Source code for camcops_server.tasks.bdi

#!/usr/bin/env python

"""
camcops_server/tasks/bdi.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
import cardinal_pythonlib.rnc_web as ws
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.schema import Column
from sqlalchemy.sql.sqltypes import Integer, String

from camcops_server.cc_modules.cc_constants import (
    CssClass,
    DATA_COLLECTION_ONLY_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, bold, td, 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_string import AS
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import Task, TaskHasPatientMixin
from camcops_server.cc_modules.cc_text import SS
from camcops_server.cc_modules.cc_trackerhelpers import TrackerInfo


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

BDI_I_QUESTION_TOPICS = {
    # from Beck 1988, https://doi.org/10.1016/0272-7358(88)90050-5
    1: "mood",  # a
    2: "pessimism",  # b
    3: "sense of failure",  # c
    4: "lack of satisfaction",  # d
    5: "guilt feelings",  # e
    6: "sense of punishment",  # f
    7: "self-dislike",  # g
    8: "self-accusation",  # h
    9: "suicidal wishes",  # i
    10: "crying",  # j
    11: "irritability",  # k
    12: "social withdrawal",  # l
    13: "indecisiveness",  # m
    14: "distortion of body image",  # n
    15: "work inhibition",  # o
    16: "sleep disturbance",  # p
    17: "fatigability",  # q
    18: "loss of appetite",  # r
    19: "weight loss",  # s
    20: "somatic preoccupation",  # t
    21: "loss of libido",  # u
}
BDI_IA_QUESTION_TOPICS = {
    # from [Beck1996b]
    1: "sadness",
    2: "pessimism",
    3: "sense of failure",
    4: "self-dissatisfaction",
    5: "guilt",
    6: "punishment",
    7: "self-dislike",
    8: "self-accusations",
    9: "suicidal ideas",
    10: "crying",
    11: "irritability",
    12: "social withdrawal",
    13: "indecisiveness",
    14: "body image change",
    15: "work difficulty",
    16: "insomnia",
    17: "fatigability",
    18: "loss of appetite",
    19: "weight loss",
    20: "somatic preoccupation",
    21: "loss of libido",
}
BDI_II_QUESTION_TOPICS = {
    # from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889520/;
    # also https://www.ncbi.nlm.nih.gov/pubmed/10100838;
    # also [Beck1996b]
    # matches BDI-II paper version
    1: "sadness",
    2: "pessimism",
    3: "past failure",
    4: "loss of pleasure",
    5: "guilty feelings",
    6: "punishment feelings",
    7: "self-dislike",
    8: "self-criticalness",
    9: "suicidal thoughts or wishes",
    10: "crying",
    11: "agitation",
    12: "loss of interest",
    13: "indecisiveness",
    14: "worthlessness",
    15: "loss of energy",
    16: "changes in sleeping pattern",  # decrease or increase
    17: "irritability",
    18: "changes in appetite",  # decrease or increase
    19: "concentration difficulty",
    20: "tiredness or fatigue",
    21: "loss of interest in sex",
}
SCALE_BDI_I = "BDI-I"  # must match client
SCALE_BDI_IA = "BDI-IA"  # must match client
SCALE_BDI_II = "BDI-II"  # must match client
TOPICS_BY_SCALE = {
    SCALE_BDI_I: BDI_I_QUESTION_TOPICS,
    SCALE_BDI_IA: BDI_IA_QUESTION_TOPICS,
    SCALE_BDI_II: BDI_II_QUESTION_TOPICS,
}

NQUESTIONS = 21
TASK_SCORED_FIELDS = strseq("q", 1, NQUESTIONS)
MAX_SCORE = NQUESTIONS * 3
SUICIDALITY_QNUM = 9  # Q9 in all versions of the BDI (I, IA, II)
SUICIDALITY_FN = "q9"  # fieldname
CUSTOM_SOMATIC_KHANDAKER_BDI_II_QNUMS = [4, 15, 16, 18, 19, 20, 21]
CUSTOM_SOMATIC_KHANDAKER_BDI_II_FIELDS = Task.fieldnames_from_list(
    "q", CUSTOM_SOMATIC_KHANDAKER_BDI_II_QNUMS)


# =============================================================================
# BDI (crippled)
# =============================================================================

class BdiMetaclass(DeclarativeMeta):
    # noinspection PyInitNewSignature
    def __init__(cls: Type['Bdi'],
                 name: str,
                 bases: Tuple[Type, ...],
                 classdict: Dict[str, Any]) -> None:
        add_multiple_columns(
            cls, "q", 1, NQUESTIONS,
            minimum=0, maximum=3,
            comment_fmt="Q{n} [{s}] (0-3, higher worse)",
            comment_strings=[
                (
                    f"BDI-I: {BDI_I_QUESTION_TOPICS[q]}; "
                    f"BDI-IA: {BDI_IA_QUESTION_TOPICS[q]}; "
                    f"BDI-II: {BDI_II_QUESTION_TOPICS[q]}"
                )
                for q in range(1, NQUESTIONS + 1)
            ]
        )
        super().__init__(name, bases, classdict)


[docs]class Bdi(TaskHasPatientMixin, Task, metaclass=BdiMetaclass): """ Server implementation of the BDI task. """ __tablename__ = "bdi" shortname = "BDI" provides_trackers = True bdi_scale = Column( "bdi_scale", String(length=10), # was Text comment="Which BDI scale (BDI-I, BDI-IA, BDI-II)?" )
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Beck Depression Inventory (data collection only)")
[docs] def is_complete(self) -> bool: return ( self.field_contents_valid() and self.bdi_scale is not None and self.all_fields_not_none(TASK_SCORED_FIELDS) )
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="BDI total score (rating depressive symptoms)", axis_label=f"Score for Q1-21 (out of {MAX_SCORE})", axis_min=-0.5, axis_max=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"{ws.webify(self.bdi_scale)} " f"total score {self.total_score()}/{MAX_SCORE}" ))]
[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 (/{MAX_SCORE})"), ]
def total_score(self) -> int: return self.sum_fields(TASK_SCORED_FIELDS) def is_bdi_ii(self) -> bool: return self.bdi_scale == SCALE_BDI_II
[docs] def get_task_html(self, req: CamcopsRequest) -> str: score = self.total_score() # Suicidal thoughts: suicidality_score = getattr(self, SUICIDALITY_FN) if suicidality_score is None: suicidality_text = bold("? (not completed)") suicidality_css_class = CssClass.INCOMPLETE elif suicidality_score == 0: suicidality_text = str(suicidality_score) suicidality_css_class = "" else: suicidality_text = bold(str(suicidality_score)) suicidality_css_class = CssClass.WARNING # Custom somatic score for Khandaker Insight study: somatic_css_class = "" if self.is_bdi_ii(): somatic_values = self.get_values( CUSTOM_SOMATIC_KHANDAKER_BDI_II_FIELDS) somatic_missing = False somatic_score = 0 for v in somatic_values: if v is None: somatic_missing = True somatic_css_class = CssClass.INCOMPLETE break else: somatic_score += int(v) somatic_text = ("incomplete" if somatic_missing else str(somatic_score)) else: somatic_text = "N/A" # not the BDI-II # Question rows: q_a = "" qdict = TOPICS_BY_SCALE.get(self.bdi_scale) topic = "?" for q in range(1, NQUESTIONS + 1): if qdict: topic = qdict.get(q, "??") q_a += tr_qa( f"{req.sstring(SS.QUESTION)} {q} ({topic})", getattr(self, "q" + str(q)) ) # HTML: tr_somatic_score = tr( td( "Custom somatic score for Insight study <sup>[2]</sup> " "(sum of scores for questions {}, for BDI-II only)".format( ", ".join("Q" + str(qnum) for qnum in CUSTOM_SOMATIC_KHANDAKER_BDI_II_QNUMS)) ), td(somatic_text, td_class=somatic_css_class), literal=True ) tr_which_scale = tr_qa( req.wappstring(AS.BDI_WHICH_SCALE) + " <sup>[3]</sup>", ws.webify(self.bdi_scale) ) return f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} {tr(req.sstring(SS.TOTAL_SCORE), answer(score) + " / {}".format(MAX_SCORE))} <tr> <td> Suicidal thoughts/wishes score (Q{SUICIDALITY_QNUM}) <sup>[1]</sup> </td> {td(suicidality_text, td_class=suicidality_css_class)} </tr> {tr_somatic_score} </table> </div> <div class="{CssClass.EXPLANATION}"> All questions are scored from 0–3 (0 free of symptoms, 3 most symptomatic). </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="70%">Question</th> <th width="30%">Answer</th> </tr> {tr_which_scale} {q_a} </table> <div class="{CssClass.FOOTNOTES}"> [1] Suicidal thoughts are asked about in Q{SUICIDALITY_QNUM} for all of: BDI-I (1961), BDI-IA (1978), and BDI-II (1996). [2] Insight study: <a href="https://doi.org/10.1186/ISRCTN16942542">doi:10.1186/ISRCTN16942542</a> [3] See the <a href="https://camcops.readthedocs.io/en/latest/tasks/bdi.html">CamCOPS BDI help</a> for full references and bibliography for the citations that follow. <b>The BDI rates “right now” [Beck1988]. The BDI-IA rates the past week [Beck1988]. The BDI-II rates the past two weeks [Beck1996b].</b> 1961 BDI(-I) question topics from [Beck1988]. 1978 BDI-IA question topics from [Beck1996b]. 1996 BDI-II question topics from [Steer1999], [Gary2018]. </ul> </div> {DATA_COLLECTION_ONLY_DIV} """ # noqa
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: scale_lookup = SnomedLookup.BDI_SCALE if self.bdi_scale in [SCALE_BDI_I, SCALE_BDI_IA]: score_lookup = SnomedLookup.BDI_SCORE proc_lookup = SnomedLookup.BDI_PROCEDURE_ASSESSMENT elif self.bdi_scale == SCALE_BDI_II: score_lookup = SnomedLookup.BDI_II_SCORE proc_lookup = SnomedLookup.BDI_II_PROCEDURE_ASSESSMENT else: return [] codes = [SnomedExpression(req.snomed(proc_lookup))] if self.is_complete(): codes.append(SnomedExpression( req.snomed(scale_lookup), { req.snomed(score_lookup): self.total_score(), } )) return codes