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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

3
src/submissions/backend/excel/parser.py
View File

@@ -648,7 +648,8 @@ class TipParser(object):
Returns:
List[dict]: List of locations
"""
return {k: v for k, v in self.submission_type.construct_tips_map()}
# return {k: v for k, v in self.submission_type.construct_tips_map()}
return {k: v for k, v in self.submission_type.construct_field_map("tip")}
def parse_tips(self) -> List[dict]:
"""

14
src/submissions/backend/excel/writer.py
View File

@@ -187,6 +187,9 @@ class InfoWriter(object):
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
except AttributeError as e:
logger.error(f"Can't write {k} to that cell due to {e}")
except ValueError as e:
logger.error(f"Can't write {v} to that cell due to {e}")
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'].name)
return self.sub_object.custom_info_writer(self.xl, info=final_info, custom_fields=self.info_map['custom'])
@@ -208,8 +211,8 @@ class ReagentWriter(object):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if isinstance(extraction_kit, str):
kit_type = KitType.query(name=extraction_kit)
reagent_map = {k: v for k, v in kit_type.construct_xl_map_for_use(submission_type)}
extraction_kit = KitType.query(name=extraction_kit)
reagent_map = {k: v for k, v in extraction_kit.construct_xl_map_for_use(submission_type)}
self.reagents = self.reconcile_map(reagent_list=reagent_list, reagent_map=reagent_map)
def reconcile_map(self, reagent_list: List[dict], reagent_map: dict) -> Generator[dict, None, None]:
@@ -359,7 +362,10 @@ class EquipmentWriter(object):
if equipment_list is None:
return
for ii, equipment in enumerate(equipment_list, start=1):
mp_info = equipment_map[equipment['role']]
try:
mp_info = equipment_map[equipment['role']]
except KeyError:
logger.error(f"No {equipment['role']} in {pformat(equipment_map)}")
# logger.debug(f"{equipment['role']} map: {mp_info}")
placeholder = copy(equipment)
if mp_info == {}:
@@ -427,7 +433,7 @@ class TipWriter(object):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
tips_map = {k: v for k, v in self.submission_type.construct_tips_map()}
tips_map = {k: v for k, v in self.submission_type.construct_field_map("tip")}
self.tips = self.reconcile_map(tips_list=tips_list, tips_map=tips_map)
def reconcile_map(self, tips_list: List[dict], tips_map: dict) -> Generator[dict, None, None]:

45
src/submissions/backend/validators/pydant.py
View File

@@ -115,7 +115,7 @@ class PydReagent(BaseModel):
fields = list(self.model_fields.keys()) + extras
return {k: getattr(self, k) for k in fields}
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, SubmissionReagentAssociation, Report]:
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, Report]:
"""
Converts this instance into a backend.db.models.kit.Reagent instance
@@ -164,13 +164,14 @@ class PydReagent(BaseModel):
report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
else:
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
else:
assoc = None
# assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
# assoc.comments = self.comment
submission.update_reagentassoc(reagent=reagent, role=self.role)
# else:
# assoc = None
# add end-of-life extension from reagent type to expiry date
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, assoc, report
return reagent, report
class PydSample(BaseModel, extra='allow'):
@@ -299,6 +300,13 @@ class PydTips(BaseModel):
lot: str | None = Field(default=None)
role: str
@field_validator('role', mode='before')
@classmethod
def get_role_name(cls, value):
if isinstance(value, TipRole):
value = value.name
return value
def to_sql(self, submission: BasicSubmission) -> SubmissionTipsAssociation:
"""
Con
@@ -324,6 +332,13 @@ class PydEquipment(BaseModel, extra='ignore'):
role: str | None
tips: List[PydTips] | None = Field(default=None)
@field_validator('role', mode='before')
@classmethod
def get_role_name(cls, value):
if isinstance(value, EquipmentRole):
value = value.name
return value
@field_validator('processes', mode='before')
@classmethod
def make_empty_list(cls, value):
@@ -786,7 +801,7 @@ class PydSubmission(BaseModel, extra='allow'):
"""
report = Report()
dicto = self.improved_dict()
logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
# logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
logger.debug(f"Result of query or create: {instance}")
@@ -807,17 +822,15 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Setting {key} to {value}")
match key:
case "reagents":
# if report.results[0].code == 1:
# instance.submission_reagent_associations = []
# logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents:
reagent, assoc, _ = reagent.toSQL(submission=instance)
logger.debug(f"Checking reagent {reagent.lot}")
reagent, _ = reagent.toSQL(submission=instance)
# logger.debug(f"Association: {assoc}")
if assoc is not None: # and assoc not in instance.submission_reagent_associations:
if assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
else:
logger.warning(f"Reagent association {assoc} is already present in {instance}")
# if assoc is not None: # and assoc not in instance.submission_reagent_associations:
# if assoc not in instance.submission_reagent_associations:
# instance.submission_reagent_associations.append(assoc)
# else:
# logger.warning(f"Reagent association {assoc} is already present in {instance.submission_reagent_associations}")
case "samples":
for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance)