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Improved form regeneration for artic.

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This commit is contained in:
Landon Wark
2024-01-04 13:29:18 -06:00
parent c688aa160c
commit 19448cc8f3
18 changed files with 519 additions and 123 deletions
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144
src/submissions/backend/db/models/kits.py
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@@ -6,7 +6,7 @@ from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Int
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging
import logging, re
from tools import check_authorization, setup_lookup, query_return, Report, Result, Settings
from typing import List
from pandas import ExcelFile
@@ -24,6 +24,14 @@ reagenttypes_reagents = Table(
extend_existing = True
)
equipmentroles_equipment = Table(
"_equipmentroles_equipment",
Base.metadata,
Column("equipment_id", INTEGER, ForeignKey("_equipment.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_equipment_roles.id")),
extend_existing=True
)
class KitType(BaseClass):
"""
Base of kits used in submission processing
@@ -589,13 +597,13 @@ class SubmissionType(BaseClass):
kit_types = association_proxy("submissiontype_kit_associations", "kit_type") #: Proxy of kittype association
submissiontype_equipment_associations = relationship(
"SubmissionTypeEquipmentAssociation",
submissiontype_equipmentrole_associations = relationship(
"SubmissionTypeEquipmentRoleAssociation",
back_populates="submission_type",
cascade="all, delete-orphan"
)
equipment = association_proxy("submissiontype_equipment_associations", "equipment")
equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role")
def __repr__(self) -> str:
return f"<SubmissionType({self.name})>"
@@ -609,34 +617,35 @@ class SubmissionType(BaseClass):
"""
return ExcelFile(self.template_file).sheet_names
def set_template_file(self, filepath:Path|str):
def set_template_file(self, ctx:Settings, filepath:Path|str):
if isinstance(filepath, str):
filepath = Path(filepath)
with open (filepath, "rb") as f:
data = f.read()
self.template_file = data
self.save()
self.save(ctx=ctx)
def get_equipment(self) -> list:
from backend.validators.pydant import PydEquipmentPool
# if static:
# return [item.equipment.to_pydantic() for item in self.submissiontype_equipment_associations if item.static==1]
# else:
preliminary1 = [item.equipment.to_pydantic(static=item.static) for item in self.submissiontype_equipment_associations]# if item.static==0]
preliminary2 = [item.equipment.to_pydantic(static=item.static) for item in self.submissiontype_equipment_associations]# if item.static==0]
def construct_equipment_map(self):
output = []
pools = list(set([item.pool_name for item in preliminary1 if item.pool_name != None]))
for pool in pools:
c_ = []
for item in preliminary1:
if item.pool_name == pool:
c_.append(item)
preliminary2.remove(item)
if len(c_) > 0:
output.append(PydEquipmentPool(name=pool, equipment=c_))
for item in preliminary2:
output.append(item)
for item in self.submissiontype_equipmentrole_associations:
map = item.uses
map['role'] = item.equipment_role.name
output.append(map)
return output
# return [item.uses for item in self.submissiontype_equipmentrole_associations]
def get_equipment(self) -> List['PydEquipmentRole']:
return [item.to_pydantic(submission_type=self) for item in self.equipment]
def get_processes_for_role(self, equipment_role:str|EquipmentRole):
match equipment_role:
case str():
relevant = [item.get_all_processes() for item in self.submissiontype_equipmentrole_associations if item.equipment_role.name==equipment_role]
case EquipmentRole():
relevant = [item.get_all_processes() for item in self.submissiontype_equipmentrole_associations if item.equipment_role==equipment_role]
case _:
raise TypeError(f"Type {type(equipment_role)} is not allowed")
return list(set([item for items in relevant for item in items if item != None ]))
@classmethod
@setup_lookup
@@ -832,7 +841,7 @@ class Equipment(BaseClass):
name = Column(String(64))
nickname = Column(String(64))
asset_number = Column(String(16))
pool_name = Column(String(16))
roles = relationship("EquipmentRole", back_populates="instances", secondary=equipmentroles_equipment)
equipment_submission_associations = relationship(
"SubmissionEquipmentAssociation",
@@ -842,16 +851,11 @@ class Equipment(BaseClass):
submissions = association_proxy("equipment_submission_associations", "submission")
equipment_submissiontype_associations = relationship(
"SubmissionTypeEquipmentAssociation",
back_populates="equipment",
cascade="all, delete-orphan",
)
submission_types = association_proxy("equipment_submission_associations", "submission_type")
def __repr__(self):
return f"<Equipment({self.name})>"
def get_processes(self, submission_type:SubmissionType):
return [assoc.process for assoc in self.equipment_submission_associations if assoc.submission.submission_type_name==submission_type.name]
@classmethod
@setup_lookup
@@ -882,14 +886,66 @@ class Equipment(BaseClass):
pass
return query_return(query=query, limit=limit)
def to_pydantic(self, static):
def to_pydantic(self, submission_type:SubmissionType):
from backend.validators.pydant import PydEquipment
return PydEquipment(static=static, **self.__dict__)
return PydEquipment(processes=self.get_processes(submission_type=submission_type), role=None, **self.__dict__)
def save(self):
self.__database_session__.add(self)
self.__database_session__.commit()
@classmethod
def get_regex(cls) -> re.Pattern:
return re.compile(r"""
(?P<PHAC>50\d{5}$)|
(?P<HC>HC-\d{6}$)|
(?P<Beckman>[^\d][A-Z0-9]{6}$)|
(?P<Axygen>[A-Z]{3}-\d{2}-[A-Z]-[A-Z]$)|
(?P<Labcon>\d{4}-\d{3}-\d{3}-\d$)""",
re.VERBOSE)
class EquipmentRole(BaseClass):
__tablename__ = "_equipment_roles"
id = Column(INTEGER, primary_key=True)
name = Column(String(32))
instances = relationship("Equipment", back_populates="roles", secondary=equipmentroles_equipment)
equipmentrole_submissiontype_associations = relationship(
"SubmissionTypeEquipmentRoleAssociation",
back_populates="equipment_role",
cascade="all, delete-orphan",
)
submission_types = association_proxy("equipmentrole_submission_associations", "submission_type")
def __repr__(self):
return f"<EquipmentRole({self.name})>"
def to_pydantic(self, submission_type:SubmissionType):
from backend.validators.pydant import PydEquipmentRole
equipment = [item.to_pydantic(submission_type=submission_type) for item in self.instances]
return PydEquipmentRole(equipment=equipment, **self.__dict__)
@classmethod
@setup_lookup
def query(cls, name:str|None=None, id:int|None=None, limit:int=0) -> EquipmentRole|List[EquipmentRole]:
query = cls.__database_session__.query(cls)
match id:
case int():
query = query.filter(cls.id==id)
limit = 1
case _:
pass
match name:
case str():
query = query.filter(cls.name==name)
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
class SubmissionEquipmentAssociation(BaseClass):
# Currently abstract until ready to implement
@@ -899,6 +955,7 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True) #: id of associated submission
role = Column(String(64), primary_key=True) #: name of the role the equipment fills
process = Column(String(64)) #: name of the process run on this equipment
start_time = Column(TIMESTAMP)
end_time = Column(TIMESTAMP)
@@ -913,27 +970,27 @@ class SubmissionEquipmentAssociation(BaseClass):
self.equipment = equipment
def to_sub_dict(self) -> dict:
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments)
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments, process=[self.process], role=self.role, nickname=self.equipment.nickname)
return output
def save(self):
self.__database_session__.add(self)
self.__database_session__.commit()
class SubmissionTypeEquipmentAssociation(BaseClass):
class SubmissionTypeEquipmentRoleAssociation(BaseClass):
# __abstract__ = True
__tablename__ = "_submissiontype_equipment"
__tablename__ = "_submissiontype_equipmentrole"
equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
equipmentrole_id = Column(INTEGER, ForeignKey("_equipment_roles.id"), primary_key=True) #: id of associated equipment
submissiontype_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of associated submission
uses = Column(JSON) #: locations of equipment on the submission type excel sheet.
static = Column(INTEGER, default=1) #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
submission_type = relationship(SubmissionType, back_populates="submissiontype_equipment_associations") #: associated submission
submission_type = relationship(SubmissionType, back_populates="submissiontype_equipmentrole_associations") #: associated submission
equipment = relationship(Equipment, back_populates="equipment_submissiontype_associations") #: associated equipment
equipment_role = relationship(EquipmentRole, back_populates="equipmentrole_submissiontype_associations") #: associated equipment
@validates('static')
def validate_age(self, key, value):
@@ -954,6 +1011,11 @@ class SubmissionTypeEquipmentAssociation(BaseClass):
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
def get_all_processes(self):
processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
processes = [item for items in processes for item in items if item != None ]
return processes
@check_authorization
def save(self, ctx:Settings):
self.__database_session__.add(self)