Source code for camcops_server.tasks.phq9

#!/usr/bin/env python

"""
camcops_server/tasks/phq9.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, Tuple, Type

from cardinal_pythonlib.stringfunc import strseq
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.sqltypes import Boolean, Integer

from camcops_server.cc_modules.cc_constants import CssClass
from camcops_server.cc_modules.cc_ctvinfo import CtvInfo, CTV_INCOMPLETE
from camcops_server.cc_modules.cc_db import add_multiple_columns
from camcops_server.cc_modules.cc_html import answer, get_yes_no, tr, 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,
    SummaryCategoryColType,
    ZERO_TO_THREE_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_text import SS
from camcops_server.cc_modules.cc_trackerhelpers import (
    TrackerAxisTick,
    TrackerInfo,
    TrackerLabel,
)


# =============================================================================
# PHQ-9
# =============================================================================

class Phq9Metaclass(DeclarativeMeta):
    # noinspection PyInitNewSignature
    def __init__(cls: Type['Phq9'],
                 name: str,
                 bases: Tuple[Type, ...],
                 classdict: Dict[str, Any]) -> None:
        add_multiple_columns(
            cls, "q", 1, cls.N_MAIN_QUESTIONS,
            minimum=0, maximum=3,
            comment_fmt="Q{n} ({s}) (0 not at all - 3 nearly every day)",
            comment_strings=[
                "anhedonia",
                "mood",
                "sleep",
                "energy",
                "appetite",
                "self-esteem/guilt",
                "concentration",
                "psychomotor",
                "death/self-harm",
            ]
        )
        super().__init__(name, bases, classdict)


[docs]class Phq9(TaskHasPatientMixin, Task, metaclass=Phq9Metaclass): """ Server implementation of the PHQ9 task. """ __tablename__ = "phq9" shortname = "PHQ-9" provides_trackers = True q10 = CamcopsColumn( "q10", Integer, permitted_value_checker=ZERO_TO_THREE_CHECKER, comment="Q10 (difficulty in activities) (0 not difficult at " "all - 3 extremely difficult)" ) N_MAIN_QUESTIONS = 9 MAX_SCORE_MAIN = 3 * N_MAIN_QUESTIONS MAIN_QUESTIONS = strseq("q", 1, N_MAIN_QUESTIONS)
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Patient Health Questionnaire-9")
[docs] def is_complete(self) -> bool: if self.any_fields_none(self.MAIN_QUESTIONS): return False if self.total_score() > 0 and self.q10 is None: return False if not self.field_contents_valid(): return False return True
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="PHQ-9 total score (rating depressive symptoms)", axis_label=f"Score for Q1-9 (out of {self.MAX_SCORE_MAIN})", axis_min=-0.5, axis_max=self.MAX_SCORE_MAIN + 0.5, axis_ticks=[ TrackerAxisTick(27, "27"), TrackerAxisTick(25, "25"), TrackerAxisTick(20, "20"), TrackerAxisTick(15, "15"), TrackerAxisTick(10, "10"), TrackerAxisTick(5, "5"), TrackerAxisTick(0, "0"), ], horizontal_lines=[ 19.5, 14.5, 9.5, 4.5 ], horizontal_labels=[ TrackerLabel(23, req.sstring(SS.SEVERE)), TrackerLabel(17, req.sstring(SS.MODERATELY_SEVERE)), TrackerLabel(12, req.sstring(SS.MODERATE)), TrackerLabel(7, req.sstring(SS.MILD)), TrackerLabel(2.25, req.sstring(SS.NONE)), ] )]
[docs] def get_clinical_text(self, req: CamcopsRequest) -> List[CtvInfo]: if not self.is_complete(): return CTV_INCOMPLETE return [CtvInfo(content=( f"PHQ-9 total score {self.total_score()}/{self.MAX_SCORE_MAIN} " f"({self.severity(req)})" ))]
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="total", coltype=Integer(), value=self.total_score(), comment=f"Total score (/{self.MAX_SCORE_MAIN})"), SummaryElement( name="n_core", coltype=Integer(), value=self.n_core(), comment="Number of core symptoms"), SummaryElement( name="n_other", coltype=Integer(), value=self.n_other(), comment="Number of other symptoms"), SummaryElement( name="n_total", coltype=Integer(), value=self.n_total(), comment="Total number of symptoms"), SummaryElement( name="is_mds", coltype=Boolean(), value=self.is_mds(), comment="PHQ9 major depressive syndrome?"), SummaryElement( name="is_ods", coltype=Boolean(), value=self.is_ods(), comment="PHQ9 other depressive syndrome?"), SummaryElement( name="severity", coltype=SummaryCategoryColType, value=self.severity(req), comment="PHQ9 depression severity"), ]
def total_score(self) -> int: return self.sum_fields(self.MAIN_QUESTIONS) def one_if_q_ge(self, qnum: int, threshold: int) -> int: value = getattr(self, "q" + str(qnum)) return 1 if value is not None and value >= threshold else 0 def n_core(self) -> int: return (self.one_if_q_ge(1, 2) + self.one_if_q_ge(2, 2)) def n_other(self) -> int: return (self.one_if_q_ge(3, 2) + self.one_if_q_ge(4, 2) + self.one_if_q_ge(5, 2) + self.one_if_q_ge(6, 2) + self.one_if_q_ge(7, 2) + self.one_if_q_ge(8, 2) + self.one_if_q_ge(9, 1)) # suicidality # suicidality counted whenever present def n_total(self) -> int: return self.n_core() + self.n_other() def is_mds(self) -> bool: return self.n_core() >= 1 and self.n_total() >= 5 def is_ods(self) -> bool: return self.n_core() >= 1 and 2 <= self.n_total() <= 4 def severity(self, req: CamcopsRequest) -> str: total = self.total_score() if total >= 20: return req.sstring(SS.SEVERE) elif total >= 15: return req.sstring(SS.MODERATELY_SEVERE) elif total >= 10: return req.sstring(SS.MODERATE) elif total >= 5: return req.sstring(SS.MILD) else: return req.sstring(SS.NONE)
[docs] def get_task_html(self, req: CamcopsRequest) -> str: main_dict = { None: None, 0: "0 — " + self.wxstring(req, "a0"), 1: "1 — " + self.wxstring(req, "a1"), 2: "2 — " + self.wxstring(req, "a2"), 3: "3 — " + self.wxstring(req, "a3") } q10_dict = { None: None, 0: "0 — " + self.wxstring(req, "fa0"), 1: "1 — " + self.wxstring(req, "fa1"), 2: "2 — " + self.wxstring(req, "fa2"), 3: "3 — " + self.wxstring(req, "fa3") } q_a = "" for i in range(1, self.N_MAIN_QUESTIONS + 1): nstr = str(i) q_a += tr_qa(self.wxstring(req, "q" + nstr), get_from_dict(main_dict, getattr(self, "q" + nstr))) q_a += tr_qa("10. " + self.wxstring(req, "finalq"), get_from_dict(q10_dict, self.q10)) h = """ <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {tr_is_complete} {total_score} {depression_severity} {n_symptoms} {mds} {ods} </table> </div> <div class="{CssClass.EXPLANATION}"> Ratings are over the last 2 weeks. </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] Sum for questions 1–9. [2] Total score ≥20 severe, ≥15 moderately severe, ≥10 moderate, ≥5 mild, &lt;5 none. [3] Number of questions 1–2 rated ≥2. [4] Number of questions 3–8 rated ≥2, or question 9 rated ≥1. [5] ≥1 core symptom and ≥5 total symptoms (as per DSM-IV-TR page 356). [6] ≥1 core symptom and 2–4 total symptoms (as per DSM-IV-TR page 775). </div> """.format( CssClass=CssClass, tr_is_complete=self.get_is_complete_tr(req), total_score=tr( req.sstring(SS.TOTAL_SCORE) + " <sup>[1]</sup>", answer(self.total_score()) + f" / {self.MAX_SCORE_MAIN}" ), depression_severity=tr_qa( self.wxstring(req, "depression_severity") + " <sup>[2]</sup>", self.severity(req) ), n_symptoms=tr( "Number of symptoms: core <sup>[3]</sup>, other " "<sup>[4]</sup>, total", answer(self.n_core()) + "/2, " + answer(self.n_other()) + "/7, " + answer(self.n_total()) + "/9" ), mds=tr_qa( self.wxstring(req, "mds") + " <sup>[5]</sup>", get_yes_no(req, self.is_mds()) ), ods=tr_qa( self.wxstring(req, "ods") + " <sup>[6]</sup>", get_yes_no(req, self.is_ods()) ), q_a=q_a, ) return h
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: procedure = req.snomed(SnomedLookup.PHQ9_PROCEDURE_DEPRESSION_SCREENING) # noqa codes = [SnomedExpression(procedure)] if self.is_complete(): scale = req.snomed(SnomedLookup.PHQ9_SCALE) score = req.snomed(SnomedLookup.PHQ9_SCORE) screen_negative = req.snomed(SnomedLookup.PHQ9_FINDING_NEGATIVE_SCREENING_FOR_DEPRESSION) # noqa screen_positive = req.snomed(SnomedLookup.PHQ9_FINDING_POSITIVE_SCREENING_FOR_DEPRESSION) # noqa if self.is_mds() or self.is_ods(): # Threshold debatable, but if you have "other depressive # syndrome", it seems wrong to say you've screened negative for # depression. procedure_result = screen_positive else: procedure_result = screen_negative codes.append(SnomedExpression(scale, {score: self.total_score()})) codes.append(SnomedExpression(procedure_result)) return codes