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

Post code clean-up, before attempt to upgrade controls to FigureWidgets

Browse Source
This commit is contained in:
lwark
2024-10-21 08:17:43 -05:00
parent 495d1a5a7f
commit 1f83b61c81
29 changed files with 441 additions and 1089 deletions
Download Patch File Download Diff File Expand all files Collapse all files

216
src/submissions/backend/db/models/kits.py
View File

@@ -2,7 +2,6 @@
All kit and reagent related models
"""
from __future__ import annotations
import datetime
import json
from pprint import pformat
@@ -152,7 +151,7 @@ class KitType(BaseClass):
submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None.
Returns:
List[ReagentRole]: List of reagents linked to this kit.
Generator[ReagentRole, None, None]: List of reagents linked to this kit.
"""
match submission_type:
case SubmissionType():
@@ -173,7 +172,7 @@ class KitType(BaseClass):
return (item.reagent_role for item in relevant_associations)
# TODO: Move to BasicSubmission?
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str)]:
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str), None, None]:
"""
Creates map of locations in Excel workbook for a SubmissionType
@@ -181,9 +180,8 @@ class KitType(BaseClass):
submission_type (str | SubmissionType): Submissiontype.name
Returns:
dict: Dictionary containing information locations.
Generator[(str, str), None, None]: Tuple containing information locations.
"""
# info_map = {}
# NOTE: Account for submission_type variable type.
match submission_type:
case str():
@@ -221,7 +219,7 @@ class KitType(BaseClass):
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns:
models.KitType|List[models.KitType]: KitType(s) of interest.
KitType|List[KitType]: KitType(s) of interest.
"""
query: Query = cls.__database_session__.query(cls)
match used_for:
@@ -257,7 +255,16 @@ class KitType(BaseClass):
def save(self):
super().save()
def to_export_dict(self, submission_type: SubmissionType):
def to_export_dict(self, submission_type: SubmissionType) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Args:
submission_type (SubmissionType): SubmissionType of interest.
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = dict(name=self.name)
base_dict['reagent roles'] = []
base_dict['equipment roles'] = []
@@ -382,7 +389,13 @@ class ReagentRole(BaseClass):
from backend.validators.pydant import PydReagent
return PydReagent(lot=None, role=self.name, name=self.name, expiry=date.today())
def to_export_dict(self):
def to_export_dict(self) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
return dict(role=self.name, extension_of_life=self.eol_ext.days)
@check_authorization
@@ -664,7 +677,7 @@ class SubmissionType(BaseClass):
"SubmissionTypeTipRoleAssociation",
back_populates="submission_type",
cascade="all, delete-orphan"
)
) #: Association of tiproles
def __repr__(self) -> str:
"""
@@ -738,12 +751,12 @@ class SubmissionType(BaseClass):
"""
return self.sample_map
def construct_equipment_map(self) -> Generator[str, dict]:
def construct_equipment_map(self) -> Generator[(str, dict), None, None]:
"""
Constructs map of equipment to excel cells.
Returns:
dict: Map equipment locations in excel sheet
Generator[(str, dict), None, None]: Map equipment locations in excel sheet
"""
# logger.debug("Iterating through equipment roles")
for item in self.submissiontype_equipmentrole_associations:
@@ -752,12 +765,12 @@ class SubmissionType(BaseClass):
emap = {}
yield item.equipment_role.name, emap
def construct_tips_map(self) -> Generator[str, dict]:
def construct_tips_map(self) -> Generator[(str, dict), None, None]:
"""
Constructs map of tips to excel cells.
Returns:
dict: Tip locations in the excel sheet.
Generator[(str, dict), None, None]: Tip locations in the excel sheet.
"""
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
@@ -770,7 +783,7 @@ class SubmissionType(BaseClass):
Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns:
List[PydEquipmentRole]: List of equipment roles
Generator['PydEquipmentRole', None, None]: List of equipment roles
"""
return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment)
@@ -846,6 +859,12 @@ class SubmissionType(BaseClass):
return cls.execute_query(query=query, limit=limit)
def to_export_dict(self):
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export')
base_dict['defaults'] = self.defaults
@@ -862,7 +881,20 @@ class SubmissionType(BaseClass):
@classmethod
@check_authorization
def import_from_json(cls, filepath: Path | str):
def import_from_json(cls, filepath: Path | str) -> SubmissionType:
"""
Creates a new SubmissionType from a yml file
Args:
filepath (Path | str): Input yml file.
Raises:
Exception: Raised if filetype is not a yml or json
Returns:
SubmissionType: Created SubmissionType
"""
full = True
yaml.add_constructor("!regex", yaml_regex_creator)
if isinstance(filepath, str):
filepath = Path(filepath)
@@ -874,70 +906,76 @@ class SubmissionType(BaseClass):
else:
raise Exception(f"Filetype {filepath.suffix} not supported.")
logger.debug(pformat(import_dict))
submission_type = cls.query(name=import_dict['name'])
if submission_type:
return submission_type
submission_type = cls()
submission_type.name = import_dict['name']
submission_type.info_map = import_dict['info']
submission_type.sample_map = import_dict['samples']
submission_type.defaults = import_dict['defaults']
for kit in import_dict['kits']:
new_kit = KitType.query(name=kit['kit_type']['name'])
if not new_kit:
new_kit = KitType(name=kit['kit_type']['name'])
for role in kit['kit_type']['reagent roles']:
new_role = ReagentRole.query(name=role['role'])
if new_role:
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
if check.lower() == "n":
new_role = None
else:
pass
if not new_role:
eol = datetime.timedelta(role['extension_of_life'])
new_role = ReagentRole(name=role['role'], eol_ext=eol)
uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet'])
ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses)
ktrr_assoc.submission_type = submission_type
ktrr_assoc.required = role['required']
ktst_assoc = SubmissionTypeKitTypeAssociation(
kit_type=new_kit,
submission_type=submission_type,
mutable_cost_sample=kit['mutable_cost_sample'],
mutable_cost_column=kit['mutable_cost_column'],
constant_cost=kit['constant_cost']
)
for role in kit['kit_type']['equipment roles']:
new_role = EquipmentRole.query(name=role['role'])
if new_role:
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
if check.lower() == "n":
new_role = None
else:
pass
if not new_role:
new_role = EquipmentRole(name=role['role'])
for equipment in Equipment.assign_equipment(equipment_role=new_role):
new_role.instances.append(equipment)
ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type,
equipment_role=new_role)
try:
uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static'])
except KeyError:
uses = None
ster_assoc.uses = uses
for process in role['processes']:
new_process = Process.query(name=process)
if not new_process:
new_process = Process(name=process)
new_process.submission_types.append(submission_type)
new_process.kit_types.append(new_kit)
new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.")
Organization.import_from_yml(filepath=filepath)
return submission_type
try:
submission_type = cls.query(name=import_dict['name'])
except KeyError:
logger.error(f"Submission type has no name")
submission_type = None
full = False
if full:
if submission_type:
return submission_type
submission_type = cls()
submission_type.name = import_dict['name']
submission_type.info_map = import_dict['info']
submission_type.sample_map = import_dict['samples']
submission_type.defaults = import_dict['defaults']
for kit in import_dict['kits']:
new_kit = KitType.query(name=kit['kit_type']['name'])
if not new_kit:
new_kit = KitType(name=kit['kit_type']['name'])
for role in kit['kit_type']['reagent roles']:
new_role = ReagentRole.query(name=role['role'])
if new_role:
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
if check.lower() == "n":
new_role = None
else:
pass
if not new_role:
eol = datetime.timedelta(role['extension_of_life'])
new_role = ReagentRole(name=role['role'], eol_ext=eol)
uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet'])
ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses)
ktrr_assoc.submission_type = submission_type
ktrr_assoc.required = role['required']
ktst_assoc = SubmissionTypeKitTypeAssociation(
kit_type=new_kit,
submission_type=submission_type,
mutable_cost_sample=kit['mutable_cost_sample'],
mutable_cost_column=kit['mutable_cost_column'],
constant_cost=kit['constant_cost']
)
for role in kit['kit_type']['equipment roles']:
new_role = EquipmentRole.query(name=role['role'])
if new_role:
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
if check.lower() == "n":
new_role = None
else:
pass
if not new_role:
new_role = EquipmentRole(name=role['role'])
for equipment in Equipment.assign_equipment(equipment_role=new_role):
new_role.instances.append(equipment)
ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type,
equipment_role=new_role)
try:
uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static'])
except KeyError:
uses = None
ster_assoc.uses = uses
for process in role['processes']:
new_process = Process.query(name=process)
if not new_process:
new_process = Process(name=process)
new_process.submission_types.append(submission_type)
new_process.kit_types.append(new_kit)
new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.")
Organization.import_from_yml(filepath=filepath)
return submission_type
class SubmissionTypeKitTypeAssociation(BaseClass):
@@ -1574,10 +1612,7 @@ class EquipmentRole(BaseClass):
"""
return dict(role=self.name,
processes=self.get_processes(submission_type=submission_type, extraction_kit=kit_type))
# base_dict['role'] = self.name
# base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
# return base_dict
class SubmissionEquipmentAssociation(BaseClass):
"""
@@ -1598,7 +1633,7 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment
def __repr__(self):
def __repr__(self) -> str:
return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num} & {self.equipment.name})>"
def __init__(self, submission, equipment, role: str = "None"):
@@ -1699,9 +1734,18 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
def save(self):
super().save()
def to_export_dict(self, kit_type: KitType):
def to_export_dict(self, extraction_kit: KitType) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Args:
kit_type (KitType): KitType of interest.
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
kit_type=kit_type).items()}
kit_type=extraction_kit).items()}
base_dict['static'] = self.static
return base_dict