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144
openpathsampling/experimental/simstore/attribute_handlers.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,144 @@ | ||
| from .my_types import parse_ndarray_type | ||
| import numpy as np | ||
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| class AttributeHandler(object): | ||
| """Abstract object to handler a given attribute type. | ||
| Each attribute in a schema entry will generate an instance of this for | ||
| the appropriate type. Different subclasses handle different types that | ||
| are supported by SimStore. | ||
| Note that you'll usually use this with the :method:`.from_type_string` | ||
| constructor, which returns None if the type string doesn't match what | ||
| this class handles. | ||
| """ | ||
| def __init__(self, type_info): | ||
| self.type_info = type_info | ||
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| @staticmethod | ||
| def is_my_type(type_str): | ||
| """Returns type info (possibly tuple) if true, None if false""" | ||
| raise NotImplementedError() | ||
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| @classmethod | ||
| def from_type_string(cls, type_str): | ||
| """Generate attribute handler based on a given type string. | ||
| Parameters | ||
| ---------- | ||
| type_str: str | ||
| the specific type string in a format understood by SimStore | ||
| Returns | ||
| ------- | ||
| :class:`.AttributeHandler` or None: | ||
| an attribute handler for the given type string, or None if this | ||
| class doesn't know how to handle that type | ||
| """ | ||
| type_info = cls.is_my_type(type_str) | ||
| if type_info: | ||
| return cls(type_info) | ||
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| def serialize(self, obj): | ||
| """Serialize the object. | ||
| Default serialization just returns the object. | ||
| Parameters | ||
| ---------- | ||
| obj : Any | ||
| object to be serialized | ||
| Returns | ||
| ------- | ||
| Any: | ||
| version ready to be written to disk; typically str or bytes but | ||
| standard types are also allowed (bool, float, int, etc.) | ||
| """ | ||
| return obj | ||
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| def deserialize(self, data, caches=None): | ||
| """Deserialize the serialized form. | ||
| Parameters | ||
| ---------- | ||
| data: Any | ||
| bytes to deserialize (usually as str or bytes) | ||
| caches: Dict | ||
| mapping of identifiers to known objects that might be components | ||
| of this object; mainly used when deserializing UUID objects. | ||
| """ | ||
| return data | ||
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| class StandardHandler(AttributeHandler): | ||
| """Attribute handler for common standard types | ||
| """ | ||
| standard_types = ['str', 'int', 'float', 'function'] | ||
| def __init__(self, type_info): | ||
| super().__init__(type_info) | ||
| self.backend_type = type_info | ||
| self.type_size = None | ||
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| @classmethod | ||
| def is_my_type(cls, type_str): | ||
| if type_str in cls.standard_types: | ||
| return type_str | ||
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| # TODO: these have not yet been implemented, but this is how it should all | ||
| # work -- everything should be managed through attribute handlers, instead | ||
| # of separate functions for serialize/deserialize | ||
| class UUIDHandler(StandardHandler): | ||
| standard_types = ['uuid', 'lazy'] | ||
| def serialize(self, obj): | ||
| pass | ||
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| def deserialize(self, data, caches=None): | ||
| pass | ||
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| class ListUUIDHandler(StandardHandler): | ||
| standard_types = ['list_uuid'] | ||
| def serialize(self, obj): | ||
| pass | ||
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| def deserialize(self, data, caches=None): | ||
| pass | ||
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| class JSONObjHandler(StandardHandler): | ||
| standard_types = ['json_obj'] | ||
| def serialize(self, obj): | ||
| pass | ||
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| def deserialize(self, data, caches=None): | ||
| pass | ||
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| class NDArrayHandler(AttributeHandler): | ||
| """Attribute handler for NumPy ndarrays. | ||
| Parameters | ||
| ---------- | ||
| type_info: Tuple | ||
| dtype and shape of the array | ||
| """ | ||
| def __init__(self, type_info): | ||
| super().__init__(type_info) | ||
| self.dtype, self.shape = type_info | ||
| self.backend_type = 'ndarray' | ||
| self.type_size = None # TODO: change this based on dtype/shape | ||
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| @classmethod | ||
| def is_my_type(cls, type_str): | ||
| return parse_ndarray_type(type_str) | ||
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| def serialize(self, obj): | ||
| return obj.astype(dtype=self.dtype, copy=False).tostring() | ||
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| def deserialize(self, data, caches=None): | ||
| return np.fromstring(data, dtype=self.dtype).reshape(self.shape) | ||
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| DEFAULT_HANDLERS = [NDArrayHandler, StandardHandler] |
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