Source code for camcops_server.tasks.hads

#!/usr/bin/env python

"""
camcops_server/tasks/hads.py

===============================================================================

    Copyright (C) 2012-2019 Rudolf Cardinal (rudolf@pobox.com).

    This file is part of CamCOPS.

    CamCOPS is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    CamCOPS is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with CamCOPS. If not, see <http://www.gnu.org/licenses/>.

===============================================================================

"""

from abc import ABC, ABCMeta
import logging
from typing import Any, Dict, List, Tuple, Type

from cardinal_pythonlib.logs import BraceStyleAdapter
from cardinal_pythonlib.stringfunc import strseq
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.sqltypes import Integer

from camcops_server.cc_modules.cc_constants import (
    CssClass,
    DATA_COLLECTION_UNLESS_UPGRADED_DIV,
)
from camcops_server.cc_modules.cc_ctvinfo import CTV_INCOMPLETE, CtvInfo
from camcops_server.cc_modules.cc_db import add_multiple_columns
from camcops_server.cc_modules.cc_html import answer, tr_qa
from camcops_server.cc_modules.cc_request import CamcopsRequest
from camcops_server.cc_modules.cc_snomed import SnomedExpression, SnomedLookup
from camcops_server.cc_modules.cc_string import AS
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import (
    Task,
    TaskHasPatientMixin,
    TaskHasRespondentMixin,
)
from camcops_server.cc_modules.cc_trackerhelpers import TrackerInfo

log = BraceStyleAdapter(logging.getLogger(__name__))


# =============================================================================
# HADS (crippled unless upgraded locally) - base classes
# =============================================================================

[docs]class HadsMetaclass(DeclarativeMeta, ABCMeta): """ We can't make this metaclass inherit from DeclarativeMeta. This works: .. :code-block:: python class MyTaskMetaclass(DeclarativeMeta): def __init__(cls, name, bases, classdict): # do useful stuff super().__init__(name, bases, classdict) class MyTask(Task, Base, metaclass=MyTaskMetaclass): __tablename__ = "mytask" ... but at the point that MyTaskMetaclass calls DeclarativeMeta.__init__, it registers "cls" (in this case MyTask) with the SQLAlchemy class registry. In this example, that's fine, because MyTask wants to be registered. But here it fails: .. :code-block:: python class OtherTaskMetaclass(DeclarativeMeta): def __init__(cls, name, bases, classdict): # do useful stuff super().__init__(name, bases, classdict) class Intermediate(Task, metaclass=OtherTaskMetaclass): pass class OtherTask(Intermediate, Base): __tablename__ = "othertask" ... and it fails because OtherTaskMetaclass calls DeclarativeMeta.__init__ and this tries to register "Intermediate" with the SQLALchemy ORM. So, it's clear that OtherTaskMetaclass shouldn't derive from DeclarativeMeta. But if we make it derive from "object" instead, we get the error .. :code-block:: none TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases because OtherTask inherits from Base, whose metaclass is DeclarativeMeta, but there is another metaclass in the metaclass set that is incompatible with this. So, is solution that OtherTaskMetaclass should derive from "type" and then to use CooperativeMeta (q.v.) for OtherTask? No, that still seems to fail (and before any CooperativeMeta code is called) -- possibly that framework is for Python 2 only. See also https://blog.ionelmc.ro/2015/02/09/understanding-python-metaclasses/ Alternative solution 1: make a new metaclass that pretends to inherit from HadsMetaclass and DeclarativeMeta. WENT WITH THIS ONE INITIALLY: .. :code-block:: python class HadsMetaclass(type): # METACLASS def __init__(cls: Type['HadsBase'], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: add_multiple_columns(...) class HadsBase(TaskHasPatientMixin, Task, # INTERMEDIATE metaclass=HadsMetaclass): ... class HadsBlendedMetaclass(HadsMetaclass, DeclarativeMeta): # ODDITY # noinspection PyInitNewSignature def __init__(cls: Type[Union[HadsBase, DeclarativeMeta]], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: HadsMetaclass.__init__(cls, name, bases, classdict) # ... will call DeclarativeMeta.__init__ via its # super().__init__() class Hads(HadsBase, # ACTUAL TASK metaclass=HadsBlendedMetaclass): __tablename__ = "hads" Alternative solution 2: continue to have the HadsMetaclass deriving from DeclarativeMeta, but add it in at the last stage. IGNORE THIS, NO LONGER TRUE: - ALL THIS SOMEWHAT REVISED to handle SQLAlchemy concrete inheritance (q.v.), with the rule that "the only things that inherit from Task are actual tasks"; Task then inherits from both AbstractConcreteBase and Base. SEE ALSO sqla_database_structure.txt FINAL ANSWER: - classes inherit in a neat chain from Base -> [+/- Task -> ...] - metaclasses inherit in a neat chain from DeclarativeMeta - abstract intermediates mark themselves with "__abstract__ = True" .. :code-block:: python class HadsMetaclass(DeclarativeMeta): # METACLASS def __init__(cls: Type['HadsBase'], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: add_multiple_columns(...) class HadsBase(TaskHasPatientMixin, Task, # INTERMEDIATE metaclass=HadsMetaclass): __abstract__ = True class Hads(HadsBase): __tablename__ = "hads" Yes, that's it. (Note that if you erroneously also add "metaclass=HadsMetaclass" on Hads, you get: "TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases.") UPDATE 2019-07-28: - To fix "class must implement all abstract methods" warning from PyCharm, add "ABCMeta" to superclass list of HadsMetaclass. """ # noinspection PyInitNewSignature def __init__(cls: Type['HadsBase'], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: add_multiple_columns( cls, "q", 1, cls.NQUESTIONS, minimum=0, maximum=3, comment_fmt="Q{n}: {s} (0-3)", comment_strings=[ "tense", "enjoy usual", "apprehensive", "laugh", "worry", "cheerful", "relaxed", "slow", "butterflies", "appearance", "restless", "anticipate", "panic", "book/TV/radio" ] ) super().__init__(name, bases, classdict)
[docs]class HadsBase(TaskHasPatientMixin, Task, ABC, metaclass=HadsMetaclass): """ Server implementation of the HADS task. """ __abstract__ = True provides_trackers = True NQUESTIONS = 14 ANXIETY_QUESTIONS = [1, 3, 5, 7, 9, 11, 13] DEPRESSION_QUESTIONS = [2, 4, 6, 8, 10, 12, 14] TASK_FIELDS = strseq("q", 1, NQUESTIONS) MAX_ANX_SCORE = 21 MAX_DEP_SCORE = 21
[docs] def is_complete(self) -> bool: return ( self.field_contents_valid() and self.all_fields_not_none(self.TASK_FIELDS) )
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [ TrackerInfo( value=self.anxiety_score(), plot_label="HADS anxiety score", axis_label=f"Anxiety score (out of {self.MAX_ANX_SCORE})", axis_min=-0.5, axis_max=self.MAX_ANX_SCORE + 0.5, ), TrackerInfo( value=self.depression_score(), plot_label="HADS depression score", axis_label=f"Depression score (out of {self.MAX_DEP_SCORE})", axis_min=-0.5, axis_max=self.MAX_DEP_SCORE + 0.5 ), ]
[docs] def get_clinical_text(self, req: CamcopsRequest) -> List[CtvInfo]: if not self.is_complete(): return CTV_INCOMPLETE return [CtvInfo(content=( f"anxiety score {self.anxiety_score()}/{self.MAX_ANX_SCORE}, " f"depression score {self.depression_score()}/{self.MAX_DEP_SCORE}" ))]
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="anxiety", coltype=Integer(), value=self.anxiety_score(), comment=f"Anxiety score (/{self.MAX_ANX_SCORE})"), SummaryElement( name="depression", coltype=Integer(), value=self.depression_score(), comment=f"Depression score (/{self.MAX_DEP_SCORE})"), ]
def score(self, questions: List[int]) -> int: fields = self.fieldnames_from_list("q", questions) return self.sum_fields(fields) def anxiety_score(self) -> int: return self.score(self.ANXIETY_QUESTIONS) def depression_score(self) -> int: return self.score(self.DEPRESSION_QUESTIONS)
[docs] def get_task_html(self, req: CamcopsRequest) -> str: min_score = 0 max_score = 3 crippled = not self.extrastrings_exist(req) a = self.anxiety_score() d = self.depression_score() h = f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} <tr> <td>{req.wappstring(AS.HADS_ANXIETY_SCORE)}</td> <td>{answer(a)} / {self.MAX_ANX_SCORE}</td> </tr> <tr> <td>{req.wappstring(AS.HADS_DEPRESSION_SCORE)}</td> <td>{answer(d)} / 21</td> </tr> </table> </div> <div class="{CssClass.EXPLANATION}"> All questions are scored from 0–3 (0 least symptomatic, 3 most symptomatic). </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="50%">Question</th> <th width="50%">Answer</th> </tr> """ for n in range(1, self.NQUESTIONS + 1): if crippled: q = f"HADS: Q{n}" else: q = f"Q{n}. {self.wxstring(req, f'q{n}_stem')}" if n in self.ANXIETY_QUESTIONS: q += " (A)" if n in self.DEPRESSION_QUESTIONS: q += " (D)" v = getattr(self, "q" + str(n)) if crippled or v is None or v < min_score or v > max_score: a = v else: a = f"{v}: {self.wxstring(req, f'q{n}_a{v}')}" h += tr_qa(q, a) h += """ </table> """ + DATA_COLLECTION_UNLESS_UPGRADED_DIV return h
# ============================================================================= # Hads # =============================================================================
[docs]class Hads(HadsBase): __tablename__ = "hads" shortname = "HADS"
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _( "Hospital Anxiety and Depression Scale (data collection only)")
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: codes = [SnomedExpression(req.snomed(SnomedLookup.HADS_PROCEDURE_ASSESSMENT))] # noqa if self.is_complete(): codes.append(SnomedExpression( req.snomed(SnomedLookup.HADS_SCALE), { req.snomed(SnomedLookup.HADS_ANXIETY_SCORE): self.anxiety_score(), # noqa req.snomed(SnomedLookup.HADS_DEPRESSION_SCORE): self.depression_score(), # noqa } )) return codes
# ============================================================================= # HadsRespondent # =============================================================================
[docs]class HadsRespondent(TaskHasRespondentMixin, HadsBase): __tablename__ = "hads_respondent" shortname = "HADS-Respondent" extrastring_taskname = "hads"
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Hospital Anxiety and Depression Scale (data collection " "only), non-patient respondent version")
# No SNOMED codes; not for the patient!