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Various bug fixes.

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This commit is contained in:
lwark
2024-05-30 13:54:35 -05:00
parent ecfc71bcc5
commit 5c52c02f7e
18 changed files with 447 additions and 375 deletions
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2
src/submissions/backend/db/models/controls.py
View File

@@ -177,6 +177,8 @@ class Control(BaseClass):
data = self.__getattribute__(mode)
except TypeError:
data = {}
if data is None:
data = {}
# logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:

399
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 sys
from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
from zipfile import ZipFile
@@ -13,7 +15,8 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLO
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError, \
ArgumentError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import pandas as pd
from openpyxl import Workbook, load_workbook
@@ -244,14 +247,22 @@ class BasicSubmission(BaseClass):
ext_info = None
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
"Submission Type": self.submission_type_name,
"Submitter Plate Number": self.submitter_plate_num,
"Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
"Submitting Lab": sub_lab,
"Sample Count": self.sample_count,
"Extraction Kit": ext_kit,
"Cost": self.run_cost,
# "Plate Number": self.rsl_plate_num,
# "Submission Type": self.submission_type_name,
# "Submitter Plate Number": self.submitter_plate_num,
# "Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
# "Submitting Lab": sub_lab,
# "Sample Count": self.sample_count,
# "Extraction Kit": ext_kit,
# "Cost": self.run_cost,
"plate_number": self.rsl_plate_num,
"submission_type": self.submission_type_name,
"submitter_plate_number": self.submitter_plate_num,
"submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
"submitting_lab": sub_lab,
"sample_count": self.sample_count,
"extraction_kit": ext_kit,
"cost": self.run_cost,
}
if report:
return output
@@ -290,17 +301,26 @@ class BasicSubmission(BaseClass):
try:
comments = self.comment
except Exception as e:
logger.error(f"Error setting comment: {self.comment}")
logger.error(f"Error setting comment: {self.comment}, {e}")
comments = None
output["Submission Category"] = self.submission_category
output["Technician"] = self.technician
# output["Submission Category"] = self.submission_category
# output["Technician"] = self.technician
# output["reagents"] = reagents
# output["samples"] = samples
# output["extraction_info"] = ext_info
# output["comment"] = comments
# output["equipment"] = equipment
# output["Cost Centre"] = cost_centre
# output["Signed By"] = self.signed_by
output["submission_category"] = self.submission_category
output["technician"] = self.technician
output["reagents"] = reagents
output["samples"] = samples
output["extraction_info"] = ext_info
output["comment"] = comments
output["equipment"] = equipment
output["Cost Centre"] = cost_centre
output["Signed By"] = self.signed_by
output["cost_centre"] = cost_centre
output["signed_by"] = self.signed_by
return output
def calculate_column_count(self) -> int:
@@ -380,7 +400,7 @@ class BasicSubmission(BaseClass):
for column in range(1, plate_columns + 1):
for row in range(1, plate_rows + 1):
try:
well = [item for item in sample_list if item['Row'] == row and item['Column'] == column][0]
well = [item for item in sample_list if item['row'] == row and item['column'] == column][0]
except IndexError:
well = dict(name="", row=row, column=column, background_color="#ffffff")
output_samples.append(well)
@@ -416,15 +436,21 @@ class BasicSubmission(BaseClass):
subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
# logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Column names: {df.columns}")
# NOTE: Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
excluded = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'signed_by']
for item in excluded:
try:
df = df.drop(item, axis=1)
except:
logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
if chronologic:
df.sort_values(by="Submitted Date", axis=0, inplace=True, ascending=False)
df.sort_values(by="id", axis=0, inplace=True, ascending=False)
# NOTE: Human friendly column labels
df.columns = [item.replace("_", " ").title() for item in df.columns]
return df
def set_attribute(self, key: str, value):
@@ -540,9 +566,9 @@ class BasicSubmission(BaseClass):
new_dict[key] = [PydEquipment(**equipment) for equipment in dicto['equipment']]
except TypeError as e:
logger.error(f"Possible no equipment error: {e}")
case "Plate Number":
case "plate_number":
new_dict['rsl_plate_num'] = dict(value=value, missing=missing)
case "Submitter Plate Number":
case "submitter_plate_number":
new_dict['submitter_plate_num'] = dict(value=value, missing=missing)
case "id":
pass
@@ -566,6 +592,10 @@ class BasicSubmission(BaseClass):
self.uploaded_by = getuser()
super().save()
@classmethod
def get_regex(cls):
return cls.construct_regex()
# Polymorphic functions
@classmethod
@@ -598,7 +628,6 @@ class BasicSubmission(BaseClass):
polymorphic_identity = polymorphic_identity['value']
if isinstance(polymorphic_identity, SubmissionType):
polymorphic_identity = polymorphic_identity.name
# if polymorphic_identity != None:
model = cls
match polymorphic_identity:
case str():
@@ -624,22 +653,6 @@ class BasicSubmission(BaseClass):
return model
# Child class custom functions
# @classmethod
# def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
# """
# Stupid stopgap solution to there being an issue with the Bacterial Culture plate map
#
# Args:
# xl (pd.ExcelFile): original xl workbook, used for child classes mostly
# plate_map (pd.DataFrame): original plate map
#
# Returns:
# pd.DataFrame: updated plate map.
# """
# logger.info(f"Calling {cls.__mapper_args__['polymorphic_identity']} plate mapper.")
# return plate_map
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
"""
@@ -723,7 +736,6 @@ class BasicSubmission(BaseClass):
data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type']
# outstr = super().enforce_name(instr=instr, data=data)
if instr in [None, ""]:
# logger.debug("Sending to RSLNamer to make new plate name.")
outstr = RSLNamer.construct_new_plate_name(data=data)
@@ -754,22 +766,7 @@ class BasicSubmission(BaseClass):
outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
abb = cls.get_default_info('abbreviation')
return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
# return outstr
# @classmethod
# def parse_pcr(cls, xl: pd.DataFrame, rsl_number: str) -> list:
# """
# Perform custom parsing of pcr info.
#
# Args:
# xl (pd.DataFrame): pcr info form
# rsl_number (str): rsl plate num of interest
#
# Returns:
# list: _description_
# """
# logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
# return []
@classmethod
def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
"""
@@ -896,15 +893,10 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Incoming kwargs: {kwargs}")
# NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
if submission_type is not None:
# if isinstance(submission_type, SubmissionType):
# model = cls.find_subclasses(submission_type=submission_type.name)
model = cls.find_polymorphic_subclass(polymorphic_identity=submission_type)
# else:
# model = cls.find_subclasses(submission_type=submission_type)
elif len(kwargs) > 0:
# find the subclass containing the relevant attributes
# logger.debug(f"Attributes for search: {kwargs}")
# model = cls.find_subclasses(attrs=kwargs)
model = cls.find_polymorphic_subclass(attrs=kwargs)
else:
model = cls
@@ -979,17 +971,6 @@ class BasicSubmission(BaseClass):
limit = 1
case _:
pass
# for k, v in kwargs.items():
# logger.debug(f"Looking up attribute: {k}")
# attr = getattr(model, k)
# logger.debug(f"Got attr: {attr}")
# query = query.filter(attr==v)
# if len(kwargs) > 0:
# limit = 1
# query = cls.query_by_keywords(query=query, model=model, **kwargs)
# if any(x in kwargs.keys() for x in cls.get_default_info('singles')):
# logger.debug(f"There's a singled out item in kwargs")
# limit = 1
if chronologic:
query.order_by(cls.submitted_date)
return cls.execute_query(query=query, model=model, limit=limit, **kwargs)
@@ -1150,7 +1131,6 @@ class BasicSubmission(BaseClass):
if fname.name == "":
# logger.debug(f"export cancelled.")
return
# pyd.filepath = fname
if full_backup:
backup = self.to_dict(full_data=True)
try:
@@ -1158,11 +1138,7 @@ class BasicSubmission(BaseClass):
yaml.dump(backup, f)
except KeyError as e:
logger.error(f"Problem saving yml backup file: {e}")
# wb = pyd.autofill_excel()
# wb = pyd.autofill_samples(wb)
# wb = pyd.autofill_equipment(wb)
writer = pyd.to_writer()
# wb.save(filename=fname.with_suffix(".xlsx"))
writer.xl.save(filename=fname.with_suffix(".xlsx"))
# Below are the custom submission types
@@ -1192,49 +1168,6 @@ class BacterialCulture(BasicSubmission):
output['controls'] = [item.to_sub_dict() for item in self.controls]
return output
# @classmethod
# def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
# """
# Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
#
# Args:
# xl (pd.ExcelFile): original xl workbook
# plate_map (pd.DataFrame): original plate map
#
# Returns:
# pd.DataFrame: updated plate map.
# """
# plate_map = super().custom_platemap(xl, plate_map)
# num1 = xl.parse("Sample List").iloc[40, 1]
# num2 = xl.parse("Sample List").iloc[41, 1]
# # logger.debug(f"Broken: {plate_map.iloc[5, 0]}, {plate_map.iloc[6, 0]}")
# # logger.debug(f"Replace: {num1}, {num2}")
# if not check_not_nan(plate_map.iloc[5, 0]):
# plate_map.iloc[5, 0] = num1
# if not check_not_nan(plate_map.iloc[6, 0]):
# plate_map.iloc[6, 0] = num2
# return plate_map
# @classmethod
# def custom_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
# """
# Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
#
# Args:
# input_excel (Workbook): Input openpyxl workbook
#
# Returns:
# Workbook: Updated openpyxl workbook
# """
# input_excel = super().custom_writer(input_excel)
# sheet = input_excel['Plate Map']
# if sheet.cell(12, 2).value == None:
# sheet.cell(row=12, column=2, value="=IF(ISBLANK('Sample List'!$B42),\"\",'Sample List'!$B42)")
# if sheet.cell(13, 2).value == None:
# sheet.cell(row=13, column=2, value="=IF(ISBLANK('Sample List'!$B43),\"\",'Sample List'!$B43)")
# input_excel["Sample List"].cell(row=15, column=2, value=getuser())
# return input_excel
@classmethod
def get_regex(cls) -> str:
"""
@@ -1336,13 +1269,13 @@ class Wastewater(BasicSubmission):
except TypeError as e:
pass
if self.ext_technician is None or self.ext_technician == "None":
output['Ext Technician'] = self.technician
output['ext_technician'] = self.technician
else:
output["Ext Technician"] = self.ext_technician
output["ext_technician"] = self.ext_technician
if self.pcr_technician is None or self.pcr_technician == "None":
output["PCR Technician"] = self.technician
output["pcr_technician"] = self.technician
else:
output['PCR Technician'] = self.pcr_technician
output['pcr_technician'] = self.pcr_technician
return output
@classmethod
@@ -1361,46 +1294,6 @@ class Wastewater(BasicSubmission):
input_dict['csv'] = xl["Copy to import file"]
return input_dict
# @classmethod
# def parse_pcr(cls, xl: pd.ExcelFile, rsl_number: str) -> list:
# """
# Parse specific to wastewater samples.
# """
# samples = super().parse_pcr(xl=xl, rsl_number=rsl_number)
# df = xl.parse(sheet_name="Results", dtype=object).fillna("")
# column_names = ["Well", "Well Position", "Omit", "Sample", "Target", "Task", " Reporter", "Quencher",
# "Amp Status", "Amp Score", "Curve Quality", "Result Quality Issues", "Cq", "Cq Confidence",
# "Cq Mean", "Cq SD", "Auto Threshold", "Threshold", "Auto Baseline", "Baseline Start",
# "Baseline End"]
# samples_df = df.iloc[23:][0:]
# logger.debug(f"Dataframe of PCR results:\n\t{samples_df}")
# samples_df.columns = column_names
# logger.debug(f"Samples columns: {samples_df.columns}")
# well_call_df = xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:, -1:]
# try:
# samples_df['Assessment'] = well_call_df.values
# except ValueError:
# logger.error("Well call number doesn't match sample number")
# logger.debug(f"Well call df: {well_call_df}")
# for _, row in samples_df.iterrows():
# try:
# sample_obj = [sample for sample in samples if sample['sample'] == row[3]][0]
# except IndexError:
# sample_obj = dict(
# sample=row['Sample'],
# plate_rsl=rsl_number,
# )
# logger.debug(f"Got sample obj: {sample_obj}")
# if isinstance(row['Cq'], float):
# sample_obj[f"ct_{row['Target'].lower()}"] = row['Cq']
# else:
# sample_obj[f"ct_{row['Target'].lower()}"] = 0.0
# try:
# sample_obj[f"{row['Target'].lower()}_status"] = row['Assessment']
# except KeyError:
# logger.error(f"No assessment for {sample_obj['sample']}")
# samples.append(sample_obj)
# return samples
@classmethod
def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
"""
@@ -1531,6 +1424,8 @@ class WastewaterArtic(BasicSubmission):
dict: dictionary used in submissions summary
"""
output = super().to_dict(full_data=full_data, backup=backup, report=report)
if self.artic_technician in [None, "None"]:
output['artic_technician'] = self.technician
if report:
return output
output['gel_info'] = self.gel_info
@@ -1770,16 +1665,13 @@ class WastewaterArtic(BasicSubmission):
Workbook: Updated workbook
"""
input_excel = super().custom_info_writer(input_excel, info, backup)
# worksheet = input_excel["First Strand List"]
# samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
# samples = sorted(samples, key=attrgetter('column', 'row'))
# logger.debug(f"Info:\n{pformat(info)}")
logger.debug(f"Info:\n{pformat(info)}")
check = 'source_plates' in info.keys() and info['source_plates'] is not None
if check:
worksheet = input_excel['First Strand List']
start_row = 8
for iii, plate in enumerate(info['source_plates']['value']):
# logger.debug(f"Plate: {plate}")
logger.debug(f"Plate: {plate}")
row = start_row + iii
try:
worksheet.cell(row=row, column=3, value=plate['plate'])
@@ -1868,12 +1760,23 @@ class WastewaterArtic(BasicSubmission):
set_plate = None
for assoc in self.submission_sample_associations:
dicto = assoc.to_sub_dict()
if self.source_plates is None:
output.append(dicto)
continue
for item in self.source_plates:
old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
if old_plate is not None:
set_plate = old_plate.submission.rsl_plate_num
logger.debug(dicto['WW Processing Num'])
if dicto['WW Processing Num'].startswith("NTC"):
dicto['Well'] = dicto['WW Processing Num']
else:
dicto['Well'] = f"{row_map[old_plate.row]}{old_plate.column}"
break
elif dicto['WW Processing Num'].startswith("NTC"):
dicto['Well'] = dicto['WW Processing Num']
dicto['plate_name'] = set_plate
logger.debug(f"Here is our raw sample: {pformat(dicto)}")
output.append(dicto)
return output
@@ -1997,8 +1900,8 @@ class BasicSample(BaseClass):
# logger.debug(f"Converting {self} to dict.")
# start = time()
sample = {}
sample['Submitter ID'] = self.submitter_id
sample['Sample Type'] = self.sample_type
sample['submitter_id'] = self.submitter_id
sample['sample_type'] = self.sample_type
if full_data:
sample['submissions'] = sorted([item.to_sub_dict() for item in self.sample_submission_associations],
key=itemgetter('submitted_date'))
@@ -2099,7 +2002,7 @@ class BasicSample(BaseClass):
@setup_lookup
def query(cls,
submitter_id: str | None = None,
sample_type: str | None = None,
sample_type: str | BasicSample | None = None,
limit: int = 0,
**kwargs
) -> BasicSample | List[BasicSample]:
@@ -2114,14 +2017,14 @@ class BasicSample(BaseClass):
Returns:
models.BasicSample|List[models.BasicSample]: Sample(s) of interest.
"""
if sample_type is None:
# model = cls.find_subclasses(attrs=kwargs)
model = cls.find_polymorphic_subclass(attrs=kwargs)
else:
model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
match sample_type:
case str():
model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
case BasicSample():
model = sample_type
case _:
model = cls.find_polymorphic_subclass(attrs=kwargs)
# logger.debug(f"Length of kwargs: {len(kwargs)}")
# model = models.BasicSample.find_subclasses(ctx=ctx, attrs=kwargs)
# query: Query = setup_lookup(ctx=ctx, locals=locals()).query(model)
query: Query = cls.__database_session__.query(model)
match submitter_id:
case str():
@@ -2130,20 +2033,7 @@ class BasicSample(BaseClass):
limit = 1
case _:
pass
# match sample_type:
# case str():
# logger.warning(f"Looking up samples with sample_type is disabled.")
# # query = query.filter(models.BasicSample.sample_type==sample_type)
# case _:
# pass
# for k, v in kwargs.items():
# attr = getattr(model, k)
# # logger.debug(f"Got attr: {attr}")
# query = query.filter(attr==v)
# if len(kwargs) > 0:
# limit = 1
return cls.execute_query(query=query, model=model, limit=limit, **kwargs)
# return cls.execute_query(query=query, limit=limit)
@classmethod
def query_or_create(cls, sample_type: str | None = None, **kwargs) -> BasicSample:
@@ -2163,10 +2053,6 @@ class BasicSample(BaseClass):
disallowed = ["id"]
if kwargs == {}:
raise ValueError("Need to narrow down query or the first available instance will be returned.")
# for key in kwargs.keys():
# if key in disallowed:
# raise ValueError(
# f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects.")
sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in disallowed}
instance = cls.query(sample_type=sample_type, limit=1, **kwargs)
# logger.debug(f"Retrieved instance: {instance}")
@@ -2177,9 +2063,85 @@ class BasicSample(BaseClass):
logger.debug(f"Creating instance: {instance}")
return instance
@classmethod
def fuzzy_search(cls,
# submitter_id: str | None = None,
sample_type: str | BasicSample | None = None,
# limit: int = 0,
**kwargs
) -> List[BasicSample]:
match sample_type:
case str():
model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
case BasicSample():
model = sample_type
case _:
model = cls.find_polymorphic_subclass(attrs=kwargs)
# logger.debug(f"Length of kwargs: {len(kwargs)}")
query: Query = cls.__database_session__.query(model)
for k, v in kwargs.items():
search = f"%{v}%"
try:
attr = getattr(model, k)
query = query.filter(attr.like(search))
except (ArgumentError, AttributeError) as e:
logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
return query.all()
def delete(self):
raise AttributeError(f"Delete not implemented for {self.__class__}")
@classmethod
def get_searchables(cls):
return [dict(label="Submitter ID", field="submitter_id")]
@classmethod
def samples_to_df(cls, sample_type: str | None | BasicSample = None, **kwargs):
# def samples_to_df(cls, sample_type:str|None|BasicSample=None, searchables:dict={}):
logger.debug(f"Checking {sample_type} with type {type(sample_type)}")
match sample_type:
case str():
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=sample_type)
case _:
try:
check = issubclass(sample_type, BasicSample)
except TypeError:
check = False
if check:
model = sample_type
else:
model = cls
q_out = model.fuzzy_search(sample_type=sample_type, **kwargs)
if not isinstance(q_out, list):
q_out = [q_out]
try:
samples = [sample.to_sub_dict() for sample in q_out]
except TypeError as e:
logger.error(f"Couldn't find any samples with data: {kwargs}\nDue to {e}")
return None
df = pd.DataFrame.from_records(samples)
# NOTE: Exclude sub information
for item in ['concentration', 'organism', 'colour', 'tooltip', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
try:
df = df.drop(item, axis=1)
except:
logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
return df
def show_details(self, obj):
"""
Creates Widget for showing submission details.
Args:
obj (_type_): parent widget
"""
# logger.debug("Hello from details")
from frontend.widgets.submission_details import SubmissionDetails
dlg = SubmissionDetails(parent=obj, sub=self)
if dlg.exec():
pass
#Below are the custom sample types
@@ -2229,10 +2191,10 @@ class WastewaterSample(BasicSample):
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
"""
sample = super().to_sub_dict(full_data=full_data)
sample['WW Processing Num'] = self.ww_processing_num
sample['Sample Location'] = self.sample_location
sample['Received Date'] = self.received_date
sample['Collection Date'] = self.collection_date
sample['ww_processing_num'] = self.ww_processing_num
sample['sample_location'] = self.sample_location
sample['received_date'] = self.received_date
sample['collection_date'] = self.collection_date
return sample
@classmethod
@@ -2257,28 +2219,9 @@ class WastewaterSample(BasicSample):
output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_num']
if output_dict['ww_full_sample_id'] is not None and output_dict["submitter_id"] in disallowed:
output_dict["submitter_id"] = output_dict['ww_full_sample_id']
# if re.search(r"^NTC", output_dict['submitter_id']):
# output_dict['submitter_id'] = "Artic-" + output_dict['submitter_id']
# Ad hoc repair method for WW (or possibly upstream) not formatting some dates properly.
# NOTE: Should be handled by validator.
# match output_dict['collection_date']:
# case str():
# try:
# output_dict['collection_date'] = parse(output_dict['collection_date']).date()
# except ParserError:
# logger.error(f"Problem parsing collection_date: {output_dict['collection_date']}")
# output_dict['collection_date'] = date(1970, 1, 1)
# case datetime():
# output_dict['collection_date'] = output_dict['collection_date'].date()
# case date():
# pass
# case _:
# del output_dict['collection_date']
return output_dict
def get_previous_ww_submission(self, current_artic_submission: WastewaterArtic):
# assocs = [assoc for assoc in self.sample_submission_associations if assoc.submission.submission_type_name=="Wastewater"]
# subs = self.submissions[:self.submissions.index(current_artic_submission)]
try:
plates = [item['plate'] for item in current_artic_submission.source_plates]
except TypeError as e:
@@ -2292,6 +2235,13 @@ class WastewaterSample(BasicSample):
except IndexError:
return None
@classmethod
def get_searchables(cls):
searchables = super().get_searchables()
for item in ["ww_processing_num", "ww_full_sample_id", "rsl_number"]:
label = item.strip("ww_").replace("_", " ").replace("rsl", "RSL").title()
searchables.append(dict(label=label, field=item))
return searchables
class BacterialCultureSample(BasicSample):
"""
@@ -2314,16 +2264,15 @@ class BacterialCultureSample(BasicSample):
"""
# start = time()
sample = super().to_sub_dict(full_data=full_data)
sample['Name'] = self.submitter_id
sample['Organism'] = self.organism
sample['Concentration'] = self.concentration
sample['name'] = self.submitter_id
sample['organism'] = self.organism
sample['concentration'] = self.concentration
if self.control != None:
sample['colour'] = [0, 128, 0]
sample['tooltip'] = f"Control: {self.control.controltype.name} - {self.control.controltype.targets}"
# logger.debug(f"Done converting to {self} to dict after {time()-start}")
return sample
# Submission to Sample Associations
class SubmissionSampleAssociation(BaseClass):
@@ -2387,15 +2336,15 @@ class SubmissionSampleAssociation(BaseClass):
# logger.debug(f"Running {self.__repr__()}")
sample = self.sample.to_sub_dict()
# logger.debug("Sample conversion complete.")
sample['Name'] = self.sample.submitter_id
sample['Row'] = self.row
sample['Column'] = self.column
sample['name'] = self.sample.submitter_id
sample['row'] = self.row
sample['column'] = self.column
try:
sample['Well'] = f"{row_map[self.row]}{self.column}"
sample['well'] = f"{row_map[self.row]}{self.column}"
except KeyError as e:
logger.error(f"Unable to find row {self.row} in row_map.")
sample['Well'] = None
sample['Plate Name'] = self.submission.rsl_plate_num
sample['plate_name'] = self.submission.rsl_plate_num
sample['positive'] = False
sample['submitted_date'] = self.submission.submitted_date
sample['submission_rank'] = self.submission_rank

13
src/submissions/backend/excel/parser.py
View File

@@ -35,7 +35,7 @@ class SheetParser(object):
Args:
filepath (Path | None, optional): file path to excel sheet. Defaults to None.
"""
logger.debug(f"\n\nParsing {filepath.__str__()}\n\n")
logger.info(f"\n\nParsing {filepath.__str__()}\n\n")
match filepath:
case Path():
self.filepath = filepath
@@ -651,6 +651,15 @@ class PCRParser(object):
info_map = self.submission_obj.get_submission_type().sample_map['pcr_general_info']
sheet = self.xl[info_map['sheet']]
iter_rows = sheet.iter_rows(min_row=info_map['start_row'], max_row=info_map['end_row'])
pcr = {row[0].value.lower().replace(' ', '_'): row[1].value for row in iter_rows}
pcr = {}
for row in iter_rows:
try:
key = row[0].value.lower().replace(' ', '_')
except AttributeError as e:
logger.error(f"No key: {row[0].value} due to {e}")
continue
value = row[1].value or ""
pcr[key] = value
pcr['imported_by'] = getuser()
# logger.debug(f"PCR: {pformat(pcr)}")
return pcr

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

@@ -23,13 +23,13 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
"""
df = DataFrame.from_records(records)
# put submissions with the same lab together
df = df.sort_values("Submitting Lab")
df = df.sort_values("submitting_lab")
# aggregate cost and sample count columns
df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
df2 = df2.rename(columns={"Extraction Kit": 'Run Count'})
df2 = df.groupby(["submitting_lab", "extraction_kit"]).agg({'extraction_kit':'count', 'cost': 'sum', 'sample_count':'sum'})
df2 = df2.rename(columns={"extraction_kit": 'run_count'})
# logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
df = df.drop('id', axis=1)
df = df.sort_values(['Submitting Lab', "Submitted Date"])
df = df.sort_values(['submitting_lab', "submitted_date"])
return df, df2
def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:

7
src/submissions/backend/excel/writer.py
View File

@@ -85,6 +85,7 @@ class SheetWriter(object):
class InfoWriter(object):
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict, sub_object:BasicSubmission|None=None):
logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if sub_object is None:
@@ -110,10 +111,15 @@ class InfoWriter(object):
dicto['value'] = v
if len(dicto) > 0:
output[k] = dicto
# logger.debug(f"Reconciled info: {pformat(output)}")
return output
def write_info(self):
for k, v in self.info.items():
# NOTE: merge all comments to fit in single cell.
if k == "comment" and isinstance(v['value'], list):
json_join = [item['text'] for item in v['value'] if 'text' in item.keys()]
v['value'] = "\n".join(json_join)
try:
locations = v['locations']
except KeyError:
@@ -183,6 +189,7 @@ class SampleWriter(object):
output = []
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
# logger.debug(f"Writing sample: {sample}")
for assoc in zip(sample['row'], sample['column'], sample['submission_rank']):
new = dict(row=assoc[0], column=assoc[1], submission_rank=assoc[2])
for k, v in sample.items():

8
src/submissions/backend/validators/__init__.py
View File

@@ -100,11 +100,15 @@ class RSLNamer(object):
regex (str): string to construct pattern
filename (str): string to be parsed
"""
# logger.debug(f"Input string to be parsed: {filename}")
logger.debug(f"Input string to be parsed: {filename}")
if regex is None:
regex = BasicSubmission.construct_regex()
else:
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
logger.debug(f"Incoming regex: {regex}")
try:
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
except re.error as e:
regex = BasicSubmission.construct_regex()
# logger.debug(f"Using regex: {regex}")
match filename:
case Path():

7
src/submissions/backend/validators/pydant.py
View File

@@ -194,7 +194,7 @@ class PydSample(BaseModel, extra='allow'):
# logger.debug(f"Data for pydsample: {data}")
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items():
print(k, v)
# print(k, v)
if k in model.timestamps():
if isinstance(v, str):
v = datetime.strptime(v, "%Y-%m-%d")
@@ -463,7 +463,10 @@ class PydSubmission(BaseModel, extra='allow'):
return value
else:
# logger.debug("Constructing plate name.")
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
output = "RSL-BS-Test001"
else:
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
data=values.data).parsed_name
return dict(value=output, missing=True)

9
src/submissions/frontend/widgets/app.py
View File

@@ -18,6 +18,7 @@ from .submission_widget import SubmissionFormContainer
from .controls_chart import ControlsViewer
from .kit_creator import KitAdder
from .submission_type_creator import SubmissionTypeAdder
from .sample_search import SearchBox
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")
@@ -71,6 +72,7 @@ class App(QMainWindow):
fileMenu.addAction(self.importAction)
# fileMenu.addAction(self.importPCRAction)
methodsMenu.addAction(self.searchLog)
methodsMenu.addAction(self.searchSample)
reportMenu.addAction(self.generateReportAction)
maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction)
@@ -102,6 +104,7 @@ class App(QMainWindow):
self.helpAction = QAction("&About", self)
self.docsAction = QAction("&Docs", self)
self.searchLog = QAction("Search Log", self)
self.searchSample = QAction("Search Sample", self)
def _connectActions(self):
"""
@@ -117,6 +120,7 @@ class App(QMainWindow):
self.helpAction.triggered.connect(self.showAbout)
self.docsAction.triggered.connect(self.openDocs)
self.searchLog.triggered.connect(self.runSearch)
self.searchSample.triggered.connect(self.runSampleSearch)
def showAbout(self):
"""
@@ -161,6 +165,10 @@ class App(QMainWindow):
dlg = LogParser(self)
dlg.exec()
def runSampleSearch(self):
dlg = SearchBox(self)
dlg.exec()
def backup_database(self):
month = date.today().strftime("%Y-%m")
# day = date.today().strftime("%Y-%m-%d")
@@ -171,6 +179,7 @@ class App(QMainWindow):
logger.info("No backup found for this month, backing up database.")
shutil.copyfile(self.ctx.database_path, current_month_bak)
class AddSubForm(QWidget):
def __init__(self, parent:QWidget):

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

@@ -18,7 +18,7 @@ class ControlsViewer(QWidget):
def __init__(self, parent: QWidget) -> None:
super().__init__(parent)
self.app = self.parent().parent()
print(f"\n\n{self.app}\n\n")
# logger.debug(f"\n\n{self.app}\n\n")
self.report = Report()
self.datepicker = ControlsDatePicker()
self.webengineview = QWebEngineView()

101
src/submissions/frontend/widgets/sample_search.py Normal file
View File

@@ -0,0 +1,101 @@
from pprint import pformat
from typing import Tuple
from pandas import DataFrame
from PyQt6.QtCore import QAbstractTableModel, Qt, QEvent, QSortFilterProxyModel
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
)
from backend.db.models import BasicSample
from .submission_table import pandasModel
from .submission_details import SubmissionDetails
import logging
logger = logging.getLogger(f"submissions.{__name__}")
class SearchBox(QDialog):
def __init__(self, parent):
super().__init__(parent)
self.layout = QGridLayout(self)
self.sample_type = QComboBox(self)
self.sample_type.setObjectName("sample_type")
self.sample_type.currentTextChanged.connect(self.update_widgets)
options = [cls.__mapper_args__['polymorphic_identity'] for cls in BasicSample.__subclasses__()]
self.sample_type.addItems(options)
self.sample_type.setEditable(False)
self.setMinimumSize(600, 600)
self.sample_type.setMinimumWidth(self.minimumWidth())
self.layout.addWidget(self.sample_type, 0, 0)
self.results = SearchResults()
self.layout.addWidget(self.results, 5, 0)
self.setLayout(self.layout)
self.update_widgets()
def update_widgets(self):
deletes = [item for item in self.findChildren(FieldSearch)]
# logger.debug(deletes)
for item in deletes:
item.setParent(None)
self.type = BasicSample.find_polymorphic_subclass(self.sample_type.currentText())
# logger.debug(f"Sample type: {self.type}")
searchables = self.type.get_searchables()
start_row = 1
for iii, item in enumerate(searchables):
widget = FieldSearch(parent=self, label=item['label'], field_name=item['field'])
self.layout.addWidget(widget, start_row+iii, 0)
def parse_form(self):
fields = [item.parse_form() for item in self.findChildren(FieldSearch)]
return {item[0]:item[1] for item in fields if item[1] is not None}
def update_data(self):
fields = self.parse_form()
data = self.type.samples_to_df(sample_type=self.type, **fields)
# logger.debug(f"Data: {data}")
self.results.setData(df=data)
class FieldSearch(QWidget):
def __init__(self, parent, label, field_name):
super().__init__(parent)
self.layout = QVBoxLayout(self)
label_widget = QLabel(label)
self.layout.addWidget(label_widget)
self.search_widget = QLineEdit()
self.search_widget.setObjectName(field_name)
self.layout.addWidget(self.search_widget)
self.setLayout(self.layout)
self.search_widget.returnPressed.connect(self.enter_pressed)
def enter_pressed(self):
self.parent().update_data()
def parse_form(self) -> Tuple:
field_value = self.search_widget.text()
if field_value == "":
field_value = None
return self.search_widget.objectName(), field_value
class SearchResults(QTableView):
def __init__(self):
super().__init__()
self.doubleClicked.connect(lambda x: BasicSample.query(submitter_id=x.sibling(x.row(), 0).data()).show_details(self))
def setData(self, df:DataFrame) -> None:
"""
sets data in model
"""
self.data = df
try:
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)
except (TypeError, KeyError):
logger.error("Couldn't format id string.")
proxy_model = QSortFilterProxyModel()
proxy_model.setSourceModel(pandasModel(self.data))
self.setModel(proxy_model)

21
src/submissions/frontend/widgets/submission_details.py
View File

@@ -25,7 +25,7 @@ class SubmissionDetails(QDialog):
"""
a window showing text details of submission
"""
def __init__(self, parent, sub:BasicSubmission) -> None:
def __init__(self, parent, sub:BasicSubmission|BasicSample) -> None:
super().__init__(parent)
try:
@@ -47,19 +47,24 @@ class SubmissionDetails(QDialog):
# NOTE: setup channel
self.channel = QWebChannel()
self.channel.registerObject('backend', self)
self.submission_details(submission=sub)
self.rsl_plate_num = sub.rsl_plate_num
match sub:
case BasicSubmission():
self.submission_details(submission=sub)
self.rsl_plate_num = sub.rsl_plate_num
case BasicSample():
self.sample_details(sample=sub)
self.webview.page().setWebChannel(self.channel)
@pyqtSlot(str)
def sample_details(self, sample:str):
def sample_details(self, sample:str|BasicSample):
"""
Changes details view to summary of Sample
Args:
sample (str): Submitter Id of the sample.
"""
sample = BasicSample.query(submitter_id=sample)
"""
if isinstance(sample, str):
sample = BasicSample.query(submitter_id=sample)
base_dict = sample.to_sub_dict(full_data=True)
base_dict, template = sample.get_details_template(base_dict=base_dict)
html = template.render(sample=base_dict)
@@ -87,6 +92,8 @@ class SubmissionDetails(QDialog):
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.webview.setHtml(self.html)
with open("test.html", "w") as f:
f.write(self.html)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
@pyqtSlot(str)
@@ -138,7 +145,7 @@ class SubmissionComment(QDialog):
super().__init__(parent)
try:
self.app = parent.parent().parent().parent().parent().parent().parent
print(f"App: {self.app}")
# logger.debug(f"App: {self.app}")
except AttributeError:
pass
self.submission = submission

9
src/submissions/frontend/widgets/submission_table.py
View File

@@ -87,11 +87,10 @@ class SubmissionsSheet(QTableView):
"""
self.data = BasicSubmission.submissions_to_df()
try:
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)
except KeyError:
pass
self.data['Id'] = self.data['Id'].apply(str)
self.data['Id'] = self.data['Id'].str.zfill(3)
except KeyError as e:
logger.error(f"Could not alter id to string due to {e}")
proxyModel = QSortFilterProxyModel()
proxyModel.setSourceModel(pandasModel(self.data))
self.setModel(proxyModel)

194
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -13,7 +13,7 @@ from tools import Report, Result, check_not_nan, workbook_2_csv
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
KitType, Organization, SubmissionType, Reagent,
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation
)
from pprint import pformat
@@ -24,9 +24,9 @@ from datetime import date
logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionFormContainer(QWidget):
# A signal carrying a path
class SubmissionFormContainer(QWidget):
# A signal carrying a path
import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None:
@@ -41,7 +41,7 @@ class SubmissionFormContainer(QWidget):
def dragEnterEvent(self, event):
"""
Allow drag if file.
"""
"""
if event.mimeData().hasUrls():
event.accept()
else:
@@ -50,16 +50,16 @@ class SubmissionFormContainer(QWidget):
def dropEvent(self, event):
"""
Sets filename when file dropped
"""
"""
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
# logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent
self.import_drag.emit(fname)
def importSubmission(self, fname:Path|None=None):
def importSubmission(self, fname: Path | None = None):
"""
import submission from excel sheet into form
"""
"""
self.app.raise_()
self.app.activateWindow()
self.import_submission_function(fname)
@@ -68,7 +68,7 @@ class SubmissionFormContainer(QWidget):
self.report = Report()
self.app.result_reporter()
def import_submission_function(self, fname:Path|None=None):
def import_submission_function(self, fname: Path | None = None):
"""
Import a new submission to the app window
@@ -77,17 +77,17 @@ class SubmissionFormContainer(QWidget):
Returns:
Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
"""
"""
logger.info(f"\n\nStarting Import...\n\n")
report = Report()
try:
self.form.setParent(None)
except AttributeError:
pass
# initialize samples
# NOTE: initialize samples
self.samples = []
self.missing_info = []
# set file dialog
# NOTE: set file dialog
if isinstance(fname, bool) or fname == None:
fname = select_open_file(self, file_extension="xlsx")
# logger.debug(f"Attempting to parse file: {fname}")
@@ -95,7 +95,7 @@ class SubmissionFormContainer(QWidget):
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
self.report.add_result(report)
return
# create sheetparser using excel sheet and context from gui
# NOTE: create sheetparser using excel sheet and context from gui
try:
self.prsr = SheetParser(filepath=fname)
except PermissionError:
@@ -108,13 +108,12 @@ class SubmissionFormContainer(QWidget):
# logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form)
# if self.prsr.sample_result != None:
# report.add_result(msg=self.prsr.sample_result, status="Warning")
self.report.add_result(report)
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
def add_reagent(self, reagent_lot: str | None = None, reagent_type: str | None = None, expiry: date | None = None,
name: str | None = None):
"""
Action to create new reagent in DB.
@@ -126,28 +125,29 @@ class SubmissionFormContainer(QWidget):
Returns:
models.Reagent: the constructed reagent object to add to submission
"""
"""
report = Report()
if isinstance(reagent_lot, bool):
reagent_lot = ""
# create form
# NOTE: create form
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
if dlg.exec():
# extract form info
info = dlg.parse_form()
# logger.debug(f"Reagent info: {info}")
# create reagent object
# NOTE: create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db
# NOTE: send reagent to db
sqlobj, result = reagent.toSQL()
sqlobj.save()
report.add_result(result)
self.app.result_reporter()
return reagent
class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission:PydSubmission) -> None:
def __init__(self, parent: QWidget, submission: PydSubmission) -> None:
super().__init__(parent)
# self.report = Report()
self.app = parent.app
@@ -157,10 +157,8 @@ class SubmissionFormWidget(QWidget):
defaults = st.get_default_info("form_recover", "form_ignore")
self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore']
# self.ignore += self.recover
# logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
self.layout = QVBoxLayout()
# for k, v in kwargs.items():
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
if k in self.ignore:
continue
@@ -176,7 +174,8 @@ class SubmissionFormWidget(QWidget):
add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.scrape_reagents(self.pyd.extraction_kit)
def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem":
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | None = None,
extraction_kit: str | None = None) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
@@ -187,7 +186,7 @@ class SubmissionFormWidget(QWidget):
Returns:
self.InfoItem: Form widget to hold name:value
"""
"""
if key not in self.ignore:
match value:
case PydReagent():
@@ -199,8 +198,8 @@ class SubmissionFormWidget(QWidget):
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
return widget
return None
def scrape_reagents(self, *args, **kwargs):#extraction_kit:str, caller:str|None=None):
def scrape_reagents(self, *args, **kwargs): #extraction_kit:str, caller:str|None=None):
"""
Extracted scrape reagents function that will run when
form 'extraction_kit' widget is updated.
@@ -211,16 +210,15 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[QMainWindow, dict]: Updated application and result
"""
"""
extraction_kit = args[0]
caller = inspect.stack()[1].function.__repr__().replace("'", "")
# self.reagents = []
# logger.debug(f"Self.reagents: {self.reagents}")
# logger.debug(f"\n\n{pformat(caller)}\n\n")
# logger.debug(f"SubmissionType: {self.submission_type}")
report = Report()
# logger.debug(f"Extraction kit: {extraction_kit}")
# Remove previous reagent widgets
# NOTE: Remove previous reagent widgets
try:
old_reagents = self.find_widgets()
except AttributeError:
@@ -230,19 +228,6 @@ class SubmissionFormWidget(QWidget):
for reagent in old_reagents:
if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
reagent.setParent(None)
# match caller:
# case "import_submission_function":
# self.reagents = self.prsr.sub['reagents']
# case _:
# already_have = [reagent for reagent in self.prsr.sub['reagents'] if not reagent.missing]
# already_have = [reagent for reagent in self.pyd.reagents if not reagent.missing]
# names = list(set([item.type for item in already_have]))
# # logger.debug(f"Already have: {already_have}")
# reagents = [item.to_pydantic() for item in KitType.query(name=extraction_kit).get_reagents(submission_type=self.pyd.submission_type) if item.name not in names]
# # logger.debug(f"Missing: {reagents}")
# self.pyd.reagents = already_have + reagents
# logger.debug(f"Reagents: {self.reagents}")
# self.kit_integrity_completion_function(extraction_kit=extraction_kit)
reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
# logger.debug(f"Missing reagents: {obj.missing_reagents}")
for reagent in reagents:
@@ -266,11 +251,11 @@ class SubmissionFormWidget(QWidget):
def clear_form(self):
"""
Removes all form widgets
"""
"""
for item in self.findChildren(QWidget):
item.setParent(None)
def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
def find_widgets(self, object_name: str | None = None) -> List[QWidget]:
"""
Gets all widgets filtered by object name
@@ -279,12 +264,12 @@ class SubmissionFormWidget(QWidget):
Returns:
List[QWidget]: Widgets matching filter
"""
"""
query = self.findChildren(QWidget)
if object_name != None:
query = [widget for widget in query if widget.objectName()==object_name]
if object_name is not None:
query = [widget for widget in query if widget.objectName() == object_name]
return query
def submit_new_sample_function(self) -> QWidget:
"""
Parse forms and add sample to the database.
@@ -294,7 +279,7 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
"""
logger.info(f"\n\nBeginning Submission\n\n")
report = Report()
result = self.parse_form()
@@ -320,8 +305,7 @@ class SubmissionFormWidget(QWidget):
case 1:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
if dlg.exec():
# Do not add duplicate reagents.
# base_submission.reagents = []
# NOTE: Do not add duplicate reagents.
result = None
else:
self.app.ctx.database_session.rollback()
@@ -347,13 +331,13 @@ class SubmissionFormWidget(QWidget):
self.app.report.add_result(report)
self.app.result_reporter()
def export_csv_function(self, fname:Path|None=None):
def export_csv_function(self, fname: Path | None = None):
"""
Save the submission's csv file.
Args:
fname (Path | None, optional): Input filename. Defaults to None.
"""
"""
if isinstance(fname, bool) or fname == None:
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try:
@@ -371,7 +355,7 @@ class SubmissionFormWidget(QWidget):
Returns:
Report: Report on status of parse.
"""
"""
report = Report()
logger.info(f"Hello from form parser!")
info = {}
@@ -397,28 +381,28 @@ class SubmissionFormWidget(QWidget):
value = getattr(self, item)
# logger.debug(f"Setting {item}")
info[item] = value
for k,v in info.items():
for k, v in info.items():
self.pyd.set_attribute(key=k, value=v)
# NOTE: return submission
report.add_result(report)
return report
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> None:
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> None:
super().__init__(parent)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type)
self.setObjectName(key)
try:
self.missing:bool = value['missing']
self.missing: bool = value['missing']
except (TypeError, KeyError):
self.missing:bool = True
if self.input != None:
self.missing: bool = True
if self.input is not None:
layout.addWidget(self.label)
layout.addWidget(self.input)
layout.setContentsMargins(0,0,0,0)
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
match self.input:
case QComboBox():
@@ -427,7 +411,7 @@ class SubmissionFormWidget(QWidget):
self.input.dateChanged.connect(self.update_missing)
case QLineEdit():
self.input.textChanged.connect(self.update_missing)
def parse_form(self) -> Tuple[str, dict]:
"""
Pulls info from widget into dict
@@ -445,8 +429,8 @@ class SubmissionFormWidget(QWidget):
case _:
return None, None
return self.input.objectName(), dict(value=value, missing=self.missing)
def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> QWidget:
"""
Creates form widget
@@ -458,7 +442,7 @@ class SubmissionFormWidget(QWidget):
Returns:
QWidget: Form object
"""
"""
try:
value = value['value']
except (TypeError, KeyError):
@@ -480,11 +464,12 @@ class SubmissionFormWidget(QWidget):
case 'extraction_kit':
# if extraction kit not available, all other values fail
if not check_not_nan(value):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!",
status="warning")
msg.exec()
# create combobox to hold looked up kits
# NOTE: create combobox to hold looked up kits
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in KitType.query(used_for=submission_type)]
obj.uses = uses
@@ -497,14 +482,13 @@ class SubmissionFormWidget(QWidget):
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
case 'submitted_date':
# uses base calendar
# NOTE: uses base calendar
add_widget = QDateEdit(calendarPopup=True)
# sets submitted date based on date found in excel sheet
# NOTE: sets submitted date based on date found in excel sheet
try:
add_widget.setDate(value)
# if not found, use today
# NOTE: if not found, use today
except:
add_widget.setDate(date.today())
case 'submission_category':
@@ -517,25 +501,25 @@ class SubmissionFormWidget(QWidget):
cats.insert(0, cats.pop(cats.index(submission_type)))
add_widget.addItems(cats)
case _:
# anything else gets added in as a line edit
# NOTE: anything else gets added in as a line edit
add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
if add_widget != None:
if add_widget is not None:
add_widget.setObjectName(key)
add_widget.setParent(parent)
return add_widget
def update_missing(self):
"""
Set widget status to updated
"""
"""
self.missing = True
self.label.updated(self.objectName())
class ParsedQLabel(QLabel):
def __init__(self, key:str, value:dict, title:bool=True, label_name:str|None=None):
def __init__(self, key: str, value: dict, title: bool = True, label_name: str | None = None):
super().__init__()
try:
check = not value['missing']
@@ -546,7 +530,7 @@ class SubmissionFormWidget(QWidget):
else:
self.setObjectName(f"{key}_label")
if title:
output = key.replace('_', ' ').title()
output = key.replace('_', ' ').title().replace("Rsl", "RSL").replace("Pcr", "PCR")
else:
output = key.replace('_', ' ')
if check:
@@ -554,43 +538,38 @@ class SubmissionFormWidget(QWidget):
else:
self.setText(f"MISSING {output}")
def updated(self, key:str, title:bool=True):
def updated(self, key: str, title: bool = True):
"""
Mark widget as updated
Args:
key (str): Name of the field
title (bool, optional): Use title case. Defaults to True.
"""
"""
if title:
output = key.replace('_', ' ').title()
output = key.replace('_', ' ').title().replace("Rsl", "RSL").replace("Pcr", "PCR")
else:
output = key.replace('_', ' ')
self.setText(f"UPDATED {output}")
class ReagentFormWidget(QWidget):
def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
def __init__(self, parent: QWidget, reagent: PydReagent, extraction_kit: str):
super().__init__(parent)
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
self.reagent = reagent
self.extraction_kit = extraction_kit
layout = QVBoxLayout()
# layout = QGridLayout()
# self.check_box = QCheckBox(self)
# self.check_box.setChecked(True)
# self.check_box.stateChanged.connect(self.check_uncheck)
# layout.addWidget(self.check_box, 0,0)
self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label)
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
layout.addWidget(self.lot)
# Remove spacing between reagents
layout.setContentsMargins(0,0,0,0)
# NOTE: Remove spacing between reagents
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.setObjectName(reagent.name)
self.missing = reagent.missing
# If changed set self.missing to True and update self.label
# NOTE: If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
def parse_form(self) -> Tuple[PydReagent, dict]:
@@ -599,40 +578,42 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[PydReagent, dict]: PydReagent and Report(?)
"""
# if not self.check_box.isChecked():
# return None, None
"""
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent == None:
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
dlg = QuestionAsker(title=f"Add {lot}?",
message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type,
expiry=self.reagent.expiry,
name=self.reagent.name)
return wanted_reagent, None
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# logger.debug("Will not add reagent.")
return None, Result(msg="Failed integrity check", status="Critical")
else:
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
rt = ReagentType.query(name=self.reagent.type)
if rt == None:
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, missing=False), None
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name,
expiry=wanted_reagent.expiry, missing=False), None
def updated(self):
"""
Set widget status to updated
"""
"""
self.missing = True
self.label.updated(self.reagent.type)
class ReagentParsedLabel(QLabel):
def __init__(self, reagent:PydReagent):
def __init__(self, reagent: PydReagent):
super().__init__()
try:
check = not reagent.missing
@@ -643,19 +624,19 @@ class SubmissionFormWidget(QWidget):
self.setText(f"Parsed {reagent.type}")
else:
self.setText(f"MISSING {reagent.type}")
def updated(self, reagent_type:str):
def updated(self, reagent_type: str):
"""
Marks widget as updated
Args:
reagent_type (str): _description_
"""
"""
self.setText(f"UPDATED {reagent_type}")
class ReagentLot(QComboBox):
def __init__(self, reagent, extraction_kit:str) -> None:
def __init__(self, reagent, extraction_kit: str) -> None:
super().__init__()
self.setEditable(True)
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
@@ -664,7 +645,7 @@ class SubmissionFormWidget(QWidget):
relevant_reagents = [str(item.lot) for item in lookup]
output_reg = []
for rel_reagent in relevant_reagents:
# extract strings from any sets.
# NOTE: extract strings from any sets.
if isinstance(rel_reagent, set):
for thing in rel_reagent:
output_reg.append(thing)
@@ -677,7 +658,8 @@ class SubmissionFormWidget(QWidget):
if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot))
else:
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type,
kit_type=extraction_kit)
try:
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
except AttributeError:

8
src/submissions/templates/basicsample_details.html
View File

@@ -42,11 +42,11 @@
{% block body %}
<h2><u>Sample Details for {{ sample['Submitter ID'] }}</u></h2>
<p>{% for key, value in sample.items() if key not in sample['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key }}: </b>{{ value }}<br>
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
{% endfor %}</p>
{% if sample['submissions'] %}<h2>Submissions:</h2>
{% for submission in sample['submissions'] %}
<p id="{{ submission['Plate Name'] }}"><b>{{ submission['Plate Name'] }}:</b> {{ submission['Well'] }}</p>
<p id="{{ submission['plate_name'] }}"><b>{{ submission['plate_name'] }}:</b> {{ submission['well'] }}</p>
{% endfor %}
{% endif %}
{% endblock %}
@@ -57,8 +57,8 @@
backend = channel.objects.backend;
});
{% for submission in sample['submissions'] %}
document.getElementById("{{ submission['Plate Name'] }}").addEventListener("dblclick", function(){
backend.submission_details("{{ submission['Plate Name'] }}");
document.getElementById("{{ submission['plate_name'] }}").addEventListener("dblclick", function(){
backend.submission_details("{{ submission['plate_name'] }}");
});
{% endfor %}
</script>

10
src/submissions/templates/basicsubmission_details.html
View File

@@ -43,7 +43,7 @@
<!-- {% set excluded = ['reagents', 'samples', 'controls', 'extraction_info', 'pcr_info', 'comment', 'barcode', 'platemap', 'export_map', 'equipment'] %} -->
<h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
<p>{% for key, value in sub.items() if key not in sub['excluded'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key }}: </b>{% if key=='Cost' %}{% if sub['Cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Pcr", "PCR") }}: </b>{% if key=='Cost' %}{% if sub['cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
{% endfor %}</p>
<h3><u>Reagents:</u></h3>
<p>{% for item in sub['reagents'] %}
@@ -58,7 +58,7 @@
{% if sub['samples'] %}
<h3><u>Samples:</u></h3>
<p>{% for item in sub['samples'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['Well'] }}:</b> {% if item['Organism'] %} {{ item['Name'] }} - ({{ item['Organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['Name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}<br>
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b> {% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}<br>
{% endfor %}</p>
{% endif %}
{% if sub['controls'] %}
@@ -129,12 +129,12 @@
backend = channel.objects.backend;
});
{% for sample in sub['samples'] %}
document.getElementById("{{sample['Submitter ID']}}").addEventListener("dblclick", function(){
backend.sample_details("{{ sample['Submitter ID'] }}");
document.getElementById("{{ sample['submitter_id'] }}").addEventListener("dblclick", function(){
backend.sample_details("{{ sample['submitter_id'] }}");
});
{% endfor %}
document.getElementById("sign_btn").addEventListener("click", function(){
backend.sign_off("{{ sub['Plate Number'] }}");
backend.sign_off("{{ sub['plate_number'] }}");
})
</script>
</html>

12
src/submissions/templates/plate_map.html
View File

@@ -1,15 +1,15 @@
<div class="gallery" style="display: grid;grid-template-columns: repeat({{ PLATE_COLUMNS }}, 7.5vw);grid-template-rows: repeat({{ PLATE_ROWS }}, 7.5vw);grid-gap: 2px;">
{% for sample in samples %}
<div class="well" id="{{sample['Submitter ID']}}" style="background-color: {{sample['background_color']}};
<div class="well" id="{{sample['submitter_id']}}" style="background-color: {{sample['background_color']}};
border: 1px solid #000;
padding: 20px;
grid-column-start: {{sample['Column']}};
grid-column-end: {{sample['Column']}};
grid-row-start: {{sample['Row']}};
grid-row-end: {{sample['Row']}};
grid-column-start: {{sample['column']}};
grid-column-end: {{sample['column']}};
grid-row-start: {{sample['row']}};
grid-row-end: {{sample['row']}};
display: flex;
">
<div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['Name'] }}
<div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['name'] }}
<span class="tooltiptext">{{ sample['tooltip'] }}</span>
</div>
</div>

8
src/submissions/templates/tooltip.html
View File

@@ -1,4 +1,4 @@
Sample name: {{ fields['Submitter ID'] }}<br>
{% if fields['Organism'] %}Organism: {{ fields['Organism'] }}<br>{% endif %}
{% if fields['Concentration'] %}Concentration: {{ fields['Concentration'] }}<br>{% endif %}
Well: {{ fields['Well'] }}<!--{{ fields['column'] }}-->
Sample name: {{ fields['submitter_id'] }}<br>
{% if fields['organism'] %}Organism: {{ fields['organism'] }}<br>{% endif %}
{% if fields['concentration'] %}Concentration: {{ fields['concentration'] }}<br>{% endif %}
Well: {{ fields['well'] }}<!--{{ fields['column'] }}-->

4
src/submissions/tools.py
View File

@@ -86,7 +86,7 @@ def check_not_nan(cell_contents) -> bool:
except TypeError:
return True
except Exception as e:
logger.debug(f"Check encountered unknown error: {type(e).__name__} - {e}")
logger.error(f"Check encountered unknown error: {type(e).__name__} - {e}")
return False
@@ -228,7 +228,7 @@ class Settings(BaseSettings, extra="allow"):
database_path = database_path
else:
raise FileNotFoundError("No database file found. Exiting program.")
logger.debug(f"Using {database_path} for database file.")
logger.info(f"Using {database_path} for database file.")
engine = create_engine(f"sqlite:///{database_path}") #, echo=True, future=True)
session = Session(engine)
# metadata.session = session