Merge branch 'release_15.07' into dev

galaxyproject · Aug 1, 2015 · 7c299fa · 7c299fa
2 parents f379de1 + 4d4c68c
commit 7c299fa
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Showing 8 changed files with 118 additions and 13 deletions.
diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py
@@ -127,9 +127,26 @@ def compare_meta_value( file_value, dataset_value ):
             return file_value == dataset_value
         assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = other_values.get( self.ref_name, None )
-        if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper ):
+        is_data = isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper )
+        is_data_list = isinstance( ref, galaxy.tools.wrappers.DatasetListWrapper ) or isinstance( ref, list )
+        is_data_or_data_list = is_data or is_data_list
+        if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not is_data_or_data_list:
             return []  # not a valid dataset
-        meta_value = ref.metadata.get( self.key, None )
+
+        if is_data_list:
+            meta_value = None
+            for single_ref in ref:
+                this_meta_value = single_ref.metadata.get( self.key, None )
+                if this_meta_value == meta_value:
+                    continue
+                elif meta_value is None:
+                    meta_value = this_meta_value
+                else:
+                    # Different values with mismatching metadata, return []
+                    return []
+        else:
+            meta_value = ref.metadata.get( self.key, None )
+
         if meta_value is None:  # assert meta_value is not None, "Required metadata value '%s' not found in referenced dataset" % self.key
             return [ ( disp_name, basic.UnvalidatedValue( optval ), selected ) for disp_name, optval, selected in options ]
 

diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
@@ -391,6 +391,8 @@ def install_package( self, elem, tool_shed_repository, tool_dependencies=None, f
                                                 # tag set that defines the recipe to install and compile from source.
                                                 log.debug( 'Proceeding with install and compile recipe for tool dependency %s.' %
                                                            str( tool_dependency.name ) )
+                                                # Reset above error to installing
+                                                tool_dependency.status = self.install_model.ToolDependency.installation_status.INSTALLING
                                                 tool_dependency = self.install_via_fabric( tool_shed_repository,
                                                                                            tool_dependency,
                                                                                            install_dir,

diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
@@ -45,6 +45,7 @@ def do_it( self, testdef ):
         job_stdio = None
         job_output_exceptions = None
         tool_execution_exception = None
+        expected_failure_occurred = False
         try:
             try:
                 tool_response = galaxy_interactor.run_tool( testdef, test_history )
@@ -53,22 +54,26 @@ def do_it( self, testdef ):
             except RunToolException as e:
                 tool_inputs = e.inputs
                 tool_execution_exception = e
-                raise e
+                if not testdef.expect_failure:
+                    raise e
+                else:
+                    expected_failure_occurred = True
             except Exception as e:
                 tool_execution_exception = e
                 raise e
 
-            self.assertTrue( data_list or data_collection_list )
+            if not expected_failure_occurred:
+                self.assertTrue( data_list or data_collection_list )
 
-            try:
-                job_stdio = self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, data_collection_list, galaxy_interactor )
-            except JobOutputsError as e:
-                job_stdio = e.job_stdio
-                job_output_exceptions = e.output_exceptions
-                raise e
-            except Exception as e:
-                job_output_exceptions = [e]
-                raise e
+                try:
+                    job_stdio = self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, data_collection_list, galaxy_interactor )
+                except JobOutputsError as e:
+                    job_stdio = e.job_stdio
+                    job_output_exceptions = e.output_exceptions
+                    raise e
+                except Exception as e:
+                    job_output_exceptions = [e]
+                    raise e
         finally:
             job_data = {}
             if tool_inputs is not None:

diff --git a/test/functional/tool-data/fasta_indexes.loc b/test/functional/tool-data/fasta_indexes.loc
@@ -0,0 +1,2 @@
+hg19	hg19	hg19	hg19
+hg18	hg18	hg18	hg18
diff --git a/test/functional/tool-data/sample_tool_data_tables.xml b/test/functional/tool-data/sample_tool_data_tables.xml
@@ -7,4 +7,8 @@
     <columns>value, path</columns>
     <file path="${__HERE__}/testbeta.loc" />
   </table>
+  <table name="test_fasta_indexes" comment_char="#">
+    <columns>value, dbkey, name, path</columns>
+    <file path="${__HERE__}/fasta_indexes.loc" />
+  </table>
 </tables>
diff --git a/test/functional/tools/dbkey_filter_input.xml b/test/functional/tools/dbkey_filter_input.xml
@@ -0,0 +1,39 @@
+<tool id="dbkey_filter_input" name="dbkey_filter_input" version="0.1.0">
+    <description>Filter (single) input on a dbkey</description>
+    <command>
+        cat $inputs > $output
+    </command>
+    <inputs>
+        <param format="txt" name="inputs" type="data" label="Inputs" help="" />
+        <param name="index" type="select" label="Using reference genome">
+          <options from_data_table="test_fasta_indexes">
+            <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
+            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+          </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+
+    <tests>
+        <!-- can choose a dbkey if it matches input -->
+        <test>
+            <param name="inputs" value="simple_line.txt" dbkey="hg19" />
+            <param name="index" value="hg19" />
+            <output name="output" file="simple_line.txt"/>
+        </test>
+        <!-- cannot pick index otherwise -->
+        <!-- Does this make sense - if no dbkey is defined there is no option
+             available? -->
+        <test expect_failure="true">
+            <param name="inputs" value="simple_line.txt" />
+            <param name="index" value="hg18" />
+            <output name="output" file="simple_line.txt"/>
+        </test>
+    </tests>
+
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/dbkey_filter_multi_input.xml b/test/functional/tools/dbkey_filter_multi_input.xml
@@ -0,0 +1,34 @@
+<tool id="dbkey_filter_multi_input" name="dbkey_filter_multi_input" version="0.1.0">
+    <description>Filter select on dbkey of multiple inputs</description>
+    <command><![CDATA[
+        #for $input in $inputs#
+        cat $input >> $output;
+        #end for#
+    ]]>
+    </command>
+    <inputs>
+        <param format="txt" name="inputs" type="data" label="Inputs" multiple="true" help="" />
+        <param name="index" type="select" label="Using reference genome">
+          <options from_data_table="test_fasta_indexes">
+            <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
+            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+          </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+
+    <tests>
+        <!-- can choose a dbkey if it matches input -->
+        <test>
+            <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19" />
+            <param name="index" value="hg19" />
+            <output name="output" file="simple_line_x2.txt"/>
+        </test>
+    </tests>
+
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
@@ -16,6 +16,8 @@
   <tool file="multi_output.xml" />
   <tool file="multi_output_configured.xml" />
   <tool file="multi_output_assign_primary.xml" />
+  <tool file="dbkey_filter_input.xml" />
+  <tool file="dbkey_filter_multi_input.xml" />
   <tool file="composite_output.xml" />
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />