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Updating method to get dict for details.

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This commit is contained in:
lwark
2025-06-10 15:05:08 -05:00
parent 58c669bc30
commit 592073c2a1
5 changed files with 124 additions and 45 deletions
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7
src/submissions/backend/db/models/__init__.py
View File

@@ -234,10 +234,9 @@ class BaseClass(Base):
@classmethod @classmethod
def query_or_create(cls, **kwargs) -> Tuple[Any, bool]: def query_or_create(cls, **kwargs) -> Tuple[Any, bool]:
new = False new = False
allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute) allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute)]
and not isinstance(v.property, _RelationshipDeclared)] # and not isinstance(v.property, _RelationshipDeclared)]
sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed} sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
logger.debug(f"Sanitized kwargs: {sanitized_kwargs}") logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
instance = cls.query(**sanitized_kwargs) instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list): if not instance or isinstance(instance, list):
@@ -554,6 +553,8 @@ class BaseClass(Base):
output_date = datetime.combine(output_date, addition_time).strftime("%Y-%m-%d %H:%M:%S") output_date = datetime.combine(output_date, addition_time).strftime("%Y-%m-%d %H:%M:%S")
return output_date return output_date
def details_dict(self):
dicto = {k:v for k,v in self.__dict__.items() if not k.startswith("_")}

123
src/submissions/backend/db/models/kits.py
View File

@@ -1082,7 +1082,7 @@ class ProcedureType(BaseClass):
equipment = association_proxy("proceduretypeequipmentroleassociation", "equipmentrole", equipment = association_proxy("proceduretypeequipmentroleassociation", "equipmentrole",
creator=lambda eq: ProcedureTypeEquipmentRoleAssociation( creator=lambda eq: ProcedureTypeEquipmentRoleAssociation(
equipment_role=eq)) #: Proxy of equipmentrole associations equipmentrole=eq)) #: Proxy of equipmentrole associations
kittypereagentroleassociation = relationship( kittypereagentroleassociation = relationship(
"KitTypeReagentRoleAssociation", "KitTypeReagentRoleAssociation",
@@ -1330,10 +1330,34 @@ class Procedure(BaseClass):
rs = results_class(procedure=self, parent=obj) rs = results_class(procedure=self, parent=obj)
def add_equipment(self, obj): def add_equipment(self, obj):
"""
Creates widget for adding equipment to this submission
Args:
obj (_type_): parent widget
"""
logger.debug(f"Add equipment")
from frontend.widgets.equipment_usage import EquipmentUsage from frontend.widgets.equipment_usage import EquipmentUsage
dlg = EquipmentUsage(parent=obj, procedure=self) dlg = EquipmentUsage(parent=obj, procedure=self)
if dlg.exec(): if dlg.exec():
pass equipment = dlg.parse_form()
for equip in equipment:
logger.debug(f"Parsed equipment: {equip}")
_, assoc = equip.to_sql(procedure=self)
logger.debug(f"Got equipment association: {assoc} for {equip}")
try:
assoc.save()
except AttributeError as e:
logger.error(f"Couldn't save association with {equip} due to {e}")
if equip.tips:
for tips in equip.tips:
# logger.debug(f"Attempting to add tips assoc: {tips} (pydantic)")
tassoc, _ = tips.to_sql(procedure=self)
# logger.debug(f"Attempting to add tips assoc: {tips.__dict__} (sql)")
if tassoc not in self.proceduretipsassociation:
tassoc.save()
else:
logger.error(f"Tips already found in submission, skipping.")
def edit(self, obj): def edit(self, obj):
logger.debug("Edit!") logger.debug("Edit!")
@@ -1348,8 +1372,6 @@ class Procedure(BaseClass):
logger.debug("Delete!") logger.debug("Delete!")
class ProcedureTypeKitTypeAssociation(BaseClass): class ProcedureTypeKitTypeAssociation(BaseClass):
""" """
Abstract of relationship between kits and their procedure type. Abstract of relationship between kits and their procedure type.
@@ -1860,7 +1882,7 @@ class Equipment(BaseClass, LogMixin):
proceduretype = ProcedureType.query(name=proceduretype) proceduretype = ProcedureType.query(name=proceduretype)
if isinstance(kittype, str): if isinstance(kittype, str):
kittype = KitType.query(name=kittype) kittype = KitType.query(name=kittype)
for process in self.processes: for process in self.process:
if proceduretype not in process.proceduretype: if proceduretype not in process.proceduretype:
continue continue
if kittype and kittype not in process.kittype: if kittype and kittype not in process.kittype:
@@ -1872,6 +1894,7 @@ class Equipment(BaseClass, LogMixin):
@classmethod @classmethod
@setup_lookup @setup_lookup
def query(cls, def query(cls,
id: int | None = None,
name: str | None = None, name: str | None = None,
nickname: str | None = None, nickname: str | None = None,
asset_number: str | None = None, asset_number: str | None = None,
@@ -1890,6 +1913,12 @@ class Equipment(BaseClass, LogMixin):
Equipment|List[Equipment]: Equipment or list of equipment matching query parameters. Equipment|List[Equipment]: Equipment or list of equipment matching query parameters.
""" """
query = cls.__database_session__.query(cls) query = cls.__database_session__.query(cls)
match id:
case int():
query = query.filter(cls.id == id)
limit = 1
case _:
pass
match name: match name:
case str(): case str():
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
@@ -1925,7 +1954,8 @@ class Equipment(BaseClass, LogMixin):
from backend.validators.pydant import PydEquipment from backend.validators.pydant import PydEquipment
processes = self.get_processes(proceduretype=proceduretype, kittype=kittype, processes = self.get_processes(proceduretype=proceduretype, kittype=kittype,
equipmentrole=equipmentrole) equipmentrole=equipmentrole)
return PydEquipment(processes=processes, role=equipmentrole, logger.debug(f"EquipmentRole: {equipmentrole}")
return PydEquipment(processes=processes, equipmentrole=equipmentrole,
**self.to_dict(processes=False)) **self.to_dict(processes=False))
@classproperty @classproperty
@@ -2046,7 +2076,7 @@ class EquipmentRole(BaseClass):
Returns: Returns:
dict: This EquipmentRole dict dict: This EquipmentRole dict
""" """
return {key: value for key, value in self.__dict__.items() if key != "process"} return {key: value for key, value in self.__dict__.items() if key != "process" and key != "equipment"}
def to_pydantic(self, proceduretype: ProcedureType, def to_pydantic(self, proceduretype: ProcedureType,
kittype: str | KitType | None = None) -> "PydEquipmentRole": kittype: str | KitType | None = None) -> "PydEquipmentRole":
@@ -2061,7 +2091,7 @@ class EquipmentRole(BaseClass):
PydEquipmentRole: This EquipmentRole as PydEquipmentRole PydEquipmentRole: This EquipmentRole as PydEquipmentRole
""" """
from backend.validators.pydant import PydEquipmentRole from backend.validators.pydant import PydEquipmentRole
equipment = [item.to_pydantic(proceduretype=proceduretype, kittype=kittype) for item in equipment = [item.to_pydantic(proceduretype=proceduretype, kittype=kittype, equipmentrole=self) for item in
self.equipment] self.equipment]
pyd_dict = self.to_dict() pyd_dict = self.to_dict()
pyd_dict['process'] = self.get_processes(proceduretype=proceduretype, kittype=kittype) pyd_dict['process'] = self.get_processes(proceduretype=proceduretype, kittype=kittype)
@@ -2131,7 +2161,7 @@ class EquipmentRole(BaseClass):
proceduretype = SubmissionType.query(name=proceduretype) proceduretype = SubmissionType.query(name=proceduretype)
if isinstance(kittype, str): if isinstance(kittype, str):
kittype = KitType.query(name=kittype) kittype = KitType.query(name=kittype)
for process in self.processes: for process in self.process:
if proceduretype and proceduretype not in process.proceduretype: if proceduretype and proceduretype not in process.proceduretype:
continue continue
if kittype and kittype not in process.kittype: if kittype and kittype not in process.kittype:
@@ -2163,10 +2193,23 @@ class ProcedureEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipmentprocedureassociation") #: associated equipment equipment = relationship(Equipment, back_populates="equipmentprocedureassociation") #: associated equipment
def __repr__(self) -> str: def __repr__(self) -> str:
try:
return f"<ProcedureEquipmentAssociation({self.procedure.name} & {self.equipment.name})>" return f"<ProcedureEquipmentAssociation({self.procedure.name} & {self.equipment.name})>"
except AttributeError:
return "<ProcedureEquipmentAssociation(Unknown)>"
def __init__(self, procedure, equipment, equipmentrole: str = "None"): def __init__(self, procedure=None, equipment=None, procedure_id:int|None=None, equipment_id:int|None=None, equipmentrole: str = "None"):
self.run = procedure if not procedure:
if procedure_id:
procedure = Procedure.query(id=procedure_id)
else:
logger.error("Creation error")
self.procedure = procedure
if not equipment:
if equipment_id:
equipment = Equipment.query(id=equipment_id)
else:
logger.error("Creation error")
self.equipment = equipment self.equipment = equipment
self.equipmentrole = equipmentrole self.equipmentrole = equipmentrole
@@ -2201,12 +2244,27 @@ class ProcedureEquipmentAssociation(BaseClass):
@classmethod @classmethod
@setup_lookup @setup_lookup
def query(cls, equipment_id: int | None = None, run_id: int | None = None, equipmentrole: str | None = None, def query(cls,
equipment: int | Equipment | None = None,
procedure: int | Procedure | None = None,
equipmentrole: str | None = None,
limit: int = 0, **kwargs) \ limit: int = 0, **kwargs) \
-> Any | List[Any]: -> Any | List[Any]:
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.equipment_id == equipment_id) match equipment:
query = query.filter(cls.run_id == run_id) case int():
query = query.filter(cls.equipment_id == equipment)
case Equipment():
query = query.filter(cls.equipment == equipment)
case _:
pass
match procedure:
case int():
query = query.filter(cls.procedure_id == procedure)
case Procedure():
query = query.filter(cls.procedure == procedure)
case _:
pass
if equipmentrole is not None: if equipmentrole is not None:
query = query.filter(cls.equipmentrole == equipmentrole) query = query.filter(cls.equipmentrole == equipmentrole)
return cls.execute_query(query=query, limit=limit, **kwargs) return cls.execute_query(query=query, limit=limit, **kwargs)
@@ -2632,7 +2690,7 @@ class ProcedureTipsAssociation(BaseClass):
back_populates="proceduretipsassociation") #: associated procedure back_populates="proceduretipsassociation") #: associated procedure
tips = relationship(Tips, tips = relationship(Tips,
back_populates="tipsprocedureassociation") #: associated equipment back_populates="tipsprocedureassociation") #: associated equipment
role_name = Column(String(32), primary_key=True) #, ForeignKey("_tiprole.name")) tiprole = Column(String(32), primary_key=True) #, ForeignKey("_tiprole.name"))
def to_sub_dict(self) -> dict: def to_sub_dict(self) -> dict:
""" """
@@ -2645,23 +2703,34 @@ class ProcedureTipsAssociation(BaseClass):
@classmethod @classmethod
@setup_lookup @setup_lookup
def query(cls, tips_id: int, role_name: str, procedure_id: int | None = None, limit: int = 0, **kwargs) \ def query(cls, tips: int|Tips, tiprole: str, procedure: int | Procedure | None = None, limit: int = 0, **kwargs) \
-> Any | List[Any]: -> Any | List[Any]:
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.tips_id == tips_id) match tips:
if procedure_id is not None: case int():
query = query.filter(cls.procedure_id == procedure_id) query = query.filter(cls.tips_id == tips)
query = query.filter(cls.role_name == role_name) case Tips():
query = query.filter(cls.tips == tips)
case _:
pass
match procedure:
case int():
query = query.filter(cls.procedure_id == procedure)
case Procedure():
query = query.filter(cls.procedure == procedure)
case _:
pass
query = query.filter(cls.tiprole == tiprole)
return cls.execute_query(query=query, limit=limit, **kwargs) return cls.execute_query(query=query, limit=limit, **kwargs)
# TODO: fold this into the BaseClass.query_or_create ? # TODO: fold this into the BaseClass.query_or_create ?
@classmethod # @classmethod
def query_or_create(cls, tips, run, role: str, **kwargs): # def query_or_create(cls, tips, procedure, role: str, **kwargs):
kwargs['limit'] = 1 # kwargs['limit'] = 1
instance = cls.query(tips_id=tips.id, role_name=role, procedure_id=run.id, **kwargs) # instance = cls.query(tips_id=tips.id, role_name=role, procedure_id=procedure.id, **kwargs)
if instance is None: # if instance is None:
instance = cls(run=run, tips=tips, role_name=role) # instance = cls(procedure=procedure, tips=tips, role_name=role)
return instance # return instance
def to_pydantic(self): def to_pydantic(self):
from backend.validators import PydTips from backend.validators import PydTips

22
src/submissions/backend/validators/pydant.py
View File

@@ -289,7 +289,8 @@ class PydTips(BaseModel):
report = Report() report = Report()
tips = Tips.query(name=self.name, limit=1) tips = Tips.query(name=self.name, limit=1)
# logger.debug(f"Tips query has yielded: {tips}") # logger.debug(f"Tips query has yielded: {tips}")
assoc = ProcedureTipsAssociation.query_or_create(tips=tips, procedure=procedure, role=self.role, limit=1) assoc = ProcedureTipsAssociation.query_or_create(tips=tips, procedure=procedure, tiprole=self.tiprole, limit=1)
logger.debug(f"Got association: {assoc}")
return assoc, report return assoc, report
@@ -297,7 +298,7 @@ class PydEquipment(BaseModel, extra='ignore'):
asset_number: str asset_number: str
name: str name: str
nickname: str | None nickname: str | None
process: List[str] | None processes: List[str] | None
equipmentrole: str | None equipmentrole: str | None
tips: List[PydTips] | None = Field(default=None) tips: List[PydTips] | None = Field(default=None)
@@ -308,9 +309,11 @@ class PydEquipment(BaseModel, extra='ignore'):
value = value.name value = value.name
return value return value
@field_validator('process', mode='before') @field_validator('processes', mode='before')
@classmethod @classmethod
def make_empty_list(cls, value): def make_empty_list(cls, value):
# if isinstance(value, dict):
# value = value['processes']
if isinstance(value, GeneratorType): if isinstance(value, GeneratorType):
value = [item.name for item in value] value = [item.name for item in value]
value = convert_nans_to_nones(value) value = convert_nans_to_nones(value)
@@ -339,20 +342,21 @@ class PydEquipment(BaseModel, extra='ignore'):
procedure = Procedure.query(name=procedure) procedure = Procedure.query(name=procedure)
if isinstance(kittype, str): if isinstance(kittype, str):
kittype = KitType.query(name=kittype) kittype = KitType.query(name=kittype)
logger.debug(f"Querying equipment: {self.asset_number}")
equipment = Equipment.query(asset_number=self.asset_number) equipment = Equipment.query(asset_number=self.asset_number)
if equipment is None: if equipment is None:
logger.error("No equipment found. Returning None.") logger.error("No equipment found. Returning None.")
return return None, None
if procedure is not None: if procedure is not None:
# NOTE: Need to make sure the same association is not added to the procedure # NOTE: Need to make sure the same association is not added to the procedure
try: try:
assoc = ProcedureEquipmentAssociation.query(equipment_id=equipment.id, submission_id=procedure.id, assoc, new = ProcedureEquipmentAssociation.query_or_create(equipment=equipment, procedure=procedure,
equipmentrole=self.equipmentrole, limit=1) equipmentrole=self.equipmentrole, limit=1)
except TypeError as e: except TypeError as e:
logger.error(f"Couldn't get association due to {e}, returning...") logger.error(f"Couldn't get association due to {e}, returning...")
assoc = None return None, None
if assoc is None: if new:
assoc = ProcedureEquipmentAssociation(submission=procedure, equipment=equipment) # assoc = ProcedureEquipmentAssociation(procedure=procedure, equipment=equipment)
# TODO: This seems precarious. What if there is more than one process? # TODO: This seems precarious. What if there is more than one process?
# NOTE: It looks like the way fetching the process is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe. # NOTE: It looks like the way fetching the process is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
# NOTE: I need to find a way to filter this by the kittype involved. # NOTE: I need to find a way to filter this by the kittype involved.
@@ -365,7 +369,7 @@ class PydEquipment(BaseModel, extra='ignore'):
logger.error(f"Found unknown process: {process}.") logger.error(f"Found unknown process: {process}.")
# logger.debug(f"Using process: {process}") # logger.debug(f"Using process: {process}")
assoc.process = process assoc.process = process
assoc.equipmentrole = self.role assoc.equipmentrole = self.equipmentrole
else: else:
logger.warning(f"Found already existing association: {assoc}") logger.warning(f"Found already existing association: {assoc}")
assoc = None assoc = None

9
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -124,9 +124,10 @@ class RoleComboBox(QWidget):
""" """
equip = self.box.currentText() equip = self.box.currentText()
equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0]) equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
logger.debug(f"Equip2: {equip2}")
with QSignalBlocker(self.process) as blocker: with QSignalBlocker(self.process) as blocker:
self.process.clear() self.process.clear()
self.process.addItems([item for item in equip2.processes if item in self.role.processes]) self.process.addItems([item for item in equip2.processes if item in self.role.process])
def update_tips(self): def update_tips(self):
""" """
@@ -137,7 +138,7 @@ class RoleComboBox(QWidget):
if process.tiprole: if process.tiprole:
for iii, tip_role in enumerate(process.tiprole): for iii, tip_role in enumerate(process.tiprole):
widget = QComboBox() widget = QComboBox()
tip_choices = [item.name for item in tip_role.control] tip_choices = [item.name for item in tip_role.tips]
widget.setEditable(False) widget.setEditable(False)
widget.addItems(tip_choices) widget.addItems(tip_choices)
widget.setObjectName(f"tips_{tip_role.name}") widget.setObjectName(f"tips_{tip_role.name}")
@@ -162,13 +163,13 @@ class RoleComboBox(QWidget):
PydEquipment|None: PydEquipment matching form PydEquipment|None: PydEquipment matching form
""" """
eq = Equipment.query(name=self.box.currentText()) eq = Equipment.query(name=self.box.currentText())
tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_"), lot="") for item in tips = [PydTips(name=item.currentText(), tiprole=item.objectName().lstrip("tips").lstrip("_"), lot="") for item in
self.findChildren(QComboBox) if item.objectName().startswith("tips")] self.findChildren(QComboBox) if item.objectName().startswith("tips")]
try: try:
return PydEquipment( return PydEquipment(
name=eq.name, name=eq.name,
processes=[self.process.currentText().strip()], processes=[self.process.currentText().strip()],
role=self.role.name, equipmentrole=self.role.name,
asset_number=eq.asset_number, asset_number=eq.asset_number,
nickname=eq.nickname, nickname=eq.nickname,
tips=tips tips=tips

4
src/submissions/frontend/widgets/submission_table.py
View File

@@ -311,7 +311,10 @@ class SubmissionsTree(QTreeView):
logger.debug(f"Parent {event.parent().data()}") logger.debug(f"Parent {event.parent().data()}")
logger.debug(f"Row: {event.row()}") logger.debug(f"Row: {event.row()}")
logger.debug(f"Sibling: {event.siblingAtRow(event.row()).data()}") logger.debug(f"Sibling: {event.siblingAtRow(event.row()).data()}")
try:
logger.debug(f"Model: {event.model().event()}") logger.debug(f"Model: {event.model().event()}")
except TypeError as e:
logger.error(f"Couldn't expand due to {e}")
def contextMenuEvent(self, event: QContextMenuEvent): def contextMenuEvent(self, event: QContextMenuEvent):
""" """
@@ -330,6 +333,7 @@ class SubmissionsTree(QTreeView):
# clientsubmission = id.model().query_group_object(id.row()) # clientsubmission = id.model().query_group_object(id.row())
self.menu = QMenu(self) self.menu = QMenu(self)
self.con_actions = query_obj.custom_context_events self.con_actions = query_obj.custom_context_events
logger.debug(f"Context menu actions: {self.con_actions}")
for key in self.con_actions.keys(): for key in self.con_actions.keys():
logger.debug(key) logger.debug(key)
match key.lower(): match key.lower():