Removed old m_x function calls.

nomad/app/api/repo.py

@@ -406,7 +406,7 @@ class EditRepoCalcsResource(Resource):
                 if quantity is None:
                     abort(400, 'Unknown quantity %s' % action_quantity_name)
 
-                quantity_flask = quantity.m_x('flask', {})
+                quantity_flask = quantity.m_get_annotations('flask', {})
                 if quantity_flask.get('admin_only', False):
                     if not g.user.is_admin():
                         abort(404, 'Only the admin user can set %s' % quantity.name)

nomad/app/optimade/filterparser.py

@@ -29,7 +29,7 @@ class FilterException(Exception):
 quantities: Dict[str, Quantity] = {
     q.name: Quantity(
         q.name, es_field='dft.optimade.%s' % q.name,
-        elastic_mapping_type=q.m_x('search').mapping.__class__)
+        elastic_mapping_type=q.a_search.mapping.__class__)
 
     for q in OptimadeEntry.m_def.all_quantities.values()
     if 'search' in q.m_annotations}

nomad/datamodel/optimade.py

@@ -2,7 +2,7 @@ from ase.data import chemical_symbols
 from elasticsearch_dsl import Keyword, Float, InnerDoc, Nested
 import numpy as np
 
-from nomad.metainfo import MSection, Section, Quantity, SubSection, MEnum, units
+from nomad.metainfo import MSection, Section, Quantity, SubSection, MEnum, units, DefinitionAnnotation
 from nomad.metainfo.search_extension import Search
 
 
@@ -25,7 +25,7 @@ class ElementRatio(InnerDoc):
             for i in range(0, entry.nelements)]
 
 
-class Optimade():
+class Optimade(DefinitionAnnotation):
     def __init__(self, query: bool = False, entry: bool = False):
         pass
 

nomad/metainfo/__init__.py

@@ -297,4 +297,6 @@ from .metainfo import (
     MResource,
     m_package,
     units,
-    Annotation)
+    Annotation,
+    DefinitionAnnotation,
+    SectionAnnotation)

nomad/metainfo/elastic_extension.py

@@ -16,7 +16,9 @@ from typing import Callable, Any, Dict, cast
 import uuid
 
 
-from .metainfo import Section, Quantity, MSection, MEnum, Datetime, Reference, Annotation, SectionAnnotation, DefinitionAnnotation
+from .metainfo import (
+    Section, Quantity, MSection, MEnum, Datetime, Reference, Annotation, SectionAnnotation,
+    DefinitionAnnotation)
 
 '''
 This module provides metainfo annotation class :class:`Elastic` and
@@ -62,7 +64,7 @@ class ElasticDocument(SectionAnnotation):
     def create_index_entry(cls, section: MSection):
         ''' Creates an elasticsearch_dsl document instance for the given section. '''
         m_def = section.m_def
-        annotation = m_def.m_x(ElasticDocument)
+        annotation = m_def.m_get_annotations(ElasticDocument)
         document_cls = ElasticDocument._all_documents[m_def.qualified_name()]
 
         if annotation is None:
@@ -75,7 +77,7 @@ class ElasticDocument(SectionAnnotation):
             obj = document_cls(meta=dict(id=id))
 
         for quantity in m_def.all_quantities.values():
-            for annotation in quantity.m_x(Elastic, as_list=True):
+            for annotation in quantity.m_get_annotations(Elastic, as_list=True):
                 if annotation.mapping is None:
                     continue
 
@@ -151,7 +153,7 @@ class ElasticDocument(SectionAnnotation):
         # create an field for each quantity
         for quantity in section.all_quantities.values():
             first = True
-            for annotation in quantity.m_x(Elastic, as_list=True):
+            for annotation in quantity.m_get_annotations(Elastic, as_list=True):
                 if annotation.mapping is None and first:
                     kwargs = dict(index=annotation.index)
                     # find a mapping based on quantity type

nomad/metainfo/metainfo.py

@@ -514,7 +514,7 @@ class MSection(metaclass=MObjectMeta):  # TODO find a way to make this a subclas
 
         # get additional annotations from the section definition
         if not is_bootstrapping:
-            for section_annotation in self.m_def.m_x(SectionAnnotation, as_list=True):
+            for section_annotation in self.m_def.m_get_annotations(SectionAnnotation, as_list=True):
                 for name, annotation in section_annotation.new(self).items():
                     self.m_annotations[name] = annotation
 
@@ -1203,10 +1203,6 @@ class MSection(metaclass=MObjectMeta):  # TODO find a way to make this a subclas
 
         return cast(MSectionBound, context)
 
-    def m_x(self, *args, **kwargs):
-        # TODO remove
-        return self.m_get_annotations(*args, **kwargs)
-
     def m_get_annotations(self, key: Union[str, type], default=None, as_list: bool = False):
         '''
         Convinience method to get annotations
@@ -1409,7 +1405,7 @@ class Definition(MSection):
         '''
 
         # initialize definition annotations
-        for annotation in self.m_x(DefinitionAnnotation, as_list=True):
+        for annotation in self.m_get_annotations(DefinitionAnnotation, as_list=True):
             annotation.init_annotation(self)
 
     @classmethod

nomad/metainfo/search_extension.py

@@ -119,7 +119,7 @@ class Search(Elastic):
 
     def register(self, prefix, field):
         # TODO support more deeply nested quantities
-        domain_or_all = self.definition.m_parent.m_x('domain', '__all__')
+        domain_or_all = self.definition.m_parent.m_get_annotations('domain', '__all__')
 
         prefix_and_dot = prefix + '.' if prefix is not None else ''
 

nomad/search.py

@@ -25,7 +25,6 @@ import json
 
 from nomad import config, datamodel, infrastructure, datamodel, utils, processing as proc
 from nomad.metainfo.search_extension import search_quantities, metrics, order_default_quantities, default_statistics
-from nomad.metainfo.elastic_extension import ElasticDocument
 
 
 path_analyzer = analyzer(
@@ -42,7 +41,7 @@ class ElasticSearchError(Exception): pass
 class ScrollIdNotFound(Exception): pass
 
 
-entry_document = datamodel.EntryMetadata.m_def.m_x(ElasticDocument).document
+entry_document = datamodel.EntryMetadata.m_def.a_elastic.document
 
 for domain in datamodel.domains:
     order_default_quantities.setdefault(domain, order_default_quantities.get('__all__'))

tests/metainfo/test_elastic_extension.py

@@ -35,7 +35,7 @@ class DFT(MSection):
         a_elastic=[Elastic(), Elastic()])
     n_atoms = Quantity(
         type=int, derived=lambda x: len(x.atoms),
-        a_eleastic=Elastic(index=False, field='natoms'))
+        a_elastic=Elastic(index=False, field='natoms'))
     only_atoms = Quantity(
         type=str, shape=['0..*'], derived=lambda x: x.atoms,
         a_elastic=Elastic(value=lambda x: ','.join(x.atoms)))
@@ -52,15 +52,15 @@ class Entry(MSection):
 
 
 def test_document():
-    annotation = Entry.m_def.m_x(ElasticDocument)
+    annotation = Entry.m_def.a_elastic
     document = annotation.document
 
     assert issubclass(document, Document)
     assert DFT.m_def.qualified_name() in ElasticDocument._all_documents
     assert EMS.m_def.qualified_name() not in ElasticDocument._all_documents
 
-    assert DFT.atoms.m_x(Elastic)[0].qualified_field == 'dft.atoms'
-    assert DFT.n_atoms.m_x(Elastic).qualified_field == 'dft.natoms'
+    assert DFT.atoms.a_elastic[0].qualified_field == 'dft.atoms'
+    assert DFT.n_atoms.a_elastic.qualified_field == 'dft.natoms'
 
 
 def test_create_entry():
@@ -68,7 +68,7 @@ def test_create_entry():
     entry = Entry(entry_id='test_id', uploader=user)
     entry.m_create(DFT).atoms = ['H', 'O']
 
-    index_entry = Entry.m_def.m_x(ElasticDocument).create_index_entry(entry)
+    index_entry = Entry.m_def.a_elastic.create_index_entry(entry)
 
     assert index_entry.entry_id == entry.entry_id
     assert index_entry.uploader.name == 'Test Tester'