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Code cleanup, dependency update, various bug fixes

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This commit is contained in:
lwark
2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
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62
src/submissions/backend/db/models/kits.py
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@@ -120,8 +120,8 @@ class KitType(BaseClass):
submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None.
Returns:
list: List of reagent types
"""
List[ReagentType]: List of reagents linked to this kit.
"""
match submission_type:
case SubmissionType():
# logger.debug(f"Getting reagents by SubmissionType {submission_type}")
@@ -152,17 +152,15 @@ class KitType(BaseClass):
dict: Dictionary containing information locations.
"""
info_map = {}
# Account for submission_type variable type.
# NOTE: Account for submission_type variable type.
match submission_type:
case str():
# logger.debug(f"Constructing xl map with str {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if
item.submission_type.name == submission_type]
# st_assoc = [item for item in self.used_for if submission_type == item.name][0]
case SubmissionType():
# logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if item.submission_type == submission_type]
# st_assoc = submission_type
case _:
raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
@@ -371,10 +369,10 @@ class Reagent(BaseClass):
dict: representation of the reagent's attributes
"""
if extraction_kit is not None:
# Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
# NOTE: Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try:
reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
# Most will be able to fall back to first ReagentType in itself because most will only have 1.
# NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
except:
reagent_role = self.type[0]
else:
@@ -383,7 +381,7 @@ class Reagent(BaseClass):
rtype = reagent_role.name.replace("_", " ")
except AttributeError:
rtype = "Unknown"
# Calculate expiry with EOL from ReagentType
# NOTE: Calculate expiry with EOL from ReagentType
try:
place_holder = self.expiry + reagent_role.eol_ext
except (TypeError, AttributeError) as e:
@@ -467,7 +465,7 @@ class Reagent(BaseClass):
match name:
case str():
# logger.debug(f"Looking up reagent by name str: {name}")
# Not limited due to multiple reagents having same name.
# NOTE: Not limited due to multiple reagents having same name.
query = query.filter(cls.name == name)
case _:
pass
@@ -475,7 +473,7 @@ class Reagent(BaseClass):
case str():
# logger.debug(f"Looking up reagent by lot number str: {lot_number}")
query = query.filter(cls.lot == lot_number)
# In this case limit number returned.
# NOTE: In this case limit number returned.
limit = 1
case _:
pass
@@ -516,10 +514,6 @@ class Discount(BaseClass):
organization (models.Organization | str | int): Organization receiving discount.
kit_type (models.KitType | str | int): Kit discount received on.
Raises:
ValueError: Invalid Organization
ValueError: Invalid kit.
Returns:
models.Discount|List[models.Discount]: Discount(s) of interest.
"""
@@ -535,7 +529,6 @@ class Discount(BaseClass):
# logger.debug(f"Looking up discount with organization id: {organization}")
query = query.join(Organization).filter(Organization.id == organization)
case _:
# raise ValueError(f"Invalid value for organization: {organization}")
pass
match kit_type:
case KitType():
@@ -548,7 +541,6 @@ class Discount(BaseClass):
# logger.debug(f"Looking up discount with kit type id: {kit_type}")
query = query.join(KitType).filter(KitType.id == kit_type)
case _:
# raise ValueError(f"Invalid value for kit type: {kit_type}")
pass
return cls.execute_query(query=query)
@@ -634,11 +626,18 @@ class SubmissionType(BaseClass):
self.save()
def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
"""
Make of map of where all fields are located in excel sheet
Args:
mode (Literal["read", "write"]): Which mode to get locations for
Returns:
dict: Map of locations
"""
info = self.info_map
# logger.debug(f"Info map: {info}")
output = {}
# for k,v in info.items():
# info[k]['write'] += info[k]['read']
match mode:
case "read":
output = {k: v[mode] for k, v in info.items() if v[mode]}
@@ -647,7 +646,13 @@ class SubmissionType(BaseClass):
output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
return output
def construct_sample_map(self):
def construct_sample_map(self) -> dict:
"""
Returns sample map
Returns:
dict: sample location map
"""
return self.sample_map
def construct_equipment_map(self) -> dict:
@@ -655,7 +660,7 @@ class SubmissionType(BaseClass):
Constructs map of equipment to excel cells.
Returns:
List[dict]: List of equipment locations in excel sheet
dict: Map equipment locations in excel sheet
"""
output = {}
# logger.debug("Iterating through equipment roles")
@@ -671,7 +676,7 @@ class SubmissionType(BaseClass):
Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns:
List['PydEquipmentRole']: List of equipment roles
List[PydEquipmentRole]: List of equipment roles
"""
return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
@@ -702,7 +707,13 @@ class SubmissionType(BaseClass):
raise TypeError(f"Type {type(equipment_role)} is not allowed")
return list(set([item for items in relevant for item in items if item != None]))
def get_submission_class(self):
def get_submission_class(self) -> "BasicSubmission":
"""
Gets submission class associated with this submission type.
Returns:
BasicSubmission: Submission class
"""
from .submissions import BasicSubmission
return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
@@ -1063,7 +1074,7 @@ class Equipment(BaseClass):
processes (bool, optional): Whether to include processes. Defaults to False.
Returns:
dict: _description_
dict: Dictionary representation of this equipment
"""
if not processes:
return {k: v for k, v in self.__dict__.items() if k != 'processes'}
@@ -1152,7 +1163,7 @@ class Equipment(BaseClass):
extraction_kit (str | KitType | None, optional): Relevant KitType. Defaults to None.
Returns:
PydEquipment: _description_
PydEquipment: pydantic equipment object
"""
from backend.validators.pydant import PydEquipment
return PydEquipment(
@@ -1179,7 +1190,6 @@ class Equipment(BaseClass):
class EquipmentRole(BaseClass):
"""
Abstract roles for equipment
"""
id = Column(INTEGER, primary_key=True) #: Role id, primary key
@@ -1331,7 +1341,7 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment
def __repr__(self):
return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num}&{self.equipment.name})>"
return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num} & {self.equipment.name})>"
def __init__(self, submission, equipment, role: str = "None"):
self.submission = submission