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Prior to merging omni_search.py and sample_search.py

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lwark
2024-11-18 09:53:03 -06:00
parent 3d6a42b36f
commit 506aac80c1
13 changed files with 162 additions and 73 deletions
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22
src/submissions/backend/db/models/__init__.py
View File

@@ -3,6 +3,8 @@ Contains all models for sqlalchemy
"""
from __future__ import annotations
import sys, logging
import pandas as pd
from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
@@ -97,6 +99,26 @@ class BaseClass(Base):
singles = list(set(cls.singles + BaseClass.singles))
return dict(singles=singles)
@classmethod
def fuzzy_search(cls, **kwargs):
query: Query = cls.__database_session__.query(cls)
# logger.debug(f"Queried model. Now running searches in {kwargs}")
for k, v in kwargs.items():
# logger.debug(f"Running fuzzy search for attribute: {k} with value {v}")
search = f"%{v}%"
try:
attr = getattr(cls, k)
# NOTE: the secret sauce is in attr.like
query = query.filter(attr.like(search))
except (ArgumentError, AttributeError) as e:
logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
return query.limit(50).all()
@classmethod
def results_to_df(cls, objects: list, **kwargs):
records = [object.to_sub_dict(**kwargs) for object in objects]
return pd.DataFrame.from_records(records)
@classmethod
def query(cls, **kwargs) -> Any | List[Any]:
"""

64
src/submissions/backend/db/models/kits.py
View File

@@ -7,8 +7,8 @@ from pprint import pformat
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
from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator
from datetime import date, datetime
from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator, timezone
from typing import List, Literal, Generator, Any
from pandas import ExcelFile
from pathlib import Path
@@ -355,7 +355,7 @@ class ReagentRole(BaseClass):
match reagent:
case str():
# logger.debug(f"Lookup ReagentType by reagent str {reagent}")
reagent = Reagent.query(lot_number=reagent)
reagent = Reagent.query(lot=reagent)
case _:
pass
assert reagent.role
@@ -405,6 +405,8 @@ class Reagent(BaseClass):
Concrete reagent instance
"""
searchables = ["lot"]
id = Column(INTEGER, primary_key=True) #: primary key
role = relationship("ReagentRole", back_populates="instances",
secondary=reagentroles_reagents) #: joined parent reagent type
@@ -430,7 +432,7 @@ class Reagent(BaseClass):
else:
return f"<Reagent({self.role.name}-{self.lot})>"
def to_sub_dict(self, extraction_kit: KitType = None, full_data: bool = False) -> dict:
def to_sub_dict(self, extraction_kit: KitType = None, full_data: bool = False, **kwargs) -> dict:
"""
dictionary containing values necessary for gui
@@ -441,6 +443,7 @@ class Reagent(BaseClass):
Returns:
dict: representation of the reagent's attributes
"""
if extraction_kit is not None:
# NOTE: Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try:
@@ -449,7 +452,10 @@ class Reagent(BaseClass):
except:
reagent_role = self.role[0]
else:
reagent_role = self.role[0]
try:
reagent_role = self.role[0]
except IndexError:
reagent_role = None
try:
rtype = reagent_role.name.replace("_", " ")
except AttributeError:
@@ -475,7 +481,8 @@ class Reagent(BaseClass):
)
if full_data:
output['submissions'] = [sub.rsl_plate_num for sub in self.submissions]
output['excluded'] = ['missing', 'submissions', 'excluded']
output['excluded'] = ['missing', 'submissions', 'excluded', 'editable']
output['editable'] = ['lot', 'expiry']
return output
def update_last_used(self, kit: KitType) -> Report:
@@ -508,8 +515,8 @@ class Reagent(BaseClass):
@setup_lookup
def query(cls,
id: int | None = None,
reagent_role: str | ReagentRole | None = None,
lot_number: str | None = None,
role: str | ReagentRole | None = None,
lot: str | None = None,
name: str | None = None,
limit: int = 0
) -> Reagent | List[Reagent]:
@@ -533,13 +540,13 @@ class Reagent(BaseClass):
limit = 1
case _:
pass
match reagent_role:
match role:
case str():
# logger.debug(f"Looking up reagents by reagent type str: {reagent_type}")
query = query.join(cls.role).filter(ReagentRole.name == reagent_role)
query = query.join(cls.role).filter(ReagentRole.name == role)
case ReagentRole():
# logger.debug(f"Looking up reagents by reagent type ReagentType: {reagent_type}")
query = query.filter(cls.role.contains(reagent_role))
query = query.filter(cls.role.contains(role))
case _:
pass
match name:
@@ -549,16 +556,43 @@ class Reagent(BaseClass):
query = query.filter(cls.name == name)
case _:
pass
match lot_number:
match lot:
case str():
# logger.debug(f"Looking up reagent by lot number str: {lot_number}")
query = query.filter(cls.lot == lot_number)
# logger.debug(f"Looking up reagent by lot number str: {lot}")
query = query.filter(cls.lot == lot)
# NOTE: In this case limit number returned.
limit = 1
case _:
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
def edit_from_search(self, **kwargs):
from frontend.widgets.misc import AddReagentForm
role = ReagentRole.query(kwargs['role'])
if role:
role_name = role.name
else:
role_name = None
dlg = AddReagentForm(reagent_lot=self.lot, reagent_role=role_name, expiry=self.expiry, reagent_name=self.name)
if dlg.exec():
vars = dlg.parse_form()
for key, value in vars.items():
match key:
case "expiry":
if not isinstance(value, date):
field_value = datetime.strptime(value, "%Y-%m-%d").date
field_value.replace(tzinfo=timezone)
else:
field_value = value
case "role":
continue
case _:
field_value = value
logger.debug(f"Setting reagent {key} to {field_value}")
self.__setattr__(key, field_value)
self.save()
class Discount(BaseClass):
"""
@@ -1278,7 +1312,7 @@ class SubmissionReagentAssociation(BaseClass):
case Reagent() | str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
if isinstance(reagent, str):
reagent = Reagent.query(lot_number=reagent)
reagent = Reagent.query(lot=reagent)
query = query.filter(cls.reagent == reagent)
case _:
pass

5
src/submissions/backend/db/models/submissions.py
View File

@@ -844,7 +844,8 @@ class BasicSubmission(BaseClass):
ws.cell(row=item['row'], column=item['column'], value=item['value'])
return input_excel
def custom_sample_writer(self, sample:dict) -> dict:
@classmethod
def custom_sample_writer(self, sample: dict) -> dict:
return sample
@classmethod
@@ -2091,7 +2092,7 @@ class WastewaterArtic(BasicSubmission):
return input_excel
@classmethod
def custom_sample_writer(self, sample:dict) -> dict:
def custom_sample_writer(self, sample: dict) -> dict:
logger.debug("Wastewater Artic custom sample writer")
if sample['source_plate_number'] in [0, "0"]:
sample['source_plate_number'] = "control"

4
src/submissions/backend/validators/pydant.py
View File

@@ -48,7 +48,7 @@ class PydReagent(BaseModel):
def rescue_type_with_lookup(cls, value, values):
if value is None and values.data['lot'] is not None:
try:
return Reagent.query(lot_number=values.data['lot'].name)
return Reagent.query(lot=values.data['lot'].name)
except AttributeError:
return value
return value
@@ -127,7 +127,7 @@ class PydReagent(BaseModel):
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
# logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot_number=self.lot, name=self.name)
reagent = Reagent.query(lot=self.lot, name=self.name)
# logger.debug(f"Result: {reagent}")
if reagent is None:
reagent = Reagent()