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Added custom validation to PydSubmission to replace 'finalize_parse'

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This commit is contained in:
lwark
2024-09-27 11:12:20 -05:00
parent 9b08fc5186
commit c0f78390b5
3 changed files with 45 additions and 30 deletions
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18
src/submissions/backend/excel/parser.py
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@@ -53,7 +53,7 @@ class SheetParser(object):
self.parse_samples()
self.parse_equipment()
self.parse_tips()
self.finalize_parse()
# self.finalize_parse()
# logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
def parse_info(self):
@@ -98,7 +98,7 @@ class SheetParser(object):
# logger.debug(f"Parsing reagents for {extraction_kit}")
parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
extraction_kit=extraction_kit)
self.sub['reagents'] = [reagent for reagent in parser.parse_reagents()]
self.sub['reagents'] = parser.parse_reagents()
def parse_samples(self):
"""
@@ -112,14 +112,14 @@ class SheetParser(object):
Calls equipment parser to pull info from the excel sheet
"""
parser = EquipmentParser(xl=self.xl, submission_type=self.submission_type)
self.sub['equipment'] = [equipment for equipment in parser.parse_equipment()]
self.sub['equipment'] = parser.parse_equipment()
def parse_tips(self):
"""
Calls tips parser to pull info from the excel sheet
"""
parser = TipParser(xl=self.xl, submission_type=self.submission_type)
self.sub['tips'] = [tip for tip in parser.parse_tips()]
self.sub['tips'] = parser.parse_tips()
def import_kit_validation_check(self):
"""
@@ -137,12 +137,6 @@ class SheetParser(object):
if isinstance(self.sub['extraction_kit'], str):
self.sub['extraction_kit'] = dict(value=self.sub['extraction_kit'], missing=True)
def finalize_parse(self):
"""
Run custom final validations of data for submission subclasses.
"""
self.sub = self.sub_object.finalize_parse(input_dict=self.sub, xl=self.xl, info_map=self.info_map)
def to_pydantic(self) -> PydSubmission:
"""
Generates a pydantic model of scraped data for validation
@@ -172,7 +166,7 @@ class SheetParser(object):
pyd_dict['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
else:
pyd_dict['tips'] = None
psm = PydSubmission(filepath=self.filepath, **pyd_dict)
psm = PydSubmission(filepath=self.filepath, run_custom=True, **pyd_dict)
return psm
@@ -524,6 +518,8 @@ class SampleParser(object):
merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
print(pformat(plate_map_samples))
print(pformat(lookup_samples))
for ii, psample in enumerate(plate_map_samples):
try:
check = psample['id'] == lookup_samples[ii][merge_on_id]