Source code for camcops_server.tasks.asdas

#!/usr/bin/env python

"""
camcops_server/tasks/asdas.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/>.

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

**Ankylosing Spondylitis Disease Activity Score (ASDAS) task.**

"""

import math
from typing import Any, Dict, List, Optional, Type, Tuple

from camcops_server.cc_modules.cc_constants import CssClass
from camcops_server.cc_modules.cc_db import add_multiple_columns
from camcops_server.cc_modules.cc_html import tr_qa, tr, answer
from camcops_server.cc_modules.cc_request import CamcopsRequest
from camcops_server.cc_modules.cc_sqla_coltypes import (
    SummaryCategoryColType,
)
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import TaskHasPatientMixin, Task
from camcops_server.cc_modules.cc_trackerhelpers import (
    TrackerAxisTick,
    TrackerInfo,
    TrackerLabel,
)

import cardinal_pythonlib.rnc_web as ws
from cardinal_pythonlib.stringfunc import strseq
from sqlalchemy import Column, Float
from sqlalchemy.ext.declarative import DeclarativeMeta


class AsdasMetaclass(DeclarativeMeta):
    # noinspection PyInitNewSignature
    def __init__(cls: Type['Asdas'],
                 name: str,
                 bases: Tuple[Type, ...],
                 classdict: Dict[str, Any]) -> None:

        add_multiple_columns(
            cls, "q", 1, cls.N_SCALE_QUESTIONS,
            minimum=0, maximum=10,
            comment_fmt="Q{n} - {s}",
            comment_strings=[
                "back pain 0-10 (None - very severe)",
                "morning stiffness 0-10 (None - 2+ hours)",
                "patient global 0-10 (Not active - very active)",
                "peripheral pain 0-10 (None - very severe)",
            ]
        )

        setattr(
            cls, cls.CRP_FIELD_NAME,
            Column(cls.CRP_FIELD_NAME, Float, comment="CRP (mg/L)")
        )

        setattr(
            cls, cls.ESR_FIELD_NAME,
            Column(cls.ESR_FIELD_NAME, Float, comment="ESR (mm/h)")
        )

        super().__init__(name, bases, classdict)


[docs]class Asdas(TaskHasPatientMixin, Task, metaclass=AsdasMetaclass): __tablename__ = "asdas" shortname = "ASDAS" provides_trackers = True N_SCALE_QUESTIONS = 4 MAX_SCORE_SCALE = 10 N_QUESTIONS = 6 SCALE_FIELD_NAMES = strseq("q", 1, N_SCALE_QUESTIONS) CRP_FIELD_NAME = "q5" ESR_FIELD_NAME = "q6" INACTIVE_MODERATE_CUTOFF = 1.3 MODERATE_HIGH_CUTOFF = 2.1 HIGH_VERY_HIGH_CUTOFF = 3.5
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Ankylosing Spondylitis Disease Activity Score")
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="asdas_crp", coltype=Float(), value=self.asdas_crp(), comment=f"ASDAS-CRP"), SummaryElement( name="activity_state_crp", coltype=SummaryCategoryColType, value=self.activity_state(req, self.asdas_crp()), comment=f"Activity state (CRP)"), SummaryElement( name="asdas_esr", coltype=Float(), value=self.asdas_esr(), comment=f"ASDAS-ESR"), SummaryElement( name="activity_state_esr", coltype=SummaryCategoryColType, value=self.activity_state(req, self.asdas_esr()), comment=f"Activity state (ESR)"), ]
[docs] def is_complete(self) -> bool: if self.any_fields_none(self.SCALE_FIELD_NAMES): return False crp = getattr(self, self.CRP_FIELD_NAME) esr = getattr(self, self.ESR_FIELD_NAME) if crp is None and esr is None: return False if not self.field_contents_valid(): return False return True
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: axis_min = -0.5 axis_max = 7.5 axis_ticks = [TrackerAxisTick(n, str(n)) for n in range(0, int(axis_max) + 1)] horizontal_lines = [ self.HIGH_VERY_HIGH_CUTOFF, self.MODERATE_HIGH_CUTOFF, self.INACTIVE_MODERATE_CUTOFF, 0, ] horizontal_labels = [ TrackerLabel(5.25, self.wxstring(req, "very_high")), TrackerLabel(2.8, self.wxstring(req, "high")), TrackerLabel(1.7, self.wxstring(req, "moderate")), TrackerLabel(0.65, self.wxstring(req, "inactive")), ] return [ TrackerInfo( value=self.asdas_crp(), plot_label="ASDAS-CRP", axis_label="ASDAS-CRP", axis_min=axis_min, axis_max=axis_max, axis_ticks=axis_ticks, horizontal_lines=horizontal_lines, horizontal_labels=horizontal_labels, ), TrackerInfo( value=self.asdas_esr(), plot_label="ASDAS-ESR", axis_label="ASDAS-ESR", axis_min=axis_min, axis_max=axis_max, axis_ticks=axis_ticks, horizontal_lines=horizontal_lines, horizontal_labels=horizontal_labels, ), ]
def back_pain(self) -> float: return getattr(self, "q1") def morning_stiffness(self) -> float: return getattr(self, "q2") def patient_global(self) -> float: return getattr(self, "q3") def peripheral_pain(self) -> float: return getattr(self, "q4") def asdas_crp(self) -> Optional[float]: crp = getattr(self, self.CRP_FIELD_NAME) if crp is None: return None crp = max(crp, 2.0) return ( 0.12 * self.back_pain() + 0.06 * self.morning_stiffness() + 0.11 * self.patient_global() + 0.07 * self.peripheral_pain() + 0.58 * math.log(crp + 1) ) def asdas_esr(self) -> Optional[float]: esr = getattr(self, self.ESR_FIELD_NAME) if esr is None: return None return ( 0.08 * self.back_pain() + 0.07 * self.morning_stiffness() + 0.11 * self.patient_global() + 0.09 * self.peripheral_pain() + 0.29 * math.sqrt(esr) ) def activity_state(self, req: CamcopsRequest, measurement: Any) -> str: if measurement is None: return self.wxstring(req, "n_a") if measurement < self.INACTIVE_MODERATE_CUTOFF: return self.wxstring(req, "inactive") if measurement < self.MODERATE_HIGH_CUTOFF: return self.wxstring(req, "moderate") if measurement > self.HIGH_VERY_HIGH_CUTOFF: return self.wxstring(req, "very_high") return self.wxstring(req, "high")
[docs] def get_task_html(self, req: CamcopsRequest) -> str: rows = "" for q_num in range(1, self.N_QUESTIONS + 1): q_field = "q" + str(q_num) qtext = self.wxstring(req, q_field) if q_num <= 4: # not for ESR, CRP min_text = self.wxstring(req, q_field + "_min") max_text = self.wxstring(req, q_field + "_max") qtext += f" <i>(0 = {min_text}, 10 = {max_text})</i>" question_cell = f"{q_num}. {qtext}" score = getattr(self, q_field) rows += tr_qa(question_cell, score) asdas_crp = ws.number_to_dp(self.asdas_crp(), 2, default="?") asdas_esr = ws.number_to_dp(self.asdas_esr(), 2, default="?") html = """ <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {tr_is_complete} {asdas_crp} {asdas_esr} </table> </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="60%">Question</th> <th width="40%">Answer</th> </tr> {rows} </table> <div class="{CssClass.FOOTNOTES}"> [1] &lt;1.3 Inactive disease, &lt;2.1 Moderate disease activity, 2.1-3.5 High disease activity, &gt;3.5 Very high disease activity.<br> [2] 0.12 × back pain + 0.06 × duration of morning stiffness + 0.11 × patient global + 0.07 × peripheral pain + 0.58 × ln(CRP + 1). CRP units: mg/L. When CRP&lt;2mg/L, use 2mg/L to calculate ASDAS-CRP.<br> [3] 0.08 x back pain + 0.07 x duration of morning stiffness + 0.11 x patient global + 0.09 x peripheral pain + 0.29 x √(ESR). ESR units: mm/h. </div> """.format( CssClass=CssClass, tr_is_complete=self.get_is_complete_tr(req), asdas_crp=tr( self.wxstring(req, "asdas_crp") + " <sup>[1][2]</sup>", "{} ({})".format( answer(asdas_crp), self.activity_state(req, self.asdas_crp()) ) ), asdas_esr=tr( self.wxstring(req, "asdas_esr") + " <sup>[1][3]</sup>", "{} ({})".format( answer(asdas_esr), self.activity_state(req, self.asdas_esr()) ) ), rows=rows, ) return html