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Missing sample message after Artic parsing.

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This commit is contained in:
Landon Wark
2023-06-16 13:58:28 -05:00
parent a7132cd1b4
commit 0bdcad0eee
11 changed files with 199 additions and 45 deletions
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18
src/submissions/frontend/main_window_functions.py
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@@ -26,7 +26,7 @@ from backend.db.functions import (
lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name,
construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range,
create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample
lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample, hitpick_plate
)
from backend.excel.parser import SheetParser, PCRParser
from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
@@ -35,6 +35,7 @@ from .custom_widgets.pop_ups import AlertPop, QuestionAsker
from .custom_widgets import ReportDatePicker, ReagentTypeForm
from .custom_widgets.misc import ImportReagent
from .visualizations.control_charts import create_charts, construct_html
from .visualizations import make_plate_map
logger = logging.getLogger(f"submissions.{__name__}")
@@ -60,6 +61,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
if prsr.sub['rsl_plate_num'] == None:
prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
logger.debug(f"prsr.sub = {prsr.sub}")
obj.current_submission_type = prsr.sub['submission_type']
# destroy any widgets from previous imports
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
@@ -111,7 +113,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
obj.ext_kit = prsr.sub[item]
else:
logger.error(f"Couldn't find prsr.sub[extraction_kit]")
logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
case 'submitted_date':
@@ -156,6 +158,9 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
if hasattr(obj, 'ext_kit'):
obj.kit_integrity_completion()
logger.debug(f"Imported reagents: {obj.reagents}")
if prsr.sample_result != None:
msg = AlertPop(message=prsr.sample_result, status="WARNING")
msg.exec()
return obj, result
def kit_reload_function(obj:QMainWindow) -> QMainWindow:
@@ -263,6 +268,7 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
# reset form
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
logger.debug(f"All attributes of obj: {pprint.pprint(obj.__dict__)}")
if hasattr(obj, 'csv'):
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
if dlg.exec():
@@ -271,6 +277,14 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
obj.csv.to_csv(fname.__str__(), index=False)
except PermissionError:
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
try:
delattr(obj, "csv")
except AttributeError:
pass
# if obj.current_submission_type == "Bacterial_Culture":
# hitpick = hitpick_plate(base_submission)
# image = make_plate_map(hitpick)
# image.show()
return obj, result
def generate_report_function(obj:QMainWindow) -> QMainWindow: