Continued to detail the metainfo implementation.

nomad/app/optimade/data.py

@@ -36,110 +36,117 @@ class StructureEntry(MObject):
         type=Enum(chemical_symbols), shape=['1..*'],
         links=optimade_links('h.6.2.1'),
         a_elastic=dict(type=Keyword),
-        a_optimade=Optimade(query=True, entry=True))
-    """ Names of the different elements present in the structure. """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            Names of the different elements present in the structure.
+        ''')
 
     nelements = Quantity(
         type=int,
         links=optimade_links('h.6.2.2'),
         a_elastic=dict(type=Integer),
-        a_optimade=Optimade(query=True, entry=True))
-    """ Number of different elements in the structure as an integer. """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            Number of different elements in the structure as an integer.
+        ''')
 
     elements_ratios = Quantity(
         type=float, shape=['nelements'],
         links=optimade_links('h.6.2.3'),
         a_elastic=dict(type=lambda: Nested(ElementRatio), mapping=ElementRatio.from_structure_entry),
-        a_optimade=Optimade(query=True, entry=True))
-    """ Relative proportions of different elements in the structure. """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            Relative proportions of different elements in the structure.
+        ''')
 
     chemical_formula_descriptive = Quantity(
         type=str,
         links=optimade_links('h.6.2.4'),
         a_elastic=dict(type=Text, other_types=dict(keyword=Keyword)),
-        a_optimade=Optimade(query=True, entry=True))
-    """
-    The chemical formula for a structure as a string in a form chosen by the API
-    implementation.
-    """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            The chemical formula for a structure as a string in a form chosen by the API
+            implementation.
+        ''')
 
     chemical_formula_reduced = Quantity(
         type=str,
         links=optimade_links('h.6.2.5'),
         a_elastic=dict(type=Text, other_types=dict(keyword=Keyword)),
-        a_optimade=Optimade(query=True, entry=True))
-    """
-    The reduced chemical formula for a structure as a string with element symbols and
-    integer chemical proportion numbers. The proportion number MUST be omitted if it is 1.
-    """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            The reduced chemical formula for a structure as a string with element symbols and
+            integer chemical proportion numbers. The proportion number MUST be omitted if it is 1.
+        ''')
 
     chemical_formula_hill = Quantity(
         type=str,
         links=optimade_links('h.6.2.6'),
         a_elastic=dict(type=Text, other_types=dict(keyword=Keyword)),
-        a_optimade=Optimade(query=True, entry=False))
-    """
-    The chemical formula for a structure in Hill form with element symbols followed by
-    integer chemical proportion numbers. The proportion number MUST be omitted if it is 1.
-    """
+        a_optimade=Optimade(query=True, entry=False),
+        description='''
+            The chemical formula for a structure in Hill form with element symbols followed by
+            integer chemical proportion numbers. The proportion number MUST be omitted if it is 1.
+        ''')
 
     chemical_formula_anonymous = Quantity(
         type=str,
         links=optimade_links('h.6.2.7'),
         a_elastic=dict(type=Text, other_types=dict(keyword=Keyword)),
-        a_optimade=Optimade(query=True, entry=True))
-    """
-    The anonymous formula is the chemical_formula_reduced, but where the elements are
-    instead first ordered by their chemical proportion number, and then, in order left to
-    right, replaced by anonymous symbols A, B, C, ..., Z, Aa, Ba, ..., Za, Ab, Bb, ... and
-    so on.
-    """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            The anonymous formula is the chemical_formula_reduced, but where the elements are
+            instead first ordered by their chemical proportion number, and then, in order left to
+            right, replaced by anonymous symbols A, B, C, ..., Z, Aa, Ba, ..., Za, Ab, Bb, ... and
+            so on.
+        ''')
 
     dimension_types = Quantity(
         type=int, shape=[3],
         links=optimade_links('h.6.2.8'),
         a_elastic=dict(type=Integer, mapping=lambda a: sum(a.dimension_types)),
-        a_optimade=Optimade(query=True, entry=True))
-    """
-    List of three integers. For each of the three directions indicated by the three lattice
-    vectors (see property lattice_vectors). This list indicates if the direction is
-    periodic (value 1) or non-periodic (value 0). Note: the elements in this list each
-    refer to the direction of the corresponding entry in lattice_vectors and not
-    the Cartesian x, y, z directions.
-    """
+        a_optimade=Optimade(query=True, entry=True),
+        description='''
+            List of three integers. For each of the three directions indicated by the three lattice
+            vectors (see property lattice_vectors). This list indicates if the direction is
+            periodic (value 1) or non-periodic (value 0). Note: the elements in this list each
+            refer to the direction of the corresponding entry in lattice_vectors and not
+            the Cartesian x, y, z directions.
+        ''')
 
     lattice_vectors = Quantity(
         type=float, shape=[3, 3], unit=units.angstrom,
         links=optimade_links('h.6.2.9'),
-        a_optimade=Optimade(query=False, entry=True))
-    """ The three lattice vectors in Cartesian coordinates, in ångström (Å). """
+        a_optimade=Optimade(query=False, entry=True),
+        description='''
+            The three lattice vectors in Cartesian coordinates, in ångström (Å).
+        ''')
 
     cartesian_site_positions = Quantity(
         type=float, shape=['nsites', 3], unit=units.angstrom,
         links=optimade_links('h.6.2.10'),
-        a_optimade=Optimade(query=False, entry=True))
-    """
-    Cartesian positions of each site. A site is an atom, a site potentially occupied by
-    an atom, or a placeholder for a virtual mixture of atoms (e.g., in a virtual crystal
-    approximation).
-    """
+        a_optimade=Optimade(query=False, entry=True), description='''
+            Cartesian positions of each site. A site is an atom, a site potentially occupied by
+            an atom, or a placeholder for a virtual mixture of atoms (e.g., in a virtual crystal
+            approximation).
+        ''')
 
     nsites = Quantity(
         type=int,
         links=optimade_links('h.6.2.11'),
         a_elastic=dict(type=Integer),
-        a_optimade=Optimade(query=True, entry=True))
-    """ An integer specifying the length of the cartesian_site_positions property. """
+        a_optimade=Optimade(query=True, entry=True), description='''
+            An integer specifying the length of the cartesian_site_positions property.
+        ''')
 
     species_at_sites = Quantity(
         type=str, shape=['nsites'],
         links=optimade_links('h.6.2.12'),
-        a_optimade=Optimade(query=False, entry=True))
-    """
-    Name of the species at each site (where values for sites are specified with the same
-    order of the cartesian_site_positions property). The properties of the species are
-    found in the species property.
-    """
+        a_optimade=Optimade(query=False, entry=True), description='''
+            Name of the species at each site (where values for sites are specified with the same
+            order of the cartesian_site_positions property). The properties of the species are
+            found in the species property.
+        ''')
 
     # TODO assemblies
 
@@ -147,16 +154,15 @@ class StructureEntry(MObject):
         type=Enum(['disorder', 'unknown_positions', 'assemblies']), shape=['1..*'],
         links=optimade_links('h.6.2.15'),
         a_elastic=dict(type=Keyword),
-        a_optimade=Optimade(query=True, entry=True))
-    """
-    A list of strings that flag which special features are used by the structure.
+        a_optimade=Optimade(query=True, entry=True), description='''
+            A list of strings that flag which special features are used by the structure.
 
-    - disorder: This flag MUST be present if any one entry in the species list has a
-      chemical_symbols list that is longer than 1 element.
-    - unknown_positions: This flag MUST be present if at least one component of the
-      cartesian_site_positions list of lists has value null.
-    - assemblies: This flag MUST be present if the assemblies list is present.
-    """
+            - disorder: This flag MUST be present if any one entry in the species list has a
+            chemical_symbols list that is longer than 1 element.
+            - unknown_positions: This flag MUST be present if at least one component of the
+            cartesian_site_positions list of lists has value null.
+            - assemblies: This flag MUST be present if the assemblies list is present.
+        ''')
 
 
 class Species(MObject):
@@ -171,59 +177,56 @@ class Species(MObject):
         links=optimade_links('h.6.2.13'))
 
     name = Quantity(
-        type=str,
-        a_optimade=Optimade(entry=True))
-    """ The name of the species; the name value MUST be unique in the species list. """
+        type=str, a_optimade=Optimade(entry=True), description='''
+            The name of the species; the name value MUST be unique in the species list.
+        ''')
 
     chemical_symbols = Quantity(
         type=Enum(chemical_symbols + ['x', 'vacancy']), shape=['1..*'],
-        a_optimade=Optimade(entry=True))
-    """
-    A list of strings of all chemical elements composing this species.
+        a_optimade=Optimade(entry=True), description='''
+            A list of strings of all chemical elements composing this species.
 
-    It MUST be one of the following:
+            It MUST be one of the following:
 
-    - a valid chemical-element name, or
-    - the special value "X" to represent a non-chemical element, or
-    - the special value "vacancy" to represent that this site has a non-zero probability
-      of having a vacancy (the respective probability is indicated in the concentration
-      list, see below).
+            - a valid chemical-element name, or
+            - the special value "X" to represent a non-chemical element, or
+            - the special value "vacancy" to represent that this site has a non-zero probability
+            of having a vacancy (the respective probability is indicated in the concentration
+            list, see below).
 
-    If any one entry in the species list has a chemical_symbols list that is longer than 1
-    element, the correct flag MUST be set in the list structure_features (see
-    structure_features)
-    """
+            If any one entry in the species list has a chemical_symbols list that is longer than 1
+            element, the correct flag MUST be set in the list structure_features (see
+            structure_features)
+        ''')
 
     concentration = Quantity(
         type=float, shape=['1..*'],
-        a_optimade=Optimade(entry=True))
-    """
-    A list of floats, with same length as chemical_symbols. The numbers represent the
-    relative concentration of the corresponding chemical symbol in this species. The
-    numbers SHOULD sum to one. Cases in which the numbers do not sum to one typically fall
-    only in the following two categories:
-
-    - Numerical errors when representing float numbers in fixed precision, e.g. for two
-      chemical symbols with concentrations 1/3 and 2/3, the concentration might look
-      something like [0.33333333333, 0.66666666666]. If the client is aware that the sum
-      is not one because of numerical precision, it can renormalize the values so that the
-      sum is exactly one.
-    - Experimental errors in the data present in the database. In this case, it is the
-      responsibility of the client to decide how to process the data.
-
-    Note that concentrations are uncorrelated between different sites (even of the same
-    species).
-    """
+        a_optimade=Optimade(entry=True), description='''
+            A list of floats, with same length as chemical_symbols. The numbers represent the
+            relative concentration of the corresponding chemical symbol in this species. The
+            numbers SHOULD sum to one. Cases in which the numbers do not sum to one typically fall
+            only in the following two categories:
+
+            - Numerical errors when representing float numbers in fixed precision, e.g. for two
+            chemical symbols with concentrations 1/3 and 2/3, the concentration might look
+            something like [0.33333333333, 0.66666666666]. If the client is aware that the sum
+            is not one because of numerical precision, it can renormalize the values so that the
+            sum is exactly one.
+            - Experimental errors in the data present in the database. In this case, it is the
+            responsibility of the client to decide how to process the data.
+
+            Note that concentrations are uncorrelated between different sites (even of the same
+            species).
+        ''')
 
     mass = Quantity(type=float, unit=units.amu, a_optimade=dict(entry='optional'))
 
-    original_name = Quantity(type=str, a_optimade=dict(entry='optional'))
-    """
-    Can be any valid Unicode string, and SHOULD contain (if specified) the name of the
-    species that is used internally in the source database.
+    original_name = Quantity(type=str, a_optimade=dict(entry='optional'), description='''
+        Can be any valid Unicode string, and SHOULD contain (if specified) the name of the
+        species that is used internally in the source database.
 
-    Note: With regards to "source database", we refer to the immediate source being
-    queried via the OPTiMaDe API implementation. The main use of this field is for source
-    databases that use species names, containing characters that are not allowed (see
-    description of the species_at_sites list).
-    """
+        Note: With regards to "source database", we refer to the immediate source being
+        queried via the OPTiMaDe API implementation. The main use of this field is for source
+        databases that use species names, containing characters that are not allowed (see
+        description of the species_at_sites list).
+        ''')

requirements.txt

@@ -48,6 +48,7 @@ pyyaml
 tabulate
 cachetools
 zipfile37
+inflection
 
 # dev/ops related
 setuptools

tests/test_metainfo.py

@@ -12,7 +12,31 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from nomad.metainfo.metainfo import MObject, Section, Quantity
+from nomad.metainfo.metainfo import MObject, Section, Quantity, Definition, sub_section
+
+
+def assert_section_def(section_def: Section):
+    assert isinstance(section_def, Section)
+    assert section_def.m_section is not None
+    assert isinstance(section_def.m_section, Section)
+    assert section_def.m_section.name is not None
+    assert section_def.m_section.m_section == Section.m_section
+
+    assert section_def.name is not None
+
+    if section_def.parent is not None:
+        if section_def.parent != section_def:
+            assert_section_def(section_def.parent)
+
+    if section_def.repeats:
+        assert section_def.parent is not None
+
+
+def assert_section_instance(section: MObject):
+    assert_section_def(section.m_section)
+
+    if section.m_parent is not None:
+        assert section.m_parent.m_sub_section(section.m_section, section.m_parent_index) == section
 
 
 class TestM3:
@@ -21,12 +45,22 @@ class TestM3:
     def test_section(self):
         assert Section.m_section == Section.m_section.m_section
         assert Section.m_section.name == 'Section'
+        assert Section.name is not None
+        assert Section.name == Definition.name
+        assert Section.name.m_section == Quantity.m_section
+        assert Section.description.description is not None
+
+        assert Section.m_section.m_sub_section(Quantity, 0).name in Section.m_section.attributes
+
+        assert_section_instance(Section.m_section)
 
     def test_quantity(self):
         assert Quantity.m_section.m_section == Section.m_section
         assert Quantity.m_section.name == 'Quantity'
         assert Quantity.m_section.parent == Section.m_section
 
+        assert_section_instance(Quantity.m_section)
+
 
 class TestPureReflection:
     """ Test for using meta-info instances without knowing/using the respective definitions. """
@@ -48,8 +82,10 @@ class Run(MObject):
     And some more description.
     """
 
-    code_name = Quantity(type=str)
-    """ The code_name description. """
+    code_name = Quantity(
+        type=str, description='''
+        The code_name description.
+        ''')
 
 
 class System(MObject):
@@ -65,6 +101,10 @@ class Parsing(MObject):
 class TestM2:
     """ Test for meta-info definitions. """
 
+    def test_basics(self):
+        assert_section_def(Run.m_section)
+        assert_section_def(System.m_section)
+
     def test_default_section_def(self):
         """ A section class without an explicit section def must set a default section def. """
         assert Run.m_section is not None
@@ -110,6 +150,7 @@ class TestM2:
 
     def test_quantity_description(self):
         assert Run.code_name.description is not None
+        assert Run.code_name.description == 'The code_name description.'
         assert Run.code_name.description.strip() == Run.code_name.description.strip()
 
 
@@ -126,6 +167,8 @@ class TestM1:
         assert run.m_section.name == 'Run'
         assert len(run.m_data) == 0
 
+        assert_section_instance(run)
+
     def test_system(self):
         class System(MObject):
             m_section = Section()
@@ -136,6 +179,8 @@ class TestM1:
         assert len(system.atom_labels) == 1
         assert len(system.m_data) == 1
 
+        assert_section_instance(system)
+
     def test_defaults(self):
         assert System().n_atoms == 0
         assert System().atom_label is None
@@ -150,6 +195,22 @@ class TestM1:
     def test_m_section(self):
         assert Run().m_section == Run.m_section
 
+    def test_children_parent(self):
+        run = Run()
+        system = run.m_create(System)
+
+        assert run.system[0] == system  # pylint: disable=E1101
+        assert run.m_sub_section(System, 0) == system
+
+    def test_children_sub_section(self):
+        setattr(Run, 'a_system_sub_section', sub_section(System))
+        run = Run()
+        system = run.m_create(System)
+
+        assert run.a_system_sub_section[0] == system  # pylint: disable=E1101
+        assert run.system[0] == system  # pylint: disable=E1101
+        assert run.m_sub_section(System, 0) == system
+
     def test_parent_repeats(self):
         run = Run()
         system = run.m_create(System)