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Preparing for production testing using Bacterial Culture

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lwark
2025-08-06 13:26:37 -05:00
parent 6f134d3870
commit 087bf9bcb7
24 changed files with 757 additions and 650 deletions
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26
src/submissions/backend/validators/__init__.py
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@@ -43,22 +43,28 @@ class ClientSubmissionNamer(DefaultNamer):
logger.warning(f"Getting submissiontype from file properties failed, falling back on preparse.\nDepending on excel structure this might yield an incorrect submissiontype")
sub_type = self.get_subtype_from_preparse()
if not sub_type:
logger.warning(f"Getting submissiontype from preparse failed, falling back on filename regex.\nDepending on excel structure this might yield an incorrect submissiontype")
logger.warning(f"Getting submissiontype from preparse failed, falling back on filename regex.\nDepending on file name this might yield an incorrect submissiontype")
sub_type = self.get_subtype_from_regex()
if not sub_type:
logger.warning(f"Getting submissiontype from regex failed, using default submissiontype.")
sub_type = SubmissionType.query(name="Test")
logger.debug(f"Submission Type: {sub_type}")
sys.exit()
return sub_type
def get_subtype_from_regex(self):
def get_subtype_from_regex(self) -> SubmissionType:
regex = SubmissionType.regex
m = regex.search(self.filepath.__str__())
try:
sub_type = m.lastgroup
sub_type = SubmissionType.query(name=sub_type)
except AttributeError as e:
sub_type = None
logger.critical(f"No procedure type found or procedure type found!: {e}")
return sub_type
def get_subtype_from_preparse(self):
def get_subtype_from_preparse(self) -> SubmissionType:
from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser
parser = ClientSubmissionInfoParser(self.filepath)
sub_type = next((value for k, value in parser.parsed_info.items() if k == "submissiontype"), None)
@@ -67,7 +73,7 @@ class ClientSubmissionNamer(DefaultNamer):
sub_type = None
return sub_type
def get_subtype_from_properties(self):
def get_subtype_from_properties(self) -> SubmissionType:
wb = load_workbook(self.filepath)
# NOTE: Gets first category in the metadata.
categories = wb.properties.category.split(";")
@@ -238,11 +244,13 @@ class RSLNamer(object):
today = datetime.now()
if isinstance(today, str):
today = datetime.strptime(today, "%Y-%m-%d")
if "name" in data.keys():
plate_number = data['name'].split("-")[-1][0]
else:
previous = Run.query(start_date=today, end_date=today, submissiontype=data['submissiontype'])
plate_number = len(previous) + 1
# if "name" in data.keys():
# logger.debug(f"Found name: {data['name']}")
# plate_number = data['name'].split("-")[-1][0]
# else:
previous = Run.query(start_date=today, end_date=today, submissiontype=data['submissiontype'])
plate_number = len(previous) + 1
logger.debug(f"Using plate number: {plate_number}")
return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
@classmethod