Merge pull request #1350 from jmchilton/dictifiable_refactor

Move Dictifiable out of model package into util.

lib/galaxy/model/__init__.py

@@ -33,7 +33,8 @@ import galaxy.model.orm.now
 import galaxy.security.passwords
 import galaxy.util
 from galaxy.datatypes.metadata import MetadataCollection
-from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
+from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.util.dictifiable import Dictifiable
 from galaxy.security import get_permitted_actions
 from galaxy.util import is_multi_byte, Params, restore_text, send_mail
 from galaxy.util import ready_name_for_url, unique_id

lib/galaxy/model/item_attrs.py

@@ -1,10 +1,7 @@
 from sqlalchemy.sql.expression import func
-from sqlalchemy.orm.collections import InstrumentedList
 # Cannot import galaxy.model b/c it creates a circular import graph.
 import galaxy
 import logging
-import datetime
-import uuid
 
 log = logging.getLogger( __name__ )
 
@@ -165,61 +162,8 @@ class UsesAnnotations:
         return getattr( galaxy.model, class_name, None )
 
 
-class Dictifiable:
-    """ Mixin that enables objects to be converted to dictionaries. This is useful
-        when for sharing objects across boundaries, such as the API, tool scripts,
-        and JavaScript code. """
-
-    def to_dict( self, view='collection', value_mapper=None ):
-        """
-        Return item dictionary.
-        """
-
-        if not value_mapper:
-            value_mapper = {}
-
-        def get_value( key, item ):
-            """
-            Recursive helper function to get item values.
-            """
-            # FIXME: why use exception here? Why not look for key in value_mapper
-            # first and then default to to_dict?
-            try:
-                return item.to_dict( view=view, value_mapper=value_mapper )
-            except:
-                if key in value_mapper:
-                    return value_mapper.get( key )( item )
-                if type(item) == datetime.datetime:
-                    return item.isoformat()
-                elif type(item) == uuid.UUID:
-                    return str(item)
-                # Leaving this for future reference, though we may want a more
-                # generic way to handle special type mappings going forward.
-                # If the item is of a class that needs to be 'stringified' before being put into a JSON data structure
-                # elif type(item) in []:
-                #    return str(item)
-                return item
-
-        # Create dict to represent item.
-        rval = dict(
-            model_class=self.__class__.__name__
-        )
-
-        # Fill item dict with visible keys.
-        try:
-            visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' )
-        except AttributeError:
-            raise Exception( 'Unknown Dictifiable view: %s' % view )
-        for key in visible_keys:
-            try:
-                item = self.__getattribute__( key )
-                if type( item ) == InstrumentedList:
-                    rval[ key ] = []
-                    for i in item:
-                        rval[ key ].append( get_value( key, i ) )
-                else:
-                    rval[ key ] = get_value( key, item )
-            except AttributeError:
-                rval[ key ] = None
-
-        return rval
+__all__ = [
+    'UsesAnnotations',
+    'UsesItemRatings',
+    'RuntimeException',
+]

lib/galaxy/model/tool_shed_install/__init__.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.bunch import Bunch
 from galaxy.util import asbool
 from tool_shed.util import common_util

lib/galaxy/tools/__init__.py

@@ -47,7 +47,7 @@ from galaxy.util.hash_util import hmac_new
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 from tool_shed.util import common_util
 from tool_shed.util import shed_util_common as suc
 

lib/galaxy/tools/data/__init__.py

@@ -20,7 +20,7 @@ from urllib2 import urlopen
 from galaxy import util
 from galaxy.util.odict import odict
 
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 
 log = logging.getLogger( __name__ )
 

lib/galaxy/tools/parameters/basic.py

@@ -23,7 +23,7 @@ from .dataset_matcher import DatasetMatcher
 from .dataset_matcher import DatasetCollectionMatcher
 # For BaseURLToolParameter
 from galaxy.web import url_for
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 import galaxy.model
 
 log = logging.getLogger(__name__)

lib/galaxy/tools/parameters/grouping.py

@@ -15,7 +15,7 @@ from galaxy.util import relpath
 from galaxy.util import sanitize_for_filename
 from galaxy.util.bunch import Bunch
 from galaxy.util.expressions import ExpressionContext
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 
 
 class Group( object, Dictifiable ):

lib/galaxy/tools/toolbox/base.py

@@ -9,7 +9,7 @@ from sqlalchemy import and_
 from markupsafe import escape
 from urlparse import urlparse
 
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 
 from galaxy.util.odict import odict
 from galaxy.util import listify

lib/galaxy/tools/toolbox/panel.py

@@ -2,7 +2,7 @@ from abc import abstractmethod
 
 from galaxy.util.odict import odict
 from galaxy.util import bunch
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 
 
 panel_item_types = bunch.Bunch(

lib/galaxy/util/dictifiable.py

@@ -0,0 +1,62 @@
+import datetime
+import uuid
+
+
+class Dictifiable:
+    """ Mixin that enables objects to be converted to dictionaries. This is useful
+        when for sharing objects across boundaries, such as the API, tool scripts,
+        and JavaScript code. """
+
+    def to_dict( self, view='collection', value_mapper=None ):
+        """
+        Return item dictionary.
+        """
+
+        if not value_mapper:
+            value_mapper = {}
+
+        def get_value( key, item ):
+            """
+            Recursive helper function to get item values.
+            """
+            # FIXME: why use exception here? Why not look for key in value_mapper
+            # first and then default to to_dict?
+            try:
+                return item.to_dict( view=view, value_mapper=value_mapper )
+            except:
+                if key in value_mapper:
+                    return value_mapper.get( key )( item )
+                if type(item) == datetime.datetime:
+                    return item.isoformat()
+                elif type(item) == uuid.UUID:
+                    return str(item)
+                # Leaving this for future reference, though we may want a more
+                # generic way to handle special type mappings going forward.
+                # If the item is of a class that needs to be 'stringified' before being put into a JSON data structure
+                # elif type(item) in []:
+                #    return str(item)
+                return item
+
+        # Create dict to represent item.
+        rval = dict(
+            model_class=self.__class__.__name__
+        )
+
+        # Fill item dict with visible keys.
+        try:
+            visible_keys = self.__getattribute__( 'dict_' + view + '_visible_keys' )
+        except AttributeError:
+            raise Exception( 'Unknown Dictifiable view: %s' % view )
+        for key in visible_keys:
+            try:
+                item = self.__getattribute__( key )
+                if isinstance( item, list ):
+                    rval[ key ] = []
+                    for i in item:
+                        rval[ key ].append( get_value( key, i ) )
+                else:
+                    rval[ key ] = get_value( key, item )
+            except AttributeError:
+                rval[ key ] = None
+
+        return rval

lib/galaxy/web/base/controller.py

@@ -23,7 +23,8 @@ from galaxy.web.form_builder import build_select_field, HistoryField, PasswordFi
 from galaxy.workflow.modules import WorkflowModuleInjector, MissingToolException
 from galaxy.security.validate_user_input import validate_publicname
 from galaxy.util.sanitize_html import sanitize_html
-from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
+from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.util.dictifiable import Dictifiable
 
 from galaxy.datatypes.interval import ChromatinInteractions
 

lib/galaxy/webapps/tool_shed/model/__init__.py

@@ -6,7 +6,7 @@ from galaxy import util
 from galaxy.util import unique_id
 from galaxy.util.bunch import Bunch
 from galaxy.util.hash_util import new_secure_hash
-from galaxy.model.item_attrs import Dictifiable
+from galaxy.util.dictifiable import Dictifiable
 import tool_shed.repository_types.util as rt_util
 
 from mercurial import hg