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

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

@@ -12,7 +12,7 @@ from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
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.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
@@ -24,7 +24,8 @@ import pandas as pd
from openpyxl import Workbook
from openpyxl.worksheet.worksheet import Worksheet
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 typing import List, Any, Tuple, Literal
from dateutil.parser import parse
@@ -160,7 +161,18 @@ class BasicSubmission(BaseClass):
return output
@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
parent_defs = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
@@ -230,6 +242,7 @@ class BasicSubmission(BaseClass):
case _:
return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
@classmethod
def construct_info_map(cls, submission_type: SubmissionType | None = None,
mode: Literal["read", "write"] = "read") -> dict:
@@ -408,8 +421,10 @@ class BasicSubmission(BaseClass):
except Exception as e:
logger.error(f"Column count error: {e}")
# NOTE: Get kit associated with this submission
assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
item.submission_type == self.submission_type][0]
# assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
# 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}")
# 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]):
@@ -453,8 +468,9 @@ 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]
except IndexError:
# well = [item for item in sample_list if item['row'] == row and item['column'] == column][0]
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")
output_samples.append(well)
env = jinja_template_loading()
@@ -498,7 +514,7 @@ class BasicSubmission(BaseClass):
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'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:
try:
df = df.drop(item, axis=1)
@@ -553,7 +569,9 @@ class BasicSubmission(BaseClass):
return
case item if item in self.jsons():
match value:
case list():
case dict():
existing = value
case _:
# logger.debug(f"Setting JSON attribute.")
existing = self.__getattribute__(key)
if value is None or value in ['', 'null']:
@@ -573,8 +591,6 @@ class BasicSubmission(BaseClass):
existing = value
else:
existing.append(value)
case _:
existing = value
self.__setattr__(key, existing)
flag_modified(self, key)
return
@@ -600,7 +616,13 @@ class BasicSubmission(BaseClass):
Returns:
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():
try:
setattr(assoc, k, v)
@@ -716,8 +738,6 @@ class BasicSubmission(BaseClass):
case str():
try:
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_
except Exception as e:
logger.error(
@@ -823,8 +843,8 @@ class BasicSubmission(BaseClass):
Workbook: Updated workbook
"""
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
logger.debug(f"Input dict: {info}")
logger.debug(f"Custom fields: {custom_fields}")
# logger.debug(f"Input dict: {info}")
# logger.debug(f"Custom fields: {custom_fields}")
for k, v in custom_fields.items():
try:
assert v['type'] in ['exempt', 'range', 'cell']
@@ -878,15 +898,9 @@ class BasicSubmission(BaseClass):
from backend.validators import RSLNamer
# logger.debug(f"instr coming into {cls}: {instr}")
logger.debug(f"data coming into {cls}: {data}")
# defaults = cls.get_default_info("abbreviation", "submission_type")
if "submission_type" not in data.keys():
data['submission_type'] = cls.__mapper_args__['polymorphic_identity']
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, ""]:
# logger.debug("Sending to RSLNamer to make new plate name.")
outstr = RSLNamer.construct_new_plate_name(data=data)
@@ -1386,8 +1400,8 @@ class BacterialCulture(BasicSubmission):
new_lot = matched.group()
try:
pos_control_reg = \
[reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control"][0]
except IndexError:
next(reg for reg in input_dict['reagents'] if reg['role'] == "Bacterial-Positive Control")
except StopIteration:
logger.error(f"No positive control reagent listed")
return input_dict
pos_control_reg['lot'] = new_lot
@@ -1615,6 +1629,7 @@ class Wastewater(BasicSubmission):
events['Link PCR'] = self.link_pcr
return events
@report_result
def link_pcr(self, obj):
"""
Adds PCR info to this submission
@@ -1624,7 +1639,11 @@ class Wastewater(BasicSubmission):
"""
from backend.excel import PCRParser
from frontend.widgets import select_open_file
report = Report()
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)
self.set_attribute("pcr_info", parser.pcr)
self.save(original=False)
@@ -1633,8 +1652,9 @@ class Wastewater(BasicSubmission):
for sample in self.samples:
# logger.debug(f"Running update on: {sample}")
try:
sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
except IndexError:
# sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
sample_dict = next(item for item in parser.samples if item['sample'] == sample.rsl_number)
except StopIteration:
continue
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'))
@@ -2119,7 +2139,11 @@ class WastewaterArtic(BasicSubmission):
"""
from frontend.widgets.gel_checker import GelBox
from frontend.widgets import select_open_file
report = Report()
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)
if dlg.exec():
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']
if polymorphic_identity is not None:
try:
return [item for item in cls.__subclasses__() if
item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
# return [item for item in cls.__subclasses__() if
# item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
model = cls