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Addition of Equipment and SubmissionType creation.

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This commit is contained in:
Landon Wark
2023-12-20 12:54:37 -06:00
parent 0dd51827a0
commit 0d64095e42
22 changed files with 755 additions and 123 deletions
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185
src/submissions/backend/db/models/kits.py
View File

@@ -10,6 +10,7 @@ import logging
from tools import check_authorization, setup_lookup, query_return, Report, Result, Settings
from typing import List
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
logger = logging.getLogger(f'submissions.{__name__}')
@@ -55,7 +56,7 @@ class KitType(BaseClass):
def __repr__(self) -> str:
return f"<KitType({self.name})>"
def get_reagents(self, required:bool=False, submission_type:str|SubmissionType|None=None) -> list:
def get_reagents(self, required:bool=False, submission_type:str|SubmissionType|None=None) -> List[ReagentType]:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
@@ -242,6 +243,10 @@ class ReagentType(BaseClass):
case _:
pass
return query_return(query=query, limit=limit)
def to_pydantic(self):
from backend.validators.pydant import PydReagent
return PydReagent(lot=None, type=self.name, name=self.name, expiry=date.today())
class KitTypeReagentTypeAssociation(BaseClass):
"""
@@ -583,6 +588,14 @@ class SubmissionType(BaseClass):
kit_types = association_proxy("submissiontype_kit_associations", "kit_type") #: Proxy of kittype association
submissiontype_equipment_associations = relationship(
"SubmissionTypeEquipmentAssociation",
back_populates="submission_type",
cascade="all, delete-orphan"
)
equipment = association_proxy("submissiontype_equipment_associations", "equipment")
def __repr__(self) -> str:
return f"<SubmissionType({self.name})>"
@@ -595,6 +608,35 @@ class SubmissionType(BaseClass):
"""
return ExcelFile(self.template_file).sheet_names
def set_template_file(self, 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()
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]
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)
return output
@classmethod
@setup_lookup
def query(cls,
@@ -772,4 +814,145 @@ class SubmissionReagentAssociation(BaseClass):
# limit = query.count()
return query_return(query=query, limit=limit)
def to_sub_dict(self, extraction_kit):
output = self.reagent.to_sub_dict(extraction_kit)
output['comments'] = self.comments
return output
class Equipment(BaseClass):
# Currently abstract until ready to implement
# __abstract__ = True
__tablename__ = "_equipment"
id = Column(INTEGER, primary_key=True)
name = Column(String(64))
nickname = Column(String(64))
asset_number = Column(String(16))
pool_name = Column(String(16))
equipment_submission_associations = relationship(
"SubmissionEquipmentAssociation",
back_populates="equipment",
cascade="all, delete-orphan",
)
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})>"
@classmethod
@setup_lookup
def query(cls,
name:str|None=None,
nickname:str|None=None,
asset_number:str|None=None,
limit:int=0
) -> Equipment|List[Equipment]:
query = cls.__database_session__.query(cls)
match name:
case str():
query = query.filter(cls.name==name)
limit = 1
case _:
pass
match nickname:
case str():
query = query.filter(cls.nickname==nickname)
limit = 1
case _:
pass
match asset_number:
case str():
query = query.filter(cls.asset_number==asset_number)
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
def to_pydantic(self, static):
from backend.validators.pydant import PydEquipment
return PydEquipment(static=static, **self.__dict__)
def save(self):
self.__database_session__.add(self)
self.__database_session__.commit()
class SubmissionEquipmentAssociation(BaseClass):
# Currently abstract until ready to implement
# __abstract__ = True
__tablename__ = "_equipment_submissions"
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
process = Column(String(64)) #: name of the process run on this equipment
start_time = Column(TIMESTAMP)
end_time = Column(TIMESTAMP)
comments = Column(String(1024))
submission = relationship("BasicSubmission", back_populates="submission_equipment_associations") #: associated submission
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated submission
def __init__(self, submission, equipment):
self.submission = submission
self.equipment = equipment
def to_sub_dict(self) -> dict:
output = dict(name=self.equipment.name, asset_number=self.equipment.asset_number, comment=self.comments)
return output
def save(self):
self.__database_session__.add(self)
self.__database_session__.commit()
class SubmissionTypeEquipmentAssociation(BaseClass):
# __abstract__ = True
__tablename__ = "_submissiontype_equipment"
equipment_id = Column(INTEGER, ForeignKey("_equipment.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
equipment = relationship(Equipment, back_populates="equipment_submissiontype_associations") #: associated equipment
@validates('static')
def validate_age(self, key, value):
"""
Ensures only 1 & 0 used in 'static'
Args:
key (str): name of attribute
value (_type_): value of attribute
Raises:
ValueError: Raised if bad value given
Returns:
_type_: value
"""
if not 0 <= value < 2:
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
def save(self):
self.__database_session__.add(self)
self.__database_session__.commit()

42
src/submissions/backend/db/models/submissions.py
View File

@@ -5,7 +5,7 @@ from __future__ import annotations
from getpass import getuser
import math, json, logging, uuid, tempfile, re, yaml
from pprint import pformat
from . import Reagent, SubmissionType, KitType, Organization
from . import Reagent, SubmissionType, KitType, Organization, Equipment, SubmissionEquipmentAssociation
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from json.decoder import JSONDecodeError
@@ -69,6 +69,13 @@ class BasicSubmission(BaseClass):
# to "keyword" attribute
reagents = association_proxy("submission_reagent_associations", "reagent") #: Association proxy to SubmissionSampleAssociation.samples
submission_equipment_associations = relationship(
"SubmissionEquipmentAssociation",
back_populates="submission",
cascade="all, delete-orphan"
)
equipment = association_proxy("submission_equipment_associations", "equipment")
# Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
__mapper_args__ = {
"polymorphic_identity": "Basic Submission",
@@ -124,7 +131,7 @@ class BasicSubmission(BaseClass):
# Updated 2023-09 to use the extraction kit to pull reagents.
if full_data:
try:
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.reagents]
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.submission_reagent_associations]
except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}")
reagents = None
@@ -138,6 +145,13 @@ class BasicSubmission(BaseClass):
except Exception as e:
logger.error(f"Error setting comment: {self.comment}")
comments = None
try:
equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
if len(equipment) == 0:
equipment = None
except Exception as e:
logger.error(f"Error setting equipment: {self.equipment}")
equipment = None
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
@@ -153,7 +167,8 @@ class BasicSubmission(BaseClass):
"reagents": reagents,
"samples": samples,
"extraction_info": ext_info,
"comment": comments
"comment": comments,
"equipment": equipment
}
return output
@@ -447,7 +462,7 @@ class BasicSubmission(BaseClass):
logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents']:
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment']:
try:
df = df.drop(item, axis=1)
except:
@@ -520,7 +535,7 @@ class BasicSubmission(BaseClass):
_type_: _description_
"""
# assoc = SubmissionSampleAssociation.query(submission=self, sample=sample, limit=1)
assoc = [item.sample 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]
for k,v in input_dict.items():
try:
setattr(assoc, k, v)
@@ -750,7 +765,8 @@ class BasicSubmission(BaseClass):
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
return instance, code, msg
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
@@ -877,6 +893,12 @@ class BacterialCulture(BasicSubmission):
template += "_{{ submitting_lab }}_{{ submitter_plate_num }}"
return template
@classmethod
def parse_info(cls, input_dict: dict, xl: pd.ExcelFile | None = None) -> dict:
input_dict = super().parse_info(input_dict, xl)
input_dict['submitted_date']['missing'] = True
return input_dict
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
@@ -1009,7 +1031,8 @@ class Wastewater(BasicSubmission):
Returns:
str: String for regex construction
"""
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789]|$)R?\d?)?)"
# return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)R?\d?)?)"
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
class WastewaterArtic(BasicSubmission):
"""
@@ -1416,7 +1439,9 @@ class BasicSample(BaseClass):
return instance
def save(self):
raise AttributeError(f"Save not implemented for {self.__class__}")
# raise AttributeError(f"Save not implemented for {self.__class__}")
self.__database_session__.add(self)
self.__database_session__.commit()
def delete(self):
raise AttributeError(f"Delete not implemented for {self.__class__}")
@@ -1735,4 +1760,3 @@ class WastewaterAssociation(SubmissionSampleAssociation):
pcr_results = Column(JSON) #: imported PCR status from QuantStudio
__mapper_args__ = {"polymorphic_identity": "Wastewater Association", "polymorphic_load": "inline"}