mirror of
https://github.com/beak-insights/felicity-lims.git
synced 2025-02-25 01:13:01 +08:00
193 lines
8 KiB
Python
193 lines
8 KiB
Python
import logging
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from typing import List
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from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, String, Table
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from sqlalchemy.dialects.postgresql import JSONB
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from sqlalchemy.orm import relationship
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from felicity.apps import Auditable, BaseAuditDBModel, DBModel
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from felicity.apps.analysis import conf as analysis_conf
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from felicity.apps.analysis.models import analysis as analysis_models
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from felicity.apps.analysis.models import qc as qc_models
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from felicity.apps.analysis.models import results as result_models
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from felicity.apps.common.models import IdSequence
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from felicity.apps.instrument.models import Instrument
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from felicity.apps.notification.utils import FelicityStreamer
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from felicity.apps.user.models import User
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from felicity.apps.worksheet import conf, schemas
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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streamer = FelicityStreamer()
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class WSBase(BaseAuditDBModel):
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__abstract__ = True
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worksheet_type = Column(String)
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reserved = Column(JSONB)
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number_of_samples = Column(Integer)
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rows = Column(Integer)
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cols = Column(Integer)
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row_wise = Column(Boolean(), default=False)
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state = Column(String)
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"""
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Many to Many Link between WorkSheetTemplate and QCLevel
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"""
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worksheet_template_qc_level = Table(
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"worksheet_template_qc_level",
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DBModel.metadata,
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Column("ws_template_uid", ForeignKey("worksheet_template.uid"), primary_key=True),
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Column("qc_level_uid", ForeignKey("qc_level.uid"), primary_key=True),
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)
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class WorkSheetTemplate(WSBase):
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"""WorkSheetTemplate
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a template has a single analyses associated in order to avoid
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cases where multi analyses can be assigned to a single ws
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"""
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__tablename__ = "worksheet_template"
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name = Column(String, unique=True, nullable=False)
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description = Column(String)
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analysis_uid = Column(String, ForeignKey("analysis.uid"), nullable=True)
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analysis = relationship(analysis_models.Analysis, lazy="selectin")
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qc_template_uid = Column(String, ForeignKey("qc_template.uid"), nullable=True)
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qc_template = relationship(qc_models.QCTemplate, lazy="selectin")
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# to help cater for those created without template we also keep the qc_levels
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qc_levels = relationship(
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qc_models.QCLevel, secondary=worksheet_template_qc_level, lazy="selectin"
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)
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instrument_uid = Column(String, ForeignKey("instrument.uid"), nullable=True)
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instrument = relationship(Instrument, lazy="selectin")
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sample_type_uid = Column(String, ForeignKey("sample_type.uid"), nullable=False)
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sample_type = relationship(analysis_models.SampleType, lazy="selectin")
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@classmethod
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async def create(cls, obj_in: dict | schemas.WSTemplateCreate) -> schemas.WSTemplate:
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data = cls._import(obj_in)
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return await super().create(**data)
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async def update(self, obj_in: dict | schemas.WSTemplateUpdate) -> schemas.WSTemplate:
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data = self._import(obj_in)
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return await super().update(**data)
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class WorkSheet(Auditable, WSBase):
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__tablename__ = "worksheet"
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template_uid = Column(String, ForeignKey("worksheet_template.uid"), nullable=False)
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template = relationship("WorkSheetTemplate", lazy="selectin")
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analyst_uid = Column(String, ForeignKey("user.uid"), nullable=False)
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analyst = relationship(User, foreign_keys=[analyst_uid], lazy="selectin")
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worksheet_id = Column(String, index=True, unique=True, nullable=False)
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analysis_uid = Column(String, ForeignKey("analysis.uid"), nullable=True)
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analysis = relationship(analysis_models.Analysis, lazy="selectin")
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instrument_uid = Column(String, ForeignKey("instrument.uid"), nullable=True)
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instrument = relationship(Instrument, backref="worksheets", lazy="selectin")
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sample_type_uid = Column(String, ForeignKey("sample_type.uid"), nullable=False)
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sample_type = relationship(analysis_models.SampleType, lazy="selectin")
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assigned_count = Column(Integer, nullable=False, default=0)
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analysis_results = relationship(
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"AnalysisResult", back_populates="worksheet", lazy="selectin"
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)
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#
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submitted_by_uid = Column(String, ForeignKey("user.uid"), nullable=True)
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submitted_by = relationship(User, foreign_keys=[submitted_by_uid], lazy="selectin")
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date_submitted = Column(DateTime, nullable=True)
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verified_by_uid = Column(String, ForeignKey("user.uid"), nullable=True)
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verified_by = relationship(User, foreign_keys=[verified_by_uid], lazy="selectin")
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date_verified = Column(DateTime, nullable=True)
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async def get_analysis_results(self):
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results: List[result_models.AnalysisResult] = []
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qc_results: List[result_models.AnalysisResult] = []
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all_results = await result_models.AnalysisResult.get_all(worksheet_uid=self.uid)
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for result in all_results:
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if result.sample.sample_type.name == "QC Sample":
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qc_results.append(result)
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else:
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results.append(result)
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return results, qc_results
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async def reset_assigned_count(self):
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# TODO: DO NOT COUNT QC SAMPLES
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analysis_results, _ = await self.get_analysis_results()
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count = len(analysis_results)
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self.assigned_count = count
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if count == 0:
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self.state = conf.worksheet_states.EMPTY
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if count > 0 and self.state == conf.worksheet_states.EMPTY:
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self.state = conf.worksheet_states.PENDING
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await self.save()
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async def change_state(self, state, updated_by_uid):
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self.state = state
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self.updated_by_uid = updated_by_uid # noqa
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await self.save()
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async def has_processed_samples(self):
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states = [
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analysis_conf.states.result.RESULTED,
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analysis_conf.states.result.APPROVED,
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]
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results, qc_results = await self.get_analysis_results()
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analysis_results = results + qc_results
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processed = any([res.status in states for res in analysis_results])
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return processed
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async def submit(self, submitter):
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if self.state != conf.worksheet_states.AWAITING:
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states = [
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analysis_conf.states.result.RESULTED,
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analysis_conf.states.result.APPROVED,
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]
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results, qc_results = await self.get_analysis_results()
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analysis_results = results + qc_results
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if all([res.status in states for res in analysis_results]):
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self.state = conf.worksheet_states.AWAITING
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self.updated_by_uid = submitter.uid # noqa
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self.submitted_by_uid = submitter.uid
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saved = await self.save()
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await streamer.stream(saved, submitter, "submitted", "worksheet")
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return saved
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return self
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async def verify(self, verified_by):
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if self.state != conf.worksheet_states.APPROVED:
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states = [
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analysis_conf.states.result.APPROVED,
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analysis_conf.states.result.RETRACTED,
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]
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results, qc_results = await self.get_analysis_results()
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analysis_results = results + qc_results
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if all([res.status in states for res in analysis_results]):
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self.state = conf.worksheet_states.APPROVED
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self.updated_by_uid = verified_by.uid # noqa
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self.verified_by_uid = verified_by.uid
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saved = await self.save()
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await streamer.stream(saved, verified_by, "verified", "worksheet")
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return saved
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return self
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@classmethod
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async def create(cls, obj_in: dict | schemas.WorkSheetCreate) -> schemas.WorkSheet:
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data = cls._import(obj_in)
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data["worksheet_id"] = (await IdSequence.get_next_number("WS"))[1]
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return await super().create(**data)
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async def update(self, obj_in: dict | schemas.WorkSheetUpdate) -> schemas.WorkSheet:
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data = self._import(obj_in)
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return await super().update(**data)
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