Beginning prelim code cleanup.
This commit is contained in:
lwark
@@ -10,7 +10,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
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class BaseOmni(BaseModel):
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instance_object: Any | None = Field(default=None)
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def __repr__(self):
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@@ -23,67 +22,107 @@ class BaseOmni(BaseModel):
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def aliases(cls):
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return cls.class_object.aliases
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# NOTE: Okay, this will not work for editing, since by definition not all attributes will line up.
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# def check_all_attributes(self, attributes: dict) -> bool:
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# """
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# Checks this instance against a dictionary of attributes to determine if they are a match.
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#
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# Args:
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# attributes (dict): A dictionary of attributes to be check for equivalence
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#
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# Returns:
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# bool: If a single unequivocal value is found will be false, else true.
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# """
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# logger.debug(f"Incoming attributes: {attributes}")
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# for key, value in attributes.items():
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# logger.debug(f"Comparing value class: {value.__class__} to omni class")
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# if isinstance(value, str):
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# try:
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# check = value.lower() == "none"
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# except AttributeError:
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# continue
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# if check:
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# value = None
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# logger.debug(f"Attempting to grab attribute: {key}")
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# try:
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# self_value = getattr(self, key)
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# class_attr = getattr(self.class_object, key)
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# except AttributeError:
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# continue
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# try:
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# logger.debug(f"Check if {self_value.__class__} is subclass of {BaseOmni}")
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# check = issubclass(self_value.__class__, BaseOmni)
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# except TypeError as e:
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# logger.error(f"Couldn't check if {self_value.__class__} is subclass of {BaseOmni} due to {e}")
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# check = False
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# if check:
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# logger.debug(f"Checking for subclass name.")
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# self_value = self_value.name
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# try:
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# logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
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# check = issubclass(value.__class__, BaseOmni)
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# except TypeError as e:
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# logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
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# check = False
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# if check:
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# logger.debug(f"Checking for subclass name.")
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# value = value.name
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# logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
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# if isinstance(class_attr, property):
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# filter = "property"
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# else:
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# filter = class_attr.property
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# match filter:
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# case ColumnProperty():
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# match class_attr.type:
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# case INTEGER():
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# if value.lower() == "true":
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# value = 1
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# elif value.lower() == "false":
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# value = 0
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# else:
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# value = int(value)
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# case FLOAT():
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# value = float(value)
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# case "property":
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# pass
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# case _RelationshipDeclared():
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# logger.debug(f"Checking relationship value: {self_value}")
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# try:
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# self_value = self_value.name
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# except AttributeError:
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# pass
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# if class_attr.property.uselist:
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# self_value = self_value.__str__()
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# logger.debug(
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# f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
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# if self_value != value:
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# output = False
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# logger.debug(f"Value {key} is False, returning.")
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# return output
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# return True
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def check_all_attributes(self, attributes: dict) -> bool:
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"""
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Checks this instance against a dictionary of attributes to determine if they are a match.
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Args:
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attributes (dict): A dictionary of attributes to be check for equivalence
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Returns:
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bool: If a single unequivocal value is found will be false, else true.
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"""
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logger.debug(f"Incoming attributes: {attributes}")
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attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
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for key, value in attributes.items():
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if value.lower() == "none":
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value = None
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logger.debug(f"Attempting to grab attribute: {key}")
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self_value = getattr(self, key)
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class_attr = getattr(self.class_object, key)
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# logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
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if isinstance(class_attr, property):
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filter = "property"
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else:
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filter = class_attr.property
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match filter:
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case ColumnProperty():
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match class_attr.type:
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case INTEGER():
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if value.lower() == "true":
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value = 1
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elif value.lower() == "false":
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value = 0
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else:
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value = int(value)
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case FLOAT():
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value = float(value)
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case "property":
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pass
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case _RelationshipDeclared():
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logger.debug(f"Checking {self_value}")
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try:
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self_value = self_value.name
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except AttributeError:
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pass
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if class_attr.property.uselist:
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self_value = self_value.__str__()
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try:
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logger.debug(f"Check if {self_value.__class__} is subclass of {self.__class__}")
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check = issubclass(self_value.__class__, self.__class__)
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logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
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check = issubclass(value.__class__, BaseOmni)
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except TypeError as e:
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logger.error(f"Couldn't check if {self_value.__class__} is subclass of {self.__class__} due to {e}")
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logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
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check = False
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if check:
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logger.debug(f"Checking for subclass name.")
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self_value = self_value.name
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logger.debug(
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f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
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if self_value != value:
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output = False
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logger.debug(f"Value {key} is False, returning.")
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return output
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value = value.name
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self_value = self.list_searchables[key]
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if value != self_value:
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logger.debug(f"Value {key} is False, these are not the same object.")
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return False
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logger.debug("Everything checks out, these are the same object.")
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return True
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def __setattr__(self, key, value):
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try:
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class_value = getattr(self.class_object, key)
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@@ -176,6 +215,13 @@ class OmniSubmissionType(BaseOmni):
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return {}
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return value
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@field_validator("template_file", mode="before")
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@classmethod
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def provide_blank_template_file(cls, value):
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if value is None:
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value = bytes()
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return value
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def __init__(self, instance_object: Any, **data):
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super().__init__(**data)
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self.instance_object = instance_object
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@@ -296,7 +342,6 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
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constant_cost=self.constant_cost
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)
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def to_sql(self):
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logger.debug(f"Self kittype: {self.submissiontype}")
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if issubclass(self.submissiontype.__class__, BaseOmni):
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@@ -315,6 +360,18 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
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instance.constant_cost = self.constant_cost
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return instance
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@property
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def list_searchables(self):
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if isinstance(self.kittype, OmniKitType):
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kit = self.kittype.name
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else:
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kit = self.kittype
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if isinstance(self.submissiontype, OmniSubmissionType):
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subtype = self.submissiontype.name
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else:
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subtype = self.submissiontype
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return dict(kittype=kit, submissiontype=subtype)
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class OmniKitTypeReagentRoleAssociation(BaseOmni):
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class_object: ClassVar[Any] = KitTypeReagentRoleAssociation
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@@ -325,6 +382,11 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
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submission_type: str | OmniSubmissionType = Field(default="", description="relationship", title="SubmissionType")
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kit_type: str | OmniKitType = Field(default="", description="relationship", title="KitType")
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def __repr__(self):
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try:
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return f"<OmniKitTypeReagentRoleAssociation({self.kit_type.name}&{self.reagent_role.name})>"
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except AttributeError:
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return f"<OmniKitTypeReagentRoleAssociation(NO NAME)>"
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@field_validator("uses", mode="before")
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@classmethod
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@@ -362,19 +424,46 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
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reagent_role = self.reagent_role.name
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else:
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reagent_role = self.reagent_role
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if issubclass(self.submission_type.__class__, BaseOmni):
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submissiontype = self.submission_type.name
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else:
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submissiontype = self.submission_type
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if issubclass(self.kit_type.__class__, BaseOmni):
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kittype = self.kit_type.name
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else:
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kittype = self.kit_type
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instance, new = self.class_object.query_or_create(
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reagentrole=reagent_role,
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kittype=self.kit_type,
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submissiontype=self.submission_type
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kittype=kittype,
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submissiontype=submissiontype
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)
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logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
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if new:
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logger.warning(f"This is a new instance: {instance.__dict__}")
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reagent_role = self.reagent_role.to_sql()
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instance.reagent_role = reagent_role
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logger.debug(f"KTRRAssoc uses: {self.uses}")
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instance.uses = self.uses
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instance.required = int(self.required)
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logger.debug(f"KitTypeReagentRoleAssociation: {pformat(instance.__dict__)}")
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return instance
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@property
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def list_searchables(self):
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if isinstance(self.kit_type, OmniKitType):
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kit = self.kit_type.name
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else:
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kit = self.kit_type
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if isinstance(self.submission_type, OmniSubmissionType):
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subtype = self.submission_type.name
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else:
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subtype = self.submission_type
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if isinstance(self.reagent_role, OmniReagentRole):
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reagentrole = self.reagent_role.name
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else:
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reagentrole = self.reagent_role
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return dict(kit_type=kit, submission_type=subtype, reagent_role=reagentrole)
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class OmniEquipmentRole(BaseOmni):
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class_object: ClassVar[Any] = EquipmentRole
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@@ -463,6 +552,7 @@ class OmniProcess(BaseOmni):
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# NOTE: How am I going to figure out relatioinships without getting into recursion issues?
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name: str = Field(default="", description="property") #: Process name
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# version: str = Field(default="", description="property") #: Version (string to account for "in_use" or whatever)
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submission_types: List[OmniSubmissionType] | List[str] = Field(default=[], description="relationship",
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title="SubmissionType")
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equipment_roles: List[OmniEquipmentRole] | List[str] = Field(default=[], description="relationship",
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@@ -491,6 +581,13 @@ class OmniProcess(BaseOmni):
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return ""
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return value
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# @field_validator("version", mode="before")
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# @classmethod
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# def rescue_name_none(cls, value):
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# if not value:
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# return "1"
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# return value
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def to_sql(self):
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instance, new = self.class_object.query_or_create(name=self.name)
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for st in self.submission_types:
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@@ -507,17 +604,21 @@ class OmniProcess(BaseOmni):
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instance.tip_roles.append(new_assoc)
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return instance
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@property
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def list_searchables(self):
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return dict(name=self.name)
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class OmniKitType(BaseOmni):
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class_object: ClassVar[Any] = KitType
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name: str = Field(default="", description="property")
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kit_submissiontype_associations: List[OmniSubmissionTypeKitTypeAssociation] | List[str] = Field(default=[],
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description="relationship",
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title="SubmissionTypeKitTypeAssociation")
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description="relationship",
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title="SubmissionTypeKitTypeAssociation")
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kit_reagentrole_associations: List[OmniKitTypeReagentRoleAssociation] | List[str] = Field(default=[],
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description="relationship",
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title="KitTypeReagentRoleAssociation")
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description="relationship",
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title="KitTypeReagentRoleAssociation")
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processes: List[OmniProcess] | List[str] = Field(default=[], description="relationship", title="Process")
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@field_validator("name", mode="before")
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@@ -548,8 +649,9 @@ class OmniKitType(BaseOmni):
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if new_assoc not in new_rr:
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logger.debug(f"Adding {new_assoc} to kit_reagentrole_associations")
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new_rr.append(new_assoc)
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logger.debug(f"Setting kit_reagentrole_associations to {new_rr}")
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logger.debug(f"Setting kit_reagentrole_associations to {pformat([item.__dict__ for item in new_rr])}")
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kit.kit_reagentrole_associations = new_rr
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# sys.exit()
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new_st = []
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for st_assoc in self.kit_submissiontype_associations:
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new_assoc = st_assoc.to_sql()
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