Source code for camcops_server.tasks.basdai

#!/usr/bin/env python

"""
camcops_server/tasks/basdai.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/>.

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

**Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) task.**

"""

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

import cardinal_pythonlib.rnc_web as ws
from cardinal_pythonlib.stringfunc import strseq
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.sqltypes import Float

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_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_task import TaskHasPatientMixin, Task
from camcops_server.cc_modules.cc_trackerhelpers import (
    TrackerAxisTick,
    TrackerInfo,
    TrackerLabel,
)


# =============================================================================
# BASDAI
# =============================================================================


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

        add_multiple_columns(
            cls,
            "q",
            1,
            cls.N_QUESTIONS,
            coltype=Float,
            minimum=0,
            maximum=10,
            comment_fmt="Q{n} - {s}",
            comment_strings=[
                "fatigue/tiredness 0-10 (none - very severe)",
                "AS neck, back, hip pain 0-10 (none - very severe)",
                "other joint pain/swelling 0-10 (none - very severe)",
                "discomfort from tender areas 0-10 (none - very severe)",
                "morning stiffness level 0-10 (none - very severe)",
                "morning stiffness duration 0-10 (none - 2 or more hours)",
            ],
        )

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


[docs]class Basdai(TaskHasPatientMixin, Task, metaclass=BasdaiMetaclass): __tablename__ = "basdai" shortname = "BASDAI" provides_trackers = True N_QUESTIONS = 6 FIELD_NAMES = strseq("q", 1, N_QUESTIONS) MINIMUM = 0.0 ACTIVE_CUTOFF = 4.0 MAXIMUM = 10.0
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("Bath Ankylosing Spondylitis Disease Activity Index")
[docs] def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: return self.standard_task_summary_fields() + [ SummaryElement( name="basdai", coltype=Float(), value=self.basdai(), comment="BASDAI", ) ]
[docs] def is_complete(self) -> bool: if self.any_fields_none(self.FIELD_NAMES): return False if not self.field_contents_valid(): return False return True
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: axis_min = self.MINIMUM - 0.5 axis_max = self.MAXIMUM + 0.5 axis_ticks = [ TrackerAxisTick(n, str(n)) for n in range(0, int(axis_max) + 1) ] horizontal_lines = [self.MAXIMUM, self.ACTIVE_CUTOFF, self.MINIMUM] horizontal_labels = [ TrackerLabel( self.ACTIVE_CUTOFF + 0.5, self.wxstring(req, "active") ), TrackerLabel( self.ACTIVE_CUTOFF - 0.5, self.wxstring(req, "inactive") ), ] return [ TrackerInfo( value=self.basdai(), plot_label="BASDAI", axis_label="BASDAI", axis_min=axis_min, axis_max=axis_max, axis_ticks=axis_ticks, horizontal_lines=horizontal_lines, horizontal_labels=horizontal_labels, ) ]
[docs] def basdai(self) -> Optional[float]: """ Calculating the BASDAI A. Add scores for questions 1 – 4 B. Calculate the mean for questions 5 and 6 C. Add A and B and divide by 5 The higher the BASDAI score, the more severe the patient’s disability due to their AS. """ if not self.is_complete(): return None score_a_field_names = strseq("q", 1, 4) score_b_field_names = strseq("q", 5, 6) a = sum([getattr(self, q) for q in score_a_field_names]) b = statistics.mean([getattr(self, q) for q in score_b_field_names]) return (a + b) / 5
def activity_state(self, req: CamcopsRequest) -> str: basdai = self.basdai() if basdai is None: return "?" if basdai < self.ACTIVE_CUTOFF: return self.wxstring(req, "inactive") return self.wxstring(req, "active")
[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.xstring(req, q_field) # includes HTML 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) basdai = ws.number_to_dp(self.basdai(), 1, default="?") html = """ <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {tr_is_complete} {basdai} </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] (A) Add scores for questions 1–4. (B) Calculate the mean for questions 5 and 6. (C) Add A and B and divide by 5, giving a total in the range 0–10. &lt;4.0 suggests inactive disease, &ge;4.0 suggests active disease. </div> """.format( CssClass=CssClass, tr_is_complete=self.get_is_complete_tr(req), basdai=tr( self.wxstring(req, "basdai") + " <sup>[1]</sup>", "{} ({})".format(answer(basdai), self.activity_state(req)), ), rows=rows, ) return html