Source code for camcops_server.tasks.eq5d5l

#!/usr/bin/env python
# camcops_server/tasks/eq5d5l.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/>.

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

- By Joe Kearney, Rudolf Cardinal.

"""

from typing import List

from cardinal_pythonlib.stringfunc import strseq
from sqlalchemy.sql.sqltypes import Integer, String

from camcops_server.cc_modules.cc_constants import CssClass
from camcops_server.cc_modules.cc_html import 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_sqla_coltypes import (
    CamcopsColumn,
    ONE_TO_FIVE_CHECKER,
    ZERO_TO_100_CHECKER,
)
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import (
    get_from_dict,
    Task,
    TaskHasPatientMixin,
)
from camcops_server.cc_modules.cc_trackerhelpers import (
    equally_spaced_int,
    regular_tracker_axis_ticks_int,
    TrackerInfo,
)


# =============================================================================
# EQ-5D-5L
# =============================================================================

[docs]class Eq5d5l(TaskHasPatientMixin, Task): """ Server implementation of the EQ-5D-5L task. Note that the "index value" summary (e.g. SNOMED-CT code 736534008) is not implemented. This is a country-specific conversion of the raw values to a unitary health value; see - https://euroqol.org/publications/key-euroqol-references/value-sets/ - https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/valuation/choosing-a-value-set/ """ # noqa __tablename__ = "eq5d5l" shortname = "EQ-5D-5L" provides_trackers = True q1 = CamcopsColumn( "q1", Integer, comment="Q1 (mobility) (1 no problems - 5 unable)", permitted_value_checker=ONE_TO_FIVE_CHECKER, ) q2 = CamcopsColumn( "q2", Integer, comment="Q2 (self-care) (1 no problems - 5 unable)", permitted_value_checker=ONE_TO_FIVE_CHECKER, ) q3 = CamcopsColumn( "q3", Integer, comment="Q3 (usual activities) (1 no problems - 5 unable)", permitted_value_checker=ONE_TO_FIVE_CHECKER, ) q4 = CamcopsColumn( "q4", Integer, comment="Q4 (pain/discomfort) (1 none - 5 extreme)", permitted_value_checker=ONE_TO_FIVE_CHECKER, ) q5 = CamcopsColumn( "q5", Integer, comment="Q5 (anxiety/depression) (1 not - 5 extremely)", permitted_value_checker=ONE_TO_FIVE_CHECKER, ) health_vas = CamcopsColumn( "health_vas", Integer, comment="Visual analogue scale for overall health (0 worst - 100 best)", # noqa permitted_value_checker=ZERO_TO_100_CHECKER, ) N_QUESTIONS = 5 MISSING_ANSWER_VALUE = 9 QUESTIONS = strseq("q", 1, N_QUESTIONS) QUESTIONS += ["health_vas"]
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("EuroQol 5-Dimension, 5-Level Health Scale")
[docs] def is_complete(self) -> bool: return self.all_fields_not_none(self.QUESTIONS)
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.health_vas, plot_label="EQ-5D-5L health visual analogue scale", axis_label="Self-rated health today (out of 100)", axis_min=-0.5, axis_max=100.5, axis_ticks=regular_tracker_axis_ticks_int(0, 100, 25), horizontal_lines=equally_spaced_int(0, 100, 25), )]
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="health_state", coltype=String(length=5), value=self.get_health_state_code(), comment="Health state as a 5-character string of numbers, " "with 9 indicating a missing value"), SummaryElement( name="visual_task_score", coltype=Integer(), value=self.get_vis_score_or_999(), comment="Visual analogue health score " "(0-100, with 999 replacing None)") ]
def get_health_state_code(self) -> str: mcq = "" for i in range(1, self.N_QUESTIONS + 1): ans = getattr(self, "q" + str(i)) if ans is None: mcq += str(self.MISSING_ANSWER_VALUE) else: mcq += str(ans) return mcq def get_vis_score_or_999(self) -> int: vis_score = self.health_vas if vis_score is None: return 999 return vis_score
[docs] def get_task_html(self, req: CamcopsRequest) -> str: q_a = "" for i in range(1, self.N_QUESTIONS + 1): nstr = str(i) answers = { None: None, 1: "1 – " + self.wxstring(req, "q" + nstr + "_o1"), 2: "2 – " + self.wxstring(req, "q" + nstr + "_o2"), 3: "3 – " + self.wxstring(req, "q" + nstr + "_o3"), 4: "4 – " + self.wxstring(req, "q" + nstr + "_o4"), 5: "5 – " + self.wxstring(req, "q" + nstr + "_o5"), } q_a += tr_qa(nstr + ". " + self.wxstring(req, "q" + nstr + "_h"), get_from_dict(answers, getattr(self, "q" + str(i)))) q_a += tr_qa( ("Self-rated health on a visual analogue scale (0–100) " "<sup>[2]</sup>"), self.health_vas) return f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} {tr_qa("Health state code <sup>[1]</sup>", self.get_health_state_code())} {tr_qa("Visual analogue scale summary number <sup>[2]</sup>", self.get_vis_score_or_999())} </table> </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="60%">Question</th> <th width="40%">Answer</th> </tr> {q_a} </table> <div class="{CssClass.FOOTNOTES}"> [1] This is a string of digits, not a directly meaningful number. Each digit corresponds to a question. A score of 1 indicates no problems in any given dimension. 5 indicates extreme problems. Missing values are coded as 9. [2] This is the visual analogue health score, with missing values coded as 999. </div> """ # noqa
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: codes = [SnomedExpression(req.snomed(SnomedLookup.EQ5D5L_PROCEDURE_ASSESSMENT))] # noqa if self.is_complete(): codes.append(SnomedExpression( req.snomed(SnomedLookup.EQ5D5L_SCALE), { # SnomedLookup.EQ5D5L_INDEX_VALUE: not used; see docstring above # noqa req.snomed(SnomedLookup.EQ5D5L_MOBILITY_SCORE): self.q1, req.snomed(SnomedLookup.EQ5D5L_SELF_CARE_SCORE): self.q2, req.snomed(SnomedLookup.EQ5D5L_USUAL_ACTIVITIES_SCORE): self.q3, # noqa req.snomed(SnomedLookup.EQ5D5L_PAIN_DISCOMFORT_SCORE): self.q4, # noqa req.snomed(SnomedLookup.EQ5D5L_ANXIETY_DEPRESSION_SCORE): self.q5, # noqa } )) return codes