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Before control chart update.

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This commit is contained in:
lwark
2024-07-31 07:50:23 -05:00
parent 2a07265cbc
commit eb6cdc63e2
10 changed files with 305 additions and 396 deletions
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4
src/submissions/backend/db/__init__.py
View File

@@ -3,6 +3,7 @@ All database related operations.
"""
from sqlalchemy import event
from sqlalchemy.engine import Engine
from tools import ctx
@event.listens_for(Engine, "connect")
@@ -17,7 +18,8 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
connection_record (_type_): _description_
"""
cursor = dbapi_connection.cursor()
# cursor.execute("PRAGMA foreign_keys=ON")
if ctx.database_schema == "sqlite":
cursor.execute("PRAGMA foreign_keys=ON")
cursor.close()

4
src/submissions/backend/db/models/__init__.py
View File

@@ -3,7 +3,7 @@ Contains all models for sqlalchemy
"""
from __future__ import annotations
import sys, logging
from sqlalchemy import Column, INTEGER, String, JSON, inspect
from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError
@@ -163,7 +163,6 @@ class BaseClass(Base):
try:
self.__database_session__.add(self)
self.__database_session__.commit()
# self.__database_session__.merge(self)
except Exception as e:
logger.critical(f"Problem saving object: {e}")
self.__database_session__.rollback()
@@ -203,4 +202,5 @@ from .organizations import *
from .kits import *
from .submissions import *
# NOTE: Add a creator to the submission for reagent association.
BasicSubmission.reagents.creator = lambda reg: SubmissionReagentAssociation(reagent=reg)

5
src/submissions/backend/db/models/kits.py
View File

@@ -467,6 +467,7 @@ class Reagent(BaseClass):
Lookup a list of reagents from the database.
Args:
id (int | None, optional): reagent id number
reagent_role (str | models.ReagentType | None, optional): Reagent type. Defaults to None.
lot_number (str | None, optional): Reagent lot number. Defaults to None.
name (str | None, optional): Reagent name. Defaults to None.
@@ -1468,7 +1469,7 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
List[Process]: All associated processes
"""
processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
# flatten list
# NOTE: flatten list
processes = [item for items in processes for item in items if item is not None]
match extraction_kit:
case str():
@@ -1523,6 +1524,7 @@ class Process(BaseClass):
Lookup Processes
Args:
id (int | None, optional): Process id. Defaults to None.
name (str | None, optional): Process name. Defaults to None.
limit (int, optional): Maximum number of results to return (0=all). Defaults to 0.
@@ -1666,7 +1668,6 @@ class SubmissionTipsAssociation(BaseClass):
back_populates="tips_submission_associations") #: associated equipment
role_name = Column(String(32), primary_key=True) #, ForeignKey("_tiprole.name"))
# role = relationship(TipRole)
def to_sub_dict(self) -> dict:
"""

43
src/submissions/backend/db/models/submissions.py
View File

@@ -27,7 +27,6 @@ from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_k
from datetime import datetime, date
from typing import List, Any, Tuple, Literal
from dateutil.parser import parse
# from dateutil.parser import ParserError
from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
@@ -370,16 +369,16 @@ class BasicSubmission(BaseClass):
"""
Calculates cost of the plate
"""
# Calculate number of columns based on largest column number
# NOTE: Calculate number of columns based on largest column number
try:
cols_count_96 = self.calculate_column_count()
except Exception as e:
logger.error(f"Column count error: {e}")
# Get kit associated with this submission
# NOTE: Get kit associated with this submission
assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
item.submission_type == self.submission_type][0]
# logger.debug(f"Came up with association: {assoc}")
# If every individual cost is 0 this is probably an old plate.
# NOTE: If every individual cost is 0 this is probably an old plate.
if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
try:
self.run_cost = self.extraction_kit.cost_per_run
@@ -446,6 +445,7 @@ class BasicSubmission(BaseClass):
Convert all submissions to dataframe
Args:
chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
limit (int, optional): Maximum number of results to return. Defaults to 0.
@@ -1047,7 +1047,7 @@ class BasicSubmission(BaseClass):
ValueError: Raised if disallowed key is passed.
Returns:
cls: _description_
cls: A BasicSubmission subclass.
"""
code = 0
msg = ""
@@ -1056,10 +1056,6 @@ class BasicSubmission(BaseClass):
if kwargs == {}:
raise ValueError("Need to narrow down query or the first available instance will be returned.")
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
# for key in kwargs.keys():
# if key in disallowed:
# raise ValueError(
# f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects. Use .query() instead.")
instance = cls.query(submission_type=submission_type, limit=1, **sanitized_kwargs)
# logger.debug(f"Retrieved instance: {instance}")
if instance is None:
@@ -1102,7 +1098,7 @@ class BasicSubmission(BaseClass):
obj (_type_, optional): Parent widget. Defaults to None.
Raises:
e: _description_
e: SQLIntegrityError or SQLOperationalError if problem with commit.
"""
from frontend.widgets.pop_ups import QuestionAsker
# logger.debug("Hello from delete")
@@ -1123,7 +1119,7 @@ class BasicSubmission(BaseClass):
Creates Widget for showing submission details.
Args:
obj (_type_): Parent widget
obj (Widget): Parent widget
"""
# logger.debug("Hello from details")
from frontend.widgets.submission_details import SubmissionDetails
@@ -1139,9 +1135,9 @@ class BasicSubmission(BaseClass):
obj (Widget): Parent widget
"""
from frontend.widgets.submission_widget import SubmissionFormWidget
for widg in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget):
# logger.debug(widg)
widg.setParent(None)
for widget in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget):
# logger.debug(widget)
widget.setParent(None)
pyd = self.to_pydantic(backup=True)
form = pyd.to_form(parent=obj, disable=['rsl_plate_num'])
obj.app.table_widget.formwidget.layout().addWidget(form)
@@ -1271,7 +1267,6 @@ class BacterialCulture(BasicSubmission):
input_dict (dict): _description_
xl (pd.ExcelFile | None, optional): _description_. Defaults to None.
info_map (dict | None, optional): _description_. Defaults to None.
plate_map (dict | None, optional): _description_. Defaults to None.
Returns:
dict: Updated dictionary.
@@ -1560,7 +1555,6 @@ class Wastewater(BasicSubmission):
well_24 = []
samples_copy = deepcopy(input_dict['samples'])
for sample in sorted(samples_copy, key=itemgetter('column', 'row')):
# for sample in input_dict['samples']:
try:
row = sample['source_row']
except KeyError:
@@ -1742,6 +1736,7 @@ class WastewaterArtic(BasicSubmission):
processed = rreplace(processed, plate_num, "")
except AttributeError:
plate_num = "1"
# NOTE: plate_num not currently used, but will keep incase it is in the future
plate_num = plate_num.strip("-")
# logger.debug(f"Processed after plate-num: {processed}")
day = re.search(r"\d{2}$", processed).group()
@@ -1827,7 +1822,6 @@ class WastewaterArtic(BasicSubmission):
"""
input_dict = super().finalize_parse(input_dict, xl, info_map)
# logger.debug(f"Incoming input_dict: {pformat(input_dict)}")
# TODO: Move to validator?
for sample in input_dict['samples']:
# logger.debug(f"Sample: {sample}")
if re.search(r"^NTC", sample['submitter_id']):
@@ -1978,7 +1972,7 @@ class WastewaterArtic(BasicSubmission):
self.comment = [com]
# logger.debug(pformat(self.gel_info))
with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
# Add a file located at the source_path to the destination within the zip
# NOTE: Add a file located at the source_path to the destination within the zip
# file. It will overwrite existing files if the names collide, but it
# will give a warning
zipf.write(img_path, self.gel_image)
@@ -1997,6 +1991,7 @@ class WastewaterArtic(BasicSubmission):
dict: Dictionary with information added.
"""
input_dict = super().custom_docx_writer(input_dict)
# NOTE: if there's a gel image, extract it.
if check_key_or_attr(key='gel_image_path', interest=input_dict, check_none=True):
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
img = zipped.read(input_dict['gel_image_path'])
@@ -2246,9 +2241,7 @@ class BasicSample(BaseClass):
@classmethod
def fuzzy_search(cls,
# submitter_id: str | None = None,
sample_type: str | BasicSample | None = None,
# limit: int = 0,
**kwargs
) -> List[BasicSample]:
"""
@@ -2315,8 +2308,8 @@ class BasicSample(BaseClass):
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
try:
df = df.drop(item, axis=1)
except:
logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
except KeyError as e:
logger.warning(f"Couldn't drop '{item}' column from submissionsheet df due to {e}.")
return df
def show_details(self, obj):
@@ -2408,7 +2401,7 @@ class WastewaterSample(BasicSample):
# logger.debug(f"Initial sample dict: {pformat(output_dict)}")
disallowed = ["", None, "None"]
try:
check = output_dict['rsl_number'] in [None, "None"]
check = output_dict['rsl_number'] in disallowed
except KeyError:
check = True
if check:
@@ -2451,7 +2444,6 @@ class BacterialCultureSample(BasicSample):
Returns:
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
"""
# start = time()
sample = super().to_sub_dict(full_data=full_data)
sample['name'] = self.submitter_id
sample['organism'] = self.organism
@@ -2553,7 +2545,7 @@ class SubmissionSampleAssociation(BaseClass):
Returns:
dict: dictionary of sample id, row and column in elution plate
"""
# Since there is no PCR, negliable result is necessary.
# NOTE: Since there is no PCR, negliable result is necessary.
sample = self.to_sub_dict()
# logger.debug(f"Sample dict to hitpick: {sample}")
env = jinja_template_loading()
@@ -2728,7 +2720,6 @@ class SubmissionSampleAssociation(BaseClass):
except StatementError:
instance = None
if instance is None:
# sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in ['id']}
used_cls = cls.find_polymorphic_subclass(polymorphic_identity=association_type)
instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
return instance