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Working new version.

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This commit is contained in:
Landon Wark
2023-09-11 13:45:10 -05:00
parent e0b80f6c7a
commit 5a978c9bff
15 changed files with 417 additions and 743 deletions
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32
src/submissions/frontend/main_window_functions.py
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@@ -25,7 +25,7 @@ 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_subsampassoc_with_pcr,
check_kit_integrity
)
from backend.excel.parser import SheetParser, PCRParser
@@ -133,7 +133,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
# lookup existing kits by 'submission_type' decided on by sheetparser
# uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'].lower())]
logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'])]
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
if check_not_nan(value['value']):
logger.debug(f"The extraction kit in parser was: {value['value']}")
@@ -365,7 +365,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
if kit_integrity != None:
return obj, dict(message=kit_integrity['message'], status="critical")
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
result = store_submission(ctx=obj.ctx, base_submission=base_submission, samples=obj.samples)
result = store_submission(ctx=obj.ctx, base_submission=base_submission)
# check result of storing for issues
# update summary sheet
obj.table_widget.sub_wid.setData()
@@ -383,7 +383,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
# excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
input_reagents = [item.to_reagent_dict() for item in parsed_reagents]
input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in parsed_reagents]
logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
if hasattr(obj, 'csv'):
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
@@ -844,10 +845,16 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
obj.ctx.database_session.commit()
logger.debug(f"Got {len(parser.samples)} samples to update!")
logger.debug(f"Parser samples: {parser.samples}")
for sample in parser.samples:
logger.debug(f"Running update on: {sample['sample']}")
sample['plate_rsl'] = sub.rsl_plate_num
update_ww_sample(ctx=obj.ctx, sample_obj=sample)
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
# sample['plate_rsl'] = sub.rsl_plate_num
# update_ww_sample(ctx=obj.ctx, sample_obj=sample)
update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
return obj, result
@@ -872,7 +879,16 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
# pare down the xl map to only the missing data.
relevant_reagent_map = {k:v for k,v in xl_map.items() if k in [reagent.type for reagent in missing_reagents]}
# pare down reagents to only what's missing
logger.debug(f"Checking {[item['type'] for item in reagents]} against {[reagent.type for reagent in missing_reagents]}")
relevant_reagents = [item for item in reagents if item['type'] in [reagent.type for reagent in missing_reagents]]
# relevant_reagents = []
# for item in reagents:
# logger.debug(f"Checking {item['type']} in {[reagent.type for reagent in missing_reagents]}")
# if item['type'] in [reagent.type for reagent in missing_reagents]:
# logger.debug("Hit!")
# relevant_reagents.append(item)
# else:
# logger.debug('Miss.')
logger.debug(f"Here are the relevant reagents: {pprint.pformat(relevant_reagents)}")
# hacky manipulation of submission type so it looks better.
# info['submission_type'] = info['submission_type'].replace("_", " ").title()