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Moments before disaster.

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This commit is contained in:
lwark
2024-12-06 12:02:39 -06:00
parent 5fc02ffeec
commit 80527355d1
23 changed files with 157 additions and 325 deletions
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8
src/submissions/backend/db/__init__.py
View File

@@ -1,10 +1,8 @@
"""
All database related operations.
"""
import sqlalchemy.orm
from sqlalchemy import event, inspect
from sqlalchemy.engine import Engine
from tools import ctx
@@ -48,7 +46,11 @@ def update_log(mapper, connection, target):
hist = attr.load_history()
if not hist.has_changes():
continue
if attr.key == "custom":
continue
added = [str(item) for item in hist.added]
if attr.key in ['submission_sample_associations', 'submission_reagent_associations']:
added = ['Numbers truncated for space purposes.']
deleted = [str(item) for item in hist.deleted]
change = dict(field=attr.key, added=added, deleted=deleted)
# logger.debug(f"Adding: {pformat(change)}")
@@ -69,6 +71,6 @@ def update_log(mapper, connection, target):
else:
logger.info(f"No changes detected, not updating logs.")
# if ctx.database_schema == "sqlite":
# if ctx.logging_enabled:
event.listen(LogMixin, 'after_update', update_log, propagate=True)
event.listen(LogMixin, 'after_insert', update_log, propagate=True)

77
src/submissions/backend/db/models/kits.py
View File

@@ -1414,25 +1414,6 @@ class Equipment(BaseClass):
if extraction_kit and extraction_kit not in process.kit_types:
continue
yield process
# processes = (process for process in self.processes if submission_type in process.submission_types)
# match extraction_kit:
# case str():
# # logger.debug(f"Filtering processes by extraction_kit str {extraction_kit}")
# processes = (process for process in processes if
# extraction_kit in [kit.name for kit in process.kit_types])
# case KitType():
# # logger.debug(f"Filtering processes by extraction_kit KitType {extraction_kit}")
# processes = (process for process in processes if extraction_kit in process.kit_types)
# case _:
# pass
# # NOTE: Convert to strings
# # processes = [process.name for process in processes]
# # assert all([isinstance(process, str) for process in processes])
# # if len(processes) == 0:
# # processes = ['']
# # return processes
# for process in processes:
# yield process.name
@classmethod
@setup_lookup
@@ -1650,25 +1631,6 @@ class EquipmentRole(BaseClass):
if extraction_kit and extraction_kit not in process.kit_types:
continue
yield process.name
# if submission_type is not None:
# # logger.debug("Getting all processes for this EquipmentRole")
# processes = [process for process in self.processes if submission_type in process.submission_types]
# else:
# processes = self.processes
# match extraction_kit:
# case str():
# # logger.debug(f"Filtering processes by extraction_kit str {extraction_kit}")
# processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_types]]
# case KitType():
# # logger.debug(f"Filtering processes by extraction_kit KitType {extraction_kit}")
# processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_types]]
# case _:
# pass
# output = [item.name for item in processes]
# if len(output) == 0:
# return ['']
# else:
# return output
def to_export_dict(self, submission_type: SubmissionType, kit_type: KitType):
"""
@@ -1730,9 +1692,8 @@ class SubmissionEquipmentAssociation(BaseClass):
@classmethod
@setup_lookup
def query(cls, equipment_id: int, submission_id: int, role: str | None = None, limit: int = 0, **kwargs) -> Any | \
List[
Any]:
def query(cls, equipment_id: int, submission_id: int, role: str | None = None, limit: int = 0, **kwargs) \
-> Any | List[Any]:
query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.equipment_id == equipment_id)
query = query.filter(cls.submission_id == submission_id)
@@ -1777,44 +1738,22 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
def get_all_processes(self, extraction_kit: KitType | str | None = None) -> List[Process]:
"""
Get all processes associated with this SubmissionTypeEquipmentRole
Args:
extraction_kit (KitType | str | None, optional): KitType of interest. Defaults to None.
Returns:
List[Process]: All associated processes
"""
processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
# NOTE: flatten list
processes = [item for items in processes for item in items if item is not None]
match extraction_kit:
case str():
# logger.debug(f"Filtering Processes by extraction_kit str {extraction_kit}")
processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_type]]
case KitType():
# logger.debug(f"Filtering Processes by extraction_kit KitType {extraction_kit}")
processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_type]]
case _:
pass
return processes
@check_authorization
def save(self):
super().save()
def to_export_dict(self, extraction_kit: KitType) -> dict:
def to_export_dict(self, extraction_kit: KitType | str) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Args:
kit_type (KitType): KitType of interest.
extraction_kit (KitType | str): KitType of interest.
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
if isinstance(extraction_kit, str):
extraction_kit = KitType.query(name=extraction_kit)
base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
kit_type=extraction_kit).items()}
base_dict['static'] = self.static
@@ -2013,8 +1952,8 @@ class SubmissionTipsAssociation(BaseClass):
@classmethod
@setup_lookup
def query(cls, tip_id: int, role: str, submission_id: int | None = None, limit: int = 0, **kwargs) -> Any | List[
Any]:
def query(cls, tip_id: int, role: str, submission_id: int | None = None, limit: int = 0, **kwargs) \
-> Any | List[Any]:
query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.tip_id == tip_id)
if submission_id is not None:

10
src/submissions/backend/db/models/submissions.py
View File

@@ -2,13 +2,10 @@
Models for the main submission and sample types.
"""
from __future__ import annotations
# import sys
# import types
# import zipfile
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
from zipfile import ZipFile
from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
@@ -20,7 +17,6 @@ from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError, \
ArgumentError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
# import pandas as pd
from openpyxl import Workbook
from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
@@ -1276,7 +1272,7 @@ class BasicSubmission(BaseClass, LogMixin):
if msg.exec():
try:
self.backup(fname=fname, full_backup=True)
except zipfile.BadZipfile:
except BadZipfile:
logger.error("Couldn't open zipfile for writing.")
self.__database_session__.delete(self)
try:
@@ -2261,7 +2257,7 @@ class WastewaterArtic(BasicSubmission):
# Sample Classes
class BasicSample(BaseClass):
class BasicSample(BaseClass, LogMixin):
"""
Base of basic sample which polymorphs into BCSample and WWSample
"""