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Bug fixing for new AddEdit forms.

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This commit is contained in:
lwark
2025-01-08 13:54:14 -06:00
parent 8662bbdc2f
commit 95ae203cc2
11 changed files with 217 additions and 85 deletions
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5
src/submissions/backend/db/models/__init__.py
View File

@@ -243,7 +243,10 @@ class BaseClass(Base):
@classmethod
def get_pydantic_model(cls):
from backend.validators import pydant
model = getattr(pydant, f"Pyd{cls.__name__}")
try:
model = getattr(pydant, f"Pyd{cls.__name__}")
except AttributeError:
return None
return model

6
src/submissions/backend/db/models/controls.py
View File

@@ -286,6 +286,10 @@ class Control(BaseClass):
"""
return None
def delete(self):
self.__database_session__.delete(self)
self.__database_session__.commit()
class PCRControl(Control):
"""
@@ -296,7 +300,7 @@ class PCRControl(Control):
subtype = Column(String(16)) #: PC or NC
target = Column(String(16)) #: N1, N2, etc.
ct = Column(FLOAT) #: PCR result
reagent_lot = Column(String(64), ForeignKey("_reagent.name", ondelete="SET NULL",
reagent_lot = Column(String(64), ForeignKey("_reagent.lot", ondelete="SET NULL",
name="fk_reagent_lot"))
reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control

18
src/submissions/backend/db/models/kits.py
View File

@@ -540,6 +540,24 @@ class Reagent(BaseClass, LogMixin):
report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
return report
@classmethod
def query_or_create(cls, **kwargs) -> Reagent:
from backend.validators.pydant import PydReagent
new = False
instance = cls.query(**kwargs)
if not instance or isinstance(instance, list):
if "role" not in kwargs:
try:
kwargs['role'] = kwargs['name']
except KeyError:
pass
instance = PydReagent(**kwargs)
new = True
instance, _ = instance.toSQL()
logger.debug(f"Instance: {instance}")
return instance, new
@classmethod
@setup_lookup
def query(cls,

19
src/submissions/backend/db/models/submissions.py
View File

@@ -936,14 +936,20 @@ class BasicSubmission(BaseClass, LogMixin):
Generator[dict, None, None]: Dictionaries of row values.
"""
location_map = cls.get_submission_type().sample_map['pcr_controls']
# logger.debug(f"Location map: {location_map}")
submission = cls.query(rsl_plate_num=rsl_plate_num)
name_column = 1
for item in location_map:
logger.debug(f"Checking {item}")
worksheet = xl[item['sheet']]
for iii, row in enumerate(worksheet.iter_rows(max_row=len(worksheet['A']), max_col=name_column), start=1):
logger.debug(f"Checking row {row}, {iii}")
for cell in row:
logger.debug(f"Checking cell: {cell}, with value {cell.value} against {item['name']}")
if cell.value == item['name']:
subtype, target = item['name'].split("-")
subtype, _ = item['name'].split("-")
target = item['target']
logger.debug(f"Subtype: {subtype}, target: {target}")
ct = worksheet.cell(row=iii, column=item['ct_column']).value
# NOTE: Kind of a stop gap solution to find control reagents.
if subtype == "PC":
@@ -955,6 +961,9 @@ class BasicSubmission(BaseClass, LogMixin):
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["molecular grade water" in item.name.lower() for item in
assoc.reagent.role])), None)
else:
ctrl = None
logger.debug(f"Control reagent: {ctrl.__dict__}")
try:
ct = float(ct)
except ValueError:
@@ -963,13 +972,15 @@ class BasicSubmission(BaseClass, LogMixin):
ctrl = ctrl.lot
else:
ctrl = None
yield dict(
name=f"{rsl_plate_num}<{item['name']}>",
output = dict(
name=f"{rsl_plate_num}<{item['name']}-{target}>",
ct=ct,
subtype=subtype,
target=target,
reagent_lot=ctrl
)
logger.debug(f"Control output: {pformat(output)}")
yield output
@classmethod
def filename_template(cls) -> str:
@@ -1663,10 +1674,12 @@ class Wastewater(BasicSubmission):
submitted_date = datetime.strptime(" ".join(parser.pcr['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
for control in pcr_controls:
logger.debug(f"Control coming into save: {control}")
new_control = PCRControl(**control)
new_control.submitted_date = submitted_date
new_control.controltype = controltype
new_control.submission = self
logger.debug(f"Control coming into save: {new_control.__dict__}")
new_control.save()
return report

8
src/submissions/backend/excel/parser.py
View File

@@ -257,9 +257,10 @@ class ReagentParser(object):
extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit)
self.map = self.fetch_kit_info_map(submission_type=submission_type)
logger.debug(f"Setting map: {self.map}")
self.xl = xl
@report_result
# @report_result
def fetch_kit_info_map(self, submission_type: str | SubmissionType) -> Tuple[Report, dict]:
"""
Gets location of kit reagents from database
@@ -298,7 +299,8 @@ class ReagentParser(object):
msg=f"No kit map found for {self.kit_object.name}.\n\n"
f"Are you sure you put the right kit in:\n\n{location_string}?",
status="Critical"))
return report, reagent_map
logger.debug(f"Here is the map coming out: {reagent_map}")
return reagent_map
def parse_reagents(self) -> Generator[dict, None, None]:
"""
@@ -310,7 +312,7 @@ class ReagentParser(object):
for sheet in self.xl.sheetnames:
ws = self.xl[sheet]
relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
if relevant == {}:
if not relevant:
continue
for item in relevant:
try:

40
src/submissions/backend/validators/pydant.py
View File

@@ -22,8 +22,8 @@ logger = logging.getLogger(f"submissions.{__name__}")
class PydReagent(BaseModel):
lot: str | None
role: str | None
expiry: date | Literal['NA'] | None
name: str | None
expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
name: str | None = Field(default=None, validate_default=True)
missing: bool = Field(default=True)
comment: str | None = Field(default="", validate_default=True)
@@ -79,6 +79,8 @@ class PydReagent(BaseModel):
case str():
return parse(value)
case date():
return datetime.combine(value, datetime.max.time())
case datetime():
return value
case _:
return convert_nans_to_nones(str(value))
@@ -939,6 +941,7 @@ class PydSubmission(BaseModel, extra='allow'):
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
# NOTE: Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.role for item in ext_kit_rtypes]
logger.debug(self.reagents)
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
missing_check = [item.role for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check and rt.role not in exempt]
@@ -956,7 +959,7 @@ class PydSubmission(BaseModel, extra='allow'):
report.add_result(result)
return output_reagents, report, missing_reagents
def check_reagent_expiries(self, exempt: List[PydReagent]=[]):
def check_reagent_expiries(self, exempt: List[PydReagent] = []):
report = Report()
expired = []
for reagent in self.reagents:
@@ -971,14 +974,11 @@ class PydSubmission(BaseModel, extra='allow'):
if expired:
output = '\n'.join(expired)
result = Result(status="Warning",
msg = f"The following reagents are expired:\n\n{output}"
msg=f"The following reagents are expired:\n\n{output}"
)
report.add_result(result)
return report
def export_csv(self, filename: Path | str):
try:
worksheet = self.csv
@@ -1009,14 +1009,34 @@ class PydContact(BaseModel):
logger.debug(f"Output phone: {value}")
return value
def toSQL(self) -> Contact:
def toSQL(self) -> Tuple[Contact, Report]:
"""
Converts this instance into a backend.db.models.organization.Contact instance
Converts this instance into a backend.db.models.organization. Contact instance.
Does not query for existing contacts.
Returns:
Contact: Contact instance
"""
return Contact(name=self.name, phone=self.phone, email=self.email)
report = Report()
instance = Contact.query(name=self.name, phone=self.phone, email=self.email)
if not instance or isinstance(instance, list):
instance = Contact()
try:
all_fields = self.model_fields + self.model_extra
except TypeError:
all_fields = self.model_fields
for field in all_fields:
value = getattr(self, field)
match field:
case "organization":
value = [Organization.query(name=value)]
case _:
pass
try:
instance.__setattr__(field, value)
except AttributeError as e:
logger.error(f"Could not set {instance} {field} to {value} due to {e}")
return instance, report
class PydOrganization(BaseModel):