Merge pull request #2390 from guerler/revise_tool_framework_000

Add a new workflow building mode variation which does access the history

lib/galaxy/tools/__init__.py

@@ -1578,7 +1578,7 @@ class Tool( object, Dictifiable ):
 
         return tool_dict
 
-    def to_json( self, trans, kwd={}, job=None, workflow_mode=False ):
+    def to_json( self, trans, kwd={}, job=None, workflow_building_mode=False ):
         """
         Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
         """
@@ -1595,7 +1595,7 @@ class Tool( object, Dictifiable ):
             raise exceptions.MessageException( '[history_id=%s] Failed to retrieve history. %s.' % ( history_id, str( e ) ) )
 
         # build request context
-        request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history, workflow_building_mode=workflow_mode )
+        request_context = WorkRequestContext( app=trans.app, user=trans.user, history=history, workflow_building_mode=workflow_building_mode )
 
         # load job parameters into incoming
         tool_message = ''

lib/galaxy/tools/parameters/basic.py

@@ -25,9 +25,12 @@ from .dataset_matcher import DatasetCollectionMatcher
 from galaxy.web import url_for
 from galaxy.util.dictifiable import Dictifiable
 import galaxy.model
+from galaxy.util.bunch import Bunch
 
 log = logging.getLogger(__name__)
 
+workflow_building_modes = Bunch( DISABLED=False, ENABLED=True, USE_HISTORY=1 )
+
 WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' )
 
 
@@ -266,7 +269,7 @@ class TextToolParameter( ToolParameter ):
 
     def validate( self, value, trans=None ):
         search = self.type == "text"
-        if not ( trans and trans.workflow_building_mode and contains_workflow_parameter(value, search=search) ):
+        if not ( trans and trans.workflow_building_mode is workflow_building_modes.ENABLED and contains_workflow_parameter(value, search=search) ):
             return super( TextToolParameter, self ).validate( value, trans )
 
     def get_initial_value( self, trans, other_values ):
@@ -333,11 +336,11 @@ class IntegerToolParameter( TextToolParameter ):
         try:
             return int( value )
         except:
-            if contains_workflow_parameter( value ) and trans.workflow_building_mode:
+            if contains_workflow_parameter( value ) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 return value
             if not value and self.optional:
                 return ""
-            if trans.workflow_building_mode:
+            if trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 raise ValueError( "An integer or workflow parameter e.g. ${name} is required" )
             else:
                 raise ValueError( "An integer is required" )
@@ -413,11 +416,11 @@ class FloatToolParameter( TextToolParameter ):
         try:
             return float( value )
         except:
-            if contains_workflow_parameter( value ) and trans.workflow_building_mode:
+            if contains_workflow_parameter( value ) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 return value
             if not value and self.optional:
                 return ""
-            if trans and trans.workflow_building_mode:
+            if trans and trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 raise ValueError( "A real number or workflow parameter e.g. ${name} is required" )
             else:
                 raise ValueError( "A real number is required" )
@@ -1860,7 +1863,7 @@ class DataToolParameter( BaseDataToolParameter ):
         return ''
 
     def from_json( self, value, trans, other_values={} ):
-        if trans.workflow_building_mode:
+        if trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return None
         if not value and not self.optional:
             raise ValueError( "History does not include a dataset of the required format / build" )
@@ -2043,7 +2046,7 @@ class DataToolParameter( BaseDataToolParameter ):
 
         # return dictionary without options if context is unavailable
         history = trans.history
-        if history is None or trans.workflow_building_mode:
+        if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return d
 
         # prepare dataset/collection matching
@@ -2144,7 +2147,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
         return field
 
     def from_json( self, value, trans, other_values={} ):
-        if trans.workflow_building_mode:
+        if trans.workflow_building_mode is workflow_building_modes.ENABLED:
             return None
         if not value and not self.optional:
             raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" )
@@ -2205,7 +2208,7 @@ class DataCollectionToolParameter( BaseDataToolParameter ):
 
         # return dictionary without options if context is unavailable
         history = trans.history
-        if history is None or trans.workflow_building_mode or other_values is None:
+        if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED or other_values is None:
             return d
 
         # prepare dataset/collection matching

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -334,7 +334,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         } )
 
         # create tool model and default tool state (if missing)
-        tool_model = module.tool.to_json( trans, tool_inputs, workflow_mode=True )
+        tool_model = module.tool.to_json( trans, tool_inputs, workflow_building_mode=True )
         module.update_state( tool_model[ 'state_inputs' ] )
         return {
             'tool_model'        : tool_model,

templates/webapps/galaxy/workflow/editor_tool_form.mako

@@ -4,7 +4,7 @@
     from galaxy.tools.parameters import params_to_incoming
     incoming = {}
     params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app )
-    self.form_config = tool.to_json(trans, incoming, workflow_mode=True)
+    self.form_config = tool.to_json(trans, incoming, workflow_building_mode=True)
     self.form_config.update({
         'id'                : tool.id,
         'job_id'            : trans.security.encode_id( job.id ) if job else None,