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Created Sample verification before import.

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This commit is contained in:
lwark
2025-03-27 15:02:18 -05:00
parent f215972b9d
commit e355aee5de
9 changed files with 179 additions and 416 deletions
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45
src/submissions/backend/db/models/submissions.py
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@@ -714,7 +714,6 @@ class BasicSubmission(BaseClass, LogMixin):
# logger.debug(f"Returning regex: {regex}")
return regex
# NOTE: Polymorphic functions
@classproperty
@@ -1130,13 +1129,13 @@ class BasicSubmission(BaseClass, LogMixin):
case date():
pass
case datetime():
end_date = end_date# + timedelta(days=1)
end_date = end_date # + timedelta(days=1)
# pass
case int():
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date()# \
# + timedelta(days=1)
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date() # \
# + timedelta(days=1)
case _:
end_date = parse(end_date).date()# + timedelta(days=1)
end_date = parse(end_date).date() # + timedelta(days=1)
# end_date = end_date.strftime("%Y-%m-%d")
start_date = datetime.combine(start_date, datetime.min.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
end_date = datetime.combine(end_date, datetime.max.time()).strftime("%Y-%m-%d %H:%M:%S.%f")
@@ -1224,10 +1223,11 @@ class BasicSubmission(BaseClass, LogMixin):
else:
from frontend.widgets.pop_ups import QuestionAsker
logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
# code = 1
# msg = "This submission already exists.\nWould you like to overwrite?"
# report.add_result(Result(msg=msg, code=code))
dlg = QuestionAsker(title="Overwrite?", message="This submission already exists.\nWould you like to overwrite?")
# code = 1
# msg = "This submission already exists.\nWould you like to overwrite?"
# report.add_result(Result(msg=msg, code=code))
dlg = QuestionAsker(title="Overwrite?",
message="This submission already exists.\nWould you like to overwrite?")
if dlg.exec():
pass
else:
@@ -1529,10 +1529,23 @@ class BacterialCulture(BasicSubmission):
main_sheet = xl[lookup_table['sheet']]
for row in main_sheet.iter_rows(min_row=lookup_table['start_row'], max_row=lookup_table['end_row']):
idx = row[0].row
sample = dict(submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
sample['concentration'] = main_sheet.cell(row=idx, column=lookup_table['sample_columns']['concentration']).value
sample = dict(
submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
sample['concentration'] = main_sheet.cell(row=idx,
column=lookup_table['sample_columns']['concentration']).value
yield sample
def get_provisional_controls(self):
if self.controls:
provs = (control.sample for control in self.controls)
else:
regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
for prov in provs:
prov.submission = self.rsl_plate_num
prov.submitted_date = self.submitted_date
yield prov
class Wastewater(BasicSubmission):
"""
@@ -1827,7 +1840,7 @@ class WastewaterArtic(BasicSubmission):
artic_date = Column(TIMESTAMP) #: Date Artic Performed
ngs_date = Column(TIMESTAMP) #: Date submission received
gel_date = Column(TIMESTAMP) #: Date submission received
gel_barcode = Column(String(16)) #: Identifier for the used gel.
gel_barcode = Column(String(16)) #: Identifier for the used gel.
__mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
polymorphic_load="inline",
@@ -2767,10 +2780,14 @@ class BacterialCultureSample(BasicSample):
sample = super().to_sub_dict(full_data=full_data)
sample['name'] = self.submitter_id
sample['organism'] = self.organism
sample['concentration'] = self.concentration
try:
sample['concentration'] = f"{float(self.concentration):.2f}"
except TypeError:
sample['concentration'] = 0.0
if self.control is not None:
sample['colour'] = [0, 128, 0]
target = next((v for k,v in self.control.controltype.targets.items() if k == self.control.subtype), "Not Available")
target = next((v for k, v in self.control.controltype.targets.items() if k == self.control.subtype),
"Not Available")
try:
target = ", ".join(target)
except: