#!/usr/bin/env python
"""
camcops_server/tasks/lynall_iam_medical.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/>.
===============================================================================
"""
from typing import Any, Dict, List, Optional, Union
from sqlalchemy.sql.schema import Column
from sqlalchemy.sql.sqltypes import Integer, UnicodeText
from camcops_server.cc_modules.cc_constants import CssClass
from camcops_server.cc_modules.cc_html import (
get_yes_no,
get_yes_no_none,
tr_qa,
)
from camcops_server.cc_modules.cc_request import CamcopsRequest
from camcops_server.cc_modules.cc_sqla_coltypes import (
BoolColumn,
CamcopsColumn,
PermittedValueChecker,
)
from camcops_server.cc_modules.cc_task import Task, TaskHasPatientMixin
from camcops_server.cc_modules.cc_text import SS
# =============================================================================
# Lynall1MedicalHistory
# =============================================================================
[docs]class LynallIamMedicalHistory(TaskHasPatientMixin, Task):
"""
Server implementation of the Lynall1IamMedicalHistory task.
"""
__tablename__ = "lynall_1_iam_medical" # historically fixed
shortname = "Lynall_IAM_Medical"
extrastring_taskname = "lynall_iam_medical"
info_filename_stem = extrastring_taskname
Q2_N_OPTIONS = 6
Q3_N_OPTIONS = 11
Q4_N_OPTIONS = 5
Q4_OPTION_PSYCH_BEFORE_PHYSICAL = 1
Q4_OPTION_PSYCH_AFTER_PHYSICAL = 2
Q8_N_OPTIONS = 2
Q7B_MIN = 1
Q7B_MAX = 10
q1_age_first_inflammatory_sx = Column(
"q1_age_first_inflammatory_sx",
Integer,
comment="Age (y) at onset of first symptoms of inflammatory disease",
)
q2_when_psych_sx_started = CamcopsColumn(
"q2_when_psych_sx_started",
Integer,
permitted_value_checker=PermittedValueChecker(
minimum=1, maximum=Q2_N_OPTIONS
),
comment="Timing of onset of psych symptoms (1 = NA, 2 = before "
"physical symptoms [Sx], 3 = same time as physical Sx but "
"before diagnosis [Dx], 4 = around time of Dx, 5 = weeks or "
"months after Dx, 6 = years after Dx)",
)
q3_worst_symptom_last_month = CamcopsColumn(
"q3_worst_symptom_last_month",
Integer,
permitted_value_checker=PermittedValueChecker(
minimum=1, maximum=Q3_N_OPTIONS
),
comment="Worst symptom in last month (1 = fatigue, 2 = low mood, 3 = "
"irritable, 4 = anxiety, 5 = brain fog/confused, 6 = pain, "
"7 = bowel Sx, 8 = mobility, 9 = skin, 10 = other, 11 = no Sx "
"in past month)",
)
q4a_symptom_timing = CamcopsColumn(
"q4a_symptom_timing",
Integer,
permitted_value_checker=PermittedValueChecker(
minimum=1, maximum=Q4_N_OPTIONS
),
comment="Timing of brain/psych Sx relative to physical Sx (1 = brain "
"before physical, 2 = brain after physical, 3 = same time, "
"4 = no relationship, 5 = none of the above)",
)
q4b_days_psych_before_phys = Column(
"q4b_days_psych_before_phys",
Integer,
comment="If Q4a == 1, number of days that brain Sx typically begin "
"before physical Sx",
)
q4c_days_psych_after_phys = Column(
"q4c_days_psych_after_phys",
Integer,
comment="If Q4a == 2, number of days that brain Sx typically begin "
"after physical Sx",
)
q5_antibiotics = BoolColumn(
"q5_antibiotics",
comment="Medication for infection (e.g. antibiotics) in past 3 months?"
" (0 = no, 1 = yes)",
)
q6a_inpatient_last_y = BoolColumn(
"q6a_inpatient_last_y",
comment="Inpatient in the last year? (0 = no, 1 = yes)",
)
q6b_inpatient_weeks = Column(
"q6b_inpatient_weeks",
Integer,
comment="If Q6a is true, approximate number of weeks spent as an "
"inpatient in the past year",
)
q7a_sx_last_2y = BoolColumn(
"q7a_sx_last_2y",
comment="Symptoms within the last 2 years? (0 = no, 1 = yes)",
)
q7b_variability = Column(
"q7b_variability",
Integer,
comment="If Q7a is true, degree of variability of symptoms (1-10 "
"where 1 = highly variable [from none to severe], 10 = "
"there all the time)",
)
q8_smoking = Column(
"q8_smoking",
Integer,
comment="Current smoking status (0 = no, 1 = yes but not every day, "
"2 = every day)",
)
q9_pregnant = BoolColumn(
"q9_pregnant", comment="Currently pregnant (0 = no or N/A, 1 = yes)"
)
q10a_effective_rx_physical = Column(
"q10a_effective_rx_physical",
UnicodeText,
comment="Most effective treatments for physical Sx",
)
q10b_effective_rx_psych = Column(
"q10b_effective_rx_psych",
UnicodeText,
comment="Most effective treatments for brain/psychiatric Sx",
)
q11a_ph_depression = BoolColumn(
"q11a_ph_depression", comment="Personal history of depression?"
)
q11b_ph_bipolar = BoolColumn(
"q11b_ph_bipolar", comment="Personal history of bipolar disorder?"
)
q11c_ph_schizophrenia = BoolColumn(
"q11c_ph_schizophrenia", comment="Personal history of schizophrenia?"
)
q11d_ph_autistic_spectrum = BoolColumn(
"q11d_ph_autistic_spectrum",
comment="Personal history of autism/Asperger's?",
)
q11e_ph_ptsd = BoolColumn(
"q11e_ph_ptsd", comment="Personal history of PTSD?"
)
q11f_ph_other_anxiety = BoolColumn(
"q11f_ph_other_anxiety",
comment="Personal history of other anxiety disorders?",
)
q11g_ph_personality_disorder = BoolColumn(
"q11g_ph_personality_disorder",
comment="Personal history of personality disorder?",
)
q11h_ph_other_psych = BoolColumn(
"q11h_ph_other_psych",
comment="Personal history of other psychiatric disorder(s)?",
)
q11h_ph_other_detail = Column(
"q11h_ph_other_detail",
UnicodeText,
comment="If q11h_ph_other_psych is true, this is the free-text "
"details field",
)
q12a_fh_depression = BoolColumn(
"q12a_fh_depression", comment="Family history of depression?"
)
q12b_fh_bipolar = BoolColumn(
"q12b_fh_bipolar", comment="Family history of bipolar disorder?"
)
q12c_fh_schizophrenia = BoolColumn(
"q12c_fh_schizophrenia", comment="Family history of schizophrenia?"
)
q12d_fh_autistic_spectrum = BoolColumn(
"q12d_fh_autistic_spectrum",
comment="Family history of autism/Asperger's?",
)
q12e_fh_ptsd = BoolColumn(
"q12e_fh_ptsd", comment="Family history of PTSD?"
)
q12f_fh_other_anxiety = BoolColumn(
"q12f_fh_other_anxiety",
comment="Family history of other anxiety disorders?",
)
q12g_fh_personality_disorder = BoolColumn(
"q12g_fh_personality_disorder",
comment="Family history of personality disorder?",
)
q12h_fh_other_psych = BoolColumn(
"q12h_fh_other_psych",
comment="Family history of other psychiatric disorder(s)?",
)
q12h_fh_other_detail = Column(
"q12h_fh_other_detail",
UnicodeText,
comment="If q12h_fh_other_psych is true, this is the free-text "
"details field",
)
q13a_behcet = BoolColumn(
"q13a_behcet", comment="Behçet’s syndrome? (0 = no, 1 = yes)"
)
q13b_oral_ulcers = BoolColumn(
"q13b_oral_ulcers",
comment="(If Behçet’s) Oral ulcers? (0 = no, 1 = yes)",
)
q13c_oral_age_first = Column(
"q13c_oral_age_first",
Integer,
comment="(If Behçet’s + oral) Age (y) at first oral ulcers",
)
q13d_oral_scarring = BoolColumn(
"q13d_oral_scarring",
comment="(If Behçet’s + oral) Oral scarring? (0 = no, 1 = yes)",
)
q13e_genital_ulcers = BoolColumn(
"q13e_genital_ulcers",
comment="(If Behçet’s) Genital ulcers? (0 = no, 1 = yes)",
)
q13f_genital_age_first = Column(
"q13f_genital_age_first",
Integer,
comment="(If Behçet’s + genital) Age (y) at first genital ulcers",
)
q13g_genital_scarring = BoolColumn(
"q13g_genital_scarring",
comment="(If Behçet’s + genital) Genital scarring? (0 = no, 1 = yes)",
)
[docs] @staticmethod
def longname(req: "CamcopsRequest") -> str:
_ = req.gettext
return _("Lynall M-E — 1 — IAM — Medical history")
[docs] def is_complete(self) -> bool:
if self.any_fields_none(
[
"q1_age_first_inflammatory_sx",
"q2_when_psych_sx_started",
"q3_worst_symptom_last_month",
"q4a_symptom_timing",
"q5_antibiotics",
"q6a_inpatient_last_y",
"q7a_sx_last_2y",
"q8_smoking",
"q9_pregnant",
"q10a_effective_rx_physical",
"q10b_effective_rx_psych",
"q13a_behcet",
]
):
return False
if self.any_fields_null_or_empty_str(
["q10a_effective_rx_physical", "q10b_effective_rx_psych"]
):
return False
q4a = self.q4a_symptom_timing
if (
q4a == self.Q4_OPTION_PSYCH_BEFORE_PHYSICAL
and self.q4b_days_psych_before_phys is None
):
return False
if (
q4a == self.Q4_OPTION_PSYCH_AFTER_PHYSICAL
and self.q4c_days_psych_after_phys is None
):
return False
if self.q6a_inpatient_last_y and self.q6b_inpatient_weeks is None:
return False
if self.q7a_sx_last_2y and self.q7b_variability is None:
return False
if self.q11h_ph_other_psych and not self.q11h_ph_other_detail:
return False
if self.q12h_fh_other_psych and not self.q12h_fh_other_detail:
return False
if self.q13a_behcet:
if self.any_fields_none(
["q13b_oral_ulcers", "q13e_genital_ulcers"]
):
return False
if self.q13b_oral_ulcers:
if self.any_fields_none(
["q13c_oral_age_first", "q13d_oral_scarring"]
):
return False
if self.q13e_genital_ulcers:
if self.any_fields_none(
["q13f_genital_age_first", "q13g_genital_scarring"]
):
return False
return True
[docs] def get_task_html(self, req: CamcopsRequest) -> str:
def plainrow(
qname: str,
xstring_name: str,
value: Any,
if_applicable: bool = False,
qsuffix: str = "",
) -> str:
ia_str = (
f"<i>[{req.wsstring(SS.IF_APPLICABLE)}]</i> "
if if_applicable
else ""
)
q = f"{ia_str}{qname}. {self.wxstring(req, xstring_name)}{qsuffix}"
return tr_qa(q, value)
def lookuprow(
qname: str,
xstring_name: str,
key: Optional[int],
lookup: Dict[int, str],
if_applicable: bool = False,
qsuffix: str = "",
) -> str:
description = lookup.get(key, None)
value = None if description is None else f"{key}: {description}"
return plainrow(
qname,
xstring_name,
value,
if_applicable=if_applicable,
qsuffix=qsuffix,
)
def boolrow(
qname: str,
xstring_name: str,
value: Optional[bool],
lookup: Dict[int, str],
if_applicable: bool = False,
qsuffix: str = "",
) -> str:
v = int(value) if value is not None else None
return lookuprow(
qname,
xstring_name,
v,
lookup,
if_applicable=if_applicable,
qsuffix=qsuffix,
)
def ynrow(
qname: str, xstring_name: str, value: Optional[Union[int, bool]]
) -> str:
return plainrow(qname, xstring_name, get_yes_no(req, value))
def ynnrow(
qname: str,
xstring_name: str,
value: Optional[Union[int, bool]],
if_applicable: bool = False,
) -> str:
return plainrow(
qname,
xstring_name,
get_yes_no_none(req, value),
if_applicable=if_applicable,
)
q2_options = self.make_options_from_xstrings(
req, "q2_option", 1, self.Q2_N_OPTIONS
)
q3_options = self.make_options_from_xstrings(
req, "q3_option", 1, self.Q3_N_OPTIONS
)
q4a_options = self.make_options_from_xstrings(
req, "q4a_option", 1, self.Q4_N_OPTIONS
)
q7a_options = self.make_options_from_xstrings(req, "q7a_option", 0, 1)
_q7b_anchors = [] # type: List[str]
for _o in (1, 10):
_wxstring = self.wxstring(req, f"q7b_anchor_{_o}")
_q7b_anchors.append(f"{_o}: {_wxstring}")
q7b_explanation = f" <i>(Anchors: {' // '.join(_q7b_anchors)})</i>"
q8_options = self.make_options_from_xstrings(
req, "q8_option", 1, self.Q8_N_OPTIONS
)
q9_options = self.make_options_from_xstrings(req, "q9_option", 0, 1)
return f"""
<div class="{CssClass.SUMMARY}">
<table class="{CssClass.SUMMARY}">
{self.get_is_complete_tr(req)}
</table>
</div>
<table class="{CssClass.TASKDETAIL}">
<tr>
<th width="60%">{req.sstring(SS.QUESTION)}</th>
<th width="40%">{req.sstring(SS.ANSWER)}</th>
</tr>
{plainrow("1", "q1_question", self.q1_age_first_inflammatory_sx)}
{lookuprow("2", "q2_question", self.q2_when_psych_sx_started, q2_options)}
{lookuprow("3", "q3_question", self.q3_worst_symptom_last_month, q3_options)}
{lookuprow("4a", "q4a_question", self.q4a_symptom_timing, q4a_options)}
{plainrow("4b", "q4b_question", self.q4b_days_psych_before_phys, True)}
{plainrow("4c", "q4c_question", self.q4c_days_psych_after_phys, True)}
{ynnrow("5", "q5_question", self.q5_antibiotics)}
{ynnrow("6a", "q6a_question", self.q6a_inpatient_last_y)}
{plainrow("6b", "q6b_question", self.q6b_inpatient_weeks, True)}
{boolrow("7a", "q7a_question", self.q7a_sx_last_2y, q7a_options)}
{plainrow("7b", "q7b_question", self.q7b_variability, True,
qsuffix=q7b_explanation)}
{lookuprow("8", "q8_question", self.q8_smoking, q8_options)}
{boolrow("9", "q9_question", self.q9_pregnant, q9_options)}
<tr class="subheading">
<td><i>{self.wxstring(req, "q10_stem")}</i></td>
<td></td>
</tr>
{plainrow("10a", "q10a_question", self.q10a_effective_rx_physical)}
{plainrow("10b", "q10b_question", self.q10b_effective_rx_psych)}
<tr class="subheading">
<td><i>{self.wxstring(req, "q11_title")}</i></td>
<td></td>
</tr>
{ynrow("11a", "depression", self.q11a_ph_depression)}
{ynrow("11b", "bipolar", self.q11b_ph_bipolar)}
{ynrow("11c", "schizophrenia", self.q11c_ph_schizophrenia)}
{ynrow("11d", "autistic_spectrum", self.q11d_ph_autistic_spectrum)}
{ynrow("11e", "ptsd", self.q11e_ph_ptsd)}
{ynrow("11f", "other_anxiety", self.q11f_ph_other_anxiety)}
{ynrow("11g", "personality_disorder", self.q11g_ph_personality_disorder)}
{ynrow("11h", "other_psych", self.q11h_ph_other_psych)}
{plainrow("11h", "other_psych", self.q11h_ph_other_detail, True)}
<tr class="subheading">
<td><i>{self.wxstring(req, "q12_title")}</i></td>
<td></td>
</tr>
{ynrow("12a", "depression", self.q12a_fh_depression)}
{ynrow("12b", "bipolar", self.q12b_fh_bipolar)}
{ynrow("12c", "schizophrenia", self.q12c_fh_schizophrenia)}
{ynrow("12d", "autistic_spectrum", self.q12d_fh_autistic_spectrum)}
{ynrow("12e", "ptsd", self.q12e_fh_ptsd)}
{ynrow("12f", "other_anxiety", self.q12f_fh_other_anxiety)}
{ynrow("12g", "personality_disorder", self.q12g_fh_personality_disorder)}
{ynrow("12h", "other_psych", self.q12h_fh_other_psych)}
{plainrow("12h", "other_psych", self.q12h_fh_other_detail, True)}
<tr class="subheading">
<td><i>{self.wxstring(req, "q13_title")}</i></td>
<td></td>
</tr>
{ynnrow("13a", "q13a_question", self.q13a_behcet)}
{ynnrow("13b", "q13b_question", self.q13b_oral_ulcers, True)}
{plainrow("13c", "q13c_question", self.q13c_oral_age_first, True)}
{ynnrow("13d", "q13d_question", self.q13d_oral_scarring, True)}
{ynnrow("13e", "q13e_question", self.q13e_genital_ulcers, True)}
{plainrow("13f", "q13f_question", self.q13f_genital_age_first, True)}
{ynnrow("13g", "q13g_question", self.q13g_genital_scarring, True)}
</table>
""" # noqa