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Database updates, scraping samples from excel sheets

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This commit is contained in:
Landon Wark
2023-01-19 11:22:57 -06:00
parent e763e7273d
commit d17ee5862d
10 changed files with 206 additions and 53 deletions
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17
src/submissions/frontend/__init__.py
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@@ -90,6 +90,7 @@ class App(QMainWindow):
def importSubmission(self):
logger.debug(self.ctx)
self.samples = []
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
logger.debug(f"Attempting to parse file: {fname}")
@@ -107,27 +108,31 @@ class App(QMainWindow):
(?P<extraction_kit>^extraction_kit$) |
(?P<submitted_date>^submitted_date$) |
(?P<submitting_lab>)^submitting_lab$ |
(?P<samples>)^samples$ |
(?P<reagent>^lot_.*$)
""", re.VERBOSE)
for item in prsr.sub:
logger.debug(f"Item: {item}")
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
try:
mo = variable_parser.fullmatch(item).lastgroup
except AttributeError:
mo = "other"
print(f"Mo: {mo}")
match mo:
case 'submitting_lab':
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
print(f"{item}: {prsr.sub[item]}")
add_widget = QComboBox()
labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
try:
labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
except TypeError:
except (TypeError, ValueError):
pass
add_widget.addItems(labs)
case 'extraction_kit':
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
if prsr.sub[item] == 'nan':
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
@@ -143,10 +148,12 @@ class App(QMainWindow):
else:
add_widget.addItems(['bacterial_culture'])
case 'submitted_date':
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QDateEdit(calendarPopup=True)
# add_widget.setDateTime(QDateTime.date(prsr.sub[item]))
add_widget.setDate(prsr.sub[item])
case 'reagent':
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QComboBox()
add_widget.setEditable(True)
# Ensure that all reagenttypes have a name that matches the items in the excel parser
@@ -169,7 +176,12 @@ class App(QMainWindow):
relevant_reagents.insert(0, str(prsr.sub[item]))
logger.debug(f"Relevant reagents: {relevant_reagents}")
add_widget.addItems(relevant_reagents)
# TODO: make samples not appear in frame.
case 'samples':
print(f"{item}: {prsr.sub[item]}")
self.samples = prsr.sub[item]
case _:
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QLineEdit()
add_widget.setText(str(prsr.sub[item]).replace("_", " "))
self.table_widget.formlayout.addWidget(add_widget)
@@ -215,6 +227,7 @@ class App(QMainWindow):
if wanted_reagent != None:
parsed_reagents.append(wanted_reagent)
logger.debug(info)
info['samples'] = self.samples
base_submission = construct_submission_info(ctx=self.ctx, info_dict=info)
for reagent in parsed_reagents:
base_submission.reagents.append(reagent)