landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Mid code cleanup

Browse Source
This commit is contained in:
lwark
2024-09-26 08:26:37 -05:00
parent 4c7b737326
commit f4e930c64e
9 changed files with 135 additions and 94 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
src/submissions/backend/db/models/__init__.py
View File

@@ -6,11 +6,10 @@ import sys, logging
from sqlalchemy import Column, INTEGER, String, JSON from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError, IntegrityError as sqlalcIntegrityError from sqlalchemy.exc import ArgumentError
from typing import Any, List from typing import Any, List
from pathlib import Path from pathlib import Path
from tools import report_result from tools import report_result
# from sqlite3 import IntegrityError as sqliteIntegrityError
# Load testing environment # Load testing environment
if 'pytest' in sys.modules: if 'pytest' in sys.modules:
@@ -155,7 +154,7 @@ class BaseClass(Base):
return query.limit(limit).all() return query.limit(limit).all()
@report_result @report_result
def save(self): def save(self) -> Report | None:
""" """
Add the object to the database and commit Add the object to the database and commit
""" """
@@ -167,21 +166,8 @@ class BaseClass(Base):
except Exception as e: except Exception as e:
logger.critical(f"Problem saving object: {e}") logger.critical(f"Problem saving object: {e}")
logger.error(f"Error message: {type(e)}") logger.error(f"Error message: {type(e)}")
# match e:
# case sqlalcIntegrityError():
# origin = e.orig.__str__().lower()
# logger.error(f"Exception origin: {origin}")
# if "unique constraint failed:" in origin:
# field = " ".join(origin.split(".")[1:]).replace("_", " ").upper()
# # logger.debug(field)
# msg = f"{field} doesn't have a unique value.\nIt must be changed."
# else:
# msg = f"Got unknown integrity error: {e}"
# case _:
# msg = f"Got generic error: {e}"
self.__database_session__.rollback() self.__database_session__.rollback()
report.add_result(Result(msg=e, status="Critical")) report.add_result(Result(msg=e, status="Critical"))
return report
class ConfigItem(BaseClass): class ConfigItem(BaseClass):
@@ -192,8 +178,8 @@ class ConfigItem(BaseClass):
key = Column(String(32)) #: Name of the configuration item. key = Column(String(32)) #: Name of the configuration item.
value = Column(JSON) #: Value associated with the config item. value = Column(JSON) #: Value associated with the config item.
def __repr__(self): def __repr__(self) -> str:
return f"ConfigItem({self.key} : {self.value})" return f"<ConfigItem({self.key} : {self.value})>"
@classmethod @classmethod
def get_config_items(cls, *args) -> ConfigItem | List[ConfigItem]: def get_config_items(cls, *args) -> ConfigItem | List[ConfigItem]:

65
src/submissions/backend/db/models/kits.py
View File

@@ -5,17 +5,14 @@ from __future__ import annotations
import datetime import datetime
import json import json
from pprint import pprint, pformat from pprint import pformat
import yaml import yaml
from jinja2 import TemplateNotFound
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date from datetime import date
import logging, re import logging, re
from tools import check_authorization, setup_lookup, Report, Result, jinja_template_loading, check_regex_match, \ from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator
yaml_regex_creator
from typing import List, Literal, Generator, Any from typing import List, Literal, Generator, Any
from pandas import ExcelFile from pandas import ExcelFile
from pathlib import Path from pathlib import Path
@@ -204,7 +201,6 @@ class KitType(BaseClass):
yield assoc.reagent_role.name, assoc.uses yield assoc.reagent_role.name, assoc.uses
except TypeError: except TypeError:
continue continue
# return info_map
@classmethod @classmethod
@setup_lookup @setup_lookup
@@ -267,17 +263,20 @@ class KitType(BaseClass):
for k, v in self.construct_xl_map_for_use(submission_type=submission_type): for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
# logger.debug(f"Value: {v}") # logger.debug(f"Value: {v}")
try: try:
assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0] # assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
except IndexError as e: assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
except StopIteration as e:
continue continue
for kk, vv in assoc.to_export_dict().items(): for kk, vv in assoc.to_export_dict().items():
v[kk] = vv v[kk] = vv
base_dict['reagent roles'].append(v) base_dict['reagent roles'].append(v)
for k, v in submission_type.construct_equipment_map(): for k, v in submission_type.construct_equipment_map():
try: try:
assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if # assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k][0] # item.equipment_role.name == k][0]
except IndexError: assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k)
except StopIteration:
continue continue
for kk, vv in assoc.to_export_dict(kit_type=self).items(): for kk, vv in assoc.to_export_dict(kit_type=self).items():
# logger.debug(f"{kk}:{vv}") # logger.debug(f"{kk}:{vv}")
@@ -858,10 +857,7 @@ class SubmissionType(BaseClass):
base_dict = dict(name=self.name) base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export') base_dict['info'] = self.construct_info_map(mode='export')
base_dict['defaults'] = self.defaults base_dict['defaults'] = self.defaults
# base_dict['excel location maps']['kits'] = [{k: v for k, v in item.kit_type.construct_xl_map_for_use(submission_type=self)} for item in
# self.submissiontype_kit_associations]
base_dict['samples'] = self.construct_sample_map() base_dict['samples'] = self.construct_sample_map()
# base_dict['excel location maps']['equipment_roles'] = {k: v for k, v in self.construct_equipment_map()}
base_dict['kits'] = [item.to_export_dict() for item in self.submissiontype_kit_associations] base_dict['kits'] = [item.to_export_dict() for item in self.submissiontype_kit_associations]
return base_dict return base_dict
@@ -878,7 +874,6 @@ class SubmissionType(BaseClass):
yaml.add_constructor("!regex", yaml_regex_creator) yaml.add_constructor("!regex", yaml_regex_creator)
if isinstance(filepath, str): if isinstance(filepath, str):
filepath = Path(filepath) filepath = Path(filepath)
with open(filepath, "r") as f: with open(filepath, "r") as f:
if filepath.suffix == ".json": if filepath.suffix == ".json":
import_dict = json.load(fp=f) import_dict = json.load(fp=f)
@@ -949,7 +944,7 @@ class SubmissionType(BaseClass):
new_process.equipment_roles.append(new_role) new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys(): if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.") logger.info("Found Organizations to be imported.")
Organization.import_from_json(filepath=filepath) Organization.import_from_yml(filepath=filepath)
return submission_type return submission_type
@@ -1031,6 +1026,12 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
return cls.execute_query(query=query, limit=limit) return cls.execute_query(query=query, limit=limit)
def to_export_dict(self): def to_export_dict(self):
"""
Creates a dictionary of relevant values in this object.
Returns:
dict: dictionary of Association and related kittype
"""
exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type'] exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude} base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude}
base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type) base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
@@ -1150,7 +1151,13 @@ class KitTypeReagentRoleAssociation(BaseClass):
limit = 1 limit = 1
return cls.execute_query(query=query, limit=limit) return cls.execute_query(query=query, limit=limit)
def to_export_dict(self): def to_export_dict(self) -> dict:
"""
Creates a dictionary of relevant values in this object.
Returns:
dict: dictionary of Association and related reagent role
"""
base_dict = {} base_dict = {}
base_dict['required'] = self.required base_dict['required'] = self.required
for k, v in self.reagent_role.to_export_dict().items(): for k, v in self.reagent_role.to_export_dict().items():
@@ -1418,6 +1425,15 @@ class Equipment(BaseClass):
@classmethod @classmethod
def assign_equipment(cls, equipment_role: EquipmentRole|str) -> List[Equipment]: def assign_equipment(cls, equipment_role: EquipmentRole|str) -> List[Equipment]:
"""
Creates a list of equipment from user input to be used in Submission Type creation
Args:
equipment_role (EquipmentRole): Equipment role to be added to.
Returns:
List[Equipment]: User selected equipment.
"""
if isinstance(equipment_role, str): if isinstance(equipment_role, str):
equipment_role = EquipmentRole.query(name=equipment_role) equipment_role = EquipmentRole.query(name=equipment_role)
equipment = cls.query() equipment = cls.query()
@@ -1468,16 +1484,7 @@ class EquipmentRole(BaseClass):
Returns: Returns:
dict: This EquipmentRole dict dict: This EquipmentRole dict
""" """
# output = {}
return {key: value for key, value in self.__dict__.items() if key != "processes"} return {key: value for key, value in self.__dict__.items() if key != "processes"}
# match key:
# case "processes":
# pass
# case _:
# value = value
# yield key, value
# # output[key] = value
# return output
def to_pydantic(self, submission_type: SubmissionType, def to_pydantic(self, submission_type: SubmissionType,
extraction_kit: str | KitType | None = None) -> "PydEquipmentRole": extraction_kit: str | KitType | None = None) -> "PydEquipmentRole":
@@ -1568,6 +1575,12 @@ class EquipmentRole(BaseClass):
return output return output
def to_export_dict(self, submission_type: SubmissionType, kit_type: KitType): def to_export_dict(self, submission_type: SubmissionType, kit_type: KitType):
"""
Creates a dictionary of relevant values in this object.
Returns:
dict: dictionary of Association and related reagent role
"""
base_dict = {} base_dict = {}
base_dict['role'] = self.name base_dict['role'] = self.name
base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type) base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)

11
src/submissions/backend/db/models/organizations.py
View File

@@ -79,7 +79,16 @@ class Organization(BaseClass):
@classmethod @classmethod
@check_authorization @check_authorization
def import_from_json(cls, filepath: Path|str): def import_from_yml(cls, filepath: Path | str):
"""
An ambitious project to create a Organization from a yml file
Args:
filepath (Path): Filepath of the yml.
Returns:
"""
if isinstance(filepath, str): if isinstance(filepath, str):
filepath = Path(filepath) filepath = Path(filepath)
if not filepath.exists(): if not filepath.exists():

81
src/submissions/backend/db/models/submissions.py
View File

@@ -12,7 +12,7 @@ from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter from operator import itemgetter
from pprint import pformat from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, Tips from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified from sqlalchemy.orm.attributes import flag_modified
@@ -24,7 +24,8 @@ import pandas as pd
from openpyxl import Workbook from openpyxl import Workbook
from openpyxl.worksheet.worksheet import Worksheet from openpyxl.worksheet.worksheet import Worksheet
from openpyxl.drawing.image import Image as OpenpyxlImage from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
report_result
from datetime import datetime, date from datetime import datetime, date
from typing import List, Any, Tuple, Literal from typing import List, Any, Tuple, Literal
from dateutil.parser import parse from dateutil.parser import parse
@@ -160,7 +161,18 @@ class BasicSubmission(BaseClass):
return output return output
@classmethod @classmethod
def get_default_info(cls, *args, submission_type: SubmissionType | None = None): def get_default_info(cls, *args, submission_type: SubmissionType | None = None) -> dict:
"""
Gets default info from the database for a given submission type.
Args:
*args (): List of fields to get
submission_type (SubmissionType): the submission type of interest. Necessary due to generic submission types.
Returns:
dict: Default info
"""
# NOTE: Create defaults for all submission_types # NOTE: Create defaults for all submission_types
parent_defs = super().get_default_info() parent_defs = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment'] recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
@@ -230,6 +242,7 @@ class BasicSubmission(BaseClass):
case _: case _:
return SubmissionType.query(cls.__mapper_args__['polymorphic_identity']) return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
@classmethod @classmethod
def construct_info_map(cls, submission_type: SubmissionType | None = None, def construct_info_map(cls, submission_type: SubmissionType | None = None,
mode: Literal["read", "write"] = "read") -> dict: mode: Literal["read", "write"] = "read") -> dict:
@@ -408,8 +421,10 @@ class BasicSubmission(BaseClass):
except Exception as e: except Exception as e:
logger.error(f"Column count error: {e}") logger.error(f"Column count error: {e}")
# NOTE: Get kit associated with this submission # NOTE: Get kit associated with this submission
assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if # assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
item.submission_type == self.submission_type][0] # item.submission_type == self.submission_type][0]
assoc = next((item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type),
None)
# logger.debug(f"Came up with association: {assoc}") # logger.debug(f"Came up with association: {assoc}")
# NOTE: If every individual cost is 0 this is probably an old plate. # NOTE: If every individual cost is 0 this is probably an old plate.
if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]): if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
@@ -453,8 +468,9 @@ class BasicSubmission(BaseClass):
for column in range(1, plate_columns + 1): for column in range(1, plate_columns + 1):
for row in range(1, plate_rows + 1): for row in range(1, plate_rows + 1):
try: 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 = next(item for item in sample_list if item['row'] == row and item['column'] == column)
except StopIteration:
well = dict(name="", row=row, column=column, background_color="#ffffff") well = dict(name="", row=row, column=column, background_color="#ffffff")
output_samples.append(well) output_samples.append(well)
env = jinja_template_loading() env = jinja_template_loading()
@@ -498,7 +514,7 @@ class BasicSubmission(BaseClass):
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre', 'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact', 'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
'tips', 'gel_image_path'] 'tips', 'gel_image_path', 'custom']
for item in excluded: for item in excluded:
try: try:
df = df.drop(item, axis=1) df = df.drop(item, axis=1)
@@ -553,7 +569,9 @@ class BasicSubmission(BaseClass):
return return
case item if item in self.jsons(): case item if item in self.jsons():
match value: match value:
case list(): case dict():
existing = value
case _:
# logger.debug(f"Setting JSON attribute.") # logger.debug(f"Setting JSON attribute.")
existing = self.__getattribute__(key) existing = self.__getattribute__(key)
if value is None or value in ['', 'null']: if value is None or value in ['', 'null']:
@@ -573,8 +591,6 @@ class BasicSubmission(BaseClass):
existing = value existing = value
else: else:
existing.append(value) existing.append(value)
case _:
existing = value
self.__setattr__(key, existing) self.__setattr__(key, existing)
flag_modified(self, key) flag_modified(self, key)
return return
@@ -600,7 +616,13 @@ class BasicSubmission(BaseClass):
Returns: Returns:
Result: _description_ Result: _description_
""" """
assoc = [item for item in self.submission_sample_associations if item.sample == sample][0] # assoc = [item for item in self.submission_sample_associations if item.sample == sample][0]
try:
assoc = next(item for item in self.submission_sample_associations if item.sample == sample)
except StopIteration:
report = Report()
report.add_result(Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
return report
for k, v in input_dict.items(): for k, v in input_dict.items():
try: try:
setattr(assoc, k, v) setattr(assoc, k, v)
@@ -716,8 +738,6 @@ class BasicSubmission(BaseClass):
case str(): case str():
try: try:
logger.info(f"Recruiting: {cls}") logger.info(f"Recruiting: {cls}")
# model = [item for item in cls.__subclasses__() if
# item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_ model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
except Exception as e: except Exception as e:
logger.error( logger.error(
@@ -823,8 +843,8 @@ class BasicSubmission(BaseClass):
Workbook: Updated workbook Workbook: Updated workbook
""" """
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill") logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
logger.debug(f"Input dict: {info}") # logger.debug(f"Input dict: {info}")
logger.debug(f"Custom fields: {custom_fields}") # logger.debug(f"Custom fields: {custom_fields}")
for k, v in custom_fields.items(): for k, v in custom_fields.items():
try: try:
assert v['type'] in ['exempt', 'range', 'cell'] assert v['type'] in ['exempt', 'range', 'cell']
@@ -878,15 +898,9 @@ class BasicSubmission(BaseClass):
from backend.validators import RSLNamer from backend.validators import RSLNamer
# logger.debug(f"instr coming into {cls}: {instr}") # logger.debug(f"instr coming into {cls}: {instr}")
logger.debug(f"data coming into {cls}: {data}") logger.debug(f"data coming into {cls}: {data}")
# defaults = cls.get_default_info("abbreviation", "submission_type")
if "submission_type" not in data.keys(): if "submission_type" not in data.keys():
data['submission_type'] = cls.__mapper_args__['polymorphic_identity'] data['submission_type'] = cls.__mapper_args__['polymorphic_identity']
data['abbreviation'] = cls.get_default_info("abbreviation", submission_type=data['submission_type']) data['abbreviation'] = cls.get_default_info("abbreviation", submission_type=data['submission_type'])
# logger.debug(f"Default info: {defaults}")
# data['abbreviation'] = defaults['abbreviation']
# if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
# data['submission_type'] = defaults['submission_type']
if instr in [None, ""]: if instr in [None, ""]:
# logger.debug("Sending to RSLNamer to make new plate name.") # logger.debug("Sending to RSLNamer to make new plate name.")
outstr = RSLNamer.construct_new_plate_name(data=data) outstr = RSLNamer.construct_new_plate_name(data=data)
@@ -1386,8 +1400,8 @@ class BacterialCulture(BasicSubmission):
new_lot = matched.group() new_lot = matched.group()
try: try:
pos_control_reg = \ pos_control_reg = \
[reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control"][0] next(reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control")
except IndexError: except StopIteration:
logger.error(f"No positive control reagent listed") logger.error(f"No positive control reagent listed")
return input_dict return input_dict
pos_control_reg['lot'] = new_lot pos_control_reg['lot'] = new_lot
@@ -1615,6 +1629,7 @@ class Wastewater(BasicSubmission):
events['Link PCR'] = self.link_pcr events['Link PCR'] = self.link_pcr
return events return events
@report_result
def link_pcr(self, obj): def link_pcr(self, obj):
""" """
Adds PCR info to this submission Adds PCR info to this submission
@@ -1624,7 +1639,11 @@ class Wastewater(BasicSubmission):
""" """
from backend.excel import PCRParser from backend.excel import PCRParser
from frontend.widgets import select_open_file from frontend.widgets import select_open_file
report = Report()
fname = select_open_file(obj=obj, file_extension="xlsx") fname = select_open_file(obj=obj, file_extension="xlsx")
if not fname:
report.add_result(Result(msg="No file selected, cancelling.", status="Warning"))
return report
parser = PCRParser(filepath=fname) parser = PCRParser(filepath=fname)
self.set_attribute("pcr_info", parser.pcr) self.set_attribute("pcr_info", parser.pcr)
self.save(original=False) self.save(original=False)
@@ -1633,8 +1652,9 @@ class Wastewater(BasicSubmission):
for sample in self.samples: for sample in self.samples:
# logger.debug(f"Running update on: {sample}") # logger.debug(f"Running update on: {sample}")
try: try:
sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0] # sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
except IndexError: sample_dict = next(item for item in parser.samples if item['sample'] == sample.rsl_number)
except StopIteration:
continue continue
self.update_subsampassoc(sample=sample, input_dict=sample_dict) self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information')) # self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
@@ -2119,7 +2139,11 @@ class WastewaterArtic(BasicSubmission):
""" """
from frontend.widgets.gel_checker import GelBox from frontend.widgets.gel_checker import GelBox
from frontend.widgets import select_open_file from frontend.widgets import select_open_file
report = Report()
fname = select_open_file(obj=obj, file_extension="jpg") fname = select_open_file(obj=obj, file_extension="jpg")
if not fname:
report.add_result(Result(msg="No file selected, cancelling.", status="Warning"))
return report
dlg = GelBox(parent=obj, img_path=fname, submission=self) dlg = GelBox(parent=obj, img_path=fname, submission=self)
if dlg.exec(): if dlg.exec():
self.dna_core_submission_number, self.gel_barcode, img_path, output, comment = dlg.parse_form() self.dna_core_submission_number, self.gel_barcode, img_path, output, comment = dlg.parse_form()
@@ -2283,8 +2307,9 @@ class BasicSample(BaseClass):
polymorphic_identity = polymorphic_identity['value'] polymorphic_identity = polymorphic_identity['value']
if polymorphic_identity is not None: if polymorphic_identity is not None:
try: try:
return [item for item in cls.__subclasses__() if # return [item for item in cls.__subclasses__() if
item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0] # item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
except Exception as e: except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}") logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
model = cls model = cls

34
src/submissions/backend/excel/writer.py
View File

@@ -541,28 +541,30 @@ class DocxWriter(object):
@classmethod @classmethod
def create_plate_map(self, sample_list: List[dict], rows: int = 0, columns: int = 0) -> List[list]: def create_plate_map(self, sample_list: List[dict], rows: int = 0, columns: int = 0) -> List[list]:
sample_list = sorted(sample_list, key=itemgetter('column', 'row')) sample_list = sorted(sample_list, key=itemgetter('column', 'row'))
# NOTE if rows or samples is default, set to maximum value in sample list
if rows == 0: if rows == 0:
rows = max([sample['row'] for sample in sample_list]) rows = max([sample['row'] for sample in sample_list])
if columns == 0: if columns == 0:
columns = max([sample['column'] for sample in sample_list]) columns = max([sample['column'] for sample in sample_list])
# output = []
for row in range(0, rows): for row in range(0, rows):
contents = [''] * columns # NOTE: Create a list with length equal to columns length
for column in range(0, columns): # contents = [''] * columns
try: contents = [next((item['submitter_id'] for item in sample_list if item['row'] == row + 1 and
ooi = [item for item in sample_list if item['row'] == row + 1 and item['column'] == column + 1][0] item['column'] == column + 1), '') for column in range(0, columns)]
except IndexError: # for column in range(0, columns):
continue # contents[column] = next((item['submitter_id'] for item in sample_list if item['row'] == row + 1 and item['column'] == column), '')
contents[column] = ooi['submitter_id'] # try:
# contents = [sample['submitter_id'] for sample in sample_list if sample['row'] == row + 1] # # ooi = [item for item in sample_list if item['row'] == row + 1 and item['column'] == column + 1][0]
# contents = [f"{sample['row']},{sample['column']}" for sample in sample_list if sample['row'] == row + 1] # ooi = next(item for item in sample_list if item['row'] == row + 1 and item['column'] == column)
if len(contents) < columns: # except StopIteration:
contents += [''] * (columns - len(contents)) # continue
if not contents: # contents[column] = ooi['submitter_id']
contents = [''] * columns # NOTE: Pad length of contents to reflect columns
# if len(contents) < columns:
# contents += [''] * (columns - len(contents))
# if not contents:
# contents = [''] * columns
yield contents yield contents
# output.append(contents)
# return output
def create_merged_template(self, *args) -> BytesIO: def create_merged_template(self, *args) -> BytesIO:
""" """

6
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -180,7 +180,11 @@ class ControlsViewer(QWidget):
safe = ['name', 'submitted_date', 'genus', 'target'] safe = ['name', 'submitted_date', 'genus', 'target']
for column in df.columns: for column in df.columns:
if "percent" in column: if "percent" in column:
count_col = [item for item in df.columns if "count" in item][0] # count_col = [item for item in df.columns if "count" in item][0]
try:
count_col = next(item for item in df.columns if "count" in item)
except StopIteration:
continue
# NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating. # NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum') df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
if column not in safe: if column not in safe:

3
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -129,7 +129,8 @@ class RoleComboBox(QWidget):
""" """
equip = self.box.currentText() equip = self.box.currentText()
# logger.debug(f"Updating equipment: {equip}") # logger.debug(f"Updating equipment: {equip}")
equip2 = [item for item in self.role.equipment if item.name == equip][0] # equip2 = [item for item in self.role.equipment if item.name == equip][0]
equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
# logger.debug(f"Using: {equip2}") # logger.debug(f"Using: {equip2}")
self.process.clear() self.process.clear()
self.process.addItems([item for item in equip2.processes if item in self.role.processes]) self.process.addItems([item for item in equip2.processes if item in self.role.processes])

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

@@ -1,10 +1,10 @@
''' '''
functions used by all windows in the application's frontend functions used by all windows in the application's frontend
NOTE: Depreciated. Moved to functions.__init__
''' '''
from pathlib import Path from pathlib import Path
import logging import logging
from PyQt6.QtWidgets import QMainWindow, QFileDialog from PyQt6.QtWidgets import QMainWindow, QFileDialog
from tools import Result
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")

5
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -146,8 +146,9 @@ class ControlsForm(QWidget):
for le in self.findChildren(QComboBox): for le in self.findChildren(QComboBox):
label = [item.strip() for item in le.objectName().split(" : ")] label = [item.strip() for item in le.objectName().split(" : ")]
try: try:
dicto = [item for item in output if item['name'] == label[0]][0] # dicto = [item for item in output if item['name'] == label[0]][0]
except IndexError: dicto = next(item for item in output if item['name'] == label[0])
except StopIteration:
dicto = dict(name=label[0], values=[]) dicto = dict(name=label[0], values=[])
dicto['values'].append(dict(name=label[1], value=le.currentText())) dicto['values'].append(dict(name=label[1], value=le.currentText()))
if label[0] not in [item['name'] for item in output]: if label[0] not in [item['name'] for item in output]: