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Pre code clean-up

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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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20
src/submissions/backend/db/models/submissions.py
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@@ -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()