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Attempting fix of failure to update reagent on edit.

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This commit is contained in:
lwark
2024-12-02 14:52:39 -06:00
parent b45a125c51
commit 2c281166d4
10 changed files with 74 additions and 38 deletions
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4
src/submissions/backend/db/__init__.py
View File

@@ -70,5 +70,5 @@ def update_log(mapper, connection, target):
logger.info(f"No changes detected, not updating logs.")
event.listen(LogMixin, 'after_update', update_log, propagate=True)
event.listen(LogMixin, 'after_insert', update_log, propagate=True)
# event.listen(LogMixin, 'after_update', update_log, propagate=True)
# event.listen(LogMixin, 'after_insert', update_log, propagate=True)

2
src/submissions/backend/db/models/__init__.py
View File

@@ -182,7 +182,7 @@ class BaseClass(Base):
query: Query = cls.__database_session__.query(model)
# logger.debug(f"Grabbing singles using {model.get_default_info}")
singles = model.get_default_info('singles')
logger.info(f"Querying: {model}, with kwargs: {kwargs}")
# logger.info(f"Querying: {model}, with kwargs: {kwargs}")
for k, v in kwargs.items():
logger.info(f"Using key: {k} with value: {v}")
try:

6
src/submissions/backend/db/models/controls.py
View File

@@ -273,7 +273,7 @@ class Control(BaseClass):
except StopIteration as e:
raise AttributeError(
f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
logger.info(f"Recruiting model: {model}")
# logger.info(f"Recruiting model: {model}")
return model
@classmethod
@@ -535,8 +535,8 @@ class IridaControl(Control):
except AttributeError:
consolidate = False
report = Report()
# logger.debug(f"settings: {pformat(chart_settings)}")
controls = cls.query(sub_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
logger.debug(f"settings: {pformat(chart_settings)}")
controls = cls.query(subtype=chart_settings['sub_type'], start_date=chart_settings['start_date'],
end_date=chart_settings['end_date'])
# logger.debug(f"Controls found: {controls}")
if not controls:

8
src/submissions/backend/db/models/kits.py
View File

@@ -12,7 +12,7 @@ from tools import check_authorization, setup_lookup, Report, Result, check_regex
from typing import List, Literal, Generator, Any
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
from . import Base, BaseClass, Organization, LogMixin
from io import BytesIO
logger = logging.getLogger(f'submissions.{__name__}')
@@ -797,7 +797,7 @@ class SubmissionType(BaseClass):
fmap = item.uses
if fmap is None:
fmap = {}
yield getattr(item, f"{field}_role"), fmap
yield getattr(item, f"{field}_role").name, fmap
def get_default_kit(self) -> KitType | None:
if len(self.kit_types) == 1:
@@ -1361,7 +1361,7 @@ class Equipment(BaseClass):
def __repr__(self) -> str:
"""
Returns:
str: represenation of this Equipment
str: representation of this Equipment
"""
return f"<Equipment({self.name})>"
@@ -1502,7 +1502,7 @@ class Equipment(BaseClass):
equipment_role = EquipmentRole.query(name=equipment_role)
equipment = cls.query()
options = "\n".join([f"{ii}. {item.name}" for ii, item in enumerate(equipment)])
choices = input(f"Enter equipment numbers to add to {equipment_role.name} (space seperated):\n{options}\n\n")
choices = input(f"Enter equipment numbers to add to {equipment_role.name} (space separated):\n{options}\n\n")
output = []
for choice in choices.split(" "):
try:

19
src/submissions/backend/db/models/submissions.py
View File

@@ -618,6 +618,17 @@ class BasicSubmission(BaseClass, LogMixin):
result = assoc.save()
return result
def update_reagentassoc(self, reagent: Reagent, role: str):
from backend.db import SubmissionReagentAssociation
# NOTE: get the first reagent assoc that fills the given role.
try:
assoc = next(item for item in self.submission_reagent_associations if item.reagent and role in [role.name for role in item.reagent.role])
assoc.reagent = reagent
except StopIteration as e:
logger.error(f"Association for {role} not found, creating new association.")
assoc = SubmissionReagentAssociation(submission=self, reagent=reagent)
self.submission_reagent_associations.append(assoc)
def to_pydantic(self, backup: bool = False) -> "PydSubmission":
"""
Converts this instance into a PydSubmission
@@ -758,7 +769,7 @@ class BasicSubmission(BaseClass, LogMixin):
except StopIteration as e:
raise AttributeError(
f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
logger.info(f"Recruiting model: {model}")
# logger.info(f"Recruiting model: {model}")
return model
# Child class custom functions
@@ -1414,7 +1425,7 @@ class BacterialCulture(BasicSubmission):
extends parent
"""
template = super().filename_template()
template += "_{{ submitting_lab }}_{{ submitter_plate_num }}"
template += "_{{ submitting_lab.name }}_{{ submitter_plate_num }}"
return template
@classmethod
@@ -2356,7 +2367,7 @@ class BasicSample(BaseClass):
except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, using {cls}")
model = cls
logger.info(f"Recruiting model: {model}")
# logger.info(f"Recruiting model: {model}")
return model
else:
model = cls
@@ -2370,7 +2381,7 @@ class BasicSample(BaseClass):
except StopIteration as e:
raise AttributeError(
f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
logger.info(f"Recruiting model: {model}")
# logger.info(f"Recruiting model: {model}")
return model
@classmethod