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Mid clean-up.

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This commit is contained in:
lwark
2025-01-10 13:49:24 -06:00
parent d93da3c90c
commit 5cded949ed
12 changed files with 178 additions and 90 deletions
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116
src/submissions/backend/db/models/kits.py
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@@ -129,8 +129,10 @@ class KitType(BaseClass):
"""
return f"<KitType({self.name})>"
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> Generator[
ReagentRole, None, None]:
def get_reagents(self,
required: bool = False,
submission_type: str | SubmissionType | None = None
) -> Generator[ReagentRole, None, None]:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
@@ -192,13 +194,13 @@ class KitType(BaseClass):
Lookup a list of or single KitType.
Args:
name (str, optional): Name of desired kit (returns single instance). Defaults to None.
used_for (str | Submissiontype | None, optional): Submission type the kit is used for. Defaults to None.
id (int | None, optional): Kit id in the database. Defaults to None.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
name (str, optional): Name of desired kit (returns single instance). Defaults to None.
used_for (str | Submissiontype | None, optional): Submission type the kit is used for. Defaults to None.
id (int | None, optional): Kit id in the database. Defaults to None.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns:
KitType|List[KitType]: KitType(s) of interest.
KitType|List[KitType]: KitType(s) of interest.
"""
query: Query = cls.__database_session__.query(cls)
match used_for:
@@ -240,23 +242,23 @@ class KitType(BaseClass):
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = dict(name=self.name, reagent_roles=[], equipment_roles=[])
for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
for key, value in self.construct_xl_map_for_use(submission_type=submission_type):
try:
assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == key)
except StopIteration as e:
continue
for kk, vv in assoc.to_export_dict().items():
v[kk] = vv
base_dict['reagent_roles'].append(v)
for k, v in submission_type.construct_field_map("equipment"):
value[kk] = vv
base_dict['reagent_roles'].append(value)
for key, value in submission_type.construct_field_map("equipment"):
try:
assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k)
item.equipment_role.name == key)
except StopIteration:
continue
for kk, vv in assoc.to_export_dict(extraction_kit=self).items():
v[kk] = vv
base_dict['equipment_roles'].append(v)
value[kk] = vv
base_dict['equipment_roles'].append(value)
return base_dict
@classmethod
@@ -402,6 +404,7 @@ class ReagentRole(BaseClass):
case _:
pass
assert reagent.role
# NOTE: Get all roles common to the reagent and the kit.
result = set(kit_type.reagent_roles).intersection(reagent.role)
return next((item for item in result), None)
match name:
@@ -500,7 +503,7 @@ class Reagent(BaseClass, LogMixin):
except (TypeError, AttributeError) as e:
place_holder = date.today()
logger.error(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
# NOTE: The notation for not having an expiry is 1970.1.1
# NOTE: The notation for not having an expiry is 1970.01.01
if self.expiry.year == 1970:
place_holder = "NA"
else:
@@ -555,7 +558,7 @@ class Reagent(BaseClass, LogMixin):
instance = PydReagent(**kwargs)
new = True
instance, _ = instance.toSQL()
logger.debug(f"Instance: {instance}")
logger.info(f"Instance from query or create: {instance}")
return instance, new
@classmethod
@@ -609,33 +612,70 @@ class Reagent(BaseClass, LogMixin):
pass
return cls.execute_query(query=query, limit=limit)
def set_attribute(self, key, value):
match key:
case "lot":
value = value.upper()
case "role":
match value:
case ReagentRole():
role = value
case str():
role = ReagentRole.query(name=value, limit=1)
case _:
return
if role and role not in self.role:
self.role.append(role)
return
case "comment":
return
case "expiry":
if isinstance(value, str):
value = date(year=1970, month=1, day=1)
# NOTE: if min time is used, any reagent set to expire today (Bac postive control, eg) will have expired at midnight and therefore be flagged.
# NOTE: Make expiry at date given, plus maximum time = end of day
value = datetime.combine(value, datetime.max.time())
value = value.replace(tzinfo=timezone)
case _:
pass
logger.debug(f"Role to be set to: {value}")
try:
self.__setattr__(key, value)
except AttributeError as e:
logger.error(f"Could not set {key} due to {e}")
@check_authorization
def edit_from_search(self, obj, **kwargs):
from frontend.widgets.misc import AddReagentForm
from frontend.widgets.omni_add_edit import AddEdit
role = ReagentRole.query(kwargs['role'])
if role:
role_name = role.name
else:
role_name = None
dlg = AddReagentForm(reagent_lot=self.lot, reagent_role=role_name, expiry=self.expiry, reagent_name=self.name)
# dlg = AddReagentForm(reagent_lot=self.lot, reagent_role=role_name, expiry=self.expiry, reagent_name=self.name)
dlg = AddEdit(parent=None, instance=self)
if dlg.exec():
vars = dlg.parse_form()
for key, value in vars.items():
match key:
case "expiry":
if isinstance(value, str):
field_value = datetime.strptime(value, "%Y-%m-%d")
elif isinstance(value, date):
field_value = datetime.combine(value, datetime.max.time())
else:
field_value = value
field_value.replace(tzinfo=timezone)
case "role":
continue
case _:
field_value = value
self.__setattr__(key, field_value)
pyd = dlg.parse_form()
for field in pyd.model_fields:
self.set_attribute(field, pyd.__getattribute__(field))
# for key, value in vars.items():
# match key:
# case "expiry":
# if isinstance(value, str):
# field_value = datetime.strptime(value, "%Y-%m-%d")
# elif isinstance(value, date):
# field_value = datetime.combine(value, datetime.max.time())
# else:
# field_value = value
# field_value.replace(tzinfo=timezone)
# case "role":
# continue
# case _:
# field_value = value
# self.__setattr__(key, field_value)
self.save()
# print(self.__dict__)
@classproperty
def add_edit_tooltips(self):
@@ -767,7 +807,7 @@ class SubmissionType(BaseClass):
Grabs the default excel template file.
Returns:
bytes: The excel sheet.
bytes: The Excel sheet.
"""
submission_type = cls.query(name="Bacterial Culture")
return submission_type.template_file
@@ -787,13 +827,13 @@ class SubmissionType(BaseClass):
def set_template_file(self, filepath: Path | str):
"""
Sets the binary store to an excel file.
Sets the binary store to an Excel file.
Args:
filepath (Path | str): Path to the template file.
Raises:
ValueError: Raised if file is not excel file.
ValueError: Raised if file is not Excel file.
"""
if isinstance(filepath, str):
filepath = Path(filepath)