Source code for camcops_server.tasks.audit

#!/usr/bin/env python

"""
camcops_server/tasks/audit.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
from sqlalchemy.ext.declarative import DeclarativeMeta
from sqlalchemy.sql.sqltypes import Integer

from camcops_server.cc_modules.cc_constants import CssClass
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,
    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_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 TrackerInfo


# =============================================================================
# AUDIT
# =============================================================================

class AuditMetaclass(DeclarativeMeta):
    # noinspection PyInitNewSignature
    def __init__(cls: Type['Audit'],
                 name: str,
                 bases: Tuple[Type, ...],
                 classdict: Dict[str, Any]) -> None:
        add_multiple_columns(
            cls, "q", 1, cls.NQUESTIONS,
            minimum=0, maximum=4,
            comment_fmt="Q{n}, {s} (0-4, higher worse)",
            comment_strings=[
                "how often drink", "drinks per day", "how often six drinks",
                "unable to stop", "unable to do what was expected",
                "eye opener", "guilt", "unable to remember", "injuries",
                "others concerned"]
        )
        super().__init__(name, bases, classdict)


[docs]class Audit(TaskHasPatientMixin, Task, metaclass=AuditMetaclass): """ Server implementation of the AUDIT task. """ __tablename__ = "audit" shortname = "AUDIT" provides_trackers = True NQUESTIONS = 10 TASK_FIELDS = strseq("q", 1, NQUESTIONS)
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("WHO Alcohol Use Disorders Identification Test")
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="AUDIT total score", axis_label="Total score (out of 40)", axis_min=-0.5, axis_max=40.5, horizontal_lines=[7.5] )]
[docs] def get_clinical_text(self, req: CamcopsRequest) -> List[CtvInfo]: if not self.is_complete(): return CTV_INCOMPLETE return [CtvInfo( content=f"AUDIT total score {self.total_score()}/40" )]
[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="Total score (/40)"), ]
# noinspection PyUnresolvedReferences
[docs] def is_complete(self) -> bool: if not self.field_contents_valid(): return False if self.q1 is None or self.q9 is None or self.q10 is None: return False if self.q1 == 0: # Special limited-information completeness return True if self.q2 is not None \ and self.q3 is not None \ and (self.q2 + self.q3 == 0): # Special limited-information completeness return True # Otherwise, any null values cause problems return self.all_fields_not_none(self.TASK_FIELDS)
def total_score(self) -> int: return self.sum_fields(self.TASK_FIELDS) # noinspection PyUnresolvedReferences
[docs] def get_task_html(self, req: CamcopsRequest) -> str: score = self.total_score() exceeds_cutoff = score >= 8 q1_dict = {None: None} q2_dict = {None: None} q3_to_8_dict = {None: None} q9_to_10_dict = {None: None} for option in range(0, 5): q1_dict[option] = str(option) + " – " + \ self.wxstring(req, "q1_option" + str(option)) q2_dict[option] = str(option) + " – " + \ self.wxstring(req, "q2_option" + str(option)) q3_to_8_dict[option] = str(option) + " – " + \ self.wxstring(req, "q3to8_option" + str(option)) if option != 1 and option != 3: q9_to_10_dict[option] = str(option) + " – " + \ self.wxstring(req, "q9to10_option" + str(option)) q_a = tr_qa(self.wxstring(req, "q1_s"), get_from_dict(q1_dict, self.q1)) q_a += tr_qa(self.wxstring(req, "q2_s"), get_from_dict(q2_dict, self.q2)) for q in range(3, 8 + 1): q_a += tr_qa( self.wxstring(req, "q" + str(q) + "_s"), get_from_dict(q3_to_8_dict, getattr(self, "q" + str(q))) ) q_a += tr_qa(self.wxstring(req, "q9_s"), get_from_dict(q9_to_10_dict, self.q9)) q_a += tr_qa(self.wxstring(req, "q10_s"), get_from_dict(q9_to_10_dict, self.q10)) return f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} {tr(req.wsstring(SS.TOTAL_SCORE), answer(score) + " / 40")} {tr_qa(self.wxstring(req, "exceeds_standard_cutoff"), get_yes_no(req, exceeds_cutoff))} </table> </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="50%">Question</th> <th width="50%">Answer</th> </tr> {q_a} </table> <div class="{CssClass.COPYRIGHT}"> AUDIT: Copyright © World Health Organization. Reproduced here under the permissions granted for NON-COMMERCIAL use only. You must obtain permission from the copyright holder for any other use. </div> """
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: codes = [SnomedExpression(req.snomed(SnomedLookup.AUDIT_PROCEDURE_ASSESSMENT))] # noqa if self.is_complete(): codes.append(SnomedExpression( req.snomed(SnomedLookup.AUDIT_SCALE), { req.snomed(SnomedLookup.AUDIT_SCORE): self.total_score(), } )) return codes
# ============================================================================= # AUDIT-C # ============================================================================= class AuditCMetaclass(DeclarativeMeta): # noinspection PyInitNewSignature def __init__(cls: Type['AuditC'], name: str, bases: Tuple[Type, ...], classdict: Dict[str, Any]) -> None: add_multiple_columns( cls, "q", 1, cls.NQUESTIONS, minimum=0, maximum=4, comment_fmt="Q{n}, {s} (0-4, higher worse)", comment_strings=[ "how often drink", "drinks per day", "how often six drinks" ] ) super().__init__(name, bases, classdict)
[docs]class AuditC(TaskHasPatientMixin, Task, metaclass=AuditMetaclass): __tablename__ = "audit_c" shortname = "AUDIT-C" extrastring_taskname = "audit" # shares strings with AUDIT NQUESTIONS = 3 TASK_FIELDS = strseq("q", 1, NQUESTIONS)
[docs] @staticmethod def longname(req: "CamcopsRequest") -> str: _ = req.gettext return _("AUDIT Alcohol Consumption Questions")
[docs] def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: return [TrackerInfo( value=self.total_score(), plot_label="AUDIT-C total score", axis_label="Total score (out of 12)", axis_min=-0.5, axis_max=12.5, )]
[docs] def get_clinical_text(self, req: CamcopsRequest) -> List[CtvInfo]: if not self.is_complete(): return CTV_INCOMPLETE return [CtvInfo( content=f"AUDIT-C total score {self.total_score()}/12" )]
[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="Total score (/12)"), ]
[docs] def is_complete(self) -> bool: return self.all_fields_not_none(self.TASK_FIELDS)
def total_score(self) -> int: return self.sum_fields(self.TASK_FIELDS)
[docs] def get_task_html(self, req: CamcopsRequest) -> str: score = self.total_score() q1_dict = {None: None} q2_dict = {None: None} q3_dict = {None: None} for option in range(0, 5): q1_dict[option] = str(option) + " – " + \ self.wxstring(req, "q1_option" + str(option)) if option == 0: # special! q2_dict[option] = str(option) + " – " + \ self.wxstring(req, "c_q2_option0") else: q2_dict[option] = str(option) + " – " + \ self.wxstring(req, "q2_option" + str(option)) q3_dict[option] = str(option) + " – " + \ self.wxstring(req, "q3to8_option" + str(option)) # noinspection PyUnresolvedReferences return f""" <div class="{CssClass.SUMMARY}"> <table class="{CssClass.SUMMARY}"> {self.get_is_complete_tr(req)} {tr(req.sstring(SS.TOTAL_SCORE), answer(score) + " / 12")} </table> </div> <table class="{CssClass.TASKDETAIL}"> <tr> <th width="50%">Question</th> <th width="50%">Answer</th> </tr> {tr_qa(self.wxstring(req, "c_q1_question"), get_from_dict(q1_dict, self.q1))} {tr_qa(self.wxstring(req, "c_q2_question"), get_from_dict(q2_dict, self.q2))} {tr_qa(self.wxstring(req, "c_q3_question"), get_from_dict(q3_dict, self.q3))} </table> <div class="{CssClass.COPYRIGHT}"> AUDIT: Copyright © World Health Organization. Reproduced here under the permissions granted for NON-COMMERCIAL use only. You must obtain permission from the copyright holder for any other use. AUDIT-C: presumed to have the same restrictions. </div> """
[docs] def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]: codes = [SnomedExpression(req.snomed(SnomedLookup.AUDITC_PROCEDURE_ASSESSMENT))] # noqa if self.is_complete(): codes.append(SnomedExpression( req.snomed(SnomedLookup.AUDITC_SCALE), { req.snomed(SnomedLookup.AUDITC_SCORE): self.total_score(), } )) return codes