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Update to reagent parser to exclude 'not applicable'

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This commit is contained in:
Landon Wark
2024-04-09 10:57:29 -05:00
parent 47bc58cd7d
commit 3889498054
4 changed files with 92 additions and 107 deletions
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25
src/submissions/backend/validators/pydant.py
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@@ -138,19 +138,19 @@ class PydReagent(BaseModel):
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, report
def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
"""
Converts this instance into a form widget
# def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
# """
# Converts this instance into a form widget
Args:
parent (QWidget): Parent widget of the constructed object
extraction_kit (str): Name of extraction kit used
# Args:
# parent (QWidget): Parent widget of the constructed object
# extraction_kit (str): Name of extraction kit used
Returns:
QComboBox: Form object.
"""
from frontend.widgets.submission_widget import ReagentFormWidget
return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
# Returns:
# QComboBox: Form object.
# """
# from frontend.widgets.submission_widget import ReagentFormWidget
# return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
class PydSample(BaseModel, extra='allow'):
@@ -705,16 +705,19 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug("Sorting samples by row/column")
samples = sorted(self.samples, key=attrgetter('column', 'row'))
submission_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
# custom function to adjust values for writing.
samples = submission_obj.adjust_autofill_samples(samples=samples)
logger.debug(f"Samples: {pformat(samples)}")
# Fail safe against multiple instances of the same sample
for iii, sample in enumerate(samples, start=1):
logger.debug(f"Sample: {sample}")
# custom function to find the row of this sample
row = submission_obj.custom_sample_autofill_row(sample, worksheet=worksheet)
logger.debug(f"Writing to {row}")
if row == None:
row = sample_info['lookup_table']['start_row'] + iii
fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
logger.debug(f"Here are the fields we are going to fill:\n\t{fields}")
for field in fields:
column = sample_info['sample_columns'][field]
value = getattr(sample, field)