Rename querybuilder join relationship names

Renames the querybuilder relationship names used for joins to the scheme.
Previously, complex names where used, but these were hard to remember. The new
scheme uses simple generic names, e.g. "with_computer" and gets the required
context from the class which is specified in the qb.append() method.

The main changes are:
1. - Change the relationship function map to a two-level dictionary, where the first
     level provides the context, indicating what class of node the relationship applies to.
2. - Add deprecation messages which are printed when the join functions are called
     using the old relationship names
3. - Remove the unimplemented "join_slaves/join_masters" methods

In addition, moving all deprecation warnings to the new system
(AiidaDeprecationWarning) and removing some very old deprecations

.pre-commit-config.yaml

@@ -208,7 +208,6 @@
         aiida/orm/calculation/job/__init__.py|
         aiida/orm/code.py|
         aiida/orm/data/array/bands.py|
-        aiida/orm/data/array/__init__.py|
         aiida/orm/data/array/kpoints.py|
         aiida/orm/data/array/projection.py|
         aiida/orm/data/array/xy.py|

aiida/backends/general/abstractqueries.py

@@ -116,7 +116,7 @@ def get_statistics_dict(dataset):
         q.append(Node, project=['id', 'ctime', 'type'], tag='node')
 
         if user_pk is not None:
-            q.append(User, creator_of='node', project='email', filters={'pk': user_pk})
+            q.append(User, with_node='node', project='email', filters={'pk': user_pk})
         qb_res = q.all()
 
         # total count
@@ -156,7 +156,7 @@ def get_bands_and_parents_structure(self, args):
             n_days_ago = now - datetime.timedelta(days=args.past_days)
             bdata_filters.update({"ctime": {'>=': n_days_ago}})
 
-        qb.append(BandsData, tag="bdata", created_by="creator",
+        qb.append(BandsData, tag="bdata", with_user="creator",
                   filters=bdata_filters,
                   project=["id", "label", "ctime"]
                   )

aiida/backends/tests/dataclasses.py

@@ -2744,7 +2744,7 @@ def test_creation(self):
         n.set_array('third', third)
 
         # Check if the arrays are there
-        self.assertEquals(set(['first', 'second', 'third']), set(n.arraynames()))
+        self.assertEquals(set(['first', 'second', 'third']), set(n.get_arraynames()))
         self.assertAlmostEquals(abs(first - n.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n.get_array('second')).max(), 0.)
         self.assertAlmostEquals(abs(third - n.get_array('third')).max(), 0.)
@@ -2765,7 +2765,7 @@ def test_creation(self):
         n.set_array('first', first)
 
         # Check if the arrays are there, and if I am getting the new one
-        self.assertEquals(set(['first', 'second']), set(n.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n.get_arraynames()))
         self.assertAlmostEquals(abs(first - n.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n.get_shape('first'))
@@ -2774,30 +2774,30 @@ def test_creation(self):
         n.store()
 
         # Same checks, after storing
-        self.assertEquals(set(['first', 'second']), set(n.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n.get_arraynames()))
         self.assertAlmostEquals(abs(first - n.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n.get_shape('first'))
         self.assertEquals(second.shape, n.get_shape('second'))
 
         # Same checks, again (this is checking the caching features)
-        self.assertEquals(set(['first', 'second']), set(n.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n.get_arraynames()))
         self.assertAlmostEquals(abs(first - n.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n.get_shape('first'))
         self.assertEquals(second.shape, n.get_shape('second'))
 
         # Same checks, after reloading
         n2 = load_node(uuid=n.uuid)
-        self.assertEquals(set(['first', 'second']), set(n2.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n2.get_arraynames()))
         self.assertAlmostEquals(abs(first - n2.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n2.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n2.get_shape('first'))
         self.assertEquals(second.shape, n2.get_shape('second'))
 
         # Same checks, after reloading with UUID
         n2 = load_node(n.uuid, sub_classes=(ArrayData,))
-        self.assertEquals(set(['first', 'second']), set(n2.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n2.get_arraynames()))
         self.assertAlmostEquals(abs(first - n2.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n2.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n2.get_shape('first'))
@@ -2811,7 +2811,7 @@ def test_creation(self):
 
         # Again same checks, to verify that the attempts to delete/overwrite
         # arrays did not damage the node content
-        self.assertEquals(set(['first', 'second']), set(n.arraynames()))
+        self.assertEquals(set(['first', 'second']), set(n.get_arraynames()))
         self.assertAlmostEquals(abs(first - n.get_array('first')).max(), 0.)
         self.assertAlmostEquals(abs(second - n.get_array('second')).max(), 0.)
         self.assertEquals(first.shape, n.get_shape('first'))

aiida/backends/tests/export_and_import.py

@@ -168,14 +168,14 @@ def test_cycle_structure_data(self):
             # Check that there is a StructureData that is an output of a CalculationNode
             qb = QueryBuilder()
             qb.append(CalculationNode, project=['uuid'], tag='calculation')
-            qb.append(StructureData, output_of='calculation')
+            qb.append(StructureData, with_incoming='calculation')
             self.assertGreater(len(qb.all()), 0)
 
             # Check that there is a RemoteData that is a child and parent of a CalculationNode
             qb = QueryBuilder()
             qb.append(CalculationNode, tag='parent')
-            qb.append(RemoteData, project=['uuid'], output_of='parent', tag='remote')
-            qb.append(CalculationNode, output_of='remote')
+            qb.append(RemoteData, project=['uuid'], with_incoming='parent', tag='remote')
+            qb.append(CalculationNode, with_incoming='remote')
             self.assertGreater(len(qb.all()), 0)
 
 
@@ -874,7 +874,7 @@ def get_hash_from_db_content(groupname):
             qb.append(ParameterData, tag='p', project='*')
             qb.append(CalculationNode, tag='c', project='*', edge_tag='p2c', edge_project=('label', 'type'))
             qb.append(ArrayData, tag='a', project='*', edge_tag='c2a', edge_project=('label', 'type'))
-            qb.append(Group, filters={'name': groupname}, project='*', tag='g', group_of='a')
+            qb.append(Group, filters={'name': groupname}, project='*', tag='g', with_node='a')
             # I want the query to contain something!
             self.assertTrue(qb.count() > 0)
             # The hash is given from the preservable entries in an export-import cycle,
@@ -1177,7 +1177,7 @@ def test_same_computer_import(self):
             # computer.
             qb = QueryBuilder()
             qb.append(Computer, tag='comp')
-            qb.append(CalcJobNode, has_computer='comp', project=['label'])
+            qb.append(CalcJobNode, with_computer='comp', project=['label'])
             self.assertEqual(qb.count(), 2, "Two calculations should be "
                                             "found.")
             ret_labels = set(_ for [_] in qb.all())
@@ -1401,7 +1401,7 @@ def test_different_computer_same_name_import(self):
             qb = QueryBuilder()
             qb.append(CalcJobNode, project=['label'], tag='jcalc')
             qb.append(Computer, project=['name'],
-                      computer_of='jcalc')
+                      with_node='jcalc')
             self.assertEqual(qb.count(), 3, "Three combinations expected.")
             res = qb.all()
             self.assertIn([calc1_label, comp1_name], res,
@@ -1538,7 +1538,7 @@ def get_all_node_links(self):
         qb = QueryBuilder()
         qb.append(Node, project='uuid', tag='input')
         qb.append(Node, project='uuid', tag='output',
-                  edge_project=['label', 'type'], output_of='input')
+                  edge_project=['label', 'type'], with_incoming='input')
         return qb.all()
 
     def test_input_and_create_links(self):

aiida/backends/tests/query.py

@@ -199,7 +199,7 @@ def test_simple_query_2(self):
                 {
                     'cls': Node,
                     'tag': 'n2',
-                    'output_of': 'n1'
+                    'with_incoming': 'n1'
                 }
             ],
             'filters': {
@@ -234,7 +234,7 @@ def test_simple_query_2(self):
                 {
                     'cls': Node,
                     'tag': 'n2',
-                    'output_of': 'n1'
+                    'with_incoming': 'n1'
                 }
             ],
             'filters': {
@@ -412,15 +412,15 @@ def test_tags(self):
         from aiida.orm.computers import Computer
         qb = QueryBuilder()
         qb.append(Node, tag='n1')
-        qb.append(Node, tag='n2', edge_tag='e1', output_of='n1')
-        qb.append(Node, tag='n3', edge_tag='e2', output_of='n2')
-        qb.append(Computer, computer_of='n3', tag='c1', edge_tag='nonsense')
+        qb.append(Node, tag='n2', edge_tag='e1', with_incoming='n1')
+        qb.append(Node, tag='n3', edge_tag='e2', with_incoming='n2')
+        qb.append(Computer, with_node='n3', tag='c1', edge_tag='nonsense')
         self.assertEqual(qb.get_used_tags(), ['n1', 'n2', 'e1', 'n3', 'e2', 'c1', 'nonsense'])
 
         # Now I am testing the default tags,
         qb = QueryBuilder().append(StructureData).append(ProcessNode).append(
             StructureData).append(
-            ParameterData, input_of=ProcessNode)
+            ParameterData, with_outgoing=ProcessNode)
         self.assertEqual(qb.get_used_tags(), [
             'StructureData_1', 'ProcessNode_1',
             'StructureData_1--ProcessNode_1', 'StructureData_2',
@@ -520,15 +520,15 @@ def test_computer_json(self):
         qb = QueryBuilder()
         qb.append(ProcessNode, project=['id'], tag='calc')
         qb.append(Computer, project=['id', 'transport_params'],
-                  outerjoin=True, computer_of='calc')
+                  outerjoin=True, with_node='calc')
         qb.all()
 
         # Checking the correct retrieval of _metadata which is
         # a JSON field (in both backends).
         qb = QueryBuilder()
         qb.append(ProcessNode, project=['id'], tag='calc')
         qb.append(Computer, project=['id', '_metadata'],
-                  outerjoin=True, computer_of='calc')
+                  outerjoin=True, with_node='calc')
         qb.all()
 
 
@@ -797,15 +797,15 @@ def test_joins3_user_group(self):
         # Search for the group of the user
         qb = orm.QueryBuilder()
         qb.append(orm.User, tag='user', filters={'id': {'==': user.id}})
-        qb.append(orm.Group, belongs_to='user',
+        qb.append(orm.Group, with_user='user',
                   filters={'id': {'==': group.id}})
         self.assertEquals(qb.count(), 1, "The expected group that belongs to "
                                          "the selected user was not found.")
 
         # Search for the user that owns a group
         qb = orm.QueryBuilder()
         qb.append(orm.Group, tag='group', filters={'id': {'==': group.id}})
-        qb.append(orm.User, owner_of='group', filters={'id': {'==': user.id}})
+        qb.append(orm.User, with_group='group', filters={'id': {'==': user.id}})
 
         self.assertEquals(qb.count(), 1, "The expected user that owns the "
                                          "selected group was not found.")

aiida/cmdline/commands/cmd_code.py

@@ -289,12 +289,12 @@ def code_list(computer, input_plugin, all_entries, all_users, show_owner):
         qb.append(Code, tag="code", filters=qb_code_filters, project=["id", "label"])
         # We have a user assigned to the code so we can ask for the
         # presence of a user even if there is no user filter
-        qb.append(orm.User, creator_of="code", project=["email"], filters=qb_user_filters)
+        qb.append(orm.User, with_node="code", project=["email"], filters=qb_user_filters)
         # We also add the filter on computer. This will automatically
         # return codes that have a computer (and of course satisfy the
         # other filters). The codes that have a computer attached are the
         # remote codes.
-        qb.append(orm.Computer, computer_of="code", project=["name"], filters=qb_computer_filters)
+        qb.append(orm.Computer, with_node="code", project=["name"], filters=qb_computer_filters)
         qb.order_by({Code: {'id': 'asc'}})
         print_list_res(qb, show_owner)
 
@@ -306,8 +306,8 @@ def code_list(computer, input_plugin, all_entries, all_users, show_owner):
         qb.append(Code, tag="code", filters=qb_code_filters, project=["id", "label"])
         # We have a user assigned to the code so we can ask for the
         # presence of a user even if there is no user filter
-        qb.append(orm.User, creator_of="code", project=["email"], filters=qb_user_filters)
-        qb.append(orm.Computer, computer_of="code", project=["name"])
+        qb.append(orm.User, with_node="code", project=["email"], filters=qb_user_filters)
+        qb.append(orm.Computer, with_node="code", project=["name"])
         qb.order_by({Code: {'id': 'asc'}})
         print_list_res(qb, show_owner)
 
@@ -323,7 +323,7 @@ def code_list(computer, input_plugin, all_entries, all_users, show_owner):
         qb.append(Code, tag="code", filters=qb_code_filters, project=["id", "label"])
         # We have a user assigned to the code so we can ask for the
         # presence of a user even if there is no user filter
-        qb.append(orm.User, creator_of="code", project=["email"], filters=qb_user_filters)
+        qb.append(orm.User, with_node="code", project=["email"], filters=qb_user_filters)
         qb.order_by({Code: {'id': 'asc'}})
         print_list_res(qb, show_owner)
 

aiida/cmdline/commands/cmd_data/cmd_array.py

@@ -30,6 +30,6 @@ def array_show(data):
 
     for node in data:
         the_dict = {}
-        for arrayname in node.arraynames():
+        for arrayname in node.get_arraynames():
             the_dict[arrayname] = node.get_array(arrayname).tolist()
         echo_dictionary(the_dict, 'json+date')

aiida/cmdline/commands/cmd_data/cmd_list.py

@@ -55,13 +55,13 @@ def query(datatype, project, past_days, group_pks, all_users):
         n_days_ago = now - datetime.timedelta(days=past_days)
         data_filters.update({"ctime": {'>=': n_days_ago}})
 
-    qbl.append(datatype, tag="data", created_by="creator", filters=data_filters, project=project)
+    qbl.append(datatype, tag="data", with_user="creator", filters=data_filters, project=project)
 
     # If there is a group restriction
     if group_pks is not None:
         group_filters = dict()
         group_filters.update({"id": {"in": group_pks}})
-        qbl.append(orm.Group, tag="group", filters=group_filters, group_of="data")
+        qbl.append(orm.Group, tag="group", filters=group_filters, with_node="data")
 
     qbl.order_by({datatype: {'ctime': 'asc'}})
 

aiida/cmdline/commands/cmd_data/cmd_upf.py

@@ -73,7 +73,7 @@ def upf_listfamilies(elements, with_description):
         query.add_filter(UpfData, {'attributes.element': {'in': elements}})
     query.append(
         orm.Group,
-        group_of='upfdata',
+        with_node='upfdata',
         tag='group',
         project=["name", "description"],
         filters={"type": {
@@ -87,7 +87,7 @@ def upf_listfamilies(elements, with_description):
             group_desc = res.get("group").get("description")
             query = orm.QueryBuilder()
             query.append(orm.Group, tag='thisgroup', filters={"name": {'like': group_name}})
-            query.append(UpfData, project=["id"], member_of='thisgroup')
+            query.append(UpfData, project=["id"], with_group='thisgroup')
 
             if with_description:
                 description_string = ": {}".format(group_desc)

aiida/cmdline/commands/cmd_node.py

@@ -159,7 +159,7 @@ def show(nodes, print_groups):
             # pylint: disable=invalid-name
             qb = QueryBuilder()
             qb.append(Node, tag='node', filters={'id': {'==': node.pk}})
-            qb.append(Group, tag='groups', group_of='node', project=['id', 'name'])
+            qb.append(Group, tag='groups', with_node='node', project=['id', 'name'])
 
             echo.echo("#### GROUPS:")
 

aiida/cmdline/utils/common.py

@@ -287,7 +287,7 @@ def get_subtree(pk, level=0):
             # In the future, we should specify here the type of link
             # for now, CALL links are the only ones allowing calc-calc
             # (we here really want instead to follow CALL links)
-            output_of='workcalculation',
+            with_incoming='workcalculation',
             tag='subworkchains')
         result = list(itertools.chain(*builder.distinct().all()))
 

aiida/common/graph.py

@@ -116,7 +116,7 @@ def draw_link_settings(inp_id, out_id, link_label, link_type):
             # This query gives me all the inputs of this node, and link labels and types!
             input_query = QueryBuilder()
             input_query.append(Node, filters={'id': node.pk}, tag='n')
-            input_query.append(Node, input_of='n', edge_project=('id', 'label', 'type'), project='*', tag='inp')
+            input_query.append(Node, with_outgoing='n', edge_project=('id', 'label', 'type'), project='*', tag='inp')
             for inp, link_id, link_label, link_type in input_query.iterall():
                 # I removed this check, to me there is no way that this link was already referred to!
                 # if link_id not in links:
@@ -131,7 +131,7 @@ def draw_link_settings(inp_id, out_id, link_label, link_type):
                 # Query for the outputs, giving me also link labels and types:
                 output_query = QueryBuilder()
                 output_query.append(Node, filters={'id': node.pk}, tag='n')
-                output_query.append(Node, output_of='n', edge_project=('id', 'label', 'type'), project='*', tag='out')
+                output_query.append(Node, with_incoming='n', edge_project=('id', 'label', 'type'), project='*', tag='out')
                 # Iterate through results
                 for out, link_id, link_label, link_type in output_query.iterall():
                     # This link might have been drawn already, because the output is maybe
@@ -160,7 +160,7 @@ def draw_link_settings(inp_id, out_id, link_label, link_type):
             # Query for the outputs:
             output_query = QueryBuilder()
             output_query.append(Node, filters={'id': node.pk}, tag='n')
-            output_query.append(Node, output_of='n', edge_project=('id', 'label', 'type'), project='*', tag='out')
+            output_query.append(Node, with_incoming='n', edge_project=('id', 'label', 'type'), project='*', tag='out')
 
             for out, link_id, link_label, link_type in output_query.iterall():
                 # Draw the link
@@ -172,7 +172,7 @@ def draw_link_settings(inp_id, out_id, link_label, link_type):
             if include_calculation_inputs and isinstance(node, ProcessNode):
                 input_query = QueryBuilder()
                 input_query.append(Node, filters={'id': node.pk}, tag='n')
-                input_query.append(Node, input_of='n', edge_project=('id', 'label', 'type'), project='*', tag='inp')
+                input_query.append(Node, with_outgoing='n', edge_project=('id', 'label', 'type'), project='*', tag='inp')
                 for inp, link_id, link_label, link_type in input_query.iterall():
                     # Also here, maybe it's just better not to check?
                     if link_id not in links:

aiida/common/hashing.py

@@ -105,7 +105,7 @@ def is_password_usable(enc_pass):
     using_sysrandom = True
 except NotImplementedError:
     import warnings
-    warnings.warn('A secure pseudo-random number generator is not available '
+    warnings.warn('A secure pseudo-random number generator is not available '  # pylint: disable=no-member
                   'on your system. Falling back to Mersenne Twister.')
     using_sysrandom = False  # pylint: disable=invalid-name