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Added in checkbox to use all samples in Concentrations tab (very slow).

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This commit is contained in:
lwark
2025-04-02 12:16:12 -05:00
parent e355aee5de
commit d3807dac57
10 changed files with 184 additions and 49 deletions
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6
src/submissions/backend/db/models/__init__.py
View File

@@ -60,7 +60,7 @@ class BaseClass(Base):
try:
return f"<{self.__class__.__name__}({self.name})>"
except AttributeError:
return f"<{self.__class__.__name__}({self.__name__})>"
return f"<{self.__class__.__name__}(Unknown)>"
# @classproperty
# def skip_on_edit(cls):
@@ -411,13 +411,13 @@ class BaseClass(Base):
except AttributeError:
return super().__setattr__(key, value)
if isinstance(field_type, InstrumentedAttribute):
logger.debug(f"{key} is an InstrumentedAttribute.")
# logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.property:
case ColumnProperty():
# logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value)
case _RelationshipDeclared():
logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
# logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
if field_type.property.uselist:
logger.debug(f"Setting with uselist")
existing = self.__getattribute__(key)

161
src/submissions/backend/db/models/submissions.py
View File

@@ -2,6 +2,8 @@
Models for the main submission and sample types.
"""
from __future__ import annotations
import pickle
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
@@ -588,7 +590,39 @@ class BasicSubmission(BaseClass, LogMixin):
except AttributeError as e:
logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
# def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Update a joined submission sample association.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
# for k, v in input_dict.items():
# try:
# # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
# setattr(assoc, k, v)
# # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
# except AttributeError:
# logger.error(f"Can't set {k} to {v}")
# return assoc
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
"""
Update a joined submission sample association.
@@ -599,19 +633,26 @@ class BasicSubmission(BaseClass, LogMixin):
Returns:
SubmissionSampleAssociation: Updated association
"""
try:
assoc = next(item for item in self.submission_sample_associations if item.sample == sample)
except StopIteration:
report = Report()
report.add_result(
Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
return report
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
for k, v in input_dict.items():
try:
# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
setattr(assoc, k, v)
# NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
except AttributeError:
logger.error(f"Can't set {k} to {v}")
# logger.error(f"Can't set {k} to {v}")
pass
return assoc
def update_reagentassoc(self, reagent: Reagent, role: str):
@@ -949,10 +990,12 @@ class BasicSubmission(BaseClass, LogMixin):
pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
main_sheet = xl[pcr_sample_map['main_sheet']]
fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']}
logger.debug(f"Fields: {fields}")
for row in main_sheet.iter_rows(min_row=pcr_sample_map['start_row']):
idx = row[0].row
sample = {}
for k, v in fields.items():
# logger.debug(f"Checking key: {k} with value {v}")
sheet = xl[v['sheet']]
sample[k] = sheet.cell(row=idx, column=v['column']).value
yield sample
@@ -1535,12 +1578,15 @@ class BacterialCulture(BasicSubmission):
column=lookup_table['sample_columns']['concentration']).value
yield sample
def get_provisional_controls(self):
if self.controls:
provs = (control.sample for control in self.controls)
def get_provisional_controls(self, controls_only: bool = True):
if controls_only:
if self.controls:
provs = (control.sample for control in self.controls)
else:
regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
else:
regex = re.compile(r"^(ATCC)|(MCS)|(EN)")
provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
provs = self.samples
for prov in provs:
prov.submission = self.rsl_plate_num
prov.submitted_date = self.submitted_date
@@ -1668,7 +1714,7 @@ class Wastewater(BasicSubmission):
# NOTE: Also, you can't change the size of a list while iterating it, so don't even think about it.
output = []
for sample in samples:
# logger.debug(sample)
logger.debug(sample)
# NOTE: remove '-{target}' from controls
sample['sample'] = re.sub('-N\\d*$', '', sample['sample'])
# NOTE: if sample is already in output skip
@@ -1679,7 +1725,7 @@ class Wastewater(BasicSubmission):
# logger.debug(f"Sample ct: {sample['ct']}")
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment
logger.debug(f"Sample assessemnt: {sample['assessment']}")
# logger.debug(f"Sample assessemnt: {sample['assessment']}")
# sample[f"{sample['target'].lower()}_status"] = sample['assessment']
# NOTE: Get sample having other target
other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']]
@@ -1694,6 +1740,11 @@ class Wastewater(BasicSubmission):
del sample['assessment']
except KeyError:
pass
# logger.debug(sample)
row = int(row_keys[sample['well'][:1]])
column = int(sample['well'][1:])
sample['row'] = row
sample['column'] = column
output.append(sample)
# NOTE: And then convert back to list to keep fidelity with parent method.
for sample in output:
@@ -1779,18 +1830,43 @@ class Wastewater(BasicSubmission):
parser = PCRParser(filepath=fname, submission=self)
self.set_attribute("pcr_info", parser.pcr_info)
# NOTE: These are generators here, need to expand.
pcr_samples = [sample for sample in parser.samples]
pcr_samples = sorted([sample for sample in parser.samples], key=itemgetter('column'))
logger.debug(f"Samples from parser: {pformat(pcr_samples)}")
# NOTE: Samples from parser check out.
pcr_controls = [control for control in parser.controls]
self.save(original=False)
for sample in self.samples:
for assoc in self.submission_sample_associations:
logger.debug(f"Checking pcr_samples for {assoc.sample.rsl_number}, {assoc.sample.ww_full_sample_id} at "
f"column {assoc.column} and row {assoc.row}")
# NOTE: Associations of interest do exist in the submission, are not being found below
# Okay, I've found the problem, at last, the problem is that only one RSL number is saved for each sample,
# Even though each instance of say "25-YUL13-PU3-0320" has multiple RSL numbers in the excel sheet.
# so, yeah, the submitters need to make sure that there are unique values for each one.
try:
# NOTE: Fix for ENs which have no rsl_number...
sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
sample_dict = next(item for item in pcr_samples if item['sample'] == assoc.sample.rsl_number
and item['row'] == assoc.row and item['column'] == assoc.column)
logger.debug(
f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
except StopIteration:
logger.error(f"Couldn't find {assoc} in the Parser samples")
continue
assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
logger.debug(f"Length of pcr_samples: {len(pcr_samples)}")
assoc = self.update_subsampassoc(assoc=assoc, input_dict=sample_dict)
result = assoc.save()
report.add_result(result)
if result:
report.add_result(result)
# for sample in self.samples:
# logger.debug(f"Checking pcr_samples for {sample.rsl_number}, {sample.ww_full_sample_id}")
# try:
# # NOTE: Fix for ENs which have no rsl_number...
# sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
# logger.debug(f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
# except StopIteration:
# logger.error(f"Couldn't find {sample} in the Parser samples")
# continue
# assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# result = assoc.save()
# report.add_result(result)
controltype = ControlType.query(name="PCR Control")
submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
@@ -1804,7 +1880,7 @@ class Wastewater(BasicSubmission):
new_control.save()
return report
def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
"""
Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
@@ -1815,13 +1891,22 @@ class Wastewater(BasicSubmission):
Returns:
SubmissionSampleAssociation: Updated association
"""
assoc = super().update_subsampassoc(sample=sample, input_dict=input_dict)
targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
assert 0 < len(targets) <= 2
for i, v in enumerate(targets.values(), start=1):
update_key = f"ct_n{i}"
if getattr(assoc, update_key) is None:
setattr(assoc, update_key, v)
# logger.debug(f"Input dict: {pformat(input_dict)}")
#
assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# assert 0 < len(targets) <= 2
# for k, v in targets.items():
# # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # update_key = f"ct_n{i}"
# current_value = getattr(assoc, k)
# logger.debug(f"Current value came back as: {current_value}")
# if current_value is None:
# setattr(assoc, k, v)
# else:
# logger.debug(f"Have a value already, {current_value}... skipping.")
if assoc.column == 3:
logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
return assoc
@@ -2105,14 +2190,20 @@ class WastewaterArtic(BasicSubmission):
Returns:
str: output name
"""
logger.debug(f"PBS adapter on {input_str}")
# NOTE: Remove letters.
processed = input_str.replace("RSL", "")
# logger.debug(processed)
# NOTE: Remove brackets at end
processed = re.sub(r"\(.*\)$", "", processed).strip()
logger.debug(processed)
processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
# NOTE: Remove any non-R letters at end.
processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
logger.debug(processed)
# NOTE: Remove trailing '-' if any
processed = processed.strip("-")
logger.debug(processed)
try:
plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "")
@@ -2126,16 +2217,24 @@ class WastewaterArtic(BasicSubmission):
repeat_num = None
if repeat_num is None and "R" in plate_num:
repeat_num = "1"
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
try:
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
except AttributeError:
logger.error(f"Problem re-evaluating plate number for {processed}")
logger.debug(processed)
# NOTE: Remove any redundant -digits
processed = re.sub(r"-\d$", "", processed)
logger.debug(processed)
day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "")
logger.debug(processed)
month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "")
processed = processed.replace("--", "")
logger.debug(processed)
year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}"
logger.debug(processed)
final_en_name = f"PBS{year}{month}{day}-{plate_num}"
return final_en_name

8
src/submissions/backend/excel/reports.py
View File

@@ -196,20 +196,22 @@ class TurnaroundMaker(ReportArchetype):
class ConcentrationMaker(ReportArchetype):
def __init__(self, start_date: date, end_date: date, submission_type: str = "Bacterial Culture"):
def __init__(self, start_date: date, end_date: date, submission_type: str = "Bacterial Culture",
controls_only: bool = True):
self.start_date = start_date
self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date,
submission_type_name=submission_type, page_size=0)
# self.known_controls = list(itertools.chain.from_iterable([sub.controls for sub in self.subs]))
self.controls = list(itertools.chain.from_iterable([sub.get_provisional_controls() for sub in self.subs]))
self.records = [self.build_record(control) for control in self.controls]
self.samples = list(itertools.chain.from_iterable([sub.get_provisional_controls(controls_only=controls_only) for sub in self.subs]))
self.records = [self.build_record(sample) for sample in self.samples]
self.df = DataFrame.from_records(self.records)
self.sheet_name = "Concentration"
@classmethod
def build_record(cls, control) -> dict:
positive = not control.submitter_id.lower().startswith("en")
try:
concentration = float(control.concentration)

4
src/submissions/backend/validators/__init__.py
View File

@@ -1,6 +1,6 @@
'''
"""
Contains all validators
'''
"""
import logging, re
import sys
from pathlib import Path

20
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -366,7 +366,10 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
if new:
logger.warning(f"This is a new instance: {instance.__dict__}")
reagent_role = self.reagent_role.to_sql()
try:
reagent_role = self.reagent_role.to_sql()
except AttributeError:
reagent_role = ReagentRole.query(name=self.reagent_role)
instance.reagent_role = reagent_role
logger.debug(f"KTRRAssoc uses: {self.uses}")
instance.uses = self.uses
@@ -509,15 +512,24 @@ class OmniProcess(BaseOmni):
def to_sql(self):
instance, new = self.class_object.query_or_create(name=self.name)
for st in self.submission_types:
new_assoc = st.to_sql()
try:
new_assoc = st.to_sql()
except AttributeError:
new_assoc = SubmissionType.query(name=st)
if new_assoc not in instance.submission_types:
instance.submission_types.append(new_assoc)
for er in self.equipment_roles:
new_assoc = er.to_sql()
try:
new_assoc = er.to_sql()
except AttributeError:
new_assoc = EquipmentRole.query(name=er)
if new_assoc not in instance.equipment_roles:
instance.equipment_roles.append(new_assoc)
for tr in self.tip_roles:
new_assoc = tr.to_sql()
try:
new_assoc = tr.to_sql()
except AttributeError:
new_assoc = TipRole.query(name=tr)
if new_assoc not in instance.tip_roles:
instance.tip_roles.append(new_assoc)
return instance