Source code for camcops_server.tasks.demqol

#!/usr/bin/env python

"""
camcops_server/tasks/demqol.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 typing import Any, Dict, List, Optional, Tuple, Type, Union

from cardinal_pythonlib.stringfunc import strseq
import cardinal_pythonlib.rnc_web as ws
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.sqltypes import Float, Integer

from camcops_server.cc_modules.cc_constants import CssClass
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,
    get_yes_no,
    subheading_spanning_two_columns,
    tr_qa,
)
from camcops_server.cc_modules.cc_request import CamcopsRequest
from camcops_server.cc_modules.cc_sqla_coltypes import (
    CamcopsColumn,
    PermittedValueChecker,
)
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import (
    get_from_dict,
    Task,
    TaskHasClinicianMixin,
    TaskHasPatientMixin,
    TaskHasRespondentMixin,
)
from camcops_server.cc_modules.cc_trackerhelpers import TrackerInfo

# =============================================================================
# Constants
# =============================================================================

DP = 2
MISSING_VALUE = -99
PERMITTED_VALUES = list(range(1, 4 + 1)) + [MISSING_VALUE]
END_DIV = f"""
    </table>
    <div class="{CssClass.FOOTNOTES}">
        [1] Extrapolated total scores are: total_for_responded_questions ×
        n_questions / n_responses.
    </div>
"""
COPYRIGHT_DIV = f"""
    <div class="{CssClass.COPYRIGHT}">
        DEMQOL/DEMQOL-Proxy: Copyright © Institute of Psychiatry, King’s
        College London. Reproduced with permission.
    </div>
"""


# =============================================================================
# DEMQOL
# =============================================================================

class DemqolMetaclass(DeclarativeMeta):
    # noinspection PyInitNewSignature
    def __init__(cls: Type['Demqol'],
                 name: str,
                 bases: Tuple[Type, ...],
                 classdict: Dict[str, Any]) -> None:
        add_multiple_columns(
            cls, "q", 1, cls.N_SCORED_QUESTIONS,
            pv=PERMITTED_VALUES,
            comment_fmt="Q{n}. {s} (1 a lot - 4 not at all; -99 no response)",
            comment_strings=[
                # 1-13
                "cheerful", "worried/anxious", "enjoying life", "frustrated",
                "confident", "full of energy", "sad", "lonely", "distressed",
                "lively", "irritable", "fed up", "couldn't do things",
                # 14-19
                "worried: forget recent", "worried: forget people",
                "worried: forget day", "worried: muddled",
                "worried: difficulty making decisions",
                "worried: poor concentration",
                # 20-28
                "worried: not enough company",
                "worried: get on with people close",
                "worried: affection", "worried: people not listening",
                "worried: making self understood", "worried: getting help",
                "worried: toilet", "worried: feel in self",
                "worried: health overall",
            ]
        )
        super().__init__(name, bases, classdict)


[docs]class Demqol(TaskHasPatientMixin, TaskHasClinicianMixin, Task, metaclass=DemqolMetaclass): """ Server implementation of the DEMQOL task. """ __tablename__ = "demqol" shortname = "DEMQOL" provides_trackers = True q29 = CamcopsColumn( "q29", Integer, permitted_value_checker=PermittedValueChecker( permitted_values=PERMITTED_VALUES), comment="Q29. Overall quality of life (1 very good - 4 poor; " "-99 no response)." ) NQUESTIONS = 29 N_SCORED_QUESTIONS = 28 MINIMUM_N_FOR_TOTAL_SCORE = 14 REVERSE_SCORE = [1, 3, 5, 6, 10, 29] # questions scored backwards MIN_SCORE = N_SCORED_QUESTIONS MAX_SCORE = MIN_SCORE * 4 COMPLETENESS_FIELDS = strseq("q", 1, NQUESTIONS)
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Dementia Quality of Life measure, self-report version")
[docs] def is_complete(self) -> bool: return ( self.all_fields_not_none(self.COMPLETENESS_FIELDS) and self.field_contents_valid() )
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="DEMQOL total score", axis_label=( f"Total score (range {self.MIN_SCORE}{self.MAX_SCORE}, " f"higher better)" ), axis_min=self.MIN_SCORE - 0.5, axis_max=self.MAX_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"Total score {ws.number_to_dp(self.total_score(), DP)} " f"(range {self.MIN_SCORE}{self.MAX_SCORE}, higher better)" ))]
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="total", coltype=Float(), value=self.total_score(), comment=f"Total score ({self.MIN_SCORE}-{self.MAX_SCORE})"), ]
def totalscore_extrapolated(self) -> Tuple[float, bool]: return calc_total_score( obj=self, n_scored_questions=self.N_SCORED_QUESTIONS, reverse_score_qs=self.REVERSE_SCORE, minimum_n_for_total_score=self.MINIMUM_N_FOR_TOTAL_SCORE ) def total_score(self) -> float: (total, extrapolated) = self.totalscore_extrapolated() return total def get_q(self, req: CamcopsRequest, n: int) -> str: nstr = str(n) return "Q" + nstr + ". " + self.wxstring(req, "proxy_q" + nstr)
[docs] def get_task_html(self, req: CamcopsRequest) -> str: (total, extrapolated) = self.totalscore_extrapolated() main_dict = { None: None, 1: "1 — " + self.wxstring(req, "a1"), 2: "2 — " + self.wxstring(req, "a2"), 3: "3 — " + self.wxstring(req, "a3"), 4: "4 — " + self.wxstring(req, "a4"), MISSING_VALUE: self.wxstring(req, "no_response") } last_q_dict = { None: None, 1: "1 — " + self.wxstring(req, "q29_a1"), 2: "2 — " + self.wxstring(req, "q29_a2"), 3: "3 — " + self.wxstring(req, "q29_a3"), 4: "4 — " + self.wxstring(req, "q29_a4"), MISSING_VALUE: self.wxstring(req, "no_response") } instruction_dict = { 1: self.wxstring(req, "instruction11"), 14: self.wxstring(req, "instruction12"), 20: self.wxstring(req, "instruction13"), 29: self.wxstring(req, "instruction14"), } # https://docs.python.org/2/library/stdtypes.html#mapping-types-dict # http://paltman.com/try-except-performance-in-python-a-simple-test/ h = f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} <tr> <td>Total score ({self.MIN_SCORE}{self.MAX_SCORE}), higher better</td> <td>{answer(ws.number_to_dp(total, DP))}</td> </tr> <tr> <td>Total score extrapolated using incomplete responses? <sup>[1]</sup></td> <td>{answer(get_yes_no(req, extrapolated))}</td> </tr> </table> </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 n in instruction_dict: h += subheading_spanning_two_columns(instruction_dict.get(n)) d = main_dict if n <= self.N_SCORED_QUESTIONS else last_q_dict q = self.get_q(req, n) a = get_from_dict(d, getattr(self, "q" + str(n))) h += tr_qa(q, a) h += END_DIV + COPYRIGHT_DIV return h
# ============================================================================= # DEMQOL-Proxy # ============================================================================= class DemqolProxyMetaclass(DeclarativeMeta): # noinspection PyInitNewSignature def __init__(cls: Type['DemqolProxy'], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: add_multiple_columns( cls, "q", 1, cls.N_SCORED_QUESTIONS, pv=PERMITTED_VALUES, comment_fmt="Q{n}. {s} (1 a lot - 4 not at all; -99 no response)", comment_strings=[ # 1-11 "cheerful", "worried/anxious", "frustrated", "full of energy", "sad", "content", "distressed", "lively", "irritable", "fed up", "things to look forward to", # 12-20 "worried: memory in general", "worried: forget distant", "worried: forget recent", "worried: forget people", "worried: forget place", "worried: forget day", "worried: muddled", "worried: difficulty making decisions", "worried: making self understood", # 21-31 "worried: keeping clean", "worried: keeping self looking nice", "worried: shopping", "worried: using money to pay", "worried: looking after finances", "worried: taking longer", "worried: getting in touch with people", "worried: not enough company", "worried: not being able to help others", "worried: not playing a useful part", "worried: physical health", ] ) super().__init__(name, bases, classdict)
[docs]class DemqolProxy(TaskHasPatientMixin, TaskHasRespondentMixin, TaskHasClinicianMixin, Task, metaclass=DemqolProxyMetaclass): __tablename__ = "demqolproxy" shortname = "DEMQOL-Proxy" extrastring_taskname = "demqol" q32 = CamcopsColumn( "q32", Integer, permitted_value_checker=PermittedValueChecker( permitted_values=PERMITTED_VALUES), comment="Q32. Overall quality of life (1 very good - 4 poor; " "-99 no response)." ) NQUESTIONS = 32 N_SCORED_QUESTIONS = 31 MINIMUM_N_FOR_TOTAL_SCORE = 16 REVERSE_SCORE = [1, 4, 6, 8, 11, 32] # questions scored backwards MIN_SCORE = N_SCORED_QUESTIONS MAX_SCORE = MIN_SCORE * 4 COMPLETENESS_FIELDS = strseq("q", 1, NQUESTIONS)
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Dementia Quality of Life measure, proxy version")
[docs] def is_complete(self) -> bool: return ( self.all_fields_not_none(self.COMPLETENESS_FIELDS) and self.field_contents_valid() )
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="DEMQOL-Proxy total score", axis_label=( f"Total score (range {self.MIN_SCORE}{self.MAX_SCORE}," f" higher better)" ), axis_min=self.MIN_SCORE - 0.5, axis_max=self.MAX_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"Total score {ws.number_to_dp(self.total_score(), DP)} " f"(range {self.MIN_SCORE}{self.MAX_SCORE}, higher better)" ))]
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="total", coltype=Float(), value=self.total_score(), comment=f"Total score ({self.MIN_SCORE}-{self.MAX_SCORE})"), ]
def totalscore_extrapolated(self) -> Tuple[float, bool]: return calc_total_score( obj=self, n_scored_questions=self.N_SCORED_QUESTIONS, reverse_score_qs=self.REVERSE_SCORE, minimum_n_for_total_score=self.MINIMUM_N_FOR_TOTAL_SCORE ) def total_score(self) -> float: (total, extrapolated) = self.totalscore_extrapolated() return total def get_q(self, req: CamcopsRequest, n: int) -> str: nstr = str(n) return "Q" + nstr + ". " + self.wxstring(req, "proxy_q" + nstr)
[docs] def get_task_html(self, req: CamcopsRequest) -> str: (total, extrapolated) = self.totalscore_extrapolated() main_dict = { None: None, 1: "1 — " + self.wxstring(req, "a1"), 2: "2 — " + self.wxstring(req, "a2"), 3: "3 — " + self.wxstring(req, "a3"), 4: "4 — " + self.wxstring(req, "a4"), MISSING_VALUE: self.wxstring(req, "no_response") } last_q_dict = { None: None, 1: "1 — " + self.wxstring(req, "q29_a1"), 2: "2 — " + self.wxstring(req, "q29_a2"), 3: "3 — " + self.wxstring(req, "q29_a3"), 4: "4 — " + self.wxstring(req, "q29_a4"), MISSING_VALUE: self.wxstring(req, "no_response") } instruction_dict = { 1: self.wxstring(req, "proxy_instruction11"), 12: self.wxstring(req, "proxy_instruction12"), 21: self.wxstring(req, "proxy_instruction13"), 32: self.wxstring(req, "proxy_instruction14"), } h = f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} <tr> <td>Total score ({self.MIN_SCORE}{self.MAX_SCORE}), higher better</td> <td>{answer(ws.number_to_dp(total, DP))}</td> </tr> <tr> <td>Total score extrapolated using incomplete responses? <sup>[1]</sup></td> <td>{answer(get_yes_no(req, extrapolated))}</td> </tr> </table> </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 n in instruction_dict: h += subheading_spanning_two_columns(instruction_dict.get(n)) d = main_dict if n <= self.N_SCORED_QUESTIONS else last_q_dict q = self.get_q(req, n) a = get_from_dict(d, getattr(self, "q" + str(n))) h += tr_qa(q, a) h += END_DIV + COPYRIGHT_DIV return h
# ============================================================================= # Common scoring function # =============================================================================
[docs]def calc_total_score(obj: Union[Demqol, DemqolProxy], n_scored_questions: int, reverse_score_qs: List[int], minimum_n_for_total_score: int) \ -> Tuple[Optional[float], bool]: """Returns (total, extrapolated?).""" n = 0 total = 0 for q in range(1, n_scored_questions + 1): x = getattr(obj, "q" + str(q)) if x is None or x == MISSING_VALUE: continue if q in reverse_score_qs: x = 5 - x n += 1 total += x if n < minimum_n_for_total_score: return None, False if n < n_scored_questions: return n_scored_questions * total / n, True return total, False