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Automated Control lot retrieval

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This commit is contained in:
Landon Wark
2024-04-17 07:53:11 -05:00
parent 9e2c66a865
commit c9bd8d1425
5 changed files with 103 additions and 54 deletions
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2
TODO.md
View File

@@ -1,3 +1,5 @@
- [ ] Fix Parsed/Missing mix ups.
- [x] Have sample parser check for controls and add to reagents?
- [x] Update controls to NestedMutableJson
- [x] Appending of qPCR results to WW not saving. Find out why.
- Possibly due to immutable JSON? But... it's worked before... Right?

15
src/submissions/backend/db/models/controls.py
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@@ -5,7 +5,7 @@ from __future__ import annotations
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
from sqlalchemy.orm import relationship, Query
from sqlalchemy_json import NestedMutableJson
import logging
import logging, re
from operator import itemgetter
from . import BaseClass
from tools import setup_lookup
@@ -25,6 +25,9 @@ class ControlType(BaseClass):
targets = Column(JSON) #: organisms checked for
instances = relationship("Control", back_populates="controltype") #: control samples created of this type.
def __repr__(self) -> str:
return f"<ControlType({self.name})>"
@classmethod
@setup_lookup
def query(cls,
@@ -74,6 +77,16 @@ class ControlType(BaseClass):
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
return subtypes
@classmethod
def get_positive_control_types(cls):
return [item for item in cls.query() if item.targets != []]
@classmethod
def build_positive_regex(cls):
strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
class Control(BaseClass):
"""
Base class of a control sample.

125
src/submissions/backend/db/models/submissions.py
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@@ -1117,6 +1117,39 @@ class BacterialCulture(BasicSubmission):
# input_dict['submitted_date']['missing'] = True
# return input_dict
@classmethod
def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None, plate_map: dict | None = None) -> dict:
"""
Extends parent. Currently finds control sample and adds to reagents.
Args:
input_dict (dict): _description_
xl (pd.ExcelFile | None, optional): _description_. Defaults to None.
info_map (dict | None, optional): _description_. Defaults to None.
plate_map (dict | None, optional): _description_. Defaults to None.
Returns:
dict: _description_
"""
from . import ControlType
input_dict = super().finalize_parse(input_dict, xl, info_map, plate_map)
# build regex for all control types that have targets
regex = ControlType.build_positive_regex()
# search samples for match
for sample in input_dict['samples']:
matched = regex.match(sample.submitter_id)
if bool(matched):
logger.debug(f"Control match found: {sample.submitter_id}")
new_lot = matched.group()
try:
pos_control_reg = [reg for reg in input_dict['reagents'] if reg.type=="Bacterial-Positive Control"][0]
except IndexError:
logger.error(f"No positive control reagent listed")
return input_dict
pos_control_reg.lot = new_lot
pos_control_reg.missing = False
return input_dict
@classmethod
def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
"""
@@ -1505,53 +1538,53 @@ class WastewaterArtic(BasicSubmission):
# logger.debug(pformat(input_dict))
# logger.debug(pformat(info_map))
# logger.debug(pformat(plate_map))
samples = []
for sample in input_dict['samples']:
logger.debug(f"Input sample: {pformat(sample.__dict__)}")
if sample.submitter_id == "NTC1":
samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=2, source_row=0, source_column=0, plate_number='control', plate=None))
continue
elif sample.submitter_id == "NTC2":
samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=5, source_row=0, source_column=0, plate_number='control', plate=None))
continue
destination_row = sample.row[0]
destination_column = sample.column[0]
# logger.debug(f"Looking up: {sample.submitter_id} friend.")
lookup_sample = BasicSample.query(submitter_id=sample.submitter_id)
lookup_ssa = SubmissionSampleAssociation.query(sample=lookup_sample, exclude_submission_type=cls.__mapper_args__['polymorphic_identity'] , chronologic=True, reverse=True, limit=1)
try:
plate = lookup_ssa.submission.rsl_plate_num
source_row = lookup_ssa.row
source_column = lookup_ssa.column
except AttributeError as e:
logger.error(f"Problem with lookup: {e}")
plate = "Error"
source_row = 0
source_column = 0
# samples = []
# for sample in input_dict['samples']:
# logger.debug(f"Input sample: {pformat(sample.__dict__)}")
# if sample.submitter_id == "NTC1":
# samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=2, source_row=0, source_column=0, plate_number='control', plate=None))
# continue
output_sample = dict(
sample=sample.submitter_id,
destination_column=destination_column,
destination_row=destination_row,
plate=plate,
source_column=source_column,
source_row = source_row
)
logger.debug(f"output sample: {pformat(output_sample)}")
samples.append(output_sample)
plates = sorted(list(set([sample['plate'] for sample in samples if sample['plate'] != None and sample['plate'] != "Error"])))
logger.debug(f"Here's what I got for plates: {plates}")
for iii, plate in enumerate(plates):
for sample in samples:
if sample['plate'] == plate:
sample['plate_number'] = iii + 1
df = pd.DataFrame.from_records(samples).fillna(value="")
try:
df.source_row = df.source_row.astype(int)
df.source_column = df.source_column.astype(int)
df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
except AttributeError as e:
logger.error(f"Couldn't construct df due to {e}")
# elif sample.submitter_id == "NTC2":
# samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=5, source_row=0, source_column=0, plate_number='control', plate=None))
# continue
# destination_row = sample.row[0]
# destination_column = sample.column[0]
# # logger.debug(f"Looking up: {sample.submitter_id} friend.")
# lookup_sample = BasicSample.query(submitter_id=sample.submitter_id)
# lookup_ssa = SubmissionSampleAssociation.query(sample=lookup_sample, exclude_submission_type=cls.__mapper_args__['polymorphic_identity'] , chronologic=True, reverse=True, limit=1)
# try:
# plate = lookup_ssa.submission.rsl_plate_num
# source_row = lookup_ssa.row
# source_column = lookup_ssa.column
# except AttributeError as e:
# logger.error(f"Problem with lookup: {e}")
# plate = "Error"
# source_row = 0
# source_column = 0
# # continue
# output_sample = dict(
# sample=sample.submitter_id,
# destination_column=destination_column,
# destination_row=destination_row,
# plate=plate,
# source_column=source_column,
# source_row = source_row
# )
# logger.debug(f"output sample: {pformat(output_sample)}")
# samples.append(output_sample)
# plates = sorted(list(set([sample['plate'] for sample in samples if sample['plate'] != None and sample['plate'] != "Error"])))
# logger.debug(f"Here's what I got for plates: {plates}")
# for iii, plate in enumerate(plates):
# for sample in samples:
# if sample['plate'] == plate:
# sample['plate_number'] = iii + 1
# df = pd.DataFrame.from_records(samples).fillna(value="")
# try:
# df.source_row = df.source_row.astype(int)
# df.source_column = df.source_column.astype(int)
# df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
# except AttributeError as e:
# logger.error(f"Couldn't construct df due to {e}")
# input_dict['csv'] = df
input_dict['csv'] = xl.parse("hitpicks_csv_to_export")
return input_dict

4
src/submissions/backend/validators/pydant.py
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@@ -809,8 +809,8 @@ class PydSubmission(BaseModel, extra='allow'):
# # what reagent types are in both lists?
# missing = list(set(ext_kit_rtypes).difference(reagenttypes))
missing = []
# output_reagents = self.reagents
output_reagents = ext_kit_rtypes
output_reagents = self.reagents
# output_reagents = ext_kit_rtypes
logger.debug(f"Already have these reagent types: {reagenttypes}")
for rt in ext_kit_rtypes:
if rt.type not in reagenttypes:

9
src/submissions/frontend/widgets/submission_widget.py
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@@ -369,7 +369,7 @@ class SubmissionFormWidget(QWidget):
match result.code:
# code 0: everything is fine.
case 0:
self.report.add_result(None)
report.add_result(None)
# code 1: ask for overwrite
case 1:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
@@ -379,11 +379,11 @@ class SubmissionFormWidget(QWidget):
result = None
else:
self.app.ctx.database_session.rollback()
self.report.add_result(Result(msg="Overwrite cancelled", status="Information"))
report.add_result(Result(msg="Overwrite cancelled", status="Information"))
return
# code 2: No RSL plate number given
case 2:
self.report.add_result(result)
report.add_result(result)
return
case _:
pass
@@ -457,7 +457,8 @@ class SubmissionFormWidget(QWidget):
for k,v in info.items():
self.pyd.set_attribute(key=k, value=v)
# return submission
self.report.add_result(report)
report.add_result(report)
return report
class InfoItem(QWidget):