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validation

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FoSpy.parsing.validation

TemplateLists module-attribute 

TemplateLists = {
    "experimenters": b.TemplateList.Simple(b.Experimenter),
    "materials": b.TemplateList.Simple(b.Material),
    "treatments": b.TemplateList.Simple(b.Treatment),
    "annealings": b.TemplateList.Simple(b.Annealing),
    "anneal_sections": b.TemplateList.Simple(
        b.AnnealSection
    ),
    "cifs": b.CifList,
}

Maps alias names to TemplateList classes for use in TemplateSet blocks.

_debug module-attribute 

_debug = Debug()

aliases module-attribute 

aliases = {
    "material": b.Material,
    "materials": b.MaterialList,
    "treatment": b.Treatment,
    "treatments": b.TreatmentList,
    "experimenter": b.Experimenter,
    "experimenters": b.ExperimenterList,
    "embed": b.EmbeddedFile,
}

Maps alias names to block classes for use in non-template SingleBlock blocks.

optional_keys module-attribute 

optional_keys = {
    b.Attachment: {
        "embedded": list,
        "path": validators.filenames.PathPosix,
    },
    b.SingleBlock: {
        "rename": validators.rename.rename_dict
    },
    b.Synthesis: {
        "cif": b.Attachment.enforce_subtype(b.CIFFile),
        "cifs": b.CifList,
        "laboratory_conditions": b.LabConditions,
        "equipment": b.EquipmentList,
    },
    b.Experimenter: {"orcid": str},
    b.Product: {
        "expected_amount": validators.numbers.positive_decimal(
            "Product/expected_amount",
            "expected_amount",
            require_unit=True,
        ),
        "expected_amount_unit": validators.units.FOSUnit.enforce_dims(
            ["[mass]", {"[length]": 3}]
        ),
        "obtained_amount": validators.numbers.positive_decimal(
            "Product/obtained_amount",
            "obtained_amount",
            require_unit=True,
        ),
        "obtained_amount_unit": validators.units.FOSUnit.enforce_dims(
            ["[mass]", {"[length]": 3}]
        ),
        "characterizations": str,
        "structure_comments": str,
    },
    b.Material: {
        "purity": validators.numbers.decimal_range(
            "b.Material/purity", "purity", 0, 1
        ),
        "treatments": b.TreatmentList,
    },
    b.Treatment: {
        "recovered_amount": validators.numbers.positive_decimal(
            "b.Treatment/recovered_amount",
            "recovered_amount",
            True,
        ),
        "recovered_amount_unit": validators.units.FOSUnit.enforce_dims(
            ["[mass]", {"[length]": 3}]
        ),
        "start_time": str,
        "end_time": str,
    },
    b.Annealing: {"gas_flow": b.FlowList},
    b.Ramp: {
        "temp": validators.numbers.positive_decimal(
            "RampNoRate/temp", "temp", True
        ),
        "time": validators.numbers.positive_decimal(
            "RampNoRate/time", "time", True
        ),
        "rate": validators.numbers.any_decimal(
            "RampNoTemp/rate", "rate", True
        ),
        "temp_unit": validators.units.FOSTempUnit,
        "time_unit": validators.units.FOSUnit.enforce_dims(
            "[time]"
        ),
        "rate_unit": validators.units.temp_rate_unit,
    },
    b.TemplateSet: TemplateLists,
}

Maps block classes to dictionaries of optional keys and their validators. Validators can be types (e.g. str, int), Block constructors, or custom validator functions.

Optional key mapping is only necessary if the expected value should be passed to a validator. Simple unexpected values can be assigned directly to SingleBlock instance attributes without validation.

required_keys module-attribute 

required_keys = {
    b.SingleBlock: {"ext": SubContainer},
    b.FileBlock: {"metadata": b.MetaData},
    b.Synthesis: {
        "metadata": b.SynthesisMeta,
        "experimenters": b.ExperimenterList,
        "reaction": b.Reaction,
        "products": b.ProductList,
        "materials": b.MaterialList,
        "treatments": b.TreatmentList,
    },
    b.TemplateBlock: {"template_name": str},
    b.MetaData: {
        "fos_id": str,
        "fos_type": str,
        "description": str,
    },
    b.SynthesisMeta: {"group_id": str, "project_id": str},
    b.Experimenter: {"name": str, "affiliation": str},
    b.Reaction: {
        "nominal_formula": chemformula.ChemFormula,
        "nominal_amount": validators.numbers.positive_decimal(
            "Reaction/nominal_amount", "nominal_amount"
        ),
        "nominal_amount_unit": validators.units.FOSUnit.enforce_dims(
            ["[mass]", {"[length]": 3}]
        ),
    },
    b.Product: {
        "name": str,
        "expected": bool,
        "obtained": bool,
        "formula": chemformula.ChemFormula,
        "observations": str,
    },
    b.Material: {
        "name": str,
        "type": str,
        "formula": chemformula.ChemFormula,
        "supplier": str,
        "cas": str,
        "form": str,
        "env": str,
        "amount": validators.numbers.positive_decimal(
            "b.Material/amount", "amount"
        ),
        "amount_unit": str,
    },
    b.Treatment: {
        "type": str,
        "repeats": int,
        "observations": str,
    },
    b.AnnealSection: {"type": str},
    b.Dwell: {
        "time": validators.numbers.positive_decimal(
            "Dwell/time", "time", True
        ),
        "time_unit": validators.units.FOSUnit.enforce_dims(
            "[time]"
        ),
    },
    b.Quench: {"medium": str},
    b.Annealing: {
        "program": b.AnnealProgram,
        "start_temp": validators.numbers.positive_decimal(
            "b.Annealing/start_temp", "start_temp", True
        ),
        "start_temp_unit": validators.units.FOSTempUnit,
    },
    b.Attachment: {
        "file_name": validators.filenames.file_name,
        "extension": validators.filenames.file_extension,
    },
}

Maps block classes to dictionaries of required keys and their validators. Validators can be types (e.g. str, int), Block constructors, or custom validator functions.

Debug

Source code in FoSpy/_debug.py 
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class Debug:
    def __init__(self):
        self.on = False

        frame = inspect.currentframe().f_back
        self.module_name = frame.f_globals.get("__name__", "<unknown>")
        self.label = f"|(Debug message from {self.module_name})"
        self.label_width = len(self.label)

    def _get_text_width(self, module=None):
        if module:
            label = f"|(Debug message from {module} via {self.module_name})"
            label_width = len(label)
        else:
            label = self.label
            label_width = self.label_width

        text_width = DEBUG_WIDTH - label_width
        return text_width, label, label_width


    def msg(self,msg, module=None):
        if not self.on:
            return

        text_width, label, label_width = self._get_text_width(module)

        wrapped = textwrap.fill(str(msg), width=text_width)

        for line in wrapped.splitlines():
            print(f'{line:<{text_width}}{label:>{label_width}}')

    def pmsg(self,msg,module=None,**kwargs):
        if not self.on:
            return

        text_width, label, label_width = self._get_text_width(module)

        buf = io.StringIO()
        pprint(msg,stream=buf, width=text_width,**kwargs)
        txt = buf.getvalue()
        for line in txt.splitlines():
            print(f'{line:<{text_width}}{label:>{label_width}}')

label instance-attribute 

label = f'|(Debug message from {self.module_name})'

label_width instance-attribute 

label_width = len(self.label)

module_name instance-attribute 

module_name = frame.f_globals.get('__name__', '<unknown>')

on instance-attribute 

on = False

__init__ 

__init__()
Source code in FoSpy/_debug.py 
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def __init__(self):
    self.on = False

    frame = inspect.currentframe().f_back
    self.module_name = frame.f_globals.get("__name__", "<unknown>")
    self.label = f"|(Debug message from {self.module_name})"
    self.label_width = len(self.label)

_get_text_width 

_get_text_width(module=None)
Source code in FoSpy/_debug.py 
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def _get_text_width(self, module=None):
    if module:
        label = f"|(Debug message from {module} via {self.module_name})"
        label_width = len(label)
    else:
        label = self.label
        label_width = self.label_width

    text_width = DEBUG_WIDTH - label_width
    return text_width, label, label_width

msg 

msg(msg, module=None)
Source code in FoSpy/_debug.py 
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def msg(self,msg, module=None):
    if not self.on:
        return

    text_width, label, label_width = self._get_text_width(module)

    wrapped = textwrap.fill(str(msg), width=text_width)

    for line in wrapped.splitlines():
        print(f'{line:<{text_width}}{label:>{label_width}}')

pmsg 

pmsg(msg, module=None, **kwargs)
Source code in FoSpy/_debug.py 
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def pmsg(self,msg,module=None,**kwargs):
    if not self.on:
        return

    text_width, label, label_width = self._get_text_width(module)

    buf = io.StringIO()
    pprint(msg,stream=buf, width=text_width,**kwargs)
    txt = buf.getvalue()
    for line in txt.splitlines():
        print(f'{line:<{text_width}}{label:>{label_width}}')

SubContainer

A simple container for storing hidden or unexpected attributes of a SingleBlock

Values are only assigned directly to SingleBlock attributes if they are an expected property. Otherwise they are assigned to a SubContainer at SingleBlock.ext. Also used for SingleBlock._meta.

Example Usage: 

class SingleBlock:
    ... 
    def __setattr__(self, name, value):
        ... 
        if name not in expected:
            return setattr(self.ext, name, value)

Source code in FoSpy/blocks/_containers.py 
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class SubContainer:
    """
    A simple container for storing hidden or unexpected attributes of a
    `SingleBlock`

    Values are only assigned directly to `SingleBlock` attributes if they are an
    expected property. Otherwise they are assigned to a `SubContainer` at
    `SingleBlock.ext`. Also used for `SingleBlock._meta`.

    Example Usage:
    ```
    class SingleBlock:
        ... 
        def __setattr__(self, name, value):
            ... 
            if name not in expected:
                return setattr(self.ext, name, value)
    ```
    """
    def __init__(self):
        pass
    def __iter__(self):
        return iter(self.__dict__)

__init__ 

__init__()
Source code in FoSpy/blocks/_containers.py 
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def __init__(self):
    pass

__iter__ 

__iter__()
Source code in FoSpy/blocks/_containers.py 
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def __iter__(self):
    return iter(self.__dict__)