Split Concentration controls on the chart so they are individually selectable.
This commit is contained in:
lwark
@@ -13,7 +13,6 @@ from zipfile import ZipFile, BadZipfile
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from tempfile import TemporaryDirectory, TemporaryFile
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from operator import itemgetter
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from pprint import pformat
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from pandas import DataFrame
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from sqlalchemy.ext.hybrid import hybrid_property
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from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
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@@ -27,10 +26,9 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
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from openpyxl import Workbook
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from openpyxl.drawing.image import Image as OpenpyxlImage
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from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
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report_result, create_holidays_for_year, check_dictionary_inclusion_equality, rectify_query_date
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from datetime import datetime, date, timedelta
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report_result, create_holidays_for_year, check_dictionary_inclusion_equality
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from datetime import datetime, date
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from typing import List, Any, Tuple, Literal, Generator, Type
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from dateutil.parser import parse
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from pathlib import Path
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from jinja2.exceptions import TemplateNotFound
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from jinja2 import Template
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@@ -271,7 +269,6 @@ class BasicSubmission(BaseClass, LogMixin):
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Returns:
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dict: sample location map
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"""
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# return cls.get_submission_type(submission_type).construct_sample_map()
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return cls.get_submission_type(submission_type).sample_map
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def generate_associations(self, name: str, extra: str | None = None):
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@@ -445,11 +442,11 @@ class BasicSubmission(BaseClass, LogMixin):
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except Exception as e:
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logger.error(f"Column count error: {e}")
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# NOTE: Get kit associated with this submission
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logger.debug(f"Checking associations with submission type: {self.submission_type_name}")
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# logger.debug(f"Checking associations with submission type: {self.submission_type_name}")
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assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if
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item.submission_type == self.submission_type),
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None)
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logger.debug(f"Got association: {assoc}")
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# logger.debug(f"Got association: {assoc}")
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# NOTE: If every individual cost is 0 this is probably an old plate.
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if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
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try:
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@@ -635,16 +632,13 @@ class BasicSubmission(BaseClass, LogMixin):
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# NOTE: No longer searches for association here, done in caller function
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for k, v in input_dict.items():
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try:
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# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
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setattr(assoc, k, v)
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# NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
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except AttributeError:
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# logger.error(f"Can't set {k} to {v}")
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pass
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return assoc
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def update_reagentassoc(self, reagent: Reagent, role: str):
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from backend.db import SubmissionReagentAssociation
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# NOTE: get the first reagent assoc that fills the given role.
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try:
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assoc = next(item for item in self.submission_reagent_associations if
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@@ -1134,7 +1128,7 @@ class BasicSubmission(BaseClass, LogMixin):
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Returns:
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models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest
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"""
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from ... import SubmissionReagentAssociation
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# from ... import SubmissionReagentAssociation
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# NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
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if submissiontype is not None:
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model = cls.find_polymorphic_subclass(polymorphic_identity=submissiontype)
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@@ -1181,8 +1175,8 @@ class BasicSubmission(BaseClass, LogMixin):
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# # start_date = start_date.strftime("%Y-%m-%d %H:%M:%S.%f")
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# # query = query.filter(model.submitted_date == start_date)
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# # else:
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start_date = rectify_query_date(start_date)
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end_date = rectify_query_date(end_date, eod=True)
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start_date = cls.rectify_query_date(start_date)
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end_date = cls.rectify_query_date(end_date, eod=True)
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query = query.filter(model.submitted_date.between(start_date, end_date))
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# NOTE: by reagent (for some reason)
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match reagent:
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@@ -1575,19 +1569,40 @@ class BacterialCulture(BasicSubmission):
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column=lookup_table['sample_columns']['concentration']).value
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yield sample
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def get_provisional_controls(self, controls_only: bool = True):
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if controls_only:
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if self.controls:
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provs = (control.sample for control in self.controls)
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else:
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regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
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provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
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else:
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provs = self.samples
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for prov in provs:
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prov.submission = self.rsl_plate_num
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prov.submitted_date = self.submitted_date
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yield prov
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# def get_provisional_controls(self, controls_only: bool = True):
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def get_provisional_controls(self, include: List[str] = []):
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# NOTE To ensure Samples are done last.
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include = sorted(include)
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logger.debug(include)
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pos_str = "(ATCC)|(MCS)"
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pos_regex = re.compile(rf"^{pos_str}")
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neg_str = "(EN)"
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neg_regex = re.compile(rf"^{neg_str}")
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total_str = pos_str + "|" + neg_str
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total_regex = re.compile(rf"^{total_str}")
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output = []
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for item in include:
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# if self.controls:
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# logger.debug(item)
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match item:
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case "Positive":
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if self.controls:
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provs = (control.sample for control in self.controls if control.is_positive_control)
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else:
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provs = (sample for sample in self.samples if bool(pos_regex.match(sample.submitter_id)))
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case "Negative":
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if self.controls:
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provs = (control.sample for control in self.controls if not control.is_positive_control)
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else:
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provs = (sample for sample in self.samples if bool(neg_regex.match(sample.submitter_id)))
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case _:
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provs = (sample for sample in self.samples if not sample.control and sample not in output)
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for prov in provs:
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# logger.debug(f"Prov: {prov}")
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prov.submission = self.rsl_plate_num
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prov.submitted_date = self.submitted_date
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output.append(prov)
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return output
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class Wastewater(BasicSubmission):
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@@ -2794,8 +2809,7 @@ class WastewaterSample(BasicSample):
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output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_num']
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if output_dict['ww_full_sample_id'] is not None and output_dict["submitter_id"] in disallowed:
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output_dict["submitter_id"] = output_dict['ww_full_sample_id']
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check = check_key_or_attr("rsl_number", output_dict, check_none=True)
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# logger.debug(pformat(output_dict, indent=4))
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# check = check_key_or_attr("rsl_number", output_dict, check_none=True)
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return output_dict
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@classproperty
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@@ -3089,7 +3103,6 @@ class SubmissionSampleAssociation(BaseClass):
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Returns:
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SubmissionSampleAssociation: Queried or new association.
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"""
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# disallowed = ['id']
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match submission:
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case BasicSubmission():
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pass
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@@ -3184,7 +3197,6 @@ class WastewaterAssociation(SubmissionSampleAssociation):
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sample['background_color'] = f"rgb({red}, {grn}, {blu})"
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try:
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sample[
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# 'tooltip'] += f"<br>- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})<br>- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
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'tooltip'] += f"<br>- ct N1: {'{:.2f}'.format(self.ct_n1)}<br>- ct N2: {'{:.2f}'.format(self.ct_n2)}"
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except (TypeError, AttributeError) as e:
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logger.error(f"Couldn't set tooltip for {self.sample.rsl_number}. Looks like there isn't PCR data.")
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