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ReagentLot add/edit updated.

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lwark
2025-09-10 12:39:02 -05:00
parent c9396d6c41
commit ba4912cab7
18 changed files with 1862 additions and 1734 deletions
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158
src/submissions/tools/__init__.py
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@@ -1,18 +1,16 @@
'''
"""
Contains miscellaenous functions used by both frontend and backend.
'''
"""
from __future__ import annotations
import builtins, importlib, time, logging, re, yaml, sys, os, stat, platform, getpass, json, numpy as np, pandas as pd
import itertools
import builtins, importlib, time, logging, re, yaml, sys, os, stat, platform, getpass, json, numpy as np, pandas as pd, \
itertools, openpyxl
from copy import copy
from collections import OrderedDict
from datetime import date, datetime, timedelta
from json import JSONDecodeError
from threading import Thread
from inspect import getmembers, isfunction, stack
from types import NoneType
from dateutil.easter import easter
from dateutil.parser import parse
from jinja2 import Environment, FileSystemLoader
from logging import handlers, Logger
from pathlib import Path
@@ -60,7 +58,6 @@ main_form_style = '''
page_size = 250
# micro_char = uni_char = "\u03BC"
def divide_chunks(input_list: list, chunk_count: int) -> Generator[Any, Any, None]:
"""
@@ -447,16 +444,18 @@ def jinja_template_loading() -> Environment:
return env
def render_details_template(template_name:str, css_in:List[str]|str=[], js_in:List[str]|str=[], **kwargs) -> str:
def render_details_template(template_name: str, css_in: List[str] | str = [], js_in: List[str] | str = [],
**kwargs) -> str:
if isinstance(css_in, str):
css_in = [css_in]
env = jinja_template_loading()
html_folder = Path(env.loader.__getattribute__("searchpath")[0])
css_in = ["styles"] + css_in
css_in = [project_path.joinpath("src", "submissions", "templates", "css", f"{c}.css") for c in css_in]
css_in = [html_folder.joinpath("css", f"{c}.css") for c in css_in]
if isinstance(js_in, str):
js_in = [js_in]
js_in = ["details"] + js_in
js_in = [project_path.joinpath("src", "submissions", "templates", "js", f"{j}.js") for j in js_in]
env = jinja_template_loading()
js_in = [html_folder.joinpath("js", f"{j}.js") for j in js_in]
template = env.get_template(f"{template_name}.html")
# template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
css_out = []
@@ -467,7 +466,6 @@ def render_details_template(template_name:str, css_in:List[str]|str=[], js_in:Li
for js in js_in:
with open(js, "r") as f:
js_out.append(f.read())
# logger.debug(f"Kwargs: {kwargs}")
return template.render(css=css_out, js=js_out, **kwargs)
@@ -489,10 +487,10 @@ def convert_well_to_row_column(input_str: str) -> Tuple[int, int]:
return None, None
return row, column
# Copy a sheet with style, format, layout, ect. from one Excel file to another Excel file
# Please add the ..path\\+\\file.. and ..sheet_name.. according to your desire.
import openpyxl
from copy import copy
def copy_xl_sheet(source_sheet, target_sheet):
@@ -509,8 +507,8 @@ def copy_sheet_attributes(source_sheet, target_sheet):
target_sheet.page_margins = copy(source_sheet.page_margins)
target_sheet.freeze_panes = copy(source_sheet.freeze_panes)
# set row dimensions
# So you cannot copy the row_dimensions attribute. Does not work (because of meta data in the attribute I think). So we copy every row's row_dimensions. That seems to work.
# NOTE: set row dimensions
# NOTE: So you cannot copy the row_dimensions attribute. Does not work (because of meta data in the attribute I think). So we copy every row's row_dimensions. That seems to work.
for rn in range(len(source_sheet.row_dimensions)):
target_sheet.row_dimensions[rn] = copy(source_sheet.row_dimensions[rn])
@@ -519,12 +517,15 @@ def copy_sheet_attributes(source_sheet, target_sheet):
else:
target_sheet.sheet_format.defaultColWidth = copy(source_sheet.sheet_format.defaultColWidth)
# set specific column width and hidden property
# we cannot copy the entire column_dimensions attribute so we copy selected attributes
# NOTE: set specific column width and hidden property
# NOTE: we cannot copy the entire column_dimensions attribute so we copy selected attributes
for key, value in source_sheet.column_dimensions.items():
target_sheet.column_dimensions[key].min = copy(source_sheet.column_dimensions[key].min) # Excel actually groups multiple columns under 1 key. Use the min max attribute to also group the columns in the targetSheet
target_sheet.column_dimensions[key].max = copy(source_sheet.column_dimensions[key].max) # https://stackoverflow.com/questions/36417278/openpyxl-can-not-read-consecutive-hidden-columns discussed the issue. Note that this is also the case for the width, not onl;y the hidden property
target_sheet.column_dimensions[key].width = copy(source_sheet.column_dimensions[key].width) # set width for every column
target_sheet.column_dimensions[key].min = copy(source_sheet.column_dimensions[
key].min) # Excel actually groups multiple columns under 1 key. Use the min max attribute to also group the columns in the targetSheet
target_sheet.column_dimensions[key].max = copy(source_sheet.column_dimensions[
key].max) # https://stackoverflow.com/questions/36417278/openpyxl-can-not-read-consecutive-hidden-columns discussed the issue. Note that this is also the case for the width, not onl;y the hidden property
target_sheet.column_dimensions[key].width = copy(
source_sheet.column_dimensions[key].width) # set width for every column
target_sheet.column_dimensions[key].hidden = copy(source_sheet.column_dimensions[key].hidden)
@@ -534,11 +535,9 @@ def copy_cells(source_sheet, target_sheet):
source_cell = cell
if isinstance(source_cell, openpyxl.cell.read_only.EmptyCell):
continue
target_cell = target_sheet.cell(column=c+1, row=r+1)
target_cell = target_sheet.cell(column=c + 1, row=r + 1)
target_cell._value = source_cell._value
target_cell.data_type = source_cell.data_type
if source_cell.has_style:
target_cell.font = copy(source_cell.font)
target_cell.border = copy(source_cell.border)
@@ -546,15 +545,13 @@ def copy_cells(source_sheet, target_sheet):
target_cell.number_format = copy(source_cell.number_format)
target_cell.protection = copy(source_cell.protection)
target_cell.alignment = copy(source_cell.alignment)
if not isinstance(source_cell, openpyxl.cell.ReadOnlyCell) and source_cell.hyperlink:
target_cell._hyperlink = copy(source_cell.hyperlink)
if not isinstance(source_cell, openpyxl.cell.ReadOnlyCell) and source_cell.comment:
target_cell.comment = copy(source_cell.comment)
def list_str_comparator(input_str:str, listy: List[str], mode: Literal["starts_with", "contains"]) -> bool:
def list_str_comparator(input_str: str, listy: List[str], mode: Literal["starts_with", "contains"]) -> bool:
match mode:
case "starts_with":
if any([input_str.startswith(item) for item in listy]):
@@ -567,6 +564,7 @@ def list_str_comparator(input_str:str, listy: List[str], mode: Literal["starts_w
else:
return False
def sort_dict_by_list(dictionary: dict, order_list: list) -> dict:
output = OrderedDict()
for item in order_list:
@@ -602,14 +600,12 @@ def setup_lookup(func):
elif v is not None:
sanitized_kwargs[k] = v
return func(*args, **sanitized_kwargs)
return wrapper
def check_object_in_manager(manager: list, object_name: object) -> Tuple[Any, bool]:
if manager is None:
return None, False
# logger.debug(f"Manager: {manager}, aliases: {manager.aliases}, Key: {object_name}")
if object_name in manager.aliases:
return manager, True
relationships = [getattr(manager.__class__, item) for item in dir(manager.__class__)
@@ -617,21 +613,17 @@ def check_object_in_manager(manager: list, object_name: object) -> Tuple[Any, bo
relationships = [item for item in relationships if isinstance(item.property, _RelationshipDeclared)]
for relationship in relationships:
if relationship.key == object_name and "association" not in relationship.key:
logger.debug(f"Checking {relationship.key}")
try:
rel_obj = getattr(manager, relationship.key)
if rel_obj is not None:
logger.debug(f"Returning {rel_obj}")
return rel_obj, False
except AttributeError:
pass
if "association" in relationship.key:
try:
logger.debug(f"Checking association {relationship.key}")
rel_obj = next((getattr(item, object_name) for item in getattr(manager, relationship.key)
if getattr(item, object_name) is not None), None)
if rel_obj is not None:
logger.debug(f"Returning {rel_obj}")
return rel_obj, False
except AttributeError:
pass
@@ -862,7 +854,6 @@ def check_authorization(func):
report.add_result(
Result(owner=func.__str__(), code=1, msg=error_msg, status="warning"))
return report, kwargs
return wrapper
@@ -888,7 +879,6 @@ def under_development(func):
Result(owner=func.__str__(), code=1, msg=error_msg,
status="warning"))
return report
return wrapper
@@ -906,7 +896,6 @@ def report_result(func):
@wraps(func)
def wrapper(*args, **kwargs):
# logger.info(f"Report result being called by {func.__name__}")
output = func(*args, **kwargs)
match output:
case Report():
@@ -931,6 +920,7 @@ def report_result(func):
logger.error(f"Problem reporting due to {e}")
logger.error(result.msg)
if output:
logger.info(f"Report result being called by {func.__name__}")
if is_list_etc(output):
true_output = tuple(item for item in output if not isinstance(item, Report))
if len(true_output) == 1:
@@ -943,7 +933,6 @@ def report_result(func):
else:
true_output = None
return true_output
return wrapper
@@ -962,11 +951,32 @@ def is_list_etc(object):
def create_holidays_for_year(year: int | None = None) -> List[date]:
def find_nth_monday(year, month, occurence: int | None = None, day: int | None = None):
if not occurence:
occurence = 1
"""
Gives stat holidays for the input year.
Args:
year (int | None, optional): The input year as an integer. Defaults to None.
Returns:
List[date]
"""
def find_nth_monday(year, month, occurrence: int | None = None, day: int | None = None) -> date:
"""
Gets the nth (eg 2nd) monday of the given month.
Args:
year (int): The year the month occurs in.
month (int): The month of interest.
occurrence (int): The n in nth.
day (int): The day of the month to start after.
Returns:
date
"""
if not occurrence:
occurrence = 1
if not day:
day = occurence * 7
day = occurrence * 7
max_days = (date(2012, month + 1, 1) - date(2012, month, 1)).days
if day > max_days:
day = max_days
@@ -977,17 +987,16 @@ def create_holidays_for_year(year: int | None = None) -> List[date]:
offset = -d.weekday() # weekday == 0 means Monday
output = d + timedelta(offset)
return output.date()
if not year:
year = date.today().year
# NOTE: Includes New Year's day for next year.
# NOTE: Static holidays. Includes New Year's day for next year.
holidays = [date(year, 1, 1), date(year, 7, 1), date(year, 9, 30),
date(year, 11, 11), date(year, 12, 25), date(year, 12, 26),
date(year + 1, 1, 1)]
# NOTE: Labour Day
holidays.append(find_nth_monday(year, 9))
# NOTE: Thanksgiving
holidays.append(find_nth_monday(year, 10, occurence=2))
holidays.append(find_nth_monday(year, 10, occurrence=2))
# NOTE: Victoria Day
holidays.append(find_nth_monday(year, 5, day=25))
# NOTE: Easter, etc
@@ -1007,7 +1016,6 @@ def check_dictionary_inclusion_equality(listo: List[dict] | dict, dicto: dict) -
Returns:
bool: True if dicto is equal to any dictionary in the list.
"""
# logger.debug(f"Comparing: {listo} and {dicto}")
if isinstance(dicto, list) and isinstance(listo, list):
return listo == dicto
elif isinstance(dicto, dict) and isinstance(listo, dict):
@@ -1018,22 +1026,39 @@ def check_dictionary_inclusion_equality(listo: List[dict] | dict, dicto: dict) -
raise TypeError(f"Unsupported variable: {type(listo)}")
def flatten_list(input_list: list):
def flatten_list(input_list: list) -> list:
"""
Takes nested lists and returns a single flat list.
Args:
input_list (list): input nested list.
Returns:
list:
"""
return list(itertools.chain.from_iterable(input_list))
def sanitize_object_for_json(input_dict: dict) -> dict:
"""
Takes an object and makes sure its components can be converted to JSON
Args:
input_dict (dict): Dictionary of interest
Returns:
dict:
"""
if not isinstance(input_dict, dict):
match input_dict:
case int() | float() | bool():
pass
case _:
try:
js = json.dumps(input_dict)
input_dict = json.dumps(input_dict)
except TypeError:
input_dict = str(input_dict)
return input_dict
# return input_dict
output = {}
for key, value in input_dict.items():
match value:
@@ -1041,22 +1066,37 @@ def sanitize_object_for_json(input_dict: dict) -> dict:
value = [sanitize_object_for_json(object) for object in value]
case dict():
value = sanitize_object_for_json(value)
case _:
try:
js = json.dumps(value)
value = json.dumps(value)
except TypeError:
value = str(value)
output[key] = value
return output
def create_plate_grid(rows: int, columns: int):
matrix = np.array([[0 for yyy in range(1, columns + 1)] for xxx in range(1, rows + 1)])
return {iii: (item[0][1]+1, item[0][0]+1) for iii, item in enumerate(np.ndenumerate(matrix), start=1)}
def create_plate_grid(rows: int, columns: int) -> dict:
"""
Makes an x by y array to represent a plate.
Args:
rows (int): Number of rows.
columns (int): Number of columns
Returns:
dict: cell number : (row, column)
"""
# NOTE: columns/rows
# matrix = np.array([[0 for yyy in range(1, columns + 1)] for xxx in range(1, rows + 1)])
# NOTE: rows/columns
matrix = np.array([[0 for xxx in range(1, rows + 1)] for yyy in range(1, columns + 1)])
return {iii: (item[0][1] + 1, item[0][0] + 1) for iii, item in enumerate(np.ndenumerate(matrix), start=1)}
class classproperty(property):
"""
Allows for properties on classes as well as objects.
"""
def __get__(self, owner_self, owner_cls):
return self.fget(owner_cls)
@@ -1396,6 +1436,16 @@ class Settings(BaseSettings, extra="allow"):
@classmethod
def get_alembic_db_path(cls, alembic_path, mode=Literal['path', 'schema', 'user', 'pass']) -> Path | str:
"""
Retrieves database variables from alembic.ini file.
Args:
alembic_path (Any): Path of the alembic.ini file.
mode (Literal['path', 'schema', 'user', 'pass']): Variable of interest.
Returns:
Path | str
"""
c = ConfigParser()
c.read(alembic_path)
url = c['alembic']['sqlalchemy.url']