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

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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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4
CHANGELOG.md
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@@ -1,3 +1,7 @@
# 202504.01
- Added in checkbox to use all samples in Concentrations tab (very slow).
# 202503.05 # 202503.05
- Created Sample verification before import. - Created Sample verification before import.

6
src/submissions/backend/db/models/__init__.py
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@@ -60,7 +60,7 @@ class BaseClass(Base):
try: try:
return f"<{self.__class__.__name__}({self.name})>" return f"<{self.__class__.__name__}({self.name})>"
except AttributeError: except AttributeError:
return f"<{self.__class__.__name__}({self.__name__})>" return f"<{self.__class__.__name__}(Unknown)>"
# @classproperty # @classproperty
# def skip_on_edit(cls): # def skip_on_edit(cls):
@@ -411,13 +411,13 @@ class BaseClass(Base):
except AttributeError: except AttributeError:
return super().__setattr__(key, value) return super().__setattr__(key, value)
if isinstance(field_type, InstrumentedAttribute): if isinstance(field_type, InstrumentedAttribute):
logger.debug(f"{key} is an InstrumentedAttribute.") # logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.property: match field_type.property:
case ColumnProperty(): case ColumnProperty():
# logger.debug(f"Setting ColumnProperty to {value}") # logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value) return super().__setattr__(key, value)
case _RelationshipDeclared(): 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: if field_type.property.uselist:
logger.debug(f"Setting with uselist") logger.debug(f"Setting with uselist")
existing = self.__getattribute__(key) existing = self.__getattribute__(key)

161
src/submissions/backend/db/models/submissions.py
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@@ -2,6 +2,8 @@
Models for the main submission and sample types. Models for the main submission and sample types.
""" """
from __future__ import annotations from __future__ import annotations
import pickle
from copy import deepcopy from copy import deepcopy
from getpass import getuser from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys 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: except AttributeError as e:
logger.error(f"Could not set {self} attribute {key} to {value} due to \n{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. Update a joined submission sample association.
@@ -599,19 +633,26 @@ class BasicSubmission(BaseClass, LogMixin):
Returns: Returns:
SubmissionSampleAssociation: Updated association SubmissionSampleAssociation: Updated association
""" """
try: # try:
assoc = next(item for item in self.submission_sample_associations if item.sample == sample) # logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
except StopIteration: # assoc = next((item for item in self.submission_sample_associations
report = Report() # if item.sample == sample and
report.add_result( # item.row == input_dict['row'] and
Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning")) # item.column == input_dict['column']))
return report # 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(): for k, v in input_dict.items():
try: try:
# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
setattr(assoc, k, v) setattr(assoc, k, v)
# NOTE: for some reason I don't think assoc.__setattr__(k, v) works here. # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
except AttributeError: except AttributeError:
logger.error(f"Can't set {k} to {v}") # logger.error(f"Can't set {k} to {v}")
pass
return assoc return assoc
def update_reagentassoc(self, reagent: Reagent, role: str): 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'] pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
main_sheet = xl[pcr_sample_map['main_sheet']] 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']} 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']): for row in main_sheet.iter_rows(min_row=pcr_sample_map['start_row']):
idx = row[0].row idx = row[0].row
sample = {} sample = {}
for k, v in fields.items(): for k, v in fields.items():
# logger.debug(f"Checking key: {k} with value {v}")
sheet = xl[v['sheet']] sheet = xl[v['sheet']]
sample[k] = sheet.cell(row=idx, column=v['column']).value sample[k] = sheet.cell(row=idx, column=v['column']).value
yield sample yield sample
@@ -1535,12 +1578,15 @@ class BacterialCulture(BasicSubmission):
column=lookup_table['sample_columns']['concentration']).value column=lookup_table['sample_columns']['concentration']).value
yield sample yield sample
def get_provisional_controls(self): def get_provisional_controls(self, controls_only: bool = True):
if self.controls: if controls_only:
provs = (control.sample for control in self.controls) 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: else:
regex = re.compile(r"^(ATCC)|(MCS)|(EN)") provs = self.samples
provs = (sample for sample in self.samples if bool(regex.match(sample.submitter_id)))
for prov in provs: for prov in provs:
prov.submission = self.rsl_plate_num prov.submission = self.rsl_plate_num
prov.submitted_date = self.submitted_date 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. # NOTE: Also, you can't change the size of a list while iterating it, so don't even think about it.
output = [] output = []
for sample in samples: for sample in samples:
# logger.debug(sample) logger.debug(sample)
# NOTE: remove '-{target}' from controls # NOTE: remove '-{target}' from controls
sample['sample'] = re.sub('-N\\d*$', '', sample['sample']) sample['sample'] = re.sub('-N\\d*$', '', sample['sample'])
# NOTE: if sample is already in output skip # NOTE: if sample is already in output skip
@@ -1679,7 +1725,7 @@ class Wastewater(BasicSubmission):
# logger.debug(f"Sample ct: {sample['ct']}") # logger.debug(f"Sample ct: {sample['ct']}")
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0 sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment # 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'] # sample[f"{sample['target'].lower()}_status"] = sample['assessment']
# NOTE: Get sample having other target # NOTE: Get sample having other target
other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']] other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']]
@@ -1694,6 +1740,11 @@ class Wastewater(BasicSubmission):
del sample['assessment'] del sample['assessment']
except KeyError: except KeyError:
pass 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) output.append(sample)
# NOTE: And then convert back to list to keep fidelity with parent method. # NOTE: And then convert back to list to keep fidelity with parent method.
for sample in output: for sample in output:
@@ -1779,18 +1830,43 @@ class Wastewater(BasicSubmission):
parser = PCRParser(filepath=fname, submission=self) parser = PCRParser(filepath=fname, submission=self)
self.set_attribute("pcr_info", parser.pcr_info) self.set_attribute("pcr_info", parser.pcr_info)
# NOTE: These are generators here, need to expand. # 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] pcr_controls = [control for control in parser.controls]
self.save(original=False) 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: try:
# NOTE: Fix for ENs which have no rsl_number... sample_dict = next(item for item in pcr_samples if item['sample'] == assoc.sample.rsl_number
sample_dict = next(item for item in pcr_samples if item['sample'] == 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: except StopIteration:
logger.error(f"Couldn't find {assoc} in the Parser samples")
continue 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() 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") controltype = ControlType.query(name="PCR Control")
submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]), submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p") "%Y-%m-%d %I:%M:%S %p")
@@ -1804,7 +1880,7 @@ class Wastewater(BasicSubmission):
new_control.save() new_control.save()
return report 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. 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: Returns:
SubmissionSampleAssociation: Updated association SubmissionSampleAssociation: Updated association
""" """
assoc = super().update_subsampassoc(sample=sample, input_dict=input_dict) # logger.debug(f"Input dict: {pformat(input_dict)}")
targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")} #
assert 0 < len(targets) <= 2 assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
for i, v in enumerate(targets.values(), start=1): # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
update_key = f"ct_n{i}" # assert 0 < len(targets) <= 2
if getattr(assoc, update_key) is None: # for k, v in targets.items():
setattr(assoc, update_key, v) # # 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 return assoc
@@ -2105,14 +2190,20 @@ class WastewaterArtic(BasicSubmission):
Returns: Returns:
str: output name str: output name
""" """
logger.debug(f"PBS adapter on {input_str}")
# NOTE: Remove letters. # NOTE: Remove letters.
processed = input_str.replace("RSL", "") processed = input_str.replace("RSL", "")
# logger.debug(processed)
# NOTE: Remove brackets at end # NOTE: Remove brackets at end
processed = re.sub(r"\(.*\)$", "", processed).strip() processed = re.sub(r"\(.*\)$", "", processed).strip()
logger.debug(processed)
processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
# NOTE: Remove any non-R letters at end. # NOTE: Remove any non-R letters at end.
processed = re.sub(r"[A-QS-Z]+\d*", "", processed) processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
logger.debug(processed)
# NOTE: Remove trailing '-' if any # NOTE: Remove trailing '-' if any
processed = processed.strip("-") processed = processed.strip("-")
logger.debug(processed)
try: try:
plate_num = re.search(r"\-\d{1}R?\d?$", processed).group() plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "") processed = rreplace(processed, plate_num, "")
@@ -2126,16 +2217,24 @@ class WastewaterArtic(BasicSubmission):
repeat_num = None repeat_num = None
if repeat_num is None and "R" in plate_num: if repeat_num is None and "R" in plate_num:
repeat_num = "1" repeat_num = "1"
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num) try:
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
except AttributeError:
logger.error(f"Problem re-evaluating plate number for {processed}")
logger.debug(processed)
# NOTE: Remove any redundant -digits # NOTE: Remove any redundant -digits
processed = re.sub(r"-\d$", "", processed) processed = re.sub(r"-\d$", "", processed)
logger.debug(processed)
day = re.search(r"\d{2}$", processed).group() day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "") processed = rreplace(processed, day, "")
logger.debug(processed)
month = re.search(r"\d{2}$", processed).group() month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "") processed = rreplace(processed, month, "")
processed = processed.replace("--", "") processed = processed.replace("--", "")
logger.debug(processed)
year = re.search(r'^(?:\d{2})?\d{2}', processed).group() year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}" year = f"20{year}"
logger.debug(processed)
final_en_name = f"PBS{year}{month}{day}-{plate_num}" final_en_name = f"PBS{year}{month}{day}-{plate_num}"
return final_en_name return final_en_name

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

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

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

@@ -1,6 +1,6 @@
''' """
Contains all validators Contains all validators
''' """
import logging, re import logging, re
import sys import sys
from pathlib import Path 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}") logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
if new: if new:
logger.warning(f"This is a new instance: {instance.__dict__}") 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 instance.reagent_role = reagent_role
logger.debug(f"KTRRAssoc uses: {self.uses}") logger.debug(f"KTRRAssoc uses: {self.uses}")
instance.uses = self.uses instance.uses = self.uses
@@ -509,15 +512,24 @@ class OmniProcess(BaseOmni):
def to_sql(self): def to_sql(self):
instance, new = self.class_object.query_or_create(name=self.name) instance, new = self.class_object.query_or_create(name=self.name)
for st in self.submission_types: 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: if new_assoc not in instance.submission_types:
instance.submission_types.append(new_assoc) instance.submission_types.append(new_assoc)
for er in self.equipment_roles: 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: if new_assoc not in instance.equipment_roles:
instance.equipment_roles.append(new_assoc) instance.equipment_roles.append(new_assoc)
for tr in self.tip_roles: 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: if new_assoc not in instance.tip_roles:
instance.tip_roles.append(new_assoc) instance.tip_roles.append(new_assoc)
return instance return instance

11
src/submissions/frontend/widgets/concentrations.py
View File

@@ -1,7 +1,7 @@
""" """
Pane showing BC control concentrations summary. Pane showing BC control concentrations summary.
""" """
from PyQt6.QtWidgets import QWidget, QPushButton from PyQt6.QtWidgets import QWidget, QPushButton, QCheckBox, QLabel
from .info_tab import InfoPane from .info_tab import InfoPane
from backend.excel.reports import ConcentrationMaker from backend.excel.reports import ConcentrationMaker
from frontend.visualizations.concentrations_chart import ConcentrationsChart from frontend.visualizations.concentrations_chart import ConcentrationsChart
@@ -20,6 +20,12 @@ class Concentrations(InfoPane):
self.export_button = QPushButton("Save Data", parent=self) self.export_button = QPushButton("Save Data", parent=self)
self.export_button.pressed.connect(self.save_excel) self.export_button.pressed.connect(self.save_excel)
self.layout.addWidget(self.export_button, 0, 3, 1, 1) self.layout.addWidget(self.export_button, 0, 3, 1, 1)
check_label = QLabel("Controls Only")
self.all_box = QCheckBox()
self.all_box.setChecked(True)
self.all_box.checkStateChanged.connect(self.update_data)
self.layout.addWidget(check_label, 1, 0, 1, 1)
self.layout.addWidget(self.all_box, 1, 1, 1, 1)
self.fig = None self.fig = None
self.report_object = None self.report_object = None
self.update_data() self.update_data()
@@ -33,7 +39,8 @@ class Concentrations(InfoPane):
""" """
super().update_data() super().update_data()
months = self.diff_month(self.start_date, self.end_date) months = self.diff_month(self.start_date, self.end_date)
chart_settings = dict(start_date=self.start_date, end_date=self.end_date) # logger.debug(f"Box checked: {self.all_box.isChecked()}")
chart_settings = dict(start_date=self.start_date, end_date=self.end_date, controls_only=self.all_box.isChecked())
self.report_obj = ConcentrationMaker(**chart_settings) self.report_obj = ConcentrationMaker(**chart_settings)
self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months) self.fig = ConcentrationsChart(df=self.report_obj.df, settings=chart_settings, modes=[], months=months)
self.webview.setHtml(self.fig.html) self.webview.setHtml(self.fig.html)

15
src/submissions/frontend/widgets/sample_checker.py
View File

@@ -1,7 +1,7 @@
import logging import logging
from pathlib import Path from pathlib import Path
from typing import List from typing import List, Generator
from PyQt6.QtCore import Qt, pyqtSlot from PyQt6.QtCore import Qt, pyqtSlot
from PyQt6.QtWebChannel import QWebChannel from PyQt6.QtWebChannel import QWebChannel
@@ -37,7 +37,7 @@ class SampleChecker(QDialog):
template_path = Path(template.environment.loader.__getattribute__("searchpath")[0]) template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
with open(template_path.joinpath("css", "styles.css"), "r") as f: with open(template_path.joinpath("css", "styles.css"), "r") as f:
css = f.read() css = f.read()
html = template.render(samples=pyd.sample_list, css=css) html = template.render(samples=self.formatted_list, css=css)
self.webview.setHtml(html) self.webview.setHtml(html)
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn) self.buttonBox = QDialogButtonBox(QBtn)
@@ -59,8 +59,19 @@ class SampleChecker(QDialog):
item = next((sample for sample in self.pyd.samples if int(submission_rank) in sample.submission_rank)) item = next((sample for sample in self.pyd.samples if int(submission_rank) in sample.submission_rank))
except StopIteration: except StopIteration:
logger.error(f"Unable to find sample {submission_rank}") logger.error(f"Unable to find sample {submission_rank}")
return
item.__setattr__(key, value) item.__setattr__(key, value)
@property
def formatted_list(self) -> List[dict]:
output = []
for sample in self.pyd.sample_list:
if sample['submitter_id'] in [item['submitter_id'] for item in output]:
sample['color'] = "red"
else:
sample['color'] = "black"
output.append(sample)
return output

2
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -140,7 +140,7 @@ class SubmissionFormContainer(QWidget):
# logger.debug(f"Samples: {pformat(self.pyd.samples)}") # logger.debug(f"Samples: {pformat(self.pyd.samples)}")
checker = SampleChecker(self, "Sample Checker", self.pyd) checker = SampleChecker(self, "Sample Checker", self.pyd)
if checker.exec(): if checker.exec():
logger.debug(pformat(self.pyd.samples)) # logger.debug(pformat(self.pyd.samples))
self.form = self.pyd.to_form(parent=self) self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form) self.layout().addWidget(self.form)
else: else:

2
src/submissions/templates/sample_checker.html
View File

@@ -15,7 +15,7 @@
&emsp;&emsp;Submitter ID&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Row&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; Column<br/> &emsp;&emsp;Submitter ID&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Row&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; Column<br/>
{% for sample in samples %} {% for sample in samples %}
{{ '%02d' % sample['submission_rank'] }} {{ '%02d' % sample['submission_rank'] }}
<input type="text" id="{{ sample['submission_rank'] }}_id" name="submitter_id" value="{{ sample['submitter_id'] }}" size="40"> <input type="text" id="{{ sample['submission_rank'] }}_id" name="submitter_id" value="{{ sample['submitter_id'] }}" size="40" style="color:{{ sample['color'] }};">>
<input type="number" id="{{ sample['submission_rank'] }}_row" name="row" value="{{ sample['row'] }}" size="5", min="1"> <input type="number" id="{{ sample['submission_rank'] }}_row" name="row" value="{{ sample['row'] }}" size="5", min="1">
<input type="number" id="{{ sample['submission_rank'] }}_col" name="column" value="{{ sample['column'] }}" size="5", min="1"> <input type="number" id="{{ sample['submission_rank'] }}_col" name="column" value="{{ sample['column'] }}" size="5", min="1">
<br/> <br/>