209 lines
7.8 KiB
Python
209 lines
7.8 KiB
Python
"""
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Contains all validators
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"""
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import logging, re
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import sys
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from pathlib import Path
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from openpyxl import load_workbook
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from backend.db.models import BasicSubmission, SubmissionType
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from tools import jinja_template_loading
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from jinja2 import Template
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from dateutil.parser import parse
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from datetime import datetime
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logger = logging.getLogger(f"submissions.{__name__}")
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class RSLNamer(object):
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"""
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Object that will enforce proper formatting on RSL plate names.
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"""
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def __init__(self, filename: str, submission_type: str | None = None, data: dict | None = None):
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# NOTE: Preferred method is path retrieval, but might also need validation for just string.
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filename = Path(filename) if Path(filename).exists() else filename
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self.submission_type = submission_type
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if not self.submission_type:
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self.submission_type = self.retrieve_submission_type(filename=filename)
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logger.info(f"got submission type: {self.submission_type}")
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if self.submission_type:
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self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
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self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(
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submission_type=submission_type))
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if not data:
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data = dict(submission_type=self.submission_type)
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if "submission_type" not in data.keys():
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data['submission_type'] = self.submission_type
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self.parsed_name = self.sub_object.enforce_name(instr=self.parsed_name, data=data)
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logger.info(f"Parsed name: {self.parsed_name}")
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@classmethod
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def retrieve_submission_type(cls, filename: str | Path) -> str:
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"""
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Gets submission type from excel file properties or sheet names or regex pattern match or user input
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Args:
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filename (str | Path): filename
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Raises:
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TypeError: Raised if unsupported variable type for filename given.
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Returns:
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str: parsed submission type
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"""
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def st_from_path(filepath: Path) -> str:
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"""
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Sub def to get submissiontype from a file path
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Args:
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filepath ():
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Returns:
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"""
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if filepath.exists():
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wb = load_workbook(filepath)
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try:
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# NOTE: Gets first category in the metadata.
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categories = wb.properties.category.split(";")
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submission_type = next(item.strip().title() for item in categories)
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except (StopIteration, AttributeError):
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sts = {item.name: item.template_file_sheets for item in SubmissionType.query() if
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item.template_file}
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try:
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submission_type = next(k.title() for k, v in sts.items() if wb.sheetnames == v)
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except StopIteration:
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# NOTE: On failure recurse using filepath as string for string method
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submission_type = cls.retrieve_submission_type(filename=filepath.stem.__str__())
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else:
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submission_type = cls.retrieve_submission_type(filename=filepath.stem.__str__())
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return submission_type
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def st_from_str(file_name: str) -> str:
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if file_name.startswith("tmp"):
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return "Bacterial Culture"
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regex = BasicSubmission.regex
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m = regex.search(file_name)
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try:
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sub_type = m.lastgroup
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except AttributeError as e:
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sub_type = None
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logger.critical(f"No submission type found or submission type found!: {e}")
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return sub_type
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match filename:
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case Path():
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submission_type = st_from_path(filepath=filename)
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case str():
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submission_type = st_from_str(file_name=filename)
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case _:
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raise TypeError(f"Unsupported filename type: {type(filename)}.")
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try:
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check = submission_type is None
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except UnboundLocalError:
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check = True
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if check:
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if "pytest" in sys.modules:
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raise ValueError("Submission Type came back as None.")
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from frontend.widgets import ObjectSelector
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dlg = ObjectSelector(title="Couldn't parse submission type.",
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message="Please select submission type from list below.",
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obj_type=SubmissionType)
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if dlg.exec():
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submission_type = dlg.parse_form()
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submission_type = submission_type.replace("_", " ")
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return submission_type
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@classmethod
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def retrieve_rsl_number(cls, filename: str | Path, regex: re.Pattern | None = None):
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"""
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Uses regex to retrieve the plate number and submission type from an input string
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Args:
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regex (str): string to construct pattern
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filename (str): string to be parsed
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"""
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if regex is None:
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regex = BasicSubmission.regex
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match filename:
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case Path():
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m = regex.search(filename.stem)
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case str():
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m = regex.search(filename)
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case _:
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m = None
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if m is not None:
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try:
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parsed_name = m.group().upper().strip(".")
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except AttributeError:
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parsed_name = None
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else:
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parsed_name = None
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return parsed_name
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@classmethod
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def construct_new_plate_name(cls, data: dict) -> str:
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"""
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Make a brand-new plate name from submission data.
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Args:
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data (dict): incoming submission data
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Returns:
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str: Output filename
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"""
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if "submitted_date" in data.keys():
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if isinstance(data['submitted_date'], dict):
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if data['submitted_date']['value'] is not None:
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today = data['submitted_date']['value']
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else:
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today = datetime.now()
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else:
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today = data['submitted_date']
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else:
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try:
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today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
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today = parse(today.group())
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except (AttributeError, KeyError):
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today = datetime.now()
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if "rsl_plate_num" in data.keys():
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plate_number = data['rsl_plate_num'].split("-")[-1][0]
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else:
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previous = BasicSubmission.query(start_date=today, end_date=today, submissiontype=data['submission_type'])
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plate_number = len(previous) + 1
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return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
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@classmethod
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def construct_export_name(cls, template: Template, **kwargs) -> str:
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"""
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Make export file name from jinja template. (currently unused)
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Args:
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template (jinja2.Template): Template stored in BasicSubmission
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Returns:
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str: output file name.
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"""
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environment = jinja_template_loading()
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template = environment.from_string(template)
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return template.render(**kwargs)
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def calculate_repeat(self) -> str:
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"""
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Determines what repeat number this plate is.
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Returns:
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str: Repeat number.
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"""
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regex = re.compile(r"-\d(?P<repeat>R\d)")
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m = regex.search(self.parsed_name)
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if m is not None:
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return m.group("repeat")
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else:
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return ""
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from .pydant import PydSubmission, PydKitType, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
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PydEquipment, PydEquipmentRole, PydTips, PydPCRControl, PydIridaControl, PydProcess, PydElastic
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