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Mid code cleanup

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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
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65
src/submissions/backend/db/models/kits.py
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@@ -5,17 +5,14 @@ from __future__ import annotations
import datetime
import json
from pprint import pprint, pformat
from pprint import pformat
import yaml
from jinja2 import TemplateNotFound
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result, jinja_template_loading, check_regex_match, \
yaml_regex_creator
from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator
from typing import List, Literal, Generator, Any
from pandas import ExcelFile
from pathlib import Path
@@ -204,7 +201,6 @@ class KitType(BaseClass):
yield assoc.reagent_role.name, assoc.uses
except TypeError:
continue
# return info_map
@classmethod
@setup_lookup
@@ -267,17 +263,20 @@ class KitType(BaseClass):
for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
# logger.debug(f"Value: {v}")
try:
assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
except IndexError as e:
# assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
except StopIteration as e:
continue
for kk, vv in assoc.to_export_dict().items():
v[kk] = vv
base_dict['reagent roles'].append(v)
for k, v in submission_type.construct_equipment_map():
try:
assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k][0]
except IndexError:
# assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if
# item.equipment_role.name == k][0]
assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
item.equipment_role.name == k)
except StopIteration:
continue
for kk, vv in assoc.to_export_dict(kit_type=self).items():
# logger.debug(f"{kk}:{vv}")
@@ -858,10 +857,7 @@ class SubmissionType(BaseClass):
base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export')
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['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]
return base_dict
@@ -878,7 +874,6 @@ class SubmissionType(BaseClass):
yaml.add_constructor("!regex", yaml_regex_creator)
if isinstance(filepath, str):
filepath = Path(filepath)
with open(filepath, "r") as f:
if filepath.suffix == ".json":
import_dict = json.load(fp=f)
@@ -949,7 +944,7 @@ class SubmissionType(BaseClass):
new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.")
Organization.import_from_json(filepath=filepath)
Organization.import_from_yml(filepath=filepath)
return submission_type
@@ -1031,6 +1026,12 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
return cls.execute_query(query=query, limit=limit)
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']
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)
@@ -1150,7 +1151,13 @@ class KitTypeReagentRoleAssociation(BaseClass):
limit = 1
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['required'] = self.required
for k, v in self.reagent_role.to_export_dict().items():
@@ -1418,6 +1425,15 @@ class Equipment(BaseClass):
@classmethod
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):
equipment_role = EquipmentRole.query(name=equipment_role)
equipment = cls.query()
@@ -1468,16 +1484,7 @@ class EquipmentRole(BaseClass):
Returns:
dict: This EquipmentRole dict
"""
# output = {}
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,
extraction_kit: str | KitType | None = None) -> "PydEquipmentRole":
@@ -1568,6 +1575,12 @@ class EquipmentRole(BaseClass):
return output
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['role'] = self.name
base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)