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Code cleanup for excel.parsers complete.

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This commit is contained in:
lwark
2025-09-04 14:35:44 -05:00
parent fcda0d873c
commit b6e1c0dee2
11 changed files with 161 additions and 138 deletions
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5
src/submissions/backend/db/models/__init__.py
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@@ -538,7 +538,10 @@ class BaseClass(Base):
case _:
return super().__setattr__(key, value)
else:
return super().__setattr__(key, value)
try:
return super().__setattr__(key, value)
except AttributeError:
raise AttributeError(f"Can't set {key} to {value}")
def delete(self, **kwargs):
logger.error(f"Delete has not been implemented for {self.__class__.__name__}")

63
src/submissions/backend/db/models/procedures.py
View File

@@ -1027,7 +1027,8 @@ class ProcedureTypeReagentRoleAssociation(BaseClass):
reagentrole_id = Column(INTEGER, ForeignKey("_reagentrole.id"),
primary_key=True) #: id of associated reagentrole
proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id"), primary_key=True) #: id of associated proceduretype
proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id"),
primary_key=True) #: id of associated proceduretype
uses = Column(JSON) #: map to location on excel sheets of different procedure types
required = Column(INTEGER) #: whether the reagent type is required for the kittype (Boolean 1 or 0)
last_used = Column(String(32)) #: last used lot number of this type of reagent
@@ -1324,7 +1325,7 @@ class ProcedureReagentLotAssociation(BaseClass):
output.update(relevant)
output['reagentrole'] = self.reagentrole
output['misc_info'] = misc
logger.debug(f"Output: {pformat(output)}")
# logger.debug(f"Output: {pformat(output)}")
return output
def delete(self, **kwargs):
@@ -1544,7 +1545,6 @@ class Equipment(BaseClass, LogMixin):
else:
return {k: v for k, v in self.__dict__.items()}
@classmethod
@setup_lookup
def query(cls,
@@ -1842,7 +1842,7 @@ class ProcessVersion(BaseClass):
@classmethod
def query(cls,
version: str | None = None,
version: str | float | None = None,
name: str | None = None,
limit: int = 0,
**kwargs) -> ReagentLot | List[ReagentLot]:
@@ -1853,8 +1853,8 @@ class ProcessVersion(BaseClass):
case _:
pass
match version:
case str():
query = query.filter(cls.version == version)
case str() | float():
query = query.filter(cls.version == float(version))
case _:
pass
return cls.execute_query(query=query, limit=limit)
@@ -1879,6 +1879,9 @@ class Tips(BaseClass):
@setup_lookup
def query(cls,
name: str | None = None,
manufacturer: str | None = None,
capacity: str | None = None,
ref: str | None = None,
limit: int = 0,
**kwargs) -> Tips | List[Tips]:
query = cls.__database_session__.query(cls)
@@ -1888,6 +1891,22 @@ class Tips(BaseClass):
limit = 1
case _:
pass
match manufacturer:
case str():
query = query.filter(cls.manufacturer == manufacturer)
case _:
pass
match capacity:
case int():
query = query.filter(cls.capacity == capacity)
case _:
pass
match ref:
case str():
query = query.filter(cls.ref == ref)
limit = 1
case _:
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
@@ -1944,15 +1963,21 @@ class TipsLot(BaseClass, LogMixin):
@property
def name(self) -> str:
return f"{self.tips.manufacturer}-{self.tips.capacity}-{self.lot}"
return f"{self.tips.manufacturer}-{self.tips.ref}-{self.lot}"
@classmethod
def query(cls, name: str | None = None, lot: str | None = None, limit: int = 0, **kwargs) -> Tips | List[Tips]:
def query(cls,
manufacturer: str | None = None,
ref: str | None = None,
lot: str | None = None,
limit: int = 0,
**kwargs) -> Tips | List[Tips]:
"""
Lookup tips
Args:
name (str | None, optional): Informal name of tips. Defaults to None.
manufacturer (str | None, optional): Name of parent tip manufacturer. Defaults to None.
ref (str | None, optional): Name of parent tip reference number. Defaults to None.
lot (str | None, optional): Lot number. Defaults to None.
limit (int, optional): Maximum number of results to return (0=all). Defaults to 0.
@@ -1960,9 +1985,17 @@ class TipsLot(BaseClass, LogMixin):
Tips | List[Tips]: Tips matching criteria
"""
query = cls.__database_session__.query(cls)
match name:
if manufacturer is not None and ref is not None:
manufacturer = None
match manufacturer:
case str():
query = query.filter(cls.name == name)
logger.debug(f"Looking for {manufacturer}")
query = query.join(Tips).filter(Tips.manufacturer == manufacturer)
case _:
pass
match ref:
case str():
query = query.join(Tips).filter(Tips.ref == ref)
case _:
pass
match lot:
@@ -2032,7 +2065,8 @@ class ProcedureEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipmentprocedureassociation") #: associated equipment
processversion = relationship(ProcessVersion, back_populates="procedureequipmentassociation") #: Associated process version
processversion = relationship(ProcessVersion,
back_populates="procedureequipmentassociation") #: Associated process version
tipslot_id = Column(INTEGER, ForeignKey("_tipslot.id", ondelete="SET NULL",
name="SEA_Tipslot_id"))
@@ -2153,7 +2187,10 @@ class ProcedureEquipmentAssociation(BaseClass):
output.update(relevant)
output['misc_info'] = misc
output['equipment_role'] = self.equipmentrole
output['processversion'] = self.processversion.details_dict()
try:
output['processversion'] = self.processversion.details_dict()
except AttributeError:
output['processversion'] = None
try:
output['tips'] = self.tipslot.details_dict()
except AttributeError: