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Mid code cleanup

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This commit is contained in:
lwark
2024-09-26 13:54:28 -05:00
parent f4e930c64e
commit 3c98d2a4ad
6 changed files with 49 additions and 62 deletions
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36
src/submissions/backend/db/models/kits.py
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@@ -263,7 +263,6 @@ class KitType(BaseClass):
for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
# logger.debug(f"Value: {v}")
try:
# assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
except StopIteration as e:
continue
@@ -272,10 +271,8 @@ class KitType(BaseClass):
base_dict['reagent roles'].append(v)
for k, v in submission_type.construct_equipment_map():
try:
# assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if
# item.equipment_role.name == k][0]
assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k)
item.equipment_role.name == k)
except StopIteration:
continue
for kk, vv in assoc.to_export_dict(kit_type=self).items():
@@ -292,7 +289,7 @@ class ReagentRole(BaseClass):
"""
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
name = Column(String(64)) #: name of role reagent plays
instances = relationship("Reagent", back_populates="role",
secondary=reagentroles_reagents) #: concrete instances of this reagent type
eol_ext = Column(Interval()) #: extension of life interval
@@ -747,15 +744,12 @@ class SubmissionType(BaseClass):
Returns:
dict: Map equipment locations in excel sheet
"""
# output = {}
# logger.debug("Iterating through equipment roles")
for item in self.submissiontype_equipmentrole_associations:
emap = item.uses
if emap is None:
emap = {}
# output[item.equipment_role.name] = emap
yield item.equipment_role.name, emap
# return output
def construct_tips_map(self) -> Generator[str, dict]:
"""
@@ -764,14 +758,11 @@ class SubmissionType(BaseClass):
Returns:
dict: Tip locations in the excel sheet.
"""
# output = {}
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
if tmap is None:
tmap = {}
# output[item.tip_role.name] = tmap
yield item.tip_role.name, tmap
# return output
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
"""
@@ -1035,7 +1026,7 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude}
base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
logger.debug(f"STKTA returning: {base_dict}")
# logger.debug(f"STKTA returning: {base_dict}")
return base_dict
@@ -1073,7 +1064,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
return f"<KitTypeReagentRoleAssociation({self.kit_type} & {self.reagent_role})>"
@validates('required')
def validate_age(self, key, value):
def validate_required(self, key, value):
"""
Ensures only 1 & 0 used in 'required'
@@ -1243,7 +1234,6 @@ class SubmissionReagentAssociation(BaseClass):
match submission:
case BasicSubmission() | str():
if isinstance(submission, str):
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_num=submission)
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
query = query.filter(cls.submission == submission)
@@ -1424,7 +1414,7 @@ class Equipment(BaseClass):
re.VERBOSE)
@classmethod
def assign_equipment(cls, equipment_role: EquipmentRole|str) -> List[Equipment]:
def assign_equipment(cls, equipment_role: EquipmentRole | str) -> List[Equipment]:
"""
Creates a list of equipment from user input to be used in Submission Type creation
@@ -1581,10 +1571,11 @@ class EquipmentRole(BaseClass):
Returns:
dict: dictionary of Association and related reagent role
"""
base_dict = {}
base_dict['role'] = self.name
base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
return base_dict
return dict(role=self.name,
processes=self.get_processes(submission_type=submission_type, extraction_kit=kit_type))
# base_dict['role'] = self.name
# base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
# return base_dict
class SubmissionEquipmentAssociation(BaseClass):
@@ -1621,6 +1612,7 @@ class SubmissionEquipmentAssociation(BaseClass):
Returns:
dict: This SubmissionEquipmentAssociation as a dictionary
"""
# TODO: Currently this will only fetch a single process, even if multiple are selectable.
try:
process = self.process.name
except AttributeError:
@@ -1707,9 +1699,9 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
super().save()
def to_export_dict(self, kit_type: KitType):
base_dict = dict(static=self.static)
for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type, kit_type=kit_type).items():
base_dict[k] = v
base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
kit_type=kit_type).items()}
base_dict['static'] = self.static
return base_dict