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Adaptations to allow for stand alone scripts.

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This commit is contained in:
Landon Wark
2024-03-18 09:47:20 -05:00
parent 2fd8a0b9b6
commit e35081392e
7 changed files with 34 additions and 20 deletions
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11
src/submissions/backend/excel/parser.py
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@@ -274,7 +274,7 @@ class SampleParser(object):
object to pull data for samples in excel sheet and construct individual sample objects
"""
def __init__(self, xl:pd.ExcelFile, submission_type:str) -> None:
def __init__(self, xl:pd.ExcelFile, submission_type:str, sample_map:dict|None=None) -> None:
"""
convert sample sub-dataframe to dictionary of records
@@ -286,7 +286,7 @@ class SampleParser(object):
self.samples = []
self.xl = xl
self.submission_type = submission_type
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type)
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
logger.debug(f"sample_info_map: {sample_info_map}")
self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
logger.debug(f"plate_map: {self.plate_map}")
@@ -298,7 +298,7 @@ class SampleParser(object):
if isinstance(self.lookup_table, pd.DataFrame):
self.parse_lookup_table()
def fetch_sample_info_map(self, submission_type:str) -> dict:
def fetch_sample_info_map(self, submission_type:str, sample_map:dict|None=None) -> dict:
"""
Gets info locations in excel book for submission type.
@@ -311,7 +311,10 @@ class SampleParser(object):
logger.debug(f"Looking up submission type: {submission_type}")
submission_type = SubmissionType.query(name=submission_type)
logger.debug(f"info_map: {pformat(submission_type.info_map)}")
sample_info_map = submission_type.info_map['samples']
if sample_map is None:
sample_info_map = submission_type.info_map['samples']
else:
sample_info_map = sample_map
self.custom_sub_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_samples
self.custom_sample_parser = BasicSample.find_polymorphic_subclass(polymorphic_identity=f"{submission_type.name} Sample").parse_sample
return sample_info_map