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Improved generic submissions to replace viral culture addition.

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This commit is contained in:
lwark
2024-09-06 11:22:05 -05:00
parent bcb6e15449
commit 7f6a476cd7
11 changed files with 166 additions and 155 deletions
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11
src/submissions/backend/excel/parser.py
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@@ -76,6 +76,7 @@ class SheetParser(object):
# NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
if v not in [None, "None", "", " "]:
self.submission_type = SubmissionType.query(name=v)
logger.debug(f"Updated self.submission_type to {self.submission_type}")
case _:
self.sub[k] = v
@@ -202,7 +203,7 @@ class InfoParser(object):
"""
self.submission_type = dict(value=self.submission_type_obj.name, missing=True)
# logger.debug(f"Looking up submission type: {self.submission_type['value']}")
info_map = self.sub_object.construct_info_map("read")
info_map = self.sub_object.construct_info_map(submission_type=self.submission_type_obj, mode="read")
# NOTE: Get the parse_info method from the submission type specified
return info_map
@@ -385,10 +386,12 @@ class SampleParser(object):
self.xl = xl
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
logger.debug(f"Sample parser is using submission type: {submission_type}")
self.submission_type = submission_type.name
self.submission_type_obj = submission_type
if sub_object is None:
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type_obj.name)
logger.warning(f"Sample parser attempting to fetch submission class with polymorphic identity: {self.submission_type}")
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.sub_object = sub_object
self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
# logger.debug(f"sample_info_map: {self.sample_info_map}")
@@ -406,12 +409,12 @@ class SampleParser(object):
dict: Info locations.
"""
# logger.debug(f"Looking up submission type: {submission_type}")
self.sample_type = self.sub_object.get_default_info("sample_type")
self.sample_type = self.sub_object.get_default_info("sample_type", submission_type=submission_type)
self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)
# logger.debug(f"Got sample class: {self.samp_object.__name__}")
# logger.debug(f"info_map: {pformat(se)}")
if sample_map is None:
sample_info_map = self.sub_object.construct_sample_map()
sample_info_map = self.sub_object.construct_sample_map(submission_type=self.submission_type_obj)
else:
sample_info_map = sample_map
return sample_info_map