Addition of Equipment and SubmissionType creation.
This commit is contained in:
Landon Wark
@@ -10,6 +10,7 @@ import logging
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from tools import check_authorization, setup_lookup, query_return, Report, Result, Settings
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from typing import List
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from pandas import ExcelFile
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from pathlib import Path
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from . import Base, BaseClass, Organization
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logger = logging.getLogger(f'submissions.{__name__}')
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@@ -55,7 +56,7 @@ class KitType(BaseClass):
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def __repr__(self) -> str:
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return f"<KitType({self.name})>"
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def get_reagents(self, required:bool=False, submission_type:str|SubmissionType|None=None) -> list:
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def get_reagents(self, required:bool=False, submission_type:str|SubmissionType|None=None) -> List[ReagentType]:
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"""
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Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
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@@ -242,6 +243,10 @@ class ReagentType(BaseClass):
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case _:
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pass
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return query_return(query=query, limit=limit)
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def to_pydantic(self):
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from backend.validators.pydant import PydReagent
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return PydReagent(lot=None, type=self.name, name=self.name, expiry=date.today())
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class KitTypeReagentTypeAssociation(BaseClass):
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"""
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@@ -583,6 +588,14 @@ class SubmissionType(BaseClass):
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kit_types = association_proxy("submissiontype_kit_associations", "kit_type") #: Proxy of kittype association
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submissiontype_equipment_associations = relationship(
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"SubmissionTypeEquipmentAssociation",
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back_populates="submission_type",
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cascade="all, delete-orphan"
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)
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equipment = association_proxy("submissiontype_equipment_associations", "equipment")
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def __repr__(self) -> str:
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return f"<SubmissionType({self.name})>"
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@@ -595,6 +608,35 @@ class SubmissionType(BaseClass):
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"""
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return ExcelFile(self.template_file).sheet_names
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def set_template_file(self, filepath:Path|str):
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if isinstance(filepath, str):
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filepath = Path(filepath)
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with open (filepath, "rb") as f:
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data = f.read()
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self.template_file = data
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self.save()
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def get_equipment(self) -> list:
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from backend.validators.pydant import PydEquipmentPool
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# if static:
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# return [item.equipment.to_pydantic() for item in self.submissiontype_equipment_associations if item.static==1]
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# else:
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preliminary1 = [item.equipment.to_pydantic(static=item.static) for item in self.submissiontype_equipment_associations]# if item.static==0]
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preliminary2 = [item.equipment.to_pydantic(static=item.static) for item in self.submissiontype_equipment_associations]# if item.static==0]
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output = []
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pools = list(set([item.pool_name for item in preliminary1 if item.pool_name != None]))
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for pool in pools:
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c_ = []
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for item in preliminary1:
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if item.pool_name == pool:
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c_.append(item)
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preliminary2.remove(item)
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if len(c_) > 0:
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output.append(PydEquipmentPool(name=pool, equipment=c_))
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for item in preliminary2:
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output.append(item)
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return output
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@classmethod
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@setup_lookup
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def query(cls,
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@@ -772,4 +814,145 @@ class SubmissionReagentAssociation(BaseClass):
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# limit = query.count()
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return query_return(query=query, limit=limit)
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def to_sub_dict(self, extraction_kit):
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output = self.reagent.to_sub_dict(extraction_kit)
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output['comments'] = self.comments
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return output
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class Equipment(BaseClass):
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# Currently abstract until ready to implement
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# __abstract__ = True
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__tablename__ = "_equipment"
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id = Column(INTEGER, primary_key=True)
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name = Column(String(64))
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nickname = Column(String(64))
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asset_number = Column(String(16))
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pool_name = Column(String(16))
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equipment_submission_associations = relationship(
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"SubmissionEquipmentAssociation",
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back_populates="equipment",
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cascade="all, delete-orphan",
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)
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submissions = association_proxy("equipment_submission_associations", "submission")
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equipment_submissiontype_associations = relationship(
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"SubmissionTypeEquipmentAssociation",
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back_populates="equipment",
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cascade="all, delete-orphan",
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)
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submission_types = association_proxy("equipment_submission_associations", "submission_type")
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def __repr__(self):
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return f"<Equipment({self.name})>"
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@classmethod
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@setup_lookup
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def query(cls,
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name:str|None=None,
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nickname:str|None=None,
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asset_number:str|None=None,
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limit:int=0
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) -> Equipment|List[Equipment]:
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query = cls.__database_session__.query(cls)
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match name:
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case str():
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query = query.filter(cls.name==name)
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limit = 1
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case _:
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pass
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match nickname:
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case str():
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query = query.filter(cls.nickname==nickname)
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limit = 1
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case _:
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pass
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match asset_number:
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case str():
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query = query.filter(cls.asset_number==asset_number)
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limit = 1
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case _:
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pass
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return query_return(query=query, limit=limit)
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def to_pydantic(self, static):
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from backend.validators.pydant import PydEquipment
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return PydEquipment(static=static, **self.__dict__)
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def save(self):
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self.__database_session__.add(self)
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self.__database_session__.commit()
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class SubmissionEquipmentAssociation(BaseClass):
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# Currently abstract until ready to implement
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# __abstract__ = True
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__tablename__ = "_equipment_submissions"
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equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
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submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True) #: id of associated submission
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process = Column(String(64)) #: name of the process run on this equipment
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start_time = Column(TIMESTAMP)
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end_time = Column(TIMESTAMP)
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comments = Column(String(1024))
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submission = relationship("BasicSubmission", back_populates="submission_equipment_associations") #: associated submission
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equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated submission
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def __init__(self, submission, equipment):
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self.submission = submission
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self.equipment = equipment
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def to_sub_dict(self) -> dict:
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output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments)
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return output
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def save(self):
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self.__database_session__.add(self)
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self.__database_session__.commit()
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class SubmissionTypeEquipmentAssociation(BaseClass):
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# __abstract__ = True
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__tablename__ = "_submissiontype_equipment"
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equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
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submissiontype_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of associated submission
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uses = Column(JSON) #: locations of equipment on the submission type excel sheet.
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static = Column(INTEGER, default=1) #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
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submission_type = relationship(SubmissionType, back_populates="submissiontype_equipment_associations") #: associated submission
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equipment = relationship(Equipment, back_populates="equipment_submissiontype_associations") #: associated equipment
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@validates('static')
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def validate_age(self, key, value):
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"""
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Ensures only 1 & 0 used in 'static'
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Args:
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key (str): name of attribute
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value (_type_): value of attribute
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Raises:
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ValueError: Raised if bad value given
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Returns:
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_type_: value
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"""
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if not 0 <= value < 2:
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raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
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return value
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def save(self):
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self.__database_session__.add(self)
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self.__database_session__.commit()
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