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Bug fixes for omni gui objects.

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This commit is contained in:
lwark
2025-04-16 13:47:07 -05:00
parent 58f5d361b3
commit 1a1f766890
6 changed files with 263 additions and 70 deletions
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22
src/submissions/backend/db/models/submissions.py
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@@ -1540,12 +1540,15 @@ class BacterialCulture(BasicSubmission):
return report
parser = ConcentrationParser(filepath=fname, submission=self)
conc_samples = [sample for sample in parser.samples]
# logger.debug(f"Concentration samples: {pformat(conc_samples)}")
for sample in self.samples:
logger.debug(f"Sample {sample.submitter_id}")
# logger.debug(f"Sample {sample.submitter_id}")
# logger.debug(f"Match {item['submitter_id']}")
try:
# NOTE: Fix for ENs which have no rsl_number...
sample_dict = next(item for item in conc_samples if item['submitter_id'] == sample.submitter_id)
sample_dict = next(item for item in conc_samples if str(item['submitter_id']).upper() == sample.submitter_id)
except StopIteration:
logger.error(f"Couldn't find sample dict for {sample.submitter_id}")
continue
logger.debug(f"Sample {sample.submitter_id} conc. = {sample_dict['concentration']}")
if sample_dict['concentration']:
@@ -1734,12 +1737,10 @@ class Wastewater(BasicSubmission):
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment
# logger.debug(f"Sample assessemnt: {sample['assessment']}")
# sample[f"{sample['target'].lower()}_status"] = sample['assessment']
# NOTE: Get sample having other target
other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']]
for s in other_targets:
sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
# sample[f"{s['target'].lower()}_status"] = s['assessment']
try:
del sample['ct']
except KeyError:
@@ -2177,7 +2178,6 @@ class WastewaterArtic(BasicSubmission):
except AttributeError:
plate_num = "1"
plate_num = plate_num.strip("-")
# repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0]
try:
repeat_num = re.search(r"R(?P<repeat>\d)?$", processed).groups()[0]
except:
@@ -2663,16 +2663,6 @@ class BasicSample(BaseClass, LogMixin):
def delete(self):
raise AttributeError(f"Delete not implemented for {self.__class__}")
# @classmethod
# def get_searchables(cls) -> List[dict]:
# """
# Delivers a list of fields that can be used in fuzzy search.
#
# Returns:
# List[str]: List of fields.
# """
# return [dict(label="Submitter ID", field="submitter_id")]
@classmethod
def samples_to_df(cls, sample_list: List[BasicSample], **kwargs) -> pd.DataFrame:
"""
@@ -2729,8 +2719,6 @@ class WastewaterSample(BasicSample):
Derivative wastewater sample
"""
# searchables = BasicSample.searchables + ['ww_processing_num', 'ww_full_sample_id', 'rsl_number']
id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
ww_processing_num = Column(String(64)) #: wastewater processing number
ww_full_sample_id = Column(String(64)) #: full id given by entrics