Merge branch 'release_15.03' into dev

lib/galaxy/tools/__init__.py

@@ -34,10 +34,10 @@ from galaxy.tools.actions.upload import UploadToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.data_manager import DataManagerToolAction
 from galaxy.tools.deps import build_dependency_manager
-from galaxy.tools.parameters import params_to_incoming, check_param, params_from_strings, params_to_strings
+from galaxy.tools.parameters import params_to_incoming, check_param, params_from_strings, params_to_strings, visit_input_values
 from galaxy.tools.parameters import output_collect
 from galaxy.tools.parameters.basic import (BaseURLToolParameter,
-                                           DataToolParameter, HiddenToolParameter, LibraryDatasetToolParameter,
+                                           DataToolParameter, DataCollectionToolParameter, HiddenToolParameter, LibraryDatasetToolParameter,
                                            SelectToolParameter, ToolParameter, UnvalidatedValue,
                                            IntegerToolParameter, FloatToolParameter)
 from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, UploadDataset
@@ -52,7 +52,7 @@ from galaxy.util import rst_to_html, string_as_bool, string_to_object
 from galaxy.tools.parameters.meta import expand_meta_parameters
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
-from galaxy.util.hash_util import hmac_new
+from galaxy.util.hash_util import hmac_new, is_hashable
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
@@ -2291,6 +2291,7 @@ class Tool( object, Dictifiable ):
             try:
                 job_params = job.get_param_values( trans.app, ignore_errors = True )
                 job_messages = self.check_and_update_param_values( job_params, trans, update_values=False )
+                self._map_source_to_history( trans, self.inputs, job_params )
                 tool_message = self._compare_tool_version(trans, job)
                 params_to_incoming( kwd, self.inputs, job_params, trans.app, to_html=False )
             except Exception, exception:
@@ -2564,6 +2565,59 @@ class Tool( object, Dictifiable ):
         # return enriched tool model
         return tool_model
 
+    def _map_source_to_history(self, trans, tool_inputs, params):
+        # Need to remap dataset parameters. Job parameters point to original
+        # dataset used; parameter should be the analygous dataset in the
+        # current history.
+        history = trans.get_history()
+        hda_source_dict = {} # Mapping from HDA in history to source HDAs.
+        for hda in history.datasets:
+            source_hda = hda.copied_from_history_dataset_association
+            while source_hda:#should this check library datasets as well?
+                #FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
+                #but is still less than perfect when eg individual datasets are copied between histories
+                if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
+                    hda_source_dict[ source_hda ] = hda
+                source_hda = source_hda.copied_from_history_dataset_association
+
+        # Ditto for dataset collections.
+        hdca_source_dict = {}
+        for hdca in history.dataset_collections:
+            source_hdca = hdca.copied_from_history_dataset_collection_association
+            while source_hdca:
+                if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
+                    hdca_source_dict[ source_hdca ] = hdca
+                source_hdca = source_hdca.copied_from_history_dataset_collection_association
+
+        # Unpack unvalidated values to strings, they'll be validated when the
+        # form is submitted (this happens when re-running a job that was
+        # initially run by a workflow)
+        #This needs to be done recursively through grouping parameters
+        def rerun_callback( input, value, prefixed_name, prefixed_label ):
+            if isinstance( value, UnvalidatedValue ):
+                try:
+                    return input.to_html_value( value.value, trans.app )
+                except Exception, e:
+                    # Need to determine when (if ever) the to_html_value call could fail.
+                    log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) )
+                    return str( value )
+            if isinstance( input, DataToolParameter ):
+                if isinstance(value,list):
+                    values = []
+                    for val in value:
+                        if is_hashable( val ):
+                            if val in history.datasets:
+                                values.append( val )
+                            elif val in hda_source_dict:
+                                values.append( hda_source_dict[ val ])
+                    return values
+                if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
+                    return hda_source_dict[ value ]
+            elif isinstance( input, DataCollectionToolParameter ):
+                if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict:
+                    return hdca_source_dict[ value ]
+        visit_input_values( tool_inputs, params, rerun_callback )
+
     def _compare_tool_version( self, trans, job ):
         """
         Compares a tool version with the tool version from a job (from ToolRunner).

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -3,7 +3,7 @@ API operations allowing clients to determine Galaxy instance's capabilities
 and configuration settings.
 """
 
-from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
 from galaxy.web import _future_expose_api as expose_api
 from galaxy.web import require_admin
 from galaxy.web.base.controller import BaseAPIController
@@ -21,7 +21,7 @@ class ConfigurationController( BaseAPIController ):
         self.config_serializer = ConfigSerializer( app )
         self.admin_config_serializer = AdminConfigSerializer( app )
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def index( self, trans, **kwd ):
         """
         GET /api/configuration
@@ -33,7 +33,7 @@ class ConfigurationController( BaseAPIController ):
         serialization_params = self._parse_serialization_params( kwd, 'all' )
         return self.get_config_dict( trans, is_admin, **serialization_params )
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def version( self, trans, **kwds ):
         """
         GET /api/version