Moments before disaster
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lwark
@@ -35,6 +35,7 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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@model_validator(mode="before")
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@classmethod
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def prevalidate(cls, data):
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# logger.debug(f"Initial data for {cls.__name__}: {pformat(data)}")
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sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
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output = {}
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try:
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@@ -72,7 +73,7 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
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def __init__(self, **data):
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# NOTE: Grab the sql model for validation purposes.
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# self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
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logger.debug(f"Initial data: {data}")
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super().__init__(**data)
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def filter_field(self, key: str) -> Any:
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@@ -284,7 +285,7 @@ class PydReagent(PydBaseClass):
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class PydSample(PydBaseClass):
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sample_id: str
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sampletype: str | None = Field(default=None)
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# sampletype: str | None = Field(default=None)
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submission_rank: int | List[int] | None = Field(default=0, validate_default=True)
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enabled: bool = Field(default=True)
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row: int = Field(default=0)
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@@ -327,7 +328,7 @@ class PydSample(PydBaseClass):
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def improved_dict(self, dictionaries: bool = True) -> dict:
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output = super().improved_dict(dictionaries=dictionaries)
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output['name'] = self.sample_id
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del output['sampletype']
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# del output['sampletype']
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return output
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def to_sql(self):
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@@ -399,22 +400,24 @@ class PydEquipment(PydBaseClass):
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@field_validator('process', mode='before')
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@classmethod
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def make_empty_list(cls, value):
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def make_empty_list(cls, value, values):
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# if isinstance(value, dict):
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# value = value['processes']
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if isinstance(value, GeneratorType):
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value = [item for item in value]
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value = convert_nans_to_nones(value)
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if not value:
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value = ['']
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# logger.debug(value)
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value = []
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logger.debug(value)
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try:
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# value = [item.strip() for item in value]
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d = next((process for process in value), None)
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logger.debug(f"Next process: {d.detail_dict()}")
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value = PydProcess(d.details_dict())
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d: Process = next((process for process in value if values.data['name'] in [item.name for item in process.equipment]), None)
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# logger.debug(f"Next process: {d.details_dict()}")
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value = d.to_pydantic()
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# value = PydProcess(**d.details_dict())
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# value = next((process.to_pydantic() for process in value))
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except AttributeError:
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except AttributeError as e:
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logger.error(f"Process Validation error due to {e}")
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pass
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return value
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@@ -1179,6 +1182,7 @@ class PydProcess(PydBaseClass, extra="allow"):
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@field_validator("proceduretype", "equipment", "equipmentrole", "tiprole", mode="before")
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@classmethod
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def enforce_list(cls, value):
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# logger.debug(f"Validating field: {value}")
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if not isinstance(value, list):
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value = [value]
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output = []
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@@ -1192,32 +1196,36 @@ class PydProcess(PydBaseClass, extra="allow"):
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@report_result
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def to_sql(self):
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report = Report()
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instance = Process.query(name=self.name)
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logger.debug(f"Query process: {self.name}, version = {self.version}")
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# NOTE: can't use query_or_create due to name not being part of ProcessVersion
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instance = ProcessVersion.query(name=self.name, version=self.version, limit=1)
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logger.debug(f"Got instance: {instance}")
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if not instance:
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instance = Process()
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fields = [item for item in self.model_fields]
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for field in fields:
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logger.debug(f"Field: {field}")
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try:
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field_type = getattr(instance.__class__, field).property
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except AttributeError:
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logger.error(f"No attribute: {field} in {instance.__class__}")
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continue
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match field_type:
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case _RelationshipDeclared():
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logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
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query_str = getattr(self, field)
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if isinstance(query_str, list):
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query_str = query_str[0]
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if query_str in ["", " ", None]:
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continue
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logger.debug(f"Querying {field_type.entity.class_} with name {query_str}")
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field_value = field_type.entity.class_.query(name=query_str)
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logger.debug(f"{field} query result: {field_value}")
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case ColumnProperty():
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logger.debug(f"{field} is a property.")
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field_value = getattr(self, field)
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instance.set_attribute(key=field, value=field_value)
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instance = ProcessVersion()
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# fields = [item for item in self.model_fields]
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# for field in fields:
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# logger.debug(f"Field: {field}")
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# try:
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# field_type = getattr(instance.__class__, field).property
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# except AttributeError:
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# logger.error(f"No attribute: {field} in {instance.__class__}")
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# continue
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# match field_type:
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# case _RelationshipDeclared():
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# logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
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# query_str = getattr(self, field)
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# if isinstance(query_str, list):
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# query_str = query_str[0]
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# if query_str in ["", " ", None]:
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# continue
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# logger.debug(f"Querying {field_type.entity.class_} with name {query_str}")
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# field_value = field_type.entity.class_.query(name=query_str)
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# logger.debug(f"{field} query result: {field_value}")
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# case ColumnProperty():
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# logger.debug(f"{field} is a property.")
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# field_value = getattr(self, field)
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# # instance.set_attribute(key=field, value=field_value)
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# setattr(instance, field, field_value)
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return instance, report
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@@ -1469,7 +1477,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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idx = 0
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insertable = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
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self.reagent.insert(idx, insertable)
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logger.debug(self.reagent)
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# logger.debug(self.reagent)
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@classmethod
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def update_new_reagents(cls, reagent: PydReagent):
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@@ -1506,9 +1514,9 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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sql.proceduretype = self.proceduretype
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# Note: convert any new reagents to sql and save
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# for reagentrole, reagents in self.reagentrole.items():
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for reagent in self.reagent:
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if not reagent.lot or reagent.name == "--New--":
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continue
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# for reagent in self.reagent:
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# if not reagent.lot or reagent.name == "--New--":
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# continue
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# self.update_new_reagents(reagent)
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# NOTE: reset reagent associations.
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# sql.procedurereagentassociation = []
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@@ -1532,7 +1540,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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r.delete()
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else:
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removable.delete()
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# logger.debug(f"Adding {reagent} to {sql}")
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logger.debug(f"Adding {reagent} to {sql}")
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reagent_assoc = ProcedureReagentLotAssociation(reagentlot=reagent, procedure=sql, reagentrole=reagentrole)
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try:
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start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
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@@ -1556,14 +1564,18 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
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row=sample.row, column=sample.column,
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procedure_rank=sample.procedure_rank)
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sys.exit(pformat(self.equipment))
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# sys.exit(pformat(self.equipment))
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for equipment in self.equipment:
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equip = Equipment.query(name=equipment.name)
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logger.debug(f"Equipment: {equipment}")
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# equip = Equipment.query(name=equipment.name)
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equip, _ = equipment.to_sql()
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logger.debug(f"Process: {equipment.process}")
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if equip not in sql.equipment:
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equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql,
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equipmentrole=equip.equipmentrole[0])
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process = equipment.process.to_sql()
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equip_assoc.process = process
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equip_assoc.processversion = process
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# sys.exit(pformat([item.__dict__ for item in sql.procedureequipmentassociation]))
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return sql, None
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