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Pre-sample/control connect

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This commit is contained in:
Landon Wark
2023-12-05 10:20:46 -06:00
parent 283e77fee5
commit cddb947ec8
29 changed files with 1357 additions and 1042 deletions
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25
src/submissions/backend/excel/reports.py
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@@ -5,7 +5,7 @@ from pandas import DataFrame
import logging
from datetime import date, timedelta
import re
from typing import Tuple
from typing import List, Tuple
from tools import jinja_template_loading, Settings
logger = logging.getLogger(f"submissions.{__name__}")
@@ -27,7 +27,7 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
df = df.sort_values("Submitting Lab")
# aggregate cost and sample count columns
df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
df2 = df2.rename(columns={"Extraction Kit": 'Plate Count'})
df2 = df2.rename(columns={"Extraction Kit": 'Run Count'})
logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
df = df.drop('id', axis=1)
df = df.sort_values(['Submitting Lab', "Submitted Date"])
@@ -57,16 +57,16 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
logger.debug(f"Name: {row[0][1]}")
data = [item for item in row[1]]
kit = dict(name=row[0][1], cost=data[1], plate_count=int(data[0]), sample_count=int(data[2]))
kit = dict(name=row[0][1], cost=data[1], run_count=int(data[0]), sample_count=int(data[2]))
# if this is the same lab as before add together
if lab == old_lab:
output[-1]['kits'].append(kit)
output[-1]['total_cost'] += kit['cost']
output[-1]['total_samples'] += kit['sample_count']
output[-1]['total_plates'] += kit['plate_count']
output[-1]['total_runs'] += kit['run_count']
# if not the same lab, make a new one
else:
adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_plates=kit['plate_count'])
adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_runs=kit['run_count'])
output.append(adder)
old_lab = lab
logger.debug(output)
@@ -83,10 +83,10 @@ def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFram
Args:
ctx (dict): settings passed from gui
input (list[dict]): list of dictionaries containing records
subtype (str | None, optional): _description_. Defaults to None.
subtype (str | None, optional): name of submission type. Defaults to None.
Returns:
DataFrame: _description_
DataFrame: dataframe of controls
"""
df = DataFrame.from_records(input)
@@ -218,5 +218,14 @@ def drop_reruns_from_df(ctx:Settings, df: DataFrame) -> DataFrame:
df = df.drop(df[df.name == first_run].index)
return df
def make_hitpicks(input:list) -> DataFrame:
def make_hitpicks(input:List[dict]) -> DataFrame:
"""
Converts lsit of dictionaries constructed by hitpicking to dataframe
Args:
input (List[dict]): list of hitpicked dictionaries
Returns:
DataFrame: constructed dataframe.
"""
return DataFrame.from_records(input)