diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 9733fbb5edd8ce81988abc9b70f2e51c519615d6..c82533058630d8bec9b03d09221e701d57b053b3 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -2718,6 +2718,7 @@ class Section(Definition):
def __init_metainfo__(self):
super().__init_metainfo__()
+ # Init extending_sections
if self.extends_base_section:
base_sections_count = len(self.base_sections)
if base_sections_count == 0:
@@ -2735,6 +2736,21 @@ class Section(Definition):
base_section.extending_sections = base_section.extending_sections + [self]
+ # Transfer properties of inherited and overwriten property definitions that
+ # have not been overwritten
+ inherited_properties: Dict[str, Property] = dict()
+ for base_section in self.all_base_sections:
+ inherited_properties.update(**base_section.all_properties)
+
+ for property in self.quantities + self.sub_sections:
+ inherited_property = inherited_properties.get(property.name)
+ if inherited_property is None:
+ continue
+
+ for m_quantity in property.m_def.all_quantities.values():
+ if not property.m_is_set(m_quantity) and inherited_property.m_is_set(m_quantity):
+ property.m_set(m_quantity, inherited_property.m_get(m_quantity))
+
# validate
def validate(definition):
errors, warnings = definition.m_all_validate()
@@ -2756,9 +2772,8 @@ class Section(Definition):
@constraint
def unique_names(self):
- # start with the names of all base_sections
names: Set[str] = set()
- for base in list(self.all_base_sections) + self.extending_sections:
+ for base in self.extending_sections:
for quantity in base.quantities + base.sub_sections:
for alias in quantity.aliases:
names.add(alias)
@@ -2947,25 +2962,23 @@ Section.event_handlers = Quantity(
@derived(cached=True)
-def inherited_sections(self) -> Set[Section]:
- result: Set[Section] = set()
- result.add(self)
- for base_section in self.base_sections:
- result.add(base_section)
- for base_base_section in base_section.all_base_sections:
- result.add(base_base_section)
+def inherited_sections(self) -> List[Section]:
+ result: List[Section] = []
+ for base_section in self.all_base_sections:
+ result.append(base_section)
for extending_section in self.extending_sections:
- result.add(extending_section)
+ result.append(extending_section)
+ result.append(self)
return result
@derived(cached=True)
-def all_base_sections(self) -> Set[Section]:
- result: Set[Section] = set()
+def all_base_sections(self) -> List[Section]:
+ result: List[Section] = []
for base_section in self.base_sections:
- result.add(base_section)
for base_base_section in base_section.all_base_sections:
- result.add(base_base_section)
+ result.append(base_base_section)
+ result.append(base_section)
return result
diff --git a/tests/metainfo/test_metainfo.py b/tests/metainfo/test_metainfo.py
index 98b0e71238973600f2f21977fef7944dd406e1db..217454d6f7d310b830ed7e55ce9772a6a4cfb58d 100644
--- a/tests/metainfo/test_metainfo.py
+++ b/tests/metainfo/test_metainfo.py
@@ -191,14 +191,15 @@ class TestM2:
class TestBase(MSection):
name = Quantity(type=str)
- with pytest.raises(MetainfoError):
- class TestSection(TestBase): # pylint: disable=unused-variable
- name = Quantity(type=int)
+ # this is possible, can overwrite existing quantity
+ class TestSection(TestBase): # pylint: disable=unused-variable
+ name = Quantity(type=int)
def test_unique_names_extends(self):
class TestBase(MSection):
name = Quantity(type=str)
+ # this is not possible, cant replace existing quantity
with pytest.raises(MetainfoError):
class TestSection(TestBase): # pylint: disable=unused-variable
m_def = Section(extends_base_section=True)
diff --git a/tests/metainfo/test_sections.py b/tests/metainfo/test_sections.py
new file mode 100644
index 0000000000000000000000000000000000000000..4ff970ea0332c0508d60e313cabc2147baa8ef85
--- /dev/null
+++ b/tests/metainfo/test_sections.py
@@ -0,0 +1,160 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# Contains more general test cases that are replaced continiously by more specialized
+# in-depth tests in test_* files of the same module.
+
+import pytest
+
+from nomad.metainfo import MSection
+from nomad.metainfo.metainfo import Quantity, SubSection, Section
+
+
+def test_base_section():
+ class BaseSection(MSection):
+ pass
+
+ class Section(BaseSection):
+ pass
+
+ assert Section.m_def.base_sections == [BaseSection.m_def]
+ assert BaseSection.m_def.base_sections == []
+
+ assert isinstance(Section(), Section)
+ assert isinstance(Section(), BaseSection)
+
+
+def test_quantity_inheritance():
+ class BaseSection(MSection):
+ test_quantity = Quantity(type=str)
+
+ class Section(BaseSection):
+ pass
+
+ assert 'test_quantity' in Section.m_def.all_properties
+ assert Section.test_quantity == BaseSection.test_quantity
+
+ section = Section(test_quantity='test_value')
+ assert section.test_quantity == 'test_value'
+ assert section.m_to_dict()['test_quantity'] == 'test_value'
+
+
+def test_quantity_overwrite():
+ class BaseSection(MSection):
+ test_quantity = Quantity(type=str)
+
+ class Section(BaseSection):
+ test_quantity = Quantity(type=int)
+
+ assert 'test_quantity' in Section.m_def.all_properties
+ assert Section.m_def.all_properties['test_quantity'] == Section.test_quantity
+ assert BaseSection.test_quantity != Section.test_quantity
+ assert BaseSection.m_def.all_properties['test_quantity'] != Section.m_def.all_properties['test_quantity']
+
+ with pytest.raises(TypeError):
+ Section(test_quantity='test_value')
+
+ section = Section(test_quantity=1)
+ assert section.test_quantity == 1
+ assert section.m_to_dict()['test_quantity'] == 1
+
+
+def test_quantity_partial_overwrite():
+ class BaseSection(MSection):
+ test_quantity = Quantity(type=str, description='test_description')
+
+ class Section(BaseSection):
+ test_quantity = Quantity(type=int)
+
+ assert Section.test_quantity.description == 'test_description'
+ assert Section.test_quantity.type == int
+
+
+def test_sub_section_inheritance():
+ class OtherSection(MSection):
+ pass
+
+ class BaseSection(MSection):
+ test_sub_section = SubSection(sub_section=OtherSection)
+
+ class Section(BaseSection):
+ pass
+
+ assert 'test_sub_section' in Section.m_def.all_properties
+ assert Section.test_sub_section == BaseSection.test_sub_section
+
+ section = Section(test_sub_section=OtherSection())
+ assert section.test_sub_section.m_def == OtherSection.m_def
+ assert section.m_to_dict()['test_sub_section'] == {}
+
+
+def test_sub_section_overwrite():
+ class OtherSection(MSection):
+ pass
+
+ class BaseSection(MSection):
+ test_sub_section = SubSection(sub_section=OtherSection)
+
+ class Section(BaseSection):
+ test_sub_section = SubSection(sub_section=OtherSection, repeats=True)
+
+ assert 'test_sub_section' in Section.m_def.all_properties
+ assert Section.m_def.all_properties['test_sub_section'] == Section.test_sub_section
+ assert BaseSection.test_sub_section != Section.test_sub_section
+ assert BaseSection.m_def.all_properties['test_sub_section'] != Section.m_def.all_properties['test_sub_section']
+
+ with pytest.raises(TypeError):
+ Section(test_sub_section=OtherSection())
+
+ section = Section(test_sub_section=[OtherSection()])
+ assert len(section.test_sub_section) == 1
+ assert section.m_to_dict()['test_sub_section'] == [{}]
+
+
+def test_sub_section_partial_overwrite():
+ class OtherSection(MSection):
+ pass
+
+ class BaseSection(MSection):
+ test_sub_section = SubSection(sub_section=OtherSection, description='test_description')
+
+ class Section(BaseSection):
+ test_sub_section = SubSection(repeats=True)
+
+ assert Section.test_sub_section.description == 'test_description'
+ assert Section.test_sub_section.sub_section == OtherSection.m_def
+ assert Section.test_sub_section.repeats
+
+
+def test_overwrite_programmatic():
+ class BaseSection(MSection):
+ test_quantity = Quantity(type=str, description='test_description')
+
+ section_def = Section(name='Section', base_sections=[BaseSection.m_def])
+ section_def.m_add_sub_section(
+ Section.quantities,
+ Quantity(name='test_quantity'))
+
+ # This happens automatically in Python class based section defintions, but
+ # has to be called manually in programatic section definitions.
+ section_def.__init_metainfo__()
+
+ section_cls = section_def.section_cls
+
+ assert section_cls.test_quantity.description == 'test_description'
+ assert section_cls.test_quantity.type == str