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During code cleanup

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This commit is contained in:
lwark
2024-05-23 15:06:22 -05:00
parent d1bf12e8d1
commit 2814be8980
10 changed files with 297 additions and 356 deletions
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18
src/submissions/backend/db/models/kits.py
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@@ -13,6 +13,8 @@ from typing import List, Literal
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
from io import BytesIO
logger = logging.getLogger(f'submissions.{__name__}')
@@ -300,7 +302,7 @@ class ReagentType(BaseClass):
# logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
# logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
result = list(set(kit_type.reagent_types).intersection(reagent.type))
logger.debug(f"Result: {result}")
# logger.debug(f"Result: {result}")
try:
return result[0]
except IndexError:
@@ -386,7 +388,7 @@ class Reagent(BaseClass):
place_holder = self.expiry + reagent_role.eol_ext
except (TypeError, AttributeError) as e:
place_holder = date.today()
logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
logger.error(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
if self.expiry.year == 1970:
place_holder = "NA"
else:
@@ -410,14 +412,14 @@ class Reagent(BaseClass):
Report: Result of operation
"""
report = Report()
logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})")
# logger.debug(f"Attempting update of last used reagent type at intersection of ({self}), ({kit})")
rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
if rt is not None:
logger.debug(f"got reagenttype {rt}")
# logger.debug(f"got reagenttype {rt}")
assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
if assoc is not None:
if assoc.last_used != self.lot:
logger.debug(f"Updating {assoc} last used to {self.lot}")
# logger.debug(f"Updating {assoc} last used to {self.lot}")
assoc.last_used = self.lot
result = assoc.save()
report.add_result(result)
@@ -607,7 +609,7 @@ class SubmissionType(BaseClass):
Returns:
List[str]: List of sheet names
"""
return ExcelFile(self.template_file).sheet_names
return ExcelFile(BytesIO(self.template_file)).sheet_names
def set_template_file(self, filepath: Path | str):
"""
@@ -633,7 +635,7 @@ class SubmissionType(BaseClass):
def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
info = self.info_map
logger.debug(f"Info map: {info}")
# logger.debug(f"Info map: {info}")
output = {}
# for k,v in info.items():
# info[k]['write'] += info[k]['read']
@@ -956,7 +958,7 @@ class SubmissionReagentAssociation(BaseClass):
Returns:
str: Representation of this SubmissionReagentAssociation
"""
return f"<{self.submission.rsl_plate_num}&{self.reagent.lot}>"
return f"<{self.submission.rsl_plate_num} & {self.reagent.lot}>"
def __init__(self, reagent=None, submission=None):
if isinstance(reagent, list):