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Pre code clean-up

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This commit is contained in:
lwark
2024-10-17 13:09:35 -05:00
parent c3a4aac68b
commit 495d1a5a7f
15 changed files with 322 additions and 263 deletions
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2
src/submissions/backend/db/models/__init__.py
View File

@@ -135,7 +135,7 @@ class BaseClass(Base):
singles = model.get_default_info('singles')
logger.info(f"Querying: {model}, with kwargs: {kwargs}")
for k, v in kwargs.items():
logger.debug(f"Using key: {k} with value: {v}")
logger.info(f"Using key: {k} with value: {v}")
try:
attr = getattr(model, k)
query = query.filter(attr == v)

17
src/submissions/backend/db/models/controls.py
View File

@@ -12,7 +12,7 @@ import logging, re
from operator import itemgetter
from . import BaseClass
from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column
from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column, super_splitter
from datetime import date, datetime, timedelta
from typing import List, Literal, Tuple, Generator
from dateutil.parser import parse
@@ -81,31 +81,33 @@ class ControlType(BaseClass):
return []
# NOTE: remove items that don't have relevant data
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
logger.debug(f"subtypes out: {pformat(subtypes)}")
# logger.debug(f"subtypes out: {pformat(subtypes)}")
return subtypes
def get_instance_class(self):
return Control.find_polymorphic_subclass(polymorphic_identity=self.name)
@classmethod
def get_positive_control_types(cls) -> Generator[ControlType, None, None]:
def get_positive_control_types(cls, control_type: str) -> Generator[str, None, None]:
"""
Gets list of Control types if they have targets
Returns:
List[ControlType]: Control types that have targets
"""
return (item for item in cls.query() if item.targets)
ct = cls.query(name=control_type).targets
return (item for item in ct.keys() if ct[item])
@classmethod
def build_positive_regex(cls) -> Pattern:
def build_positive_regex(cls, control_type:str) -> Pattern:
"""
Creates a re.Pattern that will look for positive control types
Returns:
Pattern: Constructed pattern
"""
strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
# strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
strings = list(set([super_splitter(item, "-", 0) for item in cls.get_positive_control_types(control_type)]))
return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
@@ -298,7 +300,8 @@ class PCRControl(Control):
parent.mode_typer.clear()
parent.mode_typer.setEnabled(False)
report = Report()
controls = cls.query(sub_type=chart_settings['sub_type'], start_date=chart_settings['start_date'], end_date=chart_settings['end_date'])
controls = cls.query(sub_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
end_date=chart_settings['end_date'])
data = [control.to_sub_dict() for control in controls]
df = DataFrame.from_records(data)
try:

4
src/submissions/backend/db/models/kits.py
View File

@@ -198,7 +198,7 @@ class KitType(BaseClass):
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
for assoc in assocs:
try:
logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
# logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
yield assoc.reagent_role.name, assoc.uses
except TypeError:
continue
@@ -1156,7 +1156,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
base_dict[k] = v
return base_dict
def get_all_relevant_reagents(self) -> Generator[Reagent, None, None]:
def get_all_relevant_reagents(self, override:Reagent|None=None) -> Generator[Reagent, None, None]:
"""
Creates a generator that will resolve in to a list filling the role associated with this object.

1
src/submissions/backend/db/models/organizations.py
View File

@@ -102,7 +102,6 @@ class Organization(BaseClass):
else:
raise Exception(f"Filetype {filepath.suffix} not supported.")
data = import_dict['orgs']
logger.debug(pformat(import_dict))
for org in data:
organ = Organization.query(name=org['name'])
if organ is None:

20
src/submissions/backend/db/models/submissions.py
View File

@@ -235,7 +235,7 @@ class BasicSubmission(BaseClass):
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
"""
logger.debug(f"Running search for {sub_type}")
# logger.debug(f"Running search for {sub_type}")
if isinstance(sub_type, dict):
try:
sub_type = sub_type['value']
@@ -521,7 +521,7 @@ class BasicSubmission(BaseClass):
Returns:
pd.DataFrame: Pandas Dataframe of all relevant submissions
"""
logger.debug(f"Querying Type: {submission_type}")
# logger.debug(f"Querying Type: {submission_type}")
# logger.debug(f"Using limit: {limit}")
# NOTE: use lookup function to create list of dicts
subs = [item.to_dict() for item in
@@ -827,7 +827,7 @@ class BasicSubmission(BaseClass):
return input_dict
@classmethod
def custom_validation(cls, pyd: "PydSubmission") -> dict:
def custom_validation(cls, pyd: "PydSubmission") -> "PydSubmission":
"""
Performs any final custom parsing of the excel file.
@@ -1412,14 +1412,16 @@ class BacterialCulture(BasicSubmission):
dict: Updated dictionary.
"""
from . import ControlType
# logger.debug(f"\n\nHello from BacterialCulture custom_validation")
pyd = super().custom_validation(pyd)
# NOTE: build regex for all control types that have targets
regex = ControlType.build_positive_regex()
regex = ControlType.build_positive_regex(control_type="Irida Control")
logger.debug(regex)
# NOTE: search samples for match
for sample in pyd.samples:
matched = regex.match(sample.submitter_id)
if bool(matched):
# logger.debug(f"Control match found: {sample['submitter_id']}")
# logger.debug(f"Control match found: {sample.submitter_id}")
new_lot = matched.group()
try:
pos_control_reg = \
@@ -1429,6 +1431,7 @@ class BacterialCulture(BasicSubmission):
return pyd
pos_control_reg.lot = new_lot
pos_control_reg.missing = False
# logger.debug(f"Got positive control: {pos_control_reg}")
return pyd
@classmethod
@@ -1785,6 +1788,7 @@ class WastewaterArtic(BasicSubmission):
ii in
range(source_plates_section['start_row'], source_plates_section['end_row'] + 1)]
for datum in data:
logger.debug(f"Datum: {datum}")
if datum['plate'] in ["None", None, ""]:
continue
else:
@@ -1869,7 +1873,13 @@ class WastewaterArtic(BasicSubmission):
dict: Updated sample dictionary
"""
input_dict = super().parse_samples(input_dict)
logger.debug(f"WWA input dict: {pformat(input_dict)}")
input_dict['sample_type'] = "Wastewater Sample"
# NOTE: Stop gap solution because WW is sloppy with their naming schemes
try:
input_dict['source_plate'] = input_dict['source_plate'].replace("WW20", "WW-20")
except KeyError:
pass
# NOTE: Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# at the end, this has to be done here. No moving to sqlalchemy object :(
input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()