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Moments before disaster.

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This commit is contained in:
Landon Wark
2024-01-08 08:51:23 -06:00
parent 19448cc8f3
commit 8c688df75f
10 changed files with 445 additions and 82 deletions
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200
src/submissions/backend/db/models/kits.py
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@@ -32,6 +32,22 @@ equipmentroles_equipment = Table(
extend_existing=True
)
equipmentroles_processes = Table(
"_equipmentroles_processes",
Base.metadata,
Column("process_id", INTEGER, ForeignKey("_process.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_equipment_roles.id")),
extend_existing=True
)
submissiontypes_processes = Table(
"_submissiontypes_processes",
Base.metadata,
Column("process_id", INTEGER, ForeignKey("_process.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_submission_types.id")),
extend_existing=True
)
class KitType(BaseClass):
"""
Base of kits used in submission processing
@@ -588,6 +604,7 @@ class SubmissionType(BaseClass):
instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
# regex = Column(String(512))
template_file = Column(BLOB) #: Blank form for this type stored as binary.
processes = relationship("Process", back_populates="submission_types", secondary=submissiontypes_processes)
submissiontype_kit_associations = relationship(
"SubmissionTypeKitTypeAssociation",
@@ -855,7 +872,10 @@ class Equipment(BaseClass):
return f"<Equipment({self.name})>"
def get_processes(self, submission_type:SubmissionType):
return [assoc.process for assoc in self.equipment_submission_associations if assoc.submission.submission_type_name==submission_type.name]
processes = [assoc.process for assoc in self.equipment_submission_associations if assoc.submission.submission_type_name==submission_type.name]
if len(processes) == 0:
processes = ['']
return processes
@classmethod
@setup_lookup
@@ -888,7 +908,8 @@ class Equipment(BaseClass):
def to_pydantic(self, submission_type:SubmissionType):
from backend.validators.pydant import PydEquipment
return PydEquipment(processes=self.get_processes(submission_type=submission_type), role=None, **self.__dict__)
# return PydEquipment(process=self.get_processes(submission_type=submission_type), role=None, **self.__dict__)
return PydEquipment(process=None, role=None, **self.__dict__)
def save(self):
self.__database_session__.add(self)
@@ -911,6 +932,7 @@ class EquipmentRole(BaseClass):
id = Column(INTEGER, primary_key=True)
name = Column(String(32))
instances = relationship("Equipment", back_populates="roles", secondary=equipmentroles_equipment)
processes = relationship("Process", back_populates="equipment_roles", secondary=equipmentroles_processes)
equipmentrole_submissiontype_associations = relationship(
"SubmissionTypeEquipmentRoleAssociation",
@@ -926,7 +948,9 @@ class EquipmentRole(BaseClass):
def to_pydantic(self, submission_type:SubmissionType):
from backend.validators.pydant import PydEquipmentRole
equipment = [item.to_pydantic(submission_type=submission_type) for item in self.instances]
return PydEquipmentRole(equipment=equipment, **self.__dict__)
pyd_dict = self.__dict__
pyd_dict['processes'] = self.get_processes(submission_type=submission_type)
return PydEquipmentRole(equipment=equipment, **pyd_dict)
@classmethod
@setup_lookup
@@ -945,6 +969,25 @@ class EquipmentRole(BaseClass):
case _:
pass
return query_return(query=query, limit=limit)
def get_processes(self, submission_type:str|SubmissionType|None) -> List[Process]:
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if submission_type != None:
output = [process.name for process in self.processes if submission_type in process.submission_types]
else:
output = [process.name for process in self.processes]
if len(output) == 0:
return ['']
else:
return output
def save(self):
try:
self.__database_session__.add(self)
self.__database_session__.commit()
except:
self.__database_session__.rollback()
class SubmissionEquipmentAssociation(BaseClass):
@@ -956,7 +999,8 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True) #: id of associated submission
role = Column(String(64), primary_key=True) #: name of the role the equipment fills
process = Column(String(64)) #: name of the process run on this equipment
# process = Column(String(64)) #: name of the process run on this equipment
process_id = Column(INTEGER, ForeignKey("_process.id",ondelete="SET NULL", name="SEA_Process_id"))
start_time = Column(TIMESTAMP)
end_time = Column(TIMESTAMP)
comments = Column(String(1024))
@@ -970,7 +1014,7 @@ class SubmissionEquipmentAssociation(BaseClass):
self.equipment = equipment
def to_sub_dict(self) -> dict:
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments, process=[self.process], role=self.role, nickname=self.equipment.nickname)
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments, process=self.process.name, role=self.role, nickname=self.equipment.nickname)
return output
def save(self):
@@ -1021,3 +1065,149 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
self.__database_session__.add(self)
self.__database_session__.commit()
class Process(BaseClass):
__tablename__ = "_process"
id = Column(INTEGER, primary_key=True)
name = Column(String(64))
submission_types = relationship("SubmissionType", back_populates='processes', secondary=submissiontypes_processes)
equipment_roles = relationship("EquipmentRole", back_populates='processes', secondary=equipmentroles_processes)
submissions = relationship("SubmissionEquipmentAssociation", backref='process')
def __repr__(self):
return f"<Process({self.name})"
@classmethod
@setup_lookup
def query(cls, name:str|None, limit:int=0):
query = cls.__database_session__.query(cls)
match name:
case str():
query = query.filter(cls.name==name)
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
def save(self):
try:
self.__database_session__.add(self)
self.__database_session__.commit()
except:
self.__database_session__.rollback()
# class KitTypeReagentTypeAssociation(BaseClass):
# """
# table containing reagenttype/kittype associations
# DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
# """
# __tablename__ = "_reagenttypes_kittypes"
# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
# kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
# uses = Column(JSON) #: map to location on excel sheets of different submission types
# required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0)
# last_used = Column(String(32)) #: last used lot number of this type of reagent
# kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit
# # reference to the "ReagentType" object
# reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type
# def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
# # logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
# self.kit_type = kit_type
# self.reagent_type = reagent_type
# self.uses = uses
# self.required = required
# def __repr__(self) -> str:
# return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
# @validates('required')
# def validate_age(self, key, value):
# """
# Ensures only 1 & 0 used in 'required'
# Args:
# key (str): name of attribute
# value (_type_): value of attribute
# Raises:
# ValueError: Raised if bad value given
# Returns:
# _type_: value
# """
# if not 0 <= value < 2:
# raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
# return value
# @validates('reagenttype')
# def validate_reagenttype(self, key, value):
# """
# Ensures reagenttype is an actual ReagentType
# Args:
# key (str)): name of attribute
# value (_type_): value of attribute
# Raises:
# ValueError: raised if reagenttype is not a ReagentType
# Returns:
# _type_: ReagentType
# """
# if not isinstance(value, ReagentType):
# raise ValueError(f'{value} is not a reagenttype')
# return value
# @classmethod
# @setup_lookup
# def query(cls,
# kit_type:KitType|str|None=None,
# reagent_type:ReagentType|str|None=None,
# limit:int=0
# ) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
# """
# Lookup junction of ReagentType and KitType
# Args:
# kit_type (models.KitType | str | None): KitType of interest.
# reagent_type (models.ReagentType | str | None): ReagentType of interest.
# limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
# Returns:
# models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
# """
# query: Query = cls.__database_session__.query(cls)
# match kit_type:
# case KitType():
# query = query.filter(cls.kit_type==kit_type)
# case str():
# query = query.join(KitType).filter(KitType.name==kit_type)
# case _:
# pass
# match reagent_type:
# case ReagentType():
# query = query.filter(cls.reagent_type==reagent_type)
# case str():
# query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
# case _:
# pass
# if kit_type != None and reagent_type != None:
# limit = 1
# return query_return(query=query, limit=limit)
# def save(self) -> Report:
# """
# Adds this instance to the database and commits.
# Returns:
# Report: Result of save action
# """
# report = Report()
# self.__database_session__.add(self)
# self.__database_session__.commit()
# return report