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Pre-major refactor

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This commit is contained in:
Landon Wark
2023-11-03 10:49:37 -05:00
parent 22a23b7838
commit 5570d87b7c
19 changed files with 1078 additions and 1045 deletions
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15
src/submissions/backend/excel/parser.py
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@@ -110,7 +110,8 @@ class SheetParser(object):
"""
Enforce that only allowed reagents get into the Pydantic Model
"""
kit = lookup_kit_types(ctx=self.ctx, name=self.sub['extraction_kit']['value'])
# kit = lookup_kit_types(ctx=self.ctx, name=self.sub['extraction_kit']['value'])
kit = models.KitType.query(name=self.sub['extraction_kit']['value'])
allowed_reagents = [item.name for item in kit.get_reagents()]
logger.debug(f"List of reagents for comparison with allowed_reagents: {pprint.pformat(self.sub['reagents'])}")
# self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent['value'].type in allowed_reagents]
@@ -151,7 +152,8 @@ class InfoParser(object):
if isinstance(submission_type, str):
submission_type = dict(value=submission_type, missing=True)
logger.debug(f"Looking up submission type: {submission_type['value']}")
submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type['value'])
# submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type['value'])
submission_type = models.SubmissionType.query(name=submission_type['value'])
info_map = submission_type.info_map
# Get the parse_info method from the submission type specified
self.custom_parser = models.BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_info
@@ -212,7 +214,8 @@ class ReagentParser(object):
def fetch_kit_info_map(self, extraction_kit:dict, submission_type:str):
if isinstance(extraction_kit, dict):
extraction_kit = extraction_kit['value']
kit = lookup_kit_types(ctx=self.ctx, name=extraction_kit)
# kit = lookup_kit_types(ctx=self.ctx, name=extraction_kit)
kit = models.KitType.query(name=extraction_kit)
if isinstance(submission_type, dict):
submission_type = submission_type['value']
reagent_map = kit.construct_xl_map_for_use(submission_type.title())
@@ -289,7 +292,8 @@ class SampleParser(object):
dict: Info locations.
"""
logger.debug(f"Looking up submission type: {submission_type}")
submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type)
# submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type)
submission_type = models.SubmissionType.query(name=submission_type)
logger.debug(f"info_map: {pprint.pformat(submission_type.info_map)}")
sample_info_map = submission_type.info_map['samples']
# self.custom_parser = get_polymorphic_subclass(models.BasicSubmission, submission_type.name).parse_samples
@@ -458,7 +462,8 @@ class SampleParser(object):
logger.error(f"Could not find the model {query}. Using generic.")
database_obj = models.BasicSample
logger.debug(f"Searching database for {input_dict['submitter_id']}...")
instance = lookup_samples(ctx=self.ctx, submitter_id=str(input_dict['submitter_id']))
# instance = lookup_samples(ctx=self.ctx, submitter_id=str(input_dict['submitter_id']))
instance = models.BasicSample.query(submitter_id=str(input_dict['submitter_id']))
if instance == None:
logger.debug(f"Couldn't find sample {input_dict['submitter_id']}. Creating new sample.")
instance = database_obj()