13 combinatorial library base section (#22)

* Added Combinatorial Base Sections

* Temporary Fix for Type Specialization

* Attempt at Specializing Collection Quantities

* Overloaded lab_id and entities

src/nomad_material_processing/combinatorial.py

@@ -0,0 +1,318 @@
+#
+# 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.
+#
+from typing import (
+    TYPE_CHECKING,
+)
+from nomad.metainfo import (
+    Package,
+    Quantity,
+    SubSection,
+    Section,
+)
+from nomad.datamodel.data import (
+    ArchiveSection,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    ELNComponentEnum,
+)
+from nomad.datamodel.metainfo.basesections import (
+    Collection,
+    CompositeSystem,
+    CompositeSystemReference,
+)
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import (
+        EntryArchive,
+    )
+    from structlog.stdlib import (
+        BoundLogger,
+    )
+
+m_package = Package(name='Combinatorial Synthesis')
+
+
+class CombinatorialSample(CompositeSystem):
+    '''
+    A base section for any sample of a combinatorial library.
+    '''
+    m_def = Section()
+    sample_number = Quantity(
+        type=int,
+        description='''
+        A unique number for this sample of the combinatorial library.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+        ),
+    )
+    lab_id = Quantity(
+        type=str,
+        description='''
+        A unique human readable ID for the sample within the combinatorial library.
+        Suggested to be the ID of the library followed by a dash ("-") and the sample
+        number.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.StringEditQuantity,
+            label='Sample ID',
+        ),
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `CombinatorialSample` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(CombinatorialSample, self).normalize(archive, logger)
+
+
+class CombinatorialSampleReference(CompositeSystemReference):
+    '''
+    A section containing a reference to a combinatorial sample entry.
+    '''
+    m_def = Section(
+        label_quantity='sample_number',
+    )
+    sample_number = Quantity(
+        type=int,
+        description='''
+        A unique number for this sample of the combinatorial library.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+        ),
+    )
+    reference = Quantity(
+        type=CombinatorialSample,
+        description='''
+        The reference to the combinatorial sample entry.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.ReferenceEditQuantity,
+            label='Sample Reference',
+        ),
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `CombinatorialSampleReference` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(CombinatorialSampleReference, self).normalize(archive, logger)
+
+
+class CombinatorialLibrary(Collection):
+    '''
+    A base section for any combinatorial library.
+    '''
+    m_def = Section()
+    lab_id = Quantity(
+        type=str,
+        description='''
+        A unique human readable ID for the combinatorial library.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.StringEditQuantity,
+            label='Library ID'
+        ),
+    )
+    entities = SubSection(
+        section_def=CombinatorialSampleReference,
+        description='''
+        All the investigated samples of the combinatorial library.
+        ''',
+        repeats=True,
+        a_eln=ELNAnnotation(
+            label='Samples'
+        ),
+    )
+    # lab_id = Collection.lab_id.m_copy()
+    # lab_id.description = '''
+    #     A unique human readable ID for the combinatorial library.
+    #     '''
+    # lab_id.m_annotations['eln'].label = 'Library ID'
+    # entities = Collection.entities.m_copy()
+    # entities.section_def = CombinatorialSampleReference
+    # entities.description = '''
+    #     All the investigated samples of the combinatorial library.
+    #     '''
+    # entities.m_annotations['eln'] = ELNAnnotation(
+    #     label='Samples'
+    # )  # Currently the label cannot be overwritten.
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `CombinatorialLibrary` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(CombinatorialLibrary, self).normalize(archive, logger)
+
+
+class CombinatorialSamplePosition(ArchiveSection):
+    '''
+    A section for representing the position of a sample within a continuous
+    combinatorial library.
+    If nothing else is specified it is the position relative to the center of mass of
+    the library.
+    '''
+    m_def = Section()
+    x = Quantity(
+        type=float,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='mm',
+        ),
+        unit='m',
+    )
+    y = Quantity(
+        type=float,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='mm',
+        ),
+        unit='m',
+    )
+    z = Quantity(
+        type=float,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='mm',
+        ),
+        unit='m',
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `CombinatorialSamplePosition` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(CombinatorialSamplePosition, self).normalize(archive, logger)
+
+
+class ContinuousCombiSample(CombinatorialSample):
+    '''
+    A base section for any sample of a continuous combinatorial library.
+    '''
+    m_def = Section()
+    position = SubSection(
+        section_def=CombinatorialSamplePosition,
+        description='''
+        The position of a sample within the continuous combinatorial library. If nothing 
+        else is specified it is the position relative to the center of mass of the 
+        library.
+        ''',
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `ContinuousCombiSample` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(ContinuousCombiSample, self).normalize(archive, logger)
+
+
+class ContinuousCombiSampleReference(CombinatorialSampleReference):
+    '''
+    A section containing a reference to a continuous combinatorial sample entry.
+    '''
+    m_def = Section(
+        label_quantity='sample_number',
+    )
+    reference = Quantity(
+        type=ContinuousCombiSample,
+        description='''
+        The reference to the combinatorial sample entry.
+        ''',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.ReferenceEditQuantity,
+            label='Sample Reference',
+        ),
+    )
+    # reference = CombinatorialSampleReference.reference.m_copy()
+    # reference.type = ContinuousCombiSample  # Specializing custom types is currently not supported.
+    position = SubSection(
+        section_def=CombinatorialSamplePosition,
+        description='''
+        The position of a sample within the continuous combinatorial library. If nothing 
+        else is specified it is the position relative to the center of mass of the 
+        library.
+        ''',
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `ContinuousCombiSampleReference` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(ContinuousCombiSampleReference, self).normalize(archive, logger)
+
+
+class ContinuousCombiLibrary(CombinatorialLibrary):
+    '''
+    A base section for any continuous combinatorial library.
+    '''
+    m_def = Section()
+    entities = SubSection(
+        section_def=ContinuousCombiSampleReference,
+        description='''
+        All the investigated samples of the combinatorial library.
+        ''',
+        repeats=True,
+        a_eln=ELNAnnotation(
+            label='Samples'
+        ),
+    )
+
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        '''
+        The normalizer for the `ContinuousCombiLibrary` section.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        '''
+        super(ContinuousCombiLibrary, self).normalize(archive, logger)
+
+
+m_package.__init_metainfo__()