landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Moved import PCR results to context menu.

Browse Source
This commit is contained in:
Landon Wark
2024-04-11 09:33:16 -05:00
parent dc5549486f
commit f994f81d11
5 changed files with 59 additions and 89 deletions
Download Patch File Download Diff File Expand all files Collapse all files

75
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -112,81 +112,6 @@ class SubmissionFormContainer(QWidget):
logger.debug(f"Outgoing report: {self.report.results}")
logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def import_pcr_results(self):
"""
Pull QuantStudio results into db
"""
self.import_pcr_results_function()
self.app.report.add_result(self.report)
self.report = Report()
self.app.result_reporter()
def import_pcr_results_function(self):
"""
Import Quant-studio PCR data to an imported submission
Args:
obj (QMainWindow): original app window
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
report = Report()
fname = select_open_file(self, file_extension="xlsx")
parser = PCRParser(filepath=fname)
logger.debug(f"Attempting lookup for {parser.plate_num}")
sub = BasicSubmission.query(rsl_number=parser.plate_num)
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
# If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
sub = BasicSubmission.query(rsl_number=parser.plate_num)
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
logger.error(f"Rescue of {parser.plate_num} failed.")
self.report.add_result(Result(msg="Couldn't find a submission with that RSL number.", status="Warning"))
return
# Check if PCR info already exists
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
# existing = json.loads(sub.pcr_info)
existing = sub.pcr_info
else:
existing = None
if existing != None:
# update pcr_info
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
# if json.dumps(parser.pcr) not in sub.pcr_info:
if parser.pcr not in sub.pcr_info:
existing.append(parser.pcr)
logger.debug(f"Setting: {existing}")
# sub.pcr_info = json.dumps(existing)
sub.pcr_info = existing
except TypeError:
logger.error(f"Error updating!")
# sub.pcr_info = json.dumps([parser.pcr])
sub.pcr_info = [parser.pcr]
logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
else:
# sub.pcr_info = json.dumps([parser.pcr])
sub.pcr_info = [parser.pcr]
logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
sub.save(original=False)
logger.debug(f"Got {len(parser.samples)} samples to update!")
logger.debug(f"Parser samples: {parser.samples}")
for sample in sub.samples:
logger.debug(f"Running update on: {sample}")
try:
sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
except IndexError:
continue
sub.update_subsampassoc(sample=sample, input_dict=sample_dict)
self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
"""
Action to create new reagent in DB.