Working on aiidateam#258. Added functionality to selectable descentan…

…ts_beta and Declarative DbPathBeta to behave as DbPath does,

with queryable properties being descendant_id (instead of child_id), ancestor_id (parent_id) and depth.
Possibility to add traversed path as an array, though this will only work in Postgresql, so commented out for now.
To initialize the mapper correctly, I added imports in the __init__ of backends.sqlalchemy.model
This might be also of greater convenience when importing!
Added headers to all files in the querybuild module.

aiida/backends/querybuild/dummy_model.py

@@ -1,5 +1,11 @@
 # -*- coding: utf-8 -*-
 
+__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
+__license__ = "MIT license, see LICENSE.txt file."
+__authors__ = "The AiiDA team."
+__version__ = "0.7.0"
+
+
 """
 The dummy model encodes the model defined by django in backends.djsite
 using SQLAlchemy.
@@ -38,10 +44,6 @@
 
 
 
-__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
-__license__ = "MIT license, see LICENSE.txt file."
-__authors__ = "The AiiDA team."
-__version__ = "0.7.0"
 
 Base = declarative_base()
 
@@ -386,22 +388,25 @@ def get_aiida_class(self):
 
 
 
+# Recursive query that replaces DbPath
+# Note: Does not work with sqlite
 node_aliased = aliased(DbNode)
 
 walk = select([
-        DbNode.id.label('start'),
-        DbNode.id.label('end'),
+        DbNode.id.label('ancestor_id'),
+        DbNode.id.label('descendant_id'),
         cast(-1, Integer).label('depth'),
-        array([DbNode.id]).label('path')
+        # array([DbNode.id]).label('path') Arrays can only be used with postgres, so leave it out for now
     ]).select_from(DbNode).cte(recursive=True) #, name="incl_aliased3")
 
 
 descendants_beta = walk.union_all(
     select([
-            walk.c.start,
+            walk.c.ancestor_id,
             node_aliased.id,
             walk.c.depth + cast(1, Integer),
-            (walk.c.path+array([node_aliased.id])).label('path'),
+            # This is the way to reconstruct the path (the sequence of nodes traversed)
+            # (walk.c.path+array([node_aliased.id])).label('path'), As above, but if arrays are supported
         ]).select_from(
             join(
                 node_aliased,
@@ -410,7 +415,7 @@ def get_aiida_class(self):
             )
         ).where(
             and_(
-                DbLink.input_id == walk.c.end,
+                DbLink.input_id == walk.c.descendant_id,
             )
         )
     )
@@ -423,11 +428,8 @@ def __init__(self, start, end, depth):
         self.out = end
         self.depth = depth
 
-
-
 mapper(DbPathBeta, descendants_beta)
 
-
 #~ DbAttribute.value_str = column_property(
         #~ case([
             #~ (DbAttribute.datatype == 'txt', DbAttribute.tval),

aiida/backends/querybuild/querybuilder_base.py

@@ -1,5 +1,10 @@
 # -*- coding: utf-8 -*-
 
+__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
+__license__ = "MIT license, see LICENSE.txt file."
+__authors__ = "The AiiDA team."
+__version__ = "0.7.0"
+
 
 """
 The general functionalities that all querybuilders need to have
@@ -531,6 +536,9 @@ def append(self, cls=None, type=None, tag=None,
                 aliased_edge = aliased(self.Link)
             elif joining_keyword in ('ancestor_of', 'descendant_of'):
                 aliased_edge = aliased(self.Path)
+            elif joining_keyword in ('ancestor_of_beta', 'descendant_of_beta'):
+                #~ aliased_edge = aliased(self.PathBeta)
+                aliased_edge = self.PathBeta
 
             if aliased_edge is not None:
 
@@ -1261,10 +1269,10 @@ def _join_outputs(self, joined_entity, entity_to_join, aliased_edge):
         self._query = self._query.join(
                 aliased_edge,
                 aliased_edge.input_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 aliased_edge.output_id == entity_to_join.id
-        )
+            )
 
     def _join_inputs(self, joined_entity, entity_to_join, aliased_edge):
         """
@@ -1283,12 +1291,56 @@ def _join_inputs(self, joined_entity, entity_to_join, aliased_edge):
         self._query = self._query.join(
                 aliased_edge,
                 aliased_edge.output_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 aliased_edge.input_id == entity_to_join.id
-        )
+            )
+
+    def _join_descendants_beta(self, joined_entity, entity_to_join, aliased_path):
+        """
+        Beta version, joining descendants using the recursive functionality
+        """
+        self._check_dbentities(
+                (joined_entity, self.Node),
+                (entity_to_join, self.Node),
+                'descendant_of_beta'
+            )
 
-    #~ def _join_descendants_beta(self, joined_entity, entity_to_join, aliased_path):
+        self._query = self._query.join(
+                aliased_path,
+                aliased_path.ancestor_id == joined_entity.id
+            ).join(
+                entity_to_join,
+                aliased_path.descendant_id == entity_to_join.id
+            ).filter(
+                # it is necessary to put this filter so that the
+                # the node does not include itself as a ancestor/descendant
+                aliased_path.depth > -1
+            )
+    def _join_ancestors_beta(self, joined_entity, entity_to_join, aliased_path):
+        """
+        :param joined_entity: The (aliased) ORMclass that is a descendant
+        :param entity_to_join: The (aliased) ORMClass that is an ancestor.
+        :param aliased_path: An aliased instance of DbPath
+
+        """
+        self._check_dbentities(
+                (joined_entity, self.Node),
+                (entity_to_join, self.Node),
+                'ancestor_of_beta'
+            )
+        #~ aliased_path = aliased(self.Path)
+        self._query = self._query.join(
+                aliased_path,
+                aliased_path.descendant_id == joined_entity.id
+            ).join(
+                entity_to_join,
+                aliased_path.ancestor_id == entity_to_join.id
+            ).filter(
+                # it is necessary to put this filter so that the
+                # the node does not include itself as a ancestor/descendant
+                aliased_path.depth > -1
+            )
 
     def _join_descendants(self, joined_entity, entity_to_join, aliased_path):
         """
@@ -1310,10 +1362,10 @@ def _join_descendants(self, joined_entity, entity_to_join, aliased_path):
         self._query = self._query.join(
                 aliased_path,
                 aliased_path.parent_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 aliased_path.child_id == entity_to_join.id
-        )
+            )
 
     def _join_ancestors(self, joined_entity, entity_to_join, aliased_path):
         """
@@ -1335,10 +1387,10 @@ def _join_ancestors(self, joined_entity, entity_to_join, aliased_path):
         self._query = self._query.join(
                 aliased_path,
                 aliased_path.child_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 aliased_path.parent_id == entity_to_join.id
-        )
+            )
     def _join_group_members(self, joined_entity, entity_to_join):
         """
         :param joined_entity:
@@ -1361,10 +1413,10 @@ def _join_group_members(self, joined_entity, entity_to_join):
         self._query = self._query.join(
                 aliased_group_nodes,
                 aliased_group_nodes.c.dbgroup_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 entity_to_join.id == aliased_group_nodes.c.dbnode_id
-        )
+            )
     def _join_groups(self, joined_entity, entity_to_join):
         """
         :param joined_entity: The (aliased) node in the database
@@ -1384,10 +1436,10 @@ def _join_groups(self, joined_entity, entity_to_join):
         self._query = self._query.join(
                 aliased_group_nodes,
                 aliased_group_nodes.c.dbnode_id == joined_entity.id
-        ).join(
+            ).join(
                 entity_to_join,
                 entity_to_join.id == aliased_group_nodes.c.dbgroup_id
-        )
+            )
     def _join_creator_of(self, joined_entity, entity_to_join):
         """
         :param joined_entity: the aliased node
@@ -1431,7 +1483,7 @@ def _join_to_computer_used(self, joined_entity, entity_to_join):
         self._query = self._query.join(
                 entity_to_join,
                 entity_to_join.dbcomputer_id == joined_entity.id
-        )
+            )
 
     def _join_computer(self, joined_entity, entity_to_join):
         """
@@ -1448,7 +1500,7 @@ def _join_computer(self, joined_entity, entity_to_join):
         self._query = self._query.join(
                 entity_to_join,
                 joined_entity.dbcomputer_id == entity_to_join.id
-        )
+            )
 
     def _get_function_map(self):
         d = {
@@ -1458,6 +1510,8 @@ def _get_function_map(self):
                 'master_of' : self._join_masters,# not implemented
                 'ancestor_of': self._join_ancestors,
                 'descendant_of': self._join_descendants,
+                'ancestor_of_beta': self._join_ancestors_beta, #not implemented
+                'descendant_of_beta': self._join_descendants_beta,
                 'direction' : None,
                 'group_of'  : self._join_groups,
                 'member_of' : self._join_group_members,

aiida/backends/querybuild/querybuilder_django.py

@@ -1,5 +1,11 @@
 # -*- coding: utf-8 -*-
 
+__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
+__license__ = "MIT license, see LICENSE.txt file."
+__authors__ = "The AiiDA team."
+__version__ = "0.7.0"
+
+
 from datetime import datetime
 from json import loads as json_loads
 
@@ -15,6 +21,7 @@
     DbLink      as DummyLink,
     DbCalcState as DummyState,
     DbPath      as DummyPath,
+    DbPathBeta  as DummyPathBeta,
     DbUser      as DummyUser,
     DbComputer  as DummyComputer,
     DbGroup     as DummyGroup,
@@ -50,6 +57,7 @@ def __init__(self, *args, **kwargs):
 
         self.Link               = DummyLink
         self.Path               = DummyPath
+        self.PathBeta           = DummyPathBeta
         self.Node               = DummyNode
         self.Computer           = DummyComputer
         self.User               = DummyUser

aiida/backends/querybuild/querybuilder_sa.py

@@ -1,5 +1,11 @@
 # -*- coding: utf-8 -*-
 
+__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
+__license__ = "MIT license, see LICENSE.txt file."
+__authors__ = "The AiiDA team."
+__version__ = "0.7.0"
+
+
 from datetime import datetime
 
 __copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
@@ -26,6 +32,7 @@
 from sqlalchemy_utils.types.choice import Choice
 from aiida.backends.sqlalchemy import session as sa_session
 from aiida.backends.sqlalchemy.models.node import DbNode, DbLink, DbPath
+from aiida.backends.sqlalchemy.models import DbPathBeta
 from aiida.backends.sqlalchemy.models.computer import DbComputer
 from aiida.backends.sqlalchemy.models.group import DbGroup, table_groups_nodes
 from aiida.backends.sqlalchemy.models.user import DbUser
@@ -47,6 +54,7 @@ def __init__(self, *args, **kwargs):
         from aiida.orm.implementation.sqlalchemy.user import User as AiidaUser
         self.Link               = DbLink
         self.Path               = DbPath
+        self.PathBeta           = DbPathBeta
         self.Node               = DbNode
         self.Computer           = DbComputer
         self.User               = DbUser

aiida/backends/querybuild/sa_init.py

@@ -1,4 +1,11 @@
 # -*- coding: utf-8 -*-
+
+__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved."
+__license__ = "MIT license, see LICENSE.txt file."
+__authors__ = "The AiiDA team."
+__version__ = "0.7.0"
+
+
 """
 Imports used for the QueryBuilder.
 See

aiida/backends/sqlalchemy/models/__init__.py

@@ -15,3 +15,63 @@
 # is stored in the DbSetting table and the check is done in the
 # load_dbenv() function).
 SCHEMA_VERSION = 0.1
+
+
+
+# This is convenience so that one can import all ORM classes from one module
+# from aiida.backends.sqlalchemy.models import *
+# Also, only by import
+from comment import DbComment
+from computer import DbComputer
+from group import DbGroup
+from lock import DbLock
+from log import DbLog
+from node import DbNode, DbLink, DbPath, DbCalcState
+from settings import DbSetting
+from user import DbUser
+from workflow import DbWorkflow, DbWorkflowData, DbWorkflowStep
+
+from sqlalchemy.orm import aliased, mapper
+from sqlalchemy import select, func, join, and_
+from sqlalchemy.sql.expression import cast
+from sqlalchemy.types import Integer
+
+node_aliased = aliased(DbNode)
+
+walk = select([
+        DbNode.id.label('ancestor_id'),
+        DbNode.id.label('descendant_id'),
+        cast(-1, Integer).label('depth'),
+        # array([DbNode.id]).label('path') Arrays can only be used with postgres, so leave it out for now
+    ]).select_from(DbNode).cte(recursive=True) #, name="incl_aliased3")
+
+
+descendants_beta = walk.union_all(
+    select([
+            walk.c.ancestor_id,
+            node_aliased.id,
+            walk.c.depth + cast(1, Integer),
+            # (walk.c.path+array([node_aliased.id])).label('path'), As above, but if arrays are supported
+            # This is the way to reconstruct the path (the sequence of nodes traversed)
+        ]).select_from(
+            join(
+                node_aliased,
+                DbLink,
+                DbLink.output_id==node_aliased.id,
+            )
+        ).where(
+            and_(
+                DbLink.input_id == walk.c.descendant_id,
+            )
+        )
+    )
+
+
+class DbPathBeta(object):
+
+    def __init__(self, start, end, depth):
+        self.start = start
+        self.out = end
+        self.depth = depth
+
+mapper(DbPathBeta, descendants_beta)

aiida/backends/sqlalchemy/models/node.py

@@ -3,7 +3,7 @@
 from sqlalchemy import ForeignKey, select, func, join, and_
 from sqlalchemy.orm import (
         relationship, backref, Query, mapper,
-        foreign, column_property,
+        foreign, column_property, aliased
     )
 from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.schema import Column, UniqueConstraint
@@ -382,3 +382,5 @@ class DbCalcState(Base):
     select([recent_states.c.state]).
     where(recent_states.c.dbnode_id == foreign(DbNode.id))
 )
+
+