else "data"
+            assert output2_details[ "file_ext" ] == "txt" if (use_action == "do") else "data"
+
+    @skip_without_tool( "Cut1" )
+    def test_map_over_with_complex_output_actions( self ):
+        history_id = self.dataset_populator.new_history()
+        hdca_id = self._bed_list(history_id)
+        inputs = {
+            "columnList": "c1,c2,c3,c4,c5",
+            "delimiter": "T",
+            "input": { 'batch': True, 'values': [ { 'src': 'hdca', 'id': hdca_id } ] },
+        }
+        create = self._run( 'Cut1', history_id, inputs ).json()
+        outputs = create[ 'outputs' ]
+        jobs = create[ 'jobs' ]
+        implicit_collections = create[ 'implicit_collections' ]
+        self.assertEquals( len( jobs ), 2 )
+        self.assertEquals( len( outputs ), 2 )
+        self.assertEquals( len( implicit_collections ), 1 )
+        output1 = outputs[ 0 ]
+        output2 = outputs[ 1 ]
+        output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 )
+        output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 )
+        assert output1_content.startswith("chr1")
+        assert output2_content.startswith("chr1")
+
+    def _bed_list(self, history_id):
+        bed1_contents = open(self.get_filename("1.bed"), "r").read()
+        bed2_contents = open(self.get_filename("2.bed"), "r").read()
+        contents = [bed1_contents, bed2_contents]
+        hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=contents ).json()
+        return hdca["id"]
+
     def _run_and_check_simple_collection_mapping( self, history_id, inputs ):
         create = self._run_cat1( history_id, inputs=inputs, assert_ok=True )
         outputs = create[ 'outputs' ]

test/functional/tools/output_action_change_format.xml

@@ -0,0 +1,52 @@
+<tool id="output_action_change_format" name="output_action_change_format" version="1.0.0">
+    <command>
+        echo "1\t2" > out1;
+    </command>
+    <inputs>
+        <conditional name="input_cond">
+            <param type="select" name="dispatch" label="Dispatch on type">
+                <option value="dont">Dont</option>
+                <option value="do">Do</option>
+            </param>
+            <when value="dont">
+                <param type="data" name="input" format="data" />
+            </when>
+            <when value="do">
+                <param type="data" name="input" format="data" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out1" from_work_dir="out1">
+            <actions>
+                <conditional name="input_cond.dispatch">
+                    <when value="do">
+                        <action type="format">
+                            <option type="from_param" name="input_cond.input" param_attribute="ext" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dispatch" value="dont" />
+            <param name="input" value="simple_line.txt" />
+            <output name="out1" ftype="data">
+                <assert_contents>
+                    <has_line line="1&#009;2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="dispatch" value="do" />
+            <param name="input" value="simple_line.txt" />
+            <output name="out1" ftype="txt">
+                <assert_contents>
+                    <has_line line="1&#009;2" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -35,6 +35,7 @@
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
   <tool file="tool_directory.xml" />
+  <tool file="output_action_change_format.xml" />
   <tool file="collection_paired_test.xml" />
   <tool file="collection_nested_test.xml" />
   <tool file="collection_mixed_param.xml" />