From c74f239e49d24368c5f51ce0432cee22f3a5d0dc Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Tue, 14 Jul 2020 13:42:53 +0200
Subject: [PATCH] Added the remaining datamodel packages to the overall
public/common environment and metainfo browser. #376
---
examples/access_metainfo.py | 15 ++++---
gui/src/components/Markdown.js | 2 +-
.../metaInfoBrowser/DefinitionCard.js | 2 +-
nomad/datamodel/datamodel.py | 11 +++--
nomad/datamodel/dft.py | 2 +-
nomad/datamodel/ems.py | 2 +-
nomad/datamodel/encyclopedia.py | 12 +++--
nomad/datamodel/metainfo/__init__.py | 6 +++
nomad/metainfo/legacy.py | 45 ++++++++++++++-----
9 files changed, 70 insertions(+), 27 deletions(-)
diff --git a/examples/access_metainfo.py b/examples/access_metainfo.py
index b3d9b8e12e..1d632c3a01 100644
--- a/examples/access_metainfo.py
+++ b/examples/access_metainfo.py
@@ -49,7 +49,7 @@ from nomad.datamodel.metainfo import m_env # noqa, contains all common, public,
from vaspparser.metainfo import m_env as vasp_m_env # noqa, contains also the vasp specific definitions
print(m_env.packages)
# Resolve definition by name
-print(m_env.resolve_definition('atom_labels', metainfo.Quantity))
+print(m_env.resolve_definitions('number_of_atoms', metainfo.Quantity))
# Traverse all definitions:
for definition in m_env.m_all_contents():
print(definition)
@@ -64,18 +64,14 @@ quantity = public.section_system.atom_labels
for dim in quantity.shape:
if isinstance(dim, str):
section = quantity.m_parent
- print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definition(dim, metainfo.Quantity)))
+ print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definitions(dim, metainfo.Quantity)))
# All quantities used as dimensions in a package:
for definition in public.m_package.m_all_contents():
if definition.m_def == metainfo.Quantity.m_def:
for dim in definition.shape:
if isinstance(dim, str) and '..' not in dim:
- try:
- print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definition(dim, metainfo.Quantity)))
- except KeyError:
- # metainfo is still not perfect
- print('does not exist: ' + dim)
+ print('%s[%s]: %s' % (quantity.name, dim, m_env.resolve_definitions(dim, metainfo.Quantity)))
# Categories are special classes, similar to sections and they Python definition is a
@@ -90,3 +86,8 @@ print(public.m_package.category_definitions)
print(public.m_package.section_definitions)
# Access the categories of a metainfo definition, e.g. quantity
print(public.section_single_configuration_calculation.energy_total.categories)
+
+
+print(m_env.resolve_definition('EntryMetadata', metainfo.Section).all_quantities)
+print(m_env.resolve_definition('Bulk', metainfo.Section).all_quantities)
+print(m_env.resolve_definition('OptimadeEntry', metainfo.Section).all_quantities)
\ No newline at end of file
diff --git a/gui/src/components/Markdown.js b/gui/src/components/Markdown.js
index c5618f0133..26f68dcccb 100644
--- a/gui/src/components/Markdown.js
+++ b/gui/src/components/Markdown.js
@@ -217,7 +217,7 @@ function Markdown(props) {
return (
<Typography variant="body1"
className={classes.root}
- dangerouslySetInnerHTML={{__html: marked(content)}}
+ dangerouslySetInnerHTML={{__html: marked(content || '')}}
/>
)
}
diff --git a/gui/src/components/metaInfoBrowser/DefinitionCard.js b/gui/src/components/metaInfoBrowser/DefinitionCard.js
index a60ad1d81c..7e1b77e48b 100644
--- a/gui/src/components/metaInfoBrowser/DefinitionCard.js
+++ b/gui/src/components/metaInfoBrowser/DefinitionCard.js
@@ -127,7 +127,7 @@ class DefinitionCardUnstyled extends React.Component {
}
renderDescription(description) {
- description = description.replace(/[^([A-Za-z0-9](([A-Za-z0-9]+_)+[A-Za-z0-9]+)[^)[A-Za-z0-9]/g, '`$1`')
+ description = (description || '').replace(/[^([A-Za-z0-9](([A-Za-z0-9]+_)+[A-Za-z0-9]+)[^)[A-Za-z0-9]/g, '`$1`')
return (
<Markdown>{description}</Markdown>
)
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index 1ef6454988..c7c0e22044 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -26,9 +26,14 @@ from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
from .dft import DFTMetadata
from .ems import EMSMetadata
-from .encyclopedia import EncyclopediaMetadata
-from .metainfo.public import section_run
-from .metainfo.general_experimental import section_experiment
+
+# This is usually defined automatically when the first metainfo definition is evaluated, but
+# due to the next imports requireing the m_package already, this would be too late.
+m_package = metainfo.Package()
+
+from .encyclopedia import EncyclopediaMetadata # noqa
+from .metainfo.public import section_run # noqa
+from .metainfo.general_experimental import section_experiment # noqa
def _only_atoms(atoms):
diff --git a/nomad/datamodel/dft.py b/nomad/datamodel/dft.py
index 5e5ae809bf..623d155899 100644
--- a/nomad/datamodel/dft.py
+++ b/nomad/datamodel/dft.py
@@ -19,7 +19,7 @@ DFT specific metadata
import re
from nomad import config, utils
-from nomad.metainfo import MSection, Section, Quantity, MEnum, SubSection
+from nomad.metainfo import MSection, Section, Quantity, MEnum, SubSection, Package
from nomad.metainfo.search_extension import Search
from .common import get_optional_backend_value
diff --git a/nomad/datamodel/ems.py b/nomad/datamodel/ems.py
index 89a8422bbe..0db370d554 100644
--- a/nomad/datamodel/ems.py
+++ b/nomad/datamodel/ems.py
@@ -17,7 +17,7 @@ Experimental material science specific metadata
'''
from nomad import config
-from nomad.metainfo import Quantity, MSection, Section, Datetime
+from nomad.metainfo import Quantity, MSection, Section, Datetime, Package
from nomad.metainfo.search_extension import Search
from .common import get_optional_backend_value
diff --git a/nomad/datamodel/encyclopedia.py b/nomad/datamodel/encyclopedia.py
index d8e77f19c8..a031a4d177 100644
--- a/nomad/datamodel/encyclopedia.py
+++ b/nomad/datamodel/encyclopedia.py
@@ -1,9 +1,15 @@
import numpy as np
-from nomad.metainfo import MSection, Section, SubSection, Quantity, MEnum, Reference
-from nomad.datamodel.metainfo.public import section_k_band, section_dos, section_thermodynamical_properties
-from nomad.metainfo.search_extension import Search
from elasticsearch_dsl import Text, Keyword
+from nomad.metainfo import MSection, Section, SubSection, Quantity, MEnum, Reference, Package
+from nomad.metainfo.search_extension import Search
+
+# This is usally defined automatically when the first metainfo definition is evaluated, but
+# due to the next imports requireing the m_package already, this would be too late.
+m_package = Package()
+
+from .metainfo.public import section_k_band, section_dos, section_thermodynamical_properties # noqa
+
class WyckoffVariables(MSection):
m_def = Section(
diff --git a/nomad/datamodel/metainfo/__init__.py b/nomad/datamodel/metainfo/__init__.py
index ca3964e994..08f5e9f84a 100644
--- a/nomad/datamodel/metainfo/__init__.py
+++ b/nomad/datamodel/metainfo/__init__.py
@@ -9,3 +9,9 @@ m_env = LegacyMetainfoEnvironment()
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.common'].m_package) # type: ignore
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.public'].m_package) # type: ignore
m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.metainfo.general'].m_package) # type: ignore
+
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.datamodel'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.dft'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.ems'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.encyclopedia'].m_package) # type: ignore
+m_env.m_add_sub_section(Environment.packages, sys.modules['nomad.datamodel.optimade'].m_package) # type: ignore
diff --git a/nomad/metainfo/legacy.py b/nomad/metainfo/legacy.py
index 113eb0b6a2..57b50bc011 100644
--- a/nomad/metainfo/legacy.py
+++ b/nomad/metainfo/legacy.py
@@ -54,6 +54,13 @@ class LegacyPackage(LegacyDefinition):
self.python_path = python_path
+def def_name(definition):
+ try:
+ return definition.a_legacy.name
+ except AttributeError:
+ return definition.name
+
+
def normalize_name(name: str):
return name.replace('.', '_').replace('-', '_')
@@ -100,25 +107,42 @@ class LegacyMetainfoEnvironment(Environment):
legacy_package_name = Quantity(type=str)
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.__section_to_sub_section_name = None
+
+ @property
+ def section_to_sub_section_name(self) -> Dict[str, str]:
+ if self.__section_to_sub_section_name is not None:
+ return self.__section_to_sub_section_name
+
+ self.__section_to_sub_section_name = dict()
+ for definition in self.m_all_contents():
+ if definition.m_def == SubSection.m_def:
+ self.__section_to_sub_section_name[definition.sub_section.name] = definition.name
+
+ return self.__section_to_sub_section_name
+
def legacy_info(self, definition: Definition, *args, **kwargs) -> InfoKindEl:
''' Creates a legacy metainfo object for the given definition. '''
super_names: List[str] = list()
result: Dict[str, Any] = dict(
- name=definition.a_legacy.name,
+ name=def_name(definition),
description=definition.description,
superNames=super_names)
for category in definition.categories:
- super_names.append(category.a_legacy.name)
+ super_names.append(def_name(category))
if isinstance(definition, Section):
+ sub_section_name = self.section_to_sub_section_name.get(definition.name, definition.name)
result['kindStr'] = 'type_section'
result['repeats'] = any(
sub_section.repeats
- for sub_section in self.resolve_definitions(definition.name, SubSection))
+ for sub_section in self.resolve_definitions(sub_section_name, SubSection))
- for sub_section in self.resolve_definitions(definition.name, SubSection):
- super_names.append(sub_section.m_parent_as(Definition).a_legacy.name)
+ for sub_section in self.resolve_definitions(sub_section_name, SubSection):
+ super_names.append(def_name(sub_section.m_parent_as(Definition)))
elif isinstance(definition, Quantity):
result['kindStr'] = 'type_document_content'
@@ -135,7 +159,7 @@ class LegacyMetainfoEnvironment(Environment):
elif isinstance(definition.type, Reference):
dtype_str = 'r'
result['referencedSections'] = [
- definition.type.target_section_def.m_resolved().a_legacy.name]
+ def_name(definition.type.target_section_def.m_resolved())]
elif isinstance(definition.type, MEnum):
dtype_str = 'C'
elif type(definition.type) == np.dtype:
@@ -143,12 +167,13 @@ class LegacyMetainfoEnvironment(Environment):
elif definition.type == Any:
dtype_str = 'D'
else:
- raise TypeError(
- 'Unsupported quantity type %s in %s.' % (definition.type, definition))
+ dtype_str = str(definition.type)
+ # raise TypeError(
+ # 'Unsupported quantity type %s in %s.' % (definition.type, definition))
result['dtypeStr'] = dtype_str
if definition.unit is not None:
result['units'] = str(definition.unit)
- super_names.append(definition.m_parent_as(Definition).a_legacy.name)
+ super_names.append(def_name(definition.m_parent_as(Definition)))
elif isinstance(definition, Category):
result['kindStr'] = 'type_abstract_document_content'
@@ -215,7 +240,7 @@ class LegacyMetainfoEnvironment(Environment):
'type': 'nomad_meta_info_1_0',
'description': description,
'dependencies': [
- {'relativePath': dependency.a_legacy.name}
+ {'relativePath': def_name(dependency)}
for dependency in dependencies],
'metaInfos': definitions
}
--
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