#!/usr/bin/env python
"""
camcops_server/tasks/phq9.py
===============================================================================
Copyright (C) 2012, University of Cambridge, Department of Psychiatry.
Created by Rudolf Cardinal (rnc1001@cam.ac.uk).
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 <https://www.gnu.org/licenses/>.
===============================================================================
"""
import logging
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_fhir import (
FHIRAnsweredQuestion,
FHIRAnswerType,
FHIRQuestionType,
)
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,
)
log = logging.getLogger(__name__)
# =============================================================================
# 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 "
f"{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, <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
)
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
)
screen_positive = req.snomed(
SnomedLookup.PHQ9_FINDING_POSITIVE_SCREENING_FOR_DEPRESSION
)
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
[docs] def get_fhir_questionnaire(
self, req: "CamcopsRequest"
) -> List[FHIRAnsweredQuestion]:
items = [] # type: List[FHIRAnsweredQuestion]
main_options = {} # type: Dict[int, str]
for index in range(4):
main_options[index] = self.wxstring(req, f"a{index}")
for q_field in self.MAIN_QUESTIONS:
items.append(
FHIRAnsweredQuestion(
qname=q_field,
qtext=self.xstring(req, q_field),
qtype=FHIRQuestionType.CHOICE,
answer_type=FHIRAnswerType.INTEGER,
answer=getattr(self, q_field),
answer_options=main_options,
)
)
q10_options = {}
for index in range(4):
q10_options[index] = self.wxstring(req, f"fa{index}")
items.append(
FHIRAnsweredQuestion(
qname="q10",
qtext="10. " + self.xstring(req, "finalq"),
qtype=FHIRQuestionType.CHOICE,
answer_type=FHIRAnswerType.INTEGER,
answer=self.q10,
answer_options=q10_options,
)
)
return items