##############################
# Auto-generated. Do not Edit
##############################
import re
from pylipd.utils import uniqid
[docs]
class PhysicalSample:
"""Auto-generated LinkedEarth class representing `PhysicalSample`."""
def __init__(self):
"""Initialize a new PhysicalSample instance."""
self.housedAt: str = None
self.iGSN: str = None
self.name: str = None
self.misc = {}
self.ontns = "http://linked.earth/ontology#"
self.ns = "http://linked.earth/lipd"
self.type = "http://linked.earth/ontology#PhysicalSample"
self.id = self.ns + "/" + uniqid("PhysicalSample.")
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@staticmethod
def from_data(id, data) -> 'PhysicalSample':
"""Instantiate `PhysicalSample` from an ontology-style data graph.
Parameters
----------
id : str
The node identifier for this object.
data : dict
Dictionary mapping node ids to their predicate lists.
Returns
-------
PhysicalSample
The populated `PhysicalSample` instance.
"""
self = PhysicalSample()
self.id = id
mydata = data[id]
for key in mydata:
value = mydata[key]
obj = None
if key == "type":
for val in value:
self.type = val["@id"]
elif key == "hasIGSN":
for val in value:
if "@value" in val:
obj = val["@value"]
self.iGSN = obj
elif key == "housedAt":
for val in value:
if "@value" in val:
obj = val["@value"]
self.housedAt = obj
elif key == "name":
for val in value:
if "@value" in val:
obj = val["@value"]
self.name = obj
else:
for val in value:
obj = None
if "@id" in val:
obj = data[val["@id"]]
elif "@value" in val:
obj = val["@value"]
self.set_non_standard_property(key, obj)
return self
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def to_data(self, data={}):
"""Serialize the object into a JSON-LD compatible dictionary.
Parameters
----------
data : dict, optional
Existing data dictionary to extend.
Returns
-------
dict
The updated data dictionary.
"""
data[self.id] = {}
data[self.id]["type"] = [
{
"@id": self.type,
"@type": "uri"
}
]
if self.housedAt:
value_obj = self.housedAt
obj = {
"@value": value_obj,
"@type": "literal",
"@datatype": "http://www.w3.org/2001/XMLSchema#string"
}
data[self.id]["housedAt"] = [obj]
if self.iGSN:
value_obj = self.iGSN
obj = {
"@value": value_obj,
"@type": "literal",
"@datatype": "http://www.w3.org/2001/XMLSchema#string"
}
data[self.id]["hasIGSN"] = [obj]
if self.name:
value_obj = self.name
obj = {
"@value": value_obj,
"@type": "literal",
"@datatype": "http://www.w3.org/2001/XMLSchema#string"
}
data[self.id]["name"] = [obj]
for key in self.misc:
value = self.misc[key]
data[self.id][key] = []
ptype = None
tp = type(value).__name__
if tp == "int":
ptype = "http://www.w3.org/2001/XMLSchema#integer"
elif tp == "float" or tp == "double":
ptype = "http://www.w3.org/2001/XMLSchema#float"
elif tp == "str":
if re.match(r"\d{4}-\d{2}-\d{2}( |T)\d{2}:\d{2}:\d{2}", value):
ptype = "http://www.w3.org/2001/XMLSchema#datetime"
elif re.match(r"\d{4}-\d{2}-\d{2}", value):
ptype = "http://www.w3.org/2001/XMLSchema#date"
else:
ptype = "http://www.w3.org/2001/XMLSchema#string"
elif tp == "bool":
ptype = "http://www.w3.org/2001/XMLSchema#boolean"
data[self.id][key].append({
"@value": value,
"@type": "literal",
"@datatype": ptype
})
return data
[docs]
def to_json(self):
"""Return a lightweight JSON representation (used by LiPD).
Returns
-------
dict
A dictionary representation of this object.
"""
data = {
"@id": self.id
}
if self.housedAt:
value_obj = self.housedAt
obj = value_obj
data["housedat"] = obj
if self.iGSN:
value_obj = self.iGSN
obj = value_obj
data["hasidentifier"] = obj
if self.name:
value_obj = self.name
obj = value_obj
data["hasname"] = obj
for key in self.misc:
value = self.misc[key]
data[key] = value
return data
[docs]
@staticmethod
def from_json(data) -> 'PhysicalSample':
"""Instantiate `PhysicalSample` from its lightweight JSON representation.
Parameters
----------
data : dict
The JSON dictionary to parse.
Returns
-------
PhysicalSample
The populated `PhysicalSample` instance.
"""
self = PhysicalSample()
for key in data:
pvalue = data[key]
if key == "@id":
self.id = pvalue
elif key == "hasidentifier":
value = pvalue
obj = value
self.iGSN = obj
elif key == "hasname":
value = pvalue
obj = value
self.name = obj
elif key == "housedat":
value = pvalue
obj = value
self.housedAt = obj
else:
self.set_non_standard_property(key, pvalue)
return self
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def set_non_standard_property(self, key, value):
"""Store a predicate that is not defined in the ontology schema.
This is useful for forward-compatibility with new properties that are
not yet part of the official schema.
Parameters
----------
key : str
The property name.
value : any
The property value.
"""
if key not in self.misc:
self.misc[key] = value
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def get_non_standard_property(self, key):
"""Return a single non-standard property by key.
Parameters
----------
key : str
The property name.
Returns
-------
any
The property value.
"""
return self.misc[key]
[docs]
def get_all_non_standard_properties(self):
"""Return the dictionary of all non-standard properties.
Returns
-------
dict
Dictionary of all non-standard properties.
"""
return self.misc
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def add_non_standard_property(self, key, value):
"""Append a value to a list-valued non-standard property.
Parameters
----------
key : str
The property name.
value : any
The value to append.
"""
if key not in self.misc:
self.misc[key] = []
self.misc[key].append(value)
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def getHousedAt(self) -> str:
"""Get housedAt.
Returns
-------
str
The current value of housedAt.
"""
return self.housedAt
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def setHousedAt(self, housedAt:str):
"""Set housedAt.
Parameters
----------
housedAt : str
The value to assign.
"""
assert isinstance(housedAt, str), f"Error: '{housedAt}' is not of type str"
self.housedAt = housedAt
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def getIGSN(self) -> str:
"""Get iGSN.
Returns
-------
str
The current value of iGSN.
"""
return self.iGSN
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def setIGSN(self, iGSN:str):
"""Set iGSN.
Parameters
----------
iGSN : str
The value to assign.
"""
assert isinstance(iGSN, str), f"Error: '{iGSN}' is not of type str"
self.iGSN = iGSN
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def getName(self) -> str:
"""Get name.
Returns
-------
str
The current value of name.
"""
return self.name
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def setName(self, name:str):
"""Set name.
Parameters
----------
name : str
The value to assign.
"""
assert isinstance(name, str), f"Error: '{name}' is not of type str"
self.name = name