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Updated controls to both Irida and PCR.

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This commit is contained in:
lwark
2024-10-16 15:07:43 -05:00
parent 066d1af0f2
commit c3a4aac68b
11 changed files with 750 additions and 314 deletions
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114
src/submissions/backend/db/models/submissions.py
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@@ -13,7 +13,7 @@ from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, desc
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy
@@ -22,7 +22,6 @@ from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityErr
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import pandas as pd
from openpyxl import Workbook
from openpyxl.worksheet.worksheet import Worksheet
from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
report_result
@@ -32,8 +31,6 @@ from dateutil.parser import parse
from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
from docxtpl import InlineImage
from docx.shared import Inches
from PIL import Image
logger = logging.getLogger(f"submissions.{__name__}")
@@ -74,6 +71,8 @@ class BasicSubmission(BaseClass):
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
name="fk_BS_contact_id")) #: client lab id from _organizations
custom = Column(JSON)
controls = relationship("Control", back_populates="submission",
uselist=True) #: A control sample added to submission
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
@@ -114,7 +113,6 @@ class BasicSubmission(BaseClass):
# NOTE: Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
__mapper_args__ = {
"polymorphic_identity": "Basic Submission",
# "polymorphic_on": submission_type_name,
"polymorphic_on": case(
(submission_type_name == "Wastewater", "Wastewater"),
@@ -190,7 +188,7 @@ class BasicSubmission(BaseClass):
# NOTE: Singles tells the query which fields to set limit to 1
dicto['singles'] = parent_defs['singles']
# logger.debug(dicto['singles'])
# NOTE: Grab subtype specific info.
# NOTE: Grab mode_sub_type specific info.
output = {}
for k, v in dicto.items():
if len(args) > 0 and k not in args:
@@ -960,7 +958,6 @@ class BasicSubmission(BaseClass):
pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
# logger.debug(f'sample map: {pcr_sample_map}')
main_sheet = xl[pcr_sample_map['main_sheet']]
# samples = []
fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']}
for row in main_sheet.iter_rows(min_row=pcr_sample_map['start_row']):
idx = row[0].row
@@ -969,12 +966,11 @@ class BasicSubmission(BaseClass):
sheet = xl[v['sheet']]
sample[k] = sheet.cell(row=idx, column=v['column']).value
yield sample
# samples.append(sample)
# return samples
@classmethod
def parse_pcr_controls(cls, xl: Workbook) -> list:
def parse_pcr_controls(cls, xl: Workbook, rsl_plate_num: str) -> list:
location_map = cls.get_submission_type().sample_map['pcr_controls']
submission = cls.query(rsl_plate_num=rsl_plate_num)
name_column = 1
for item in location_map:
logger.debug(f"Looking for {item['name']}")
@@ -983,7 +979,29 @@ class BasicSubmission(BaseClass):
for cell in row:
if cell.value == item['name']:
logger.debug(f"Pulling from row {iii}, column {item['ct_column']}")
yield dict(name=item['name'], ct=worksheet.cell(row=iii, column=item['ct_column']).value)
subtype, target = item['name'].split("-")
ct = worksheet.cell(row=iii, column=item['ct_column']).value
if subtype == "PC":
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["positive control" in item.name.lower() for item in assoc.reagent.role])), None)
elif subtype == "NC":
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["molecular grade water" in item.name.lower() for item in assoc.reagent.role])), None)
try:
ct = float(ct)
except ValueError:
ct = 0.0
if ctrl:
ctrl = ctrl.lot
else:
ctrl = None
yield dict(
name=f"{rsl_plate_num}<{item['name']}>",
ct=ct,
subtype=subtype,
target=target,
reagent_lot=ctrl
)
@classmethod
def filename_template(cls) -> str:
@@ -996,21 +1014,6 @@ class BasicSubmission(BaseClass):
"""
return "{{ rsl_plate_num }}"
# @classmethod
# def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
# """
# Updates row information
#
# Args:
# sample (_type_): _description_
# worksheet (Workbook): _description_
#
# Returns:
# int: New row number
# """
# logger.debug(f"Sample from args: {sample}")
# return None
@classmethod
def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
"""
@@ -1025,19 +1028,6 @@ class BasicSubmission(BaseClass):
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} sampler")
return samples
# def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
# """
# Updates sample dictionaries with custom values
#
# Args:
# backup (bool, optional): Whether to perform backup. Defaults to False.
#
# Returns:
# List[dict]: Updated dictionaries
# """
# # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
# return [item.to_sub_dict() for item in self.submission_sample_associations]
@classmethod
def get_details_template(cls, base_dict: dict) -> Template:
"""
@@ -1380,8 +1370,7 @@ class BacterialCulture(BasicSubmission):
derivative submission type from BasicSubmission
"""
id = Column(INTEGER, ForeignKey('_basicsubmission.id'), primary_key=True)
controls = relationship("Control", back_populates="submission",
uselist=True) #: A control sample added to submission
__mapper_args__ = dict(polymorphic_identity="Bacterial Culture",
polymorphic_load="inline",
inherit_condition=(id == BasicSubmission.id))
@@ -1442,25 +1431,6 @@ class BacterialCulture(BasicSubmission):
pos_control_reg.missing = False
return pyd
# @classmethod
# def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
# """
# Extends parent
# """
# # logger.debug(f"Checking {sample.well}")
# # logger.debug(f"here's the worksheet: {worksheet}")
# row = super().custom_sample_autofill_row(sample, worksheet)
# df = pd.DataFrame(list(worksheet.values))
# # logger.debug(f"Here's the dataframe: {df}")
# idx = df[df[0] == sample.well]
# if idx.empty:
# new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
# # logger.debug(f"Checking: {new}")
# idx = df[df[0] == new]
# # logger.debug(f"Here is the row: {idx}")
# row = idx.index.to_list()[0]
# return row + 1
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
@@ -1548,7 +1518,7 @@ class Wastewater(BasicSubmission):
for sample in samples:
# NOTE: remove '-{target}' from controls
sample['sample'] = re.sub('-N\\d$', '', sample['sample'])
# # NOTE: if sample is already in output skip
# NOTE: if sample is already in output skip
if sample['sample'] in [item['sample'] for item in output]:
logger.warning(f"Already have {sample['sample']}")
continue
@@ -1577,8 +1547,6 @@ class Wastewater(BasicSubmission):
# @classmethod
# def parse_pcr_controls(cls, xl: Workbook, location_map: list) -> list:
@classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
"""
@@ -1681,15 +1649,17 @@ class Wastewater(BasicSubmission):
obj (_type_): Parent widget
"""
from backend.excel import PCRParser
from backend.db import PCRControl, ControlType
from frontend.widgets import select_open_file
report = Report()
fname = select_open_file(obj=obj, file_extension="xlsx")
if not fname:
report.add_result(Result(msg="No file selected, cancelling.", status="Warning"))
return report
parser = PCRParser(filepath=fname)
parser = PCRParser(filepath=fname, submission=self)
self.set_attribute("pcr_info", parser.pcr)
pcr_samples = [sample for sample in parser.samples]
pcr_controls = [control for control in parser.controls]
self.save(original=False)
# logger.debug(f"Got {len(parser.samples)} samples to update!")
# logger.debug(f"Parser samples: {parser.samples}")
@@ -1700,6 +1670,16 @@ class Wastewater(BasicSubmission):
except StopIteration:
continue
self.update_subsampassoc(sample=sample, input_dict=sample_dict)
controltype = ControlType.query(name="PCR Control")
logger.debug(parser.pcr)
submitted_date = datetime.strptime(" ".join(parser.pcr['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
for control in pcr_controls:
new_control = PCRControl(**control)
new_control.submitted_date = submitted_date
new_control.controltype = controltype
new_control.submission = self
new_control.save()
class WastewaterArtic(BasicSubmission):
@@ -2207,7 +2187,7 @@ class BasicSample(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
submitter_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
sample_type = Column(String(32)) #: subtype of sample
sample_type = Column(String(32)) #: mode_sub_type of sample
sample_submission_associations = relationship(
"SubmissionSampleAssociation",
@@ -2632,7 +2612,7 @@ class BacterialCultureSample(BasicSample):
id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
organism = Column(String(64)) #: bacterial specimen
concentration = Column(String(16)) #: sample concentration
control = relationship("Control", back_populates="sample", uselist=False)
control = relationship("IridaControl", back_populates="sample", uselist=False)
__mapper_args__ = dict(polymorphic_identity="Bacterial Culture Sample",
polymorphic_load="inline",
inherit_condition=(id == BasicSample.id))
@@ -2677,7 +2657,7 @@ class SubmissionSampleAssociation(BaseClass):
# reference to the Sample object
sample = relationship(BasicSample, back_populates="sample_submission_associations") #: associated sample
base_sub_type = Column(String) #: string of subtype name
base_sub_type = Column(String) #: string of mode_sub_type name
# Refers to the type of parent.
# Hooooooo boy, polymorphic association type, now we're getting into the weeds!