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Pre- pydsubmission toForm method.

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Landon Wark
2023-10-25 14:58:41 -05:00
parent 4b1f88f1d0
commit f3a7d75c6a
11 changed files with 298 additions and 115 deletions
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14
src/submissions/backend/excel/parser.py
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@@ -112,7 +112,8 @@ class SheetParser(object):
kit = lookup_kit_types(ctx=self.ctx, 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]
# self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent['value'].type in allowed_reagents]
self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent.type in allowed_reagents]
def to_pydantic(self) -> PydSubmission:
"""
@@ -231,8 +232,9 @@ class ReagentParser(object):
lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
except (KeyError, IndexError):
listo.append(dict(value=PydReagent(ctx=self.ctx, type=item.strip(), lot=None, exp=None, name=None), parsed=False))
listo.append(PydReagent(ctx=self.ctx, type=item.strip(), lot=None, exp=None, name=None, parsed=False))
continue
# If the cell is blank tell the PydReagent
if check_not_nan(lot):
parsed = True
else:
@@ -240,7 +242,7 @@ class ReagentParser(object):
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot)
logger.debug(f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}")
listo.append(dict(value=PydReagent(ctx=self.ctx, type=item.strip(), lot=lot, exp=expiry, name=name), parsed=parsed))
listo.append(PydReagent(ctx=self.ctx, type=item.strip(), lot=lot, expiry=expiry, name=name, parsed=parsed))
logger.debug(f"Returning listo: {listo}")
return listo
@@ -387,7 +389,11 @@ class SampleParser(object):
# Set row in lookup table to blank values to prevent multipe lookups.
try:
self.lookup_table.loc[self.lookup_table['Sample #']==addition['Sample #']] = np.nan
except ValueError:
except (ValueError, KeyError):
pass
try:
self.lookup_table.loc[self.lookup_table['Well']==addition['Well']] = np.nan
except (ValueError, KeyError):
pass
logger.debug(f"Output sample dict: {sample}")
logger.debug(f"Final lookup_table: \n\n {self.lookup_table}")