Updated documentation. Improved import completion.
This commit is contained in:
Landon Wark
@@ -3,6 +3,7 @@ Operations for all user interactions.
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'''
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import json
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import re
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import sys
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from PyQt6.QtWidgets import (
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QMainWindow, QLabel, QToolBar,
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QTabWidget, QWidget, QVBoxLayout,
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@@ -32,7 +33,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
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)
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from backend.db import lookup_kittype_by_name
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from .functions import extract_form_info
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from tools import check_not_nan, check_kit_integrity
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from tools import check_not_nan, check_kit_integrity, check_if_app
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# from backend.excel.reports import
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from frontend.custom_widgets import SubmissionsSheet, AlertPop, QuestionAsker, AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
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import logging
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@@ -40,6 +41,7 @@ import difflib
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from getpass import getuser
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from datetime import date
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from frontend.visualizations import create_charts
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import webbrowser
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logger = logging.getLogger(f'submissions.{__name__}')
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logger.info("Hello, I am a logger")
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@@ -49,6 +51,7 @@ class App(QMainWindow):
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def __init__(self, ctx: dict = {}):
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super().__init__()
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self.ctx = ctx
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# indicate version and database connected in title bar
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try:
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self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
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except AttributeError:
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@@ -84,6 +87,7 @@ class App(QMainWindow):
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maintenanceMenu = menuBar.addMenu("&Monthly")
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helpMenu = menuBar.addMenu("&Help")
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helpMenu.addAction(self.helpAction)
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helpMenu.addAction(self.docsAction)
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fileMenu.addAction(self.importAction)
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reportMenu.addAction(self.generateReportAction)
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maintenanceMenu.addAction(self.joinControlsAction)
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@@ -111,6 +115,7 @@ class App(QMainWindow):
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self.joinControlsAction = QAction("Link Controls")
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self.joinExtractionAction = QAction("Link Ext Logs")
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self.helpAction = QAction("&About", self)
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self.docsAction = QAction("&Docs", self)
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def _connectActions(self):
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@@ -129,12 +134,20 @@ class App(QMainWindow):
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self.joinControlsAction.triggered.connect(self.linkControls)
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self.joinExtractionAction.triggered.connect(self.linkExtractions)
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self.helpAction.triggered.connect(self.showAbout)
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self.docsAction.triggered.connect(self.openDocs)
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def showAbout(self):
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output = f"Version: {self.ctx['package'].__version__}\n\nAuthor: {self.ctx['package'].__author__['name']} - {self.ctx['package'].__author__['email']}\n\nCopyright: {self.ctx['package'].__copyright__}"
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about = AlertPop(message=output, status="information")
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about.exec()
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def openDocs(self):
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if check_if_app():
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url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
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else:
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url = Path("docs\\build\\index.html").absolute()
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logger.debug(f"Attempting to open {url}")
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webbrowser.get('windows-default').open(f"file://{url.__str__()}")
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def importSubmission(self):
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@@ -365,24 +378,19 @@ class App(QMainWindow):
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# Custom two date picker for start & end dates
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dlg = ReportDatePicker()
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if dlg.exec():
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# labels, values = extract_form_info(dlg)
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# info = {item[0]:item[1] for item in zip(labels, values)}
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info = extract_form_info(dlg)
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logger.debug(f"Report info: {info}")
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# find submissions based on date range
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subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
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# convert each object to dict
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records = [item.report_dict() for item in subs]
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# make dataframe from record dictionaries
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df = make_report_xlsx(records=records)
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html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
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# make dataframe from record dictionaries
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# df = make_report_xlsx(records=records)
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# setup filedialog to handle save location of report
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home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
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# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
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fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
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# logger.debug(f"report output name: {fname}")
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# df.to_excel(fname, engine='openpyxl')
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with open(fname, "w+b") as f:
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pisa.CreatePDF(html, dest=f)
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writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
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@@ -398,14 +406,7 @@ class App(QMainWindow):
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worksheet.column_dimensions[get_column_letter(idx)].width = max_len
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except ValueError:
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pass
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# set_column(idx, idx, max_len) # set column width
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# colu = worksheet.column_dimensions["C"]
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# style = NamedStyle(name="custom_currency", number_format='Currency')
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for cell in worksheet['D']:
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# try:
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# check = int(cell.row)
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# except TypeError:
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# continue
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if cell.row > 1:
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cell.style = 'Currency'
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writer.close()
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@@ -431,19 +432,11 @@ class App(QMainWindow):
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return
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# send to kit creator function
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result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
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# msg = QMessageBox()
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# msg.setIcon(QMessageBox.critical)
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match result['code']:
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case 0:
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msg = AlertPop(message=result['message'], status='info')
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# msg.setText("Kit added")
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# msg.setInformativeText(result['message'])
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# msg.setWindowTitle("Kit added")
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case 1:
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msg = AlertPop(message=result['message'], status='critical')
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# msg.setText("Permission Error")
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# msg.setInformativeText(result['message'])
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# msg.setWindowTitle("Permission Error")
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msg.exec()
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@@ -467,19 +460,11 @@ class App(QMainWindow):
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return
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# send to kit creator function
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result = create_org_from_yaml(ctx=self.ctx, org=org)
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# msg = QMessageBox()
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# msg.setIcon(QMessageBox.critical)
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match result['code']:
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case 0:
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msg = AlertPop(message=result['message'], status='information')
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# msg.setText("Organization added")
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# msg.setInformativeText(result['message'])
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# msg.setWindowTitle("Kit added")
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case 1:
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msg = AlertPop(message=result['message'], status='critical')
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# msg.setText("Permission Error")
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# msg.setInformativeText(result['message'])
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# msg.setWindowTitle("Permission Error")
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msg.exec()
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@@ -537,20 +522,12 @@ class App(QMainWindow):
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controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
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# if no data found from query set fig to none for reporting in webview
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if controls == None:
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# return
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fig = None
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else:
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# data = []
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# for control in controls:
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# # change each control to list of dicts
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# # dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
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# dicts = control.convert_by_mode(mode=self.mode)
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# data.append(dicts)
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# change each control to list of dicts
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data = [control.convert_by_mode(mode=self.mode) for control in controls]
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# flatten data to one dimensional list
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data = [item for sublist in data for item in sublist]
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# logger.debug(data)
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# send to dataframe creator
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df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
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if self.subtype == None:
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@@ -567,16 +544,12 @@ class App(QMainWindow):
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else:
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html += "<h1>No data was retrieved for the given parameters.</h1>"
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html += '</body></html>'
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# with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
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# f.write(html)
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# add html to webview and update.
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self.table_widget.webengineview.setHtml(html)
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self.table_widget.webengineview.update()
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logger.debug("Figure updated... I hope.")
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def linkControls(self):
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# all_bcs = self.ctx['database_session'].query(models.BacterialCulture).all()
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all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
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logger.debug(all_bcs)
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all_controls = get_all_controls(self.ctx)
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@@ -588,9 +561,6 @@ class App(QMainWindow):
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samples = [sample.sample_id for sample in bcs.samples]
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logger.debug(bcs.controls)
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for sample in samples:
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# if "Jan" in sample and "EN" in sample:
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# sample = sample.replace("EN-", "EN1-")
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# logger.debug(f"Checking for {sample}")
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# replace below is a stopgap method because some dingus decided to add spaces in some of the ATCC49... so it looks like "ATCC 49"...
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if " " in sample:
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logger.warning(f"There is not supposed to be a space in the sample name!!!")
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@@ -601,10 +571,8 @@ class App(QMainWindow):
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else:
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for control in all_controls:
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diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
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# if diff > 0.955:
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if control.name.startswith(sample):
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logger.debug(f"Checking {sample} against {control.name}... {diff}")
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# if sample == control.name:
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logger.debug(f"Found match:\n\tSample: {sample}\n\tControl: {control.name}\n\tDifference: {diff}")
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if control in bcs.controls:
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logger.debug(f"{control.name} already in {bcs.rsl_plate_num}, skipping")
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@@ -618,28 +586,22 @@ class App(QMainWindow):
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self.ctx["database_session"].add(control)
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count += 1
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self.ctx["database_session"].add(bcs)
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# logger.debug(f"To be added: {ctx['database_session'].new}")
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logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
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# p = ctx["database_session"].query(models.BacterialCulture).filter(models.BacterialCulture.rsl_plate_num==bcs.rsl_plate_num).first()
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result = f"We added {count} controls to bacterial cultures."
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logger.debug(result)
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# logger.debug(ctx["database_session"].new)
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self.ctx['database_session'].commit()
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msg = QMessageBox()
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# msg.setIcon(QMessageBox.critical)
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msg.setText("Controls added")
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msg.setInformativeText(result)
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msg.setWindowTitle("Controls added")
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msg.exec()
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def linkExtractions(self):
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home_dir = str(Path(self.ctx["directory_path"]))
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fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
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with open(fname.__str__(), 'r') as f:
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runs = [col.strip().split(",") for col in f.readlines()]
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# check = []
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count = 0
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for run in runs:
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obj = dict(
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@@ -652,21 +614,14 @@ class App(QMainWindow):
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)
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for ii in range(6, len(run)):
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obj[f"column{str(ii-5)}_vol"] = run[ii]
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# check.append(json.dumps(obj))
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# sub = self.ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(obj["rsl_plate_num"])).first()
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sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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count += 1
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except AttributeError:
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continue
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# output = json.dumps(obj)
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if sub.extraction_info != None:
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# try:
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# logger.debug(f"Attempting update on ext info: {sub.extraction_info} for {sub.rsl_plate_num}")
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existing = json.loads(sub.extraction_info)
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# except:
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# existing = None
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else:
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existing = None
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try:
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@@ -677,7 +632,6 @@ class App(QMainWindow):
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pass
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if existing != None:
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try:
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# sub.extraction_info += output
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logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
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existing.append(obj)
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logger.debug(f"Setting: {existing}")
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@@ -694,7 +648,6 @@ class App(QMainWindow):
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dlg.exec()
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class AddSubForm(QWidget):
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def __init__(self, parent):
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