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Added importing of PCR results.

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This commit is contained in:
Landon Wark
2023-03-28 14:44:13 -05:00
parent d50a9793c7
commit 3c9f095937
16 changed files with 562 additions and 70 deletions
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210
src/submissions/frontend/__init__.py
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@@ -1,6 +1,7 @@
'''
Operations for all user interactions.
'''
import inspect
import json
import re
import sys
@@ -23,15 +24,15 @@ from xhtml2pdf import pisa
# import plotly.express as px
import yaml
import pprint
from backend.excel import convert_data_list_to_df, make_report_xlsx, make_report_html, SheetParser
from backend.excel import convert_data_list_to_df, make_report_xlsx, make_report_html, SheetParser, PCRParser
from backend.db import (construct_submission_info, lookup_reagent,
construct_reagent, store_submission, lookup_kittype_by_use,
lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
create_org_from_yaml, store_reagent
create_org_from_yaml, store_reagent, lookup_ww_sample_by_rsl_sample_number, lookup_kittype_by_name,
update_ww_sample
)
from backend.db import lookup_kittype_by_name
from .functions import extract_form_info
from tools import check_not_nan, check_kit_integrity, check_if_app
# from backend.excel.reports import
@@ -89,9 +90,11 @@ class App(QMainWindow):
helpMenu.addAction(self.helpAction)
helpMenu.addAction(self.docsAction)
fileMenu.addAction(self.importAction)
fileMenu.addAction(self.importPCRAction)
reportMenu.addAction(self.generateReportAction)
maintenanceMenu.addAction(self.joinControlsAction)
maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction)
def _createToolBar(self):
"""
@@ -107,13 +110,15 @@ class App(QMainWindow):
"""
creates actions
"""
self.importAction = QAction("&Import", self)
self.importAction = QAction("&Import Submission", self)
self.importPCRAction = QAction("&Import PCR Results", self)
self.addReagentAction = QAction("Add Reagent", self)
self.generateReportAction = QAction("Make Report", self)
self.addKitAction = QAction("Import Kit", self)
self.addOrgAction = QAction("Import Org", self)
self.joinControlsAction = QAction("Link Controls")
self.joinExtractionAction = QAction("Link Ext Logs")
self.joinExtractionAction = QAction("Link Extraction Logs")
self.joinPCRAction = QAction("Link PCR Logs")
self.helpAction = QAction("&About", self)
self.docsAction = QAction("&Docs", self)
@@ -123,6 +128,7 @@ class App(QMainWindow):
connect menu and tool bar item to functions
"""
self.importAction.triggered.connect(self.importSubmission)
self.importPCRAction.triggered.connect(self.importPCRResults)
self.addReagentAction.triggered.connect(self.add_reagent)
self.generateReportAction.triggered.connect(self.generateReport)
self.addKitAction.triggered.connect(self.add_kit)
@@ -133,6 +139,7 @@ class App(QMainWindow):
self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
self.joinControlsAction.triggered.connect(self.linkControls)
self.joinExtractionAction.triggered.connect(self.linkExtractions)
self.joinPCRAction.triggered.connect(self.linkPCR)
self.helpAction.triggered.connect(self.showAbout)
self.docsAction.triggered.connect(self.openDocs)
@@ -180,7 +187,8 @@ class App(QMainWindow):
(?P<submitted_date>^submitted_date$) |
(?P<submitting_lab>)^submitting_lab$ |
(?P<samples>)^samples$ |
(?P<reagent>^lot_.*$)
(?P<reagent>^lot_.*$) |
(?P<csv>^csv$)
""", re.VERBOSE)
for item in prsr.sub:
logger.debug(f"Item: {item}")
@@ -213,14 +221,19 @@ class App(QMainWindow):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
msg.exec()
# create combobox to hold looked up kits
# add_widget = KitSelector(ctx=self.ctx, submission_type=prsr.sub['submission_type'], parent=self)
add_widget = QComboBox()
# add_widget.currentTextChanged.connect(self.kit_reload)
# lookup existing kits by 'submission_type' decided on by sheetparser
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
# if len(uses) > 0:
add_widget.addItems(uses)
# else:
# add_widget.addItems(['bacterial_culture'])
self.ext_kit = prsr.sub[item]
if check_not_nan(prsr.sub[item]):
self.ext_kit = prsr.sub[item]
else:
self.ext_kit = add_widget.currentText()
case 'submitted_date':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
@@ -234,7 +247,9 @@ class App(QMainWindow):
add_widget.setDate(date.today())
case 'reagent':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
reg_label = QLabel(item.replace("_", " ").title())
reg_label.setObjectName(f"lot_{item}_label")
self.table_widget.formlayout.addWidget(reg_label)
# create reagent choice widget
add_widget = ImportReagent(ctx=self.ctx, item=item, prsr=prsr)
self.reagents[item] = prsr.sub[item]
@@ -243,10 +258,13 @@ class App(QMainWindow):
logger.debug(f"{item}: {prsr.sub[item]}")
self.samples = prsr.sub[item]
add_widget = None
case 'csv':
self.csv = prsr.sub[item]
case _:
# anything else gets added in as a line edit
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QLineEdit()
logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
add_widget.setText(str(prsr.sub[item]).replace("_", " "))
try:
add_widget.setObjectName(item)
@@ -256,21 +274,59 @@ class App(QMainWindow):
logger.error(e)
# compare self.reagents with expected reagents in kit
if hasattr(self, 'ext_kit'):
kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
kit_integrity = check_kit_integrity(kit, [item.replace("lot_", "") for item in self.reagents])
if kit_integrity != None:
msg = AlertPop(message=kit_integrity['message'], status="critical")
msg.exec()
for item in kit_integrity['missing']:
self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
add_widget = ImportReagent(ctx=self.ctx, item=item)
self.table_widget.formlayout.addWidget(add_widget)
self.kit_integrity_completion()
# create submission button
# submit_btn = QPushButton("Submit")
# submit_btn.setObjectName("submit_btn")
# self.table_widget.formlayout.addWidget(submit_btn)
# submit_btn.clicked.connect(self.submit_new_sample)
logger.debug(f"Imported reagents: {self.reagents}")
def kit_reload(self):
"""
Removes all reagents from form before running kit integrity completion.
"""
for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
# item.setParent(None)
if isinstance(item, QLabel):
if item.text().startswith("Lot"):
item.setParent(None)
else:
logger.debug(f"Type of {item.objectName()} is {type(item)}")
if item.objectName().startswith("lot_"):
item.setParent(None)
self.kit_integrity_completion()
def kit_integrity_completion(self):
"""
Performs check of imported reagents
NOTE: this will not change self.reagents which should be fine
since it's only used when looking up
"""
logger.debug(inspect.currentframe().f_back.f_code.co_name)
kit_widget = self.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
logger.debug(f"Kit selector: {kit_widget}")
self.ext_kit = kit_widget.currentText()
logger.debug(f"Checking integrity of {self.ext_kit}")
kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
reagents_to_lookup = [item.replace("lot_", "") for item in self.reagents]
logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
if kit_integrity != None:
msg = AlertPop(message=kit_integrity['message'], status="critical")
msg.exec()
for item in kit_integrity['missing']:
self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
add_widget = ImportReagent(ctx=self.ctx, item=item)
self.table_widget.formlayout.addWidget(add_widget)
submit_btn = QPushButton("Submit")
submit_btn.setObjectName("lot_submit_btn")
self.table_widget.formlayout.addWidget(submit_btn)
submit_btn.clicked.connect(self.submit_new_sample)
logger.debug(f"Imported reagents: {self.reagents}")
def submit_new_sample(self):
"""
Attempt to add sample to database when 'submit' button clicked
@@ -341,6 +397,15 @@ class App(QMainWindow):
# reset form
for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
if hasattr(self, 'csv'):
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
if dlg.exec():
home_dir = Path(self.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
try:
self.csv.to_csv(fname.__str__(), index=False)
except PermissionError:
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None):
@@ -468,8 +533,6 @@ class App(QMainWindow):
msg.exec()
def _controls_getter(self):
"""
Lookup controls from database and send to chartmaker
@@ -550,6 +613,9 @@ class App(QMainWindow):
def linkControls(self):
"""
Adds controls pulled from irida to relevant submissions
"""
all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
logger.debug(all_bcs)
all_controls = get_all_controls(self.ctx)
@@ -598,6 +664,9 @@ class App(QMainWindow):
def linkExtractions(self):
"""
Links extraction logs from .csv files to relevant submissions.
"""
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
with open(fname.__str__(), 'r') as f:
@@ -648,6 +717,107 @@ class App(QMainWindow):
dlg.exec()
def linkPCR(self):
"""
Links PCR logs from .csv files to relevant submissions.
"""
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
with open(fname.__str__(), 'r') as f:
runs = [col.strip().split(",") for col in f.readlines()]
count = 0
for run in runs:
obj = dict(
start_time=run[0].strip(),
rsl_plate_num=run[1].strip(),
biomek_status=run[2].strip(),
quant_status=run[3].strip(),
experiment_name=run[4].strip(),
end_time=run[5].strip()
)
# for ii in range(6, len(run)):
# obj[f"column{str(ii-5)}_vol"] = run[ii]
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
continue
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
existing = json.loads(sub.pcr_info)
else:
existing = None
try:
if json.dumps(obj) in sub.pcr_info:
logger.debug(f"Looks like we already have that info.")
continue
else:
count += 1
except TypeError:
logger.error(f"No json to dump")
if existing != None:
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
existing.append(obj)
logger.debug(f"Setting: {existing}")
sub.pcr_info = json.dumps(existing)
except TypeError:
logger.error(f"Error updating!")
sub.pcr_info = json.dumps([obj])
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
sub.pcr_info = json.dumps([obj])
self.ctx['database_session'].add(sub)
self.ctx["database_session"].commit()
dlg = AlertPop(message=f"We added {count} logs to the database.", status='information')
dlg.exec()
def importPCRResults(self):
"""
Imports results exported from Design and Analysis .eds files
"""
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "xlsx(*.xlsx)")[0])
parser = PCRParser(ctx=self.ctx, filepath=fname)
logger.debug(f"Attempting lookup for {parser.plate_num}")
sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=parser.plate_num)
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
logger.error(f"Submission of number {parser.plate_num} not found.")
return
# jout = json.dumps(parser.pcr)
count = 0
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
existing = json.loads(sub.pcr_info)
else:
# jout = None
existing = None
if existing != None:
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
if json.dumps(parser.pcr) not in sub.pcr_info:
existing.append(parser.pcr)
logger.debug(f"Setting: {existing}")
sub.pcr_info = json.dumps(existing)
except TypeError:
logger.error(f"Error updating!")
sub.pcr_info = json.dumps([parser.pcr])
logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
sub.pcr_info = json.dumps([parser.pcr])
self.ctx['database_session'].add(sub)
logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
self.ctx["database_session"].commit()
logger.debug(f"Got {len(parser.samples)} to update!")
for sample in parser.samples:
logger.debug(f"Running update on: {sample['sample']}")
update_ww_sample(ctx=self.ctx, sample_obj=sample)
dlg = AlertPop(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
dlg.exec()
class AddSubForm(QWidget):
def __init__(self, parent):