started general module (#66)

* started general module

* added recipes

* added descriptions

* removed unnecessary imports

* made annealing as a step shaped process

* final refinements

* added ontology links

* Apply suggestions from code review

Co-authored-by: Hampus Näsström <[email protected]>

* removed annealing reagnets

---------

Co-authored-by: Hampus Näsström <[email protected]>

src/nomad_material_processing/general/schema.py

@@ -0,0 +1,271 @@
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from nomad.datamodel.datamodel import (
+        EntryArchive,
+    )
+    from structlog.stdlib import (
+        BoundLogger,
+    )
+
+from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
+
+import numpy as np
+from nomad.datamodel.data import EntryData, ArchiveSection
+
+from nomad.metainfo import (
+    Quantity,
+    SubSection,
+    Section,
+    MEnum,
+)
+
+from nomad.datamodel.metainfo.basesections import (
+    CompositeSystem,
+    ProcessStep,
+    Process,
+    CompositeSystemReference,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    ELNComponentEnum,
+)
+
+from nomad.metainfo import (
+    SectionProxy,
+    Reference,
+)
+
+
+class Recipe(ArchiveSection):
+    """
+    A Recipe for a material processing experiment.
+
+    This class will be subclassed for each process that needs a recipe.
+
+    The subclass will inherit Recipe and a specific Process class.
+
+    The only difference between the Recipe and the actual Process is that
+    the datetime and the input samples Entities are hidden in the Recipe.
+    """
+
+    pass
+
+
+class EtchingStep(ProcessStep):
+    """
+    A step of etching process.
+    """
+
+    m_def = Section()
+    duration = Quantity(
+        type=np.float64,
+        description='The elapsed time since the annealing process started.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
+        ),
+        unit='second',
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description='The temperature of the etching process.',
+        a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'celsius'},
+        unit='celsius',
+    )
+    agitation = Quantity(
+        type=MEnum(
+            'Magnetic Stirring',
+            'Sonication',
+        ),
+        description='The agitation method used during the etching process.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.EnumEditQuantity,
+        ),
+    )
+    etching_reagents = SubSection(section_def=CompositeSystem, repeats=True)
+
+
+class Etching(Process, EntryData):
+    """
+    Selectively remove material from a surface using chemical or physical processes
+    to create specific patterns or structures.
+    """
+
+    m_def = Section(
+        a_eln=None,
+        links=['http://purl.obolibrary.org/obo/CHMO_0001558'],
+    )
+    recipe = Quantity(
+        type=Reference(SectionProxy('EtchingRecipe')),
+        description=""" The recipe used for the process. If a recipe is found,
+           all the data is copied from the Recipe within the Process.
+           """,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.ReferenceEditQuantity,
+        ),
+    )
+    steps = SubSection(
+        description="""
+        The steps of the etching process.
+        """,
+        section_def=EtchingStep,
+        repeats=True,
+    )
+
+
+class EtchingRecipe(Etching, Recipe, EntryData):
+    """
+    A Recipe for an etching process.
+    """
+
+    m_def = Section(
+        a_eln={'hide': ['datetime', 'samples']},
+    )
+
+
+class AnnealingStep(ProcessStep):
+    """
+    A step of annealing process.
+    """
+
+    m_def = Section()
+    duration = Quantity(
+        type=np.float64,
+        description='The elapsed time since the annealing process started.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
+        ),
+        unit='second',
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description='The temperature of the etching process.',
+        a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'celsius'},
+        unit='celsius',
+    )
+
+
+class Annealing(Process, EntryData):
+    """
+    Heat treatment process used to alter the material's properties,
+    such as reducing defects, improving crystallinity, or relieving internal stresses.
+    """
+
+    m_def = Section(
+        links=['http://purl.obolibrary.org/obo/CHMO_0001465'],
+    )
+    recipe = Quantity(
+        type=Reference(SectionProxy('AnnealingRecipe')),
+        description=""" The recipe used for the process. If a recipe is found,
+           all the data is copied from the Recipe within the Process.
+           """,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.ReferenceEditQuantity,
+        ),
+    )
+    duration = Quantity(
+        type=np.float64,
+        description='The elapsed time since the annealing process started.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
+        ),
+        unit='second',
+    )
+    steps = SubSection(
+        description="""
+        The steps of the annealing process.
+        """,
+        section_def=AnnealingStep,
+        repeats=True,
+    )
+
+
+class AnnealingRecipe(Annealing, Recipe, EntryData):
+    """
+    A Recipe for an annealing process.
+    """
+
+    m_def = Section(
+        a_eln={'hide': ['datetime', 'samples']},
+    )
+
+
+class CleaningStep(ProcessStep):
+    """
+    A step of cleaning process.
+    """
+
+    m_def = Section()
+    duration = Quantity(
+        type=np.float64,
+        description='The elapsed time since the cleaning process started.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
+        ),
+        unit='second',
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description='The temperature of the cleaning process.',
+        a_eln={'component': 'NumberEditQuantity', 'defaultDisplayUnit': 'celsius'},
+        unit='celsius',
+    )
+    agitation = Quantity(
+        type=MEnum(
+            'Magnetic Stirring',
+            'Sonication',
+        ),
+        description='The agitation method used during the cleaning process.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.EnumEditQuantity,
+        ),
+    )
+    cleaning_reagents = SubSection(
+        section_def=CompositeSystemReference,
+    )
+
+
+class Cleaning(Process, EntryData):
+    """
+    Surface cleaning in thin film material science involves removing contaminants
+    and residues from a substrate's surface to ensure proper adhesion
+    and uniformity of the thin film deposition.
+    """
+
+    m_def = Section(
+        a_eln={'hide': ['steps']},
+    )
+    recipe = Quantity(
+        type=Reference(SectionProxy('CleaningRecipe')),
+        description=""" The recipe used for the process. If a recipe is found,
+           all the data is copied from the Recipe within the Process.
+           """,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.ReferenceEditQuantity,
+        ),
+    )
+    duration = Quantity(
+        type=np.float64,
+        description='The elapsed time since the annealing process started.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity, defaultDisplayUnit='minute'
+        ),
+        unit='second',
+    )
+    steps = SubSection(
+        description="""
+        The steps of the cleaning process.
+        """,
+        section_def=CleaningStep,
+        repeats=True,
+    )
+
+
+class CleaningRecipe(Cleaning, Recipe, EntryData):
+    """
+    A Recipe for an cleaning process.
+    """
+
+    m_def = Section(
+        a_eln={'hide': ['datetime', 'samples']},
+    )