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Preparing for production testing using Bacterial Culture

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This commit is contained in:
lwark
2025-08-06 13:26:37 -05:00
parent 6f134d3870
commit 087bf9bcb7
24 changed files with 757 additions and 650 deletions
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143
src/submissions/backend/excel/parsers/clientsubmission_parser.py
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@@ -5,14 +5,12 @@ from __future__ import annotations
import logging
from pathlib import Path
from string import ascii_lowercase
from typing import Generator
from typing import Generator, TYPE_CHECKING, Literal
from openpyxl.reader.excel import load_workbook
from tools import row_keys
# from backend.db.models import SubmissionType
from . import DefaultKEYVALUEParser, DefaultTABLEParser
if TYPE_CHECKING:
from backend.db.models import SubmissionType
logger = logging.getLogger(f"submissions.{__name__}")
@@ -20,7 +18,16 @@ logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionTyperMixin(object):
@classmethod
def retrieve_submissiontype(cls, filepath: Path):
def retrieve_submissiontype(cls, filepath: Path) -> "SubmissionType":
"""
Gets the submission type from a file.
Args:
filepath (Path): The import file
Returns:
SubmissionType: The determined submissiontype
"""
# NOTE: Attempt 1, get from form properties:
sub_type = cls.get_subtype_from_properties(filepath=filepath)
if not sub_type:
@@ -35,7 +42,16 @@ class SubmissionTyperMixin(object):
return sub_type
@classmethod
def get_subtype_from_regex(cls, filepath: Path):
def get_subtype_from_regex(cls, filepath: Path) -> "SubmissionType":
"""
Uses regex of the file name to determine submissiontype
Args:
filepath (Path): The import file
Returns:
SubmissionType: The determined submissiontype
"""
from backend.db.models import SubmissionType
regex = SubmissionType.regex
m = regex.search(filepath.__str__())
@@ -43,21 +59,42 @@ class SubmissionTyperMixin(object):
sub_type = m.lastgroup
except AttributeError as e:
sub_type = None
logger.critical(f"No procedure type found or procedure type found!: {e}")
logger.critical(f"No submission type or procedure type found!: {e}")
sub_type = SubmissionType.query(name=sub_type, limit=1)
if not sub_type:
return
return sub_type
@classmethod
def get_subtype_from_preparse(cls, filepath: Path):
def get_subtype_from_preparse(cls, filepath: Path) -> "SubmissionType":
"""
Performs a default parse of the file in an attempt to find the submission type.
Args:
filepath (Path): The import file
Returns:
SubmissionType: The determined submissiontype
"""
from backend.db.models import SubmissionType
parser = ClientSubmissionInfoParser(filepath)
sub_type = next((value for k, value in parser.parsed_info.items() if k == "submissiontype"), None)
sub_type = SubmissionType.query(name=sub_type)
parser = ClientSubmissionInfoParser(filepath=filepath, submissiontype=SubmissionType.query(name="Test"))
sub_type = next((value for k, value in parser.parsed_info.items() if k == "submissiontype" or k == "submission_type"), None)
sub_type = SubmissionType.query(name=sub_type.title())
if isinstance(sub_type, list):
sub_type = None
return
return sub_type
@classmethod
def get_subtype_from_properties(cls, filepath: Path):
def get_subtype_from_properties(cls, filepath: Path) -> "SubmissionType":
"""
Attempts to get submission type from the xl metadata.
Args:
filepath (Path): The import file
Returns:
SubmissionType: The determined submissiontype
"""
from backend.db.models import SubmissionType
wb = load_workbook(filepath)
# NOTE: Gets first category in the metadata.
@@ -65,62 +102,56 @@ class SubmissionTyperMixin(object):
sub_type = next((item.strip().title() for item in categories), None)
sub_type = SubmissionType.query(name=sub_type)
if isinstance(sub_type, list):
sub_type = None
return
return sub_type
class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
"""
Object for retrieving submitter info from "sample list" sheet
Object for retrieving submitter info from "Client Info" sheet
"""
pyd_name = "PydClientSubmission"
default_range_dict = [dict(
start_row=2,
end_row=16,
key_column=1,
value_column=2,
sheet="Sample List"
)]
def __init__(self, filepath: Path | str, submissiontype:"SubmissionType"|None=None, *args, **kwargs):
from frontend.widgets.pop_ups import QuestionAsker
from backend.managers import procedures as procedure_managers
def __init__(self, filepath: Path | str, submissiontype: "SubmissionType" | None = None, *args, **kwargs):
logger.debug(f"Set submission type: {submissiontype}")
if not submissiontype:
self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
else:
self.submissiontype = submissiontype
# if "range_dict" not in kwargs:
# kwargs['range_dict'] = self.submissiontype.info_map
super().__init__(filepath=filepath, range_dict=[dict(sheet="Client Info")], **kwargs)
allowed_procedure_types = [item.name for item in self.submissiontype.proceduretype]
for name in allowed_procedure_types:
if name in self.workbook.sheetnames:
# TODO: check if run with name already exists
add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
if add_run.accepted:
# NOTE: recruit parser.
try:
manager = getattr(procedure_managers, name)
except AttributeError:
manager = procedure_managers.DefaultManager
self.manager = manager(proceduretype=name)
pass
super().__init__(filepath=filepath, sheet="Client Info", start_row=1, **kwargs)
# NOTE: move to the manager class.
# allowed_procedure_types = [item.name for item in self.submissiontype.proceduretype]
# for name in allowed_procedure_types:
# if name in self.workbook.sheetnames:
# # TODO: check if run with name already exists
# add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
# if add_run.accepted:
# # NOTE: recruit parser.
# try:
# manager = getattr(procedure_managers, name)
# except AttributeError:
# manager = procedure_managers.DefaultManager
# self.manager = manager(proceduretype=name)
# pass
@property
def parsed_info(self):
output = {k:v for k, v in super().parsed_info}
output = {k: v for k, v in super().parsed_info}
try:
output['clientlab'] = output['client_lab']
except KeyError:
pass
# output['submissiontype'] = dict(value=self.submissiontype.name.title())
try:
output['submissiontype'] = output['submission_type']
output['submissiontype']['value'] = self.submissiontype.name.title()
except KeyError:
pass
logger.debug(f"Data: {output}")
output['submissiontype'] = self.submissiontype.name
return output
class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
"""
Object for retrieving submitter samples from "sample list" sheet
@@ -128,32 +159,26 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
pyd_name = "PydSample"
default_range_dict = [dict(
header_row=18,
end_row=114,
sheet="Sample List"
)]
def __init__(self, filepath: Path | str, submissiontype: "SubmissionType"|None=None, *args, **kwargs):
def __init__(self, filepath: Path | str, submissiontype: "SubmissionType" | None = None, start_row: int = 1, *args,
**kwargs):
if not submissiontype:
self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
else:
self.submissiontype = submissiontype
if "range_dict" not in kwargs:
kwargs['range_dict'] = self.submissiontype.sample_map
super().__init__(filepath=filepath, **kwargs)
super().__init__(filepath=filepath, sheet="Client Info", start_row=start_row, **kwargs)
@property
def parsed_info(self) -> Generator[dict, None, None]:
output = super().parsed_info
for ii, sample in enumerate(output):
logger.debug(f"Parsed info sample: {sample}")
for ii, sample in enumerate(output, start=1):
# logger.debug(f"Parsed info sample: {sample}")
if isinstance(sample["row"], str) and sample["row"].lower() in ascii_lowercase[0:8]:
try:
sample["row"] = row_keys[sample["row"]]
except KeyError:
pass
sample['submission_rank'] = ii + 1
sample['submission_rank'] = ii
yield sample
def to_pydantic(self):