Merge remote-tracking branch 'upstream/release_16.10' into dev

lib/galaxy/datatypes/data.py

@@ -506,7 +506,7 @@ class Data( object ):
         """Returns ( target_ext, existing converted dataset )"""
         return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd )
 
-    def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None):
+    def convert_dataset(self, trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None):
         """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure."""
         converter = trans.app.datatypes_registry.get_converter_by_target_type( original_dataset.ext, target_type )
 
@@ -529,7 +529,7 @@ class Data( object ):
         params[input_name] = original_dataset
 
         # Run converter, job is dispatched through Queue
-        converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible )[1]
+        converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, history=history )[1]
         if len(params) > 0:
             trans.log_event( "Converter params: %s" % (str(params)), tool_id=converter.id )
         if not visible:

lib/galaxy/model/__init__.py

@@ -2045,7 +2045,7 @@ class DatasetInstance( object ):
             depends_list = []
         return dict([ (dep, self.get_converted_dataset(trans, dep)) for dep in depends_list ])
 
-    def get_converted_dataset(self, trans, target_ext, target_context=None):
+    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
         """
         Return converted dataset(s) if they exist, along with a dict of dependencies.
         If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -2084,7 +2084,7 @@ class DatasetInstance( object ):
             raise NoConverterException("A dependency (%s) is missing a converter." % dependency)
         except KeyError:
             pass  # No deps
-        new_dataset = next(iter(self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context ).values()))
+        new_dataset = next(iter(self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context, history=history ).values()))
         new_dataset.name = self.name
         self.copy_attributes( new_dataset )
         assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False )

lib/galaxy/tools/actions/__init__.py

@@ -41,7 +41,7 @@ class ToolAction( object ):
 class DefaultToolAction( object ):
     """Default tool action is to run an external command"""
 
-    def collect_input_datasets( self, tool, param_values, trans, current_user_roles=None ):
+    def _collect_input_datasets( self, tool, param_values, trans, history, current_user_roles=None ):
         """
         Collect any dataset inputs from incoming. Returns a mapping from
         parameter name to Dataset instance for each tool parameter that is
@@ -66,7 +66,7 @@ class DefaultToolAction( object ):
                         if converted_dataset:
                             data = converted_dataset
                         else:
-                            data = data.get_converted_dataset( trans, target_ext, target_context=parent )
+                            data = data.get_converted_dataset( trans, target_ext, target_context=parent, history=history )
 
                 if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ):
                     raise Exception( "User does not have permission to use a dataset (%s) provided for input." % data.id )
@@ -189,7 +189,7 @@ class DefaultToolAction( object ):
         # input datasets can process these normally.
         inp_dataset_collections = self.collect_input_dataset_collections( tool, incoming )
         # Collect any input datasets from the incoming parameters
-        inp_data = self.collect_input_datasets( tool, incoming, trans, current_user_roles=current_user_roles )
+        inp_data = self._collect_input_datasets( tool, incoming, trans, history=history, current_user_roles=current_user_roles )
 
         return history, inp_data, inp_dataset_collections
 

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -150,6 +150,7 @@ class RemoteUser( object ):
                 '/user/api_keys',
                 '/user/edit_username',
                 '/user/dbkeys',
+                '/user/logout',
                 '/user/toolbox_filters',
                 '/user/set_default_permissions',
                 '/user/change_communication',

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -1052,6 +1052,10 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
                 history=history
             )
         else:
+            # If there is just one dataset name selected or one dataset collection, these
+            # come through as string types instead of lists. xref #3247.
+            dataset_names = util.listify(dataset_names)
+            dataset_collection_names = util.listify(dataset_collection_names)
             stored_workflow = extract_workflow(
                 trans,
                 user=user,

test/functional/tools/implicit_conversion.xml

@@ -0,0 +1,23 @@
+<tool id="implicit_conversion" name="implicit_conversion">
+  <command>
+    cut -f 1 '$input1' > 'col_output'
+  </command>
+  <inputs>
+    <param type="data" format="tabular" name="input1" label="Input 1" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="tabular" from_work_dir="col_output" />
+  </outputs>
+  <tests>
+    <!-- Test implicit conversion. -->
+    <test>
+      <param name="input1" value="1.fasta" ftype="fasta" />
+      <param name="col" value="1" />
+      <output name="output1">
+        <assert_contents>
+          <has_line line="hg17" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>

test/functional/tools/sample_datatypes_conf.xml

@@ -6,7 +6,9 @@
     <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." >
     </datatype>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" />
+    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
+        <converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
+    </datatype>
     <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" />
     <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true" />
     <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" />

test/functional/tools/samples_tool_conf.xml

@@ -74,6 +74,7 @@
   <tool file="validation_repeat.xml" />
   <tool file="empty_output.xml" />
   <tool file="validation_empty_dataset.xml" />
+  <tool file="implicit_conversion.xml" />
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
   <tool file="identifier_collection.xml" />