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Renaming ReagentType to ReagentRole

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This commit is contained in:
lwark
2024-06-03 13:32:04 -05:00
parent 1a716984a7
commit cdcce80898
10 changed files with 182 additions and 140 deletions
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5
src/submissions/backend/excel/parser.py
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@@ -139,6 +139,7 @@ class SheetParser(object):
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
pyd_dict = copy(self.sub)
pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
# logger.debug(f"Equipment: {self.sub['equipment']}")
try:
@@ -307,7 +308,7 @@ class ReagentParser(object):
comment = ""
except (KeyError, IndexError):
listo.append(
PydReagent(type=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True))
PydReagent(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True))
continue
# NOTE: If the cell is blank tell the PydReagent
if check_not_nan(lot):
@@ -324,7 +325,7 @@ class ReagentParser(object):
logger.warning(f"name is not a string.")
check = True
if check:
listo.append(dict(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
listo.append(dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
missing=missing))
return listo