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Overhauling database.

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This commit is contained in:
lwark
2025-05-13 13:20:01 -05:00
parent 0dbb4ae77a
commit 75c665ea05
21 changed files with 729 additions and 1727 deletions
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22
src/submissions/backend/excel/reports.py
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@@ -7,7 +7,7 @@ from pandas import DataFrame, ExcelWriter
from pathlib import Path
from datetime import date
from typing import Tuple, List
from backend.db.models import BasicSubmission
from backend.db.models import BasicRun
from tools import jinja_template_loading, get_first_blank_df_row, row_map, flatten_list
from PyQt6.QtWidgets import QWidget
from openpyxl.worksheet.worksheet import Worksheet
@@ -45,9 +45,9 @@ class ReportMaker(object):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, page_size=0)
self.runs = BasicRun.query(start_date=start_date, end_date=end_date, page_size=0)
if organizations is not None:
self.subs = [sub for sub in self.subs if sub.client_submission.submitting_lab.name in organizations]
self.runs = [run for run in self.runs if run.client_submission.submitting_lab.name in organizations]
self.detailed_df, self.summary_df = self.make_report_xlsx()
self.html = self.make_report_html(df=self.summary_df)
@@ -58,9 +58,9 @@ class ReportMaker(object):
Returns:
DataFrame: output dataframe
"""
if not self.subs:
if not self.runs:
return DataFrame(), DataFrame()
df = DataFrame.from_records([item.to_dict(report=True) for item in self.subs])
df = DataFrame.from_records([item.to_dict(report=True) for item in self.runs])
# NOTE: put submissions with the same lab together
df = df.sort_values("submitting_lab")
# NOTE: aggregate cost and sample count columns
@@ -156,19 +156,19 @@ class TurnaroundMaker(ReportArchetype):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
self.subs = BasicRun.query(start_date=start_date, end_date=end_date,
submission_type_name=submission_type, page_size=0)
records = [self.build_record(sub) for sub in self.subs]
self.df = DataFrame.from_records(records)
self.sheet_name = "Turnaround"
@classmethod
def build_record(cls, sub: BasicSubmission) -> dict:
def build_record(cls, sub: BasicRun) -> dict:
"""
Build a turnaround dictionary from a submission
Build a turnaround dictionary from a run
Args:
sub (BasicSubmission): The submission to be processed.
sub (BasicRun): The run to be processed.
Returns:
@@ -203,9 +203,9 @@ class ConcentrationMaker(ReportArchetype):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
self.subs = BasicRun.query(start_date=start_date, end_date=end_date,
submission_type_name=submission_type, page_size=0)
# self.samples = flatten_list([sub.get_provisional_controls(controls_only=controls_only) for sub in self.subs])
# self.samples = flatten_list([sub.get_provisional_controls(controls_only=controls_only) for sub in self.runs])
self.samples = flatten_list([sub.get_provisional_controls(include=include) for sub in self.subs])
self.records = [self.build_record(sample) for sample in self.samples]
self.df = DataFrame.from_records(self.records)