diff --git a/gui/src/components/archive/MetainfoBrowser.js b/gui/src/components/archive/MetainfoBrowser.js
index 4f255f94d72e4823d99baef548cdb6e41625a96a..63eaebed5f321ebf1bca40490d9699fac8e45bd9 100644
--- a/gui/src/components/archive/MetainfoBrowser.js
+++ b/gui/src/components/archive/MetainfoBrowser.js
@@ -68,6 +68,8 @@ If you bookmark this page, you can save the definition represented by the highli
To learn more about the meta-info, visit the [meta-info documentation](${appBase}/docs/metainfo.html).
`
+const showInnerSectionDefinitions = false
+
function defCompare(a, b) {
return a.name.localeCompare(b.name)
}
@@ -328,7 +330,7 @@ class CategoryDefAdaptor extends MetainfoAdaptor {
}
}
-function SectionDef({def}) {
+function SectionDefContent({def}) {
const config = useRecoilValue(configState)
const metainfoConfig = useRecoilValue(metainfoConfigState)
const filter = def.extends_base_section ? () => true : def => {
@@ -347,8 +349,7 @@ function SectionDef({def}) {
return false
}
- return <Content style={{backgroundColor: 'grey'}}>
- <Definition def={def} kindLabel="section definition" />
+ return <React.Fragment>
<DefinitionProperties def={def} />
{def.base_sections.length > 0 &&
<Compartment title="base section">
@@ -394,7 +395,7 @@ function SectionDef({def}) {
})
}
</Compartment>
- <Compartment title="inner section definitions">
+ {showInnerSectionDefinitions && <Compartment title="inner section definitions">
{def.inner_section_definitions.filter(filter)
.map(innerSectionDef => {
const key = `innerSectionDef@${innerSectionDef.name}`
@@ -411,8 +412,18 @@ function SectionDef({def}) {
</Item>
})
}
- </Compartment>
+ </Compartment>}
<DefinitionDetails def={def} />
+ </React.Fragment>
+}
+SectionDefContent.propTypes = ({
+ def: PropTypes.object
+})
+
+function SectionDef({def}) {
+ return <Content style={{backgroundColor: 'grey'}}>
+ <Definition def={def} kindLabel="section definition" />
+ <SectionDefContent def={def} />
</Content>
}
SectionDef.propTypes = ({
@@ -420,14 +431,13 @@ SectionDef.propTypes = ({
})
function SubSectionDef({def}) {
+ const sectionDef = resolveRef(def.sub_section)
return <React.Fragment>
<Content>
- <Definition def={def} kindLabel="sub section definition"/>
- <DefinitionProperties def={def}>
- {def.repeats && <Typography><b>repeats</b>: true</Typography>}
- </DefinitionProperties>
+ <Title def={def} isDefinition kindLabel="sub section definition" />
+ <DefinitionDocs def={sectionDef} />
+ <SectionDefContent def={sectionDef} />
</Content>
- <SectionDef def={resolveRef(def.sub_section)} />
</React.Fragment>
}
SubSectionDef.propTypes = ({
@@ -482,9 +492,8 @@ QuantityDef.propTypes = ({
def: PropTypes.object
})
-function Definition({def, ...props}) {
+function DefinitionDocs({def}) {
return <React.Fragment>
- <Title def={def} isDefinition {...props} />
{def.description && !def.extends_base_section &&
<Compartment title="description">
<Box marginTop={1} marginBottom={1}>
@@ -503,6 +512,16 @@ function Definition({def, ...props}) {
}
</React.Fragment>
}
+DefinitionDocs.propTypes = {
+ def: PropTypes.object.isRequired
+}
+
+function Definition({def, ...props}) {
+ return <React.Fragment>
+ <Title def={def} isDefinition {...props} />
+ <DefinitionDocs def={def} />
+ </React.Fragment>
+}
Definition.propTypes = {
def: PropTypes.object.isRequired
}
diff --git a/nomad/datamodel/metainfo/nexus.py b/nomad/datamodel/metainfo/nexus.py
index e2b03ebc3a3b983b16a16d38a5502e815124b212..f8655b562be8e3ee64fe6ed26fadfec8de052750 100644
--- a/nomad/datamodel/metainfo/nexus.py
+++ b/nomad/datamodel/metainfo/nexus.py
@@ -43,6 +43,19 @@ _definition_sections: Dict[str, Section] = dict()
_xml_parent_map: Dict[ET.Element, ET.Element] = None
_nx_doc_base = 'https://manual.nexusformat.org/classes'
+# TODO There are more types in nxdl, but they are not used by the current base classes and
+# application definitions.
+_nx_types = {
+ 'NX_FLOAT': np.dtype(np.float64),
+ 'NX_CHAR': str,
+ 'NX_BOOLEAN': bool,
+ 'NX_INT': np.dtype(np.int64),
+ 'NX_NUMBER': np.dtype(np.number),
+ 'NX_POSINT': np.dtype(np.uint64),
+ 'NX_BINARY': Bytes,
+ 'NX_DATE_TIME': Datetime
+}
+
def to_camel_case(snake_str: str, upper: bool = False) -> str:
components = snake_str.split('_')
@@ -69,7 +82,7 @@ def nx_documenation_url(xml_node: ET.Element, nx_type: str):
return doc_url
-def get_section(name: str, **kwargs) -> Section:
+def get_or_create_section(name: str, **kwargs) -> Section:
'''
Returns the 'existing' metainfo section for a given top-level nexus base-class name.
@@ -82,34 +95,48 @@ def get_section(name: str, **kwargs) -> Section:
section.more.update(**kwargs)
return section
- section = Section(validate=validate, name=name, more=kwargs)
+ section = Section(validate=validate, name=name, **kwargs)
current_package.section_definitions.append(section)
_definition_sections[section.name] = section
return section
-def add_definition_properties(xml_node: ET.Element, definition: Definition, nx_type: str = None):
+def get_enum(xml_node: ET.Element):
+ enumeration = xml_node.find('nx:enumeration', xml_namespaces)
+ if enumeration is not None:
+ enum_values = []
+ for enum_value in enumeration.findall('nx:item', xml_namespaces):
+ enum_values.append(enum_value.attrib['value'])
+ return MEnum(*enum_values)
+ return None
+
+
+def add_common_properties(xml_node: ET.Element, definition: Definition):
'''
- Adds general metainfo definition properties (e.g. name, deprecated, description)
+ Adds general metainfo definition properties (e.g. deprecated, docs, optional, ...)
from the given nexus XML node to the given metainfo definition.
'''
+ nx_kind = definition.more.get('nx_kind')
xml_attrs = xml_node.attrib
- if 'name' in xml_attrs:
- name = xml_attrs['name']
- if nx_type and nx_type != 'class':
- name = f'nx_{nx_type}_{name}'
- definition.name = name
+ # Read properties from potential base section. Those are not inherited, but we
+ # duplicate them for a nicer presentation
+ if isinstance(definition, Section) and len(definition.base_sections) > 0:
+ base_section = definition.base_sections[0]
+ if base_section.description:
+ definition.description = base_section.description
+ if base_section.deprecated:
+ definition.deprecated = base_section.deprecated
+ if len(base_section.more) > 0:
+ definition.more.update(**base_section.more)
- # Add a link to the nexus classes documentation
links = []
- if nx_type is not None:
- doc_url = nx_documenation_url(xml_node, nx_type)
+ if nx_kind is not None:
+ doc_url = nx_documenation_url(xml_node, nx_kind)
if doc_url:
links.append(doc_url)
- # Read additional urls from the XML doc element
doc = xml_node.find('nx:doc', xml_namespaces)
if doc is not None and doc.text is not None:
definition.description = strip(doc.text)
@@ -134,17 +161,7 @@ def add_definition_properties(xml_node: ET.Element, definition: Definition, nx_t
if 'recommended' in xml_attrs:
definition.more['nx_recommended'] = xml_attrs['recommended']
- # TODO there are probably even more nxdl attributes
-
-
-def get_enum(xml_node: ET.Element):
- enumeration = xml_node.find('nx:enumeration', xml_namespaces)
- if enumeration is not None:
- enum_values = []
- for enum_value in enumeration.findall('nx:item', xml_namespaces):
- enum_values.append(enum_value.attrib['value'])
- return MEnum(*enum_values)
- return None
+ # TODO there are probably even more nxdl attributes?
def add_attributes(xml_node: ET.Element, section: Section):
@@ -156,54 +173,84 @@ def add_attributes(xml_node: ET.Element, section: Section):
type: Any = get_enum(xml_node)
if type is None:
type = str
- quantity = Quantity(type=type, nx_kind='attribute')
- add_definition_properties(attribute, quantity)
+ quantity = Quantity(type=type, nx_kind='attribute', name=attribute.attrib['name'])
+ add_common_properties(attribute, quantity)
section.quantities.append(quantity)
-# TODO There are more types in nxdl, but they are not used by the current base classes and
-# application definitions.
-_nx_types = {
- 'NX_FLOAT': np.dtype(np.float64),
- 'NX_CHAR': str,
- 'NX_BOOLEAN': bool,
- 'NX_INT': np.dtype(np.int64),
- 'NX_NUMBER': np.dtype(np.number),
- 'NX_POSINT': np.dtype(np.uint64),
- 'NX_BINARY': Bytes,
- 'NX_DATE_TIME': Datetime
-}
+def add_group_properties(xml_node: ET.Element, section: Section):
+ '''
+ Adds all properties that can be generated from the given nexus group XML node to
+ the given (empty) metainfo section definition.
+ '''
+ for group in xml_node.findall('nx:group', xml_namespaces):
+ group_section = create_group_section(group)
+ section.inner_section_definitions.append(group_section)
+
+ if 'name' in group.attrib:
+ name = f'nx_group_{group.attrib["name"]}'
+ else:
+ name = group.attrib['type'].replace('NX', 'nx_group_')
+
+ max_occurs = group.attrib.get('maxOccurs', '0')
+ repeats = max_occurs == 'unbounded' or int(max_occurs) > 1
+ section.sub_sections.append(SubSection(
+ section_def=group_section, nx_kind='group', name=name, repeats=repeats))
+
+ for field in xml_node.findall('nx:field', xml_namespaces):
+ field_section = create_field_section(field)
+ section.inner_section_definitions.append(field_section)
+
+ section.sub_sections.append(SubSection(
+ section_def=field_section, nx_kind='field',
+ name=f'nx_field_{field.attrib["name"]}'))
+
+ add_attributes(xml_node, section)
-def section_from_field(xml_node: ET.Element) -> Section:
+def add_template_properties(xml_node: ET.Element, section: Section):
'''
- Generates a metainfo section for the given nexus field XML node.
+ Adds potential abilities of a group or field section to act as a TEMPLATE or
+ nameType="any" definition.
'''
- xml_attrs = xml_node.attrib
- nx_name = xml_attrs['name']
- name = to_camel_case(nx_name, True) + 'Field'
- section = Section(validate=validate, name=name, more=dict(nx_kind='field'))
- if nx_name.lower() != nx_name:
+ is_template = section.name.lower() != section.name or xml_node.attrib.get('nameType', '') == 'any'
+ if is_template:
section.quantities.append(Quantity(
name='nx_name', type=str, description='''
This is a nexus template property. This quantity holds the actual name used
in the nexus data.'''))
- value = Quantity(name='nx_value', description='The value for this nexus field')
- section.quantities.append(value)
+
+
+def create_field_section(xml_node: ET.Element):
+ '''
+ Creates a metainfo section from the nexus field given as xml node.
+ '''
+ xml_attrs = xml_node.attrib
+
+ assert 'name' in xml_attrs, 'field has not name'
+ field_section = Section(
+ validate=validate, nx_kind='field',
+ name=to_camel_case(xml_attrs['name'], True) + 'Field')
+
+ add_template_properties(xml_node, field_section)
+
+ value_quantity = Quantity(name='nx_value', description='The value for this nexus field')
+ field_section.quantities.append(value_quantity)
if 'type' in xml_attrs:
nx_type = xml_attrs['type']
if nx_type not in _nx_types:
raise NotImplementedError(f'type {nx_type} is not supported')
- value.type = _nx_types[nx_type]
+ value_quantity.type = _nx_types[nx_type]
+ field_section.more['nx_type'] = nx_type
else:
- value.type = get_enum(xml_node)
- if value.type is None:
- value.type = Any
+ value_quantity.type = get_enum(xml_node)
+ if value_quantity.type is None:
+ value_quantity.type = Any
- if 'unit' in xml_attrs:
- # TODO map unit
- pass
+ if 'units' in xml_attrs:
+ field_section.more['nx_units'] = xml_attrs['units']
+ # TODO map unit to value
dimensions = xml_node.find('nx:dimensions', xml_namespaces)
if dimensions is not None:
@@ -215,90 +262,60 @@ def section_from_field(xml_node: ET.Element) -> Section:
except ValueError:
pass
shape.append(dimension_value)
- value.shape = shape
+ value_quantity.shape = shape
- add_attributes(xml_node, section)
+ add_common_properties(xml_node, field_section)
+ add_attributes(xml_node, field_section)
- return section
+ return field_section
-def add_group_properties(xml_node: ET.Element, definition_section: Section):
+def create_group_section(xml_node: ET.Element) -> Section:
'''
- Adds all properties that can be generated from the given nexus group XML node to
- the given (empty) metainfo section definition.
+ Creates a metainfo section from the nexus group given as xml node.
'''
- add_attributes(xml_node, definition_section)
-
- for group in xml_node.findall('nx:group', xml_namespaces):
- assert 'type' in group.attrib, 'group has not type'
-
- type = group.attrib['type']
- base_section = get_section(type)
- empty_definition = len(group) == 0 or (
- len(group) == 1 and group.find('nx:doc', xml_namespaces) is not None)
- if empty_definition:
- # The group does not define anything new, we can directly use the base definition
- group_section = base_section
- else:
- if 'name' in group.attrib:
- name = to_camel_case(group.attrib['name'], True) + 'Group'
- else:
- name = to_camel_case(type, True) + 'Group'
-
- group_section = Section(validate=validate, name=name)
- group_section.base_sections = [base_section]
- definition_section.inner_section_definitions.append(group_section)
- add_group_properties(group, group_section)
-
- sub_section = SubSection(section_def=group_section, nx_kind='group')
- add_definition_properties(group, sub_section, nx_type='group')
- if sub_section.name is None:
- sub_section.name = type.replace('NX', 'nx_group_')
- definition_section.sub_sections.append(sub_section)
+ xml_attrs = xml_node.attrib
+ type = xml_attrs['type']
- for field in xml_node.findall('nx:field', xml_namespaces):
- assert 'name' in field.attrib, 'field has not name'
+ if 'name' in xml_attrs:
+ name = to_camel_case(xml_attrs['name'], True) + 'Group'
+ else:
+ name = to_camel_case(type, True) + 'Group'
- field_section = section_from_field(field)
- definition_section.inner_section_definitions.append(field_section)
+ group_section = Section(
+ validate=validate, nx_kind='group', name=name,
+ base_sections=[get_or_create_section(type)])
- more = dict(nx_kind='field')
- more.update(**{
- f'nx_{key}': field.attrib[key]
- for key in ['type', 'units'] if key in field.attrib})
- field_sub_section = SubSection(section_def=field_section, **more)
- add_definition_properties(field, field_sub_section, nx_type='field')
- definition_section.sub_sections.append(field_sub_section)
+ add_common_properties(xml_node, group_section)
+ add_template_properties(xml_node, group_section)
+ add_group_properties(xml_node, group_section)
- return definition_section
+ return group_section
-def section_from_class(nxdl_file: str):
+def create_class_section(xml_node: ET.Element) -> Section:
'''
- Creates a metainfo section from the top-level nexus group definition in the given
- nxdl file and adds it to the current metainfo package.
+ Creates a metainfo section from the top-level nexus definition given as xml node.
'''
- xml_tree = ET.parse(nxdl_file)
- definition = xml_tree.getroot()
- xml_attrs = definition.attrib
- global _xml_parent_map
- _xml_parent_map = {child: parent for parent in xml_tree.iter() for child in parent}
-
- assert xml_attrs.get('type') == 'group', 'definition is not a group'
+ xml_attrs = xml_node.attrib
assert 'name' in xml_attrs
- definition_section = get_section(xml_attrs['name'], nx_kind=xml_attrs['type'])
+ class_section = get_or_create_section(xml_attrs['name'], nx_kind=xml_attrs['type'])
+
if 'extends' in xml_attrs:
- base_section = get_section(xml_attrs['extends'])
- definition_section.base_sections = [base_section]
- add_group_properties(definition, definition_section)
- add_definition_properties(definition, definition_section, nx_type='class')
+ base_section = get_or_create_section(xml_attrs['extends'])
+ class_section.base_sections = [base_section]
+
+ add_common_properties(xml_node, class_section)
+ add_group_properties(xml_node, class_section)
+ return class_section
-def package_from_directory(path: str, package_name: str) -> Package:
+
+def create_package_from_nxdl_directory(path: str, package_name: str) -> Package:
'''
- Creates a metainfo package from the given nexus directory. Will the respective
- metainfo definitions generated from all the nxdl files in that directory.
+ Creates a metainfo package from the given nexus directory. Will generate the respective
+ metainfo definitions from all the nxdl files in that directory.
'''
global current_package
current_package = Package(name=package_name)
@@ -308,8 +325,19 @@ def package_from_directory(path: str, package_name: str) -> Package:
continue
try:
- section_from_class(
- os.path.join(path, nxdl_file))
+ nxdl_path = os.path.join(path, nxdl_file)
+ xml_tree = ET.parse(nxdl_path)
+ xml_node = xml_tree.getroot()
+
+ global _xml_parent_map
+ _xml_parent_map = {child: parent for parent in xml_tree.iter() for child in parent}
+
+ assert xml_node.attrib.get('type') == 'group', 'definition is not a group'
+
+ # The section gets already implicitly added to current_package by
+ # get_or_create_section
+ create_class_section(xml_node)
+
except Exception as e:
print(f'Exception while mapping {nxdl_file}', file=sys.stderr)
raise e
@@ -327,7 +355,7 @@ nx_definitions_path = os.path.join(
packages: List[Package] = []
for nx_package in ['base_classes', 'applications']:
path = os.path.join(nx_definitions_path, nx_package)
- packages.append(package_from_directory(path, f'nexus_{nx_package}'))
+ packages.append(create_package_from_nxdl_directory(path, f'nexus_{nx_package}'))
# TODO there are problems generating with nx_package='contributed_definitions'
diff --git a/tests/metainfo/test_metainfo.py b/tests/metainfo/test_metainfo.py
index 217454d6f7d310b830ed7e55ce9772a6a4cfb58d..aabab5c27982c83d0991e0750c925b630be2a844 100644
--- a/tests/metainfo/test_metainfo.py
+++ b/tests/metainfo/test_metainfo.py
@@ -318,11 +318,15 @@ class TestM2:
class TestSection(MSection):
m_def = Section(this_does_not_exist_in_metainfo='value')
test_quantity = Quantity(type=str, also_no_metainfo_quantity=1, one_more=False)
+ test_delayed_more_quantity = Quantity(type=str)
another_test_quantity = Quantity(type=str)
+ TestSection.test_delayed_more_quantity.more = dict(one_more='test')
+
assert TestSection.m_def.more['this_does_not_exist_in_metainfo'] == 'value'
assert TestSection.test_quantity.more['also_no_metainfo_quantity'] == 1
assert not TestSection.test_quantity.more['one_more']
+ assert TestSection.test_delayed_more_quantity.more['one_more'] == 'test'
assert len(TestSection.another_test_quantity.more) == 0
assert TestSection.m_def.this_does_not_exist_in_metainfo == 'value'