def export_task(req: "CamcopsRequest", recipient: ExportRecipient,
task: Task) -> None:
"""
Exports a single task, checking that it remains valid to do so.
Args:
req: a :class:`camcops_server.cc_modules.cc_request.CamcopsRequest`
recipient: an :class:`camcops_server.cc_modules.cc_exportmodels.ExportRecipient`
task: a :class:`camcops_server.cc_modules.cc_task.Task`
""" # noqa
# Double-check it's OK! Just in case, for example, an old backend task has
# persisted, or someone's managed to get an iffy back-end request in some
# other way.
if not recipient.is_task_suitable(task):
# Warning will already have been emitted.
return
cfg = req.config
lockfilename = cfg.get_export_lockfilename_task(
recipient_name=recipient.recipient_name,
basetable=task.tablename,
pk=task.get_pk(),
)
dbsession = req.dbsession
try:
with lockfile.FileLock(lockfilename, timeout=0): # doesn't wait
# We recheck the export status once we hold the lock, in case
# multiple jobs are competing to export it.
if ExportedTask.task_already_exported(
dbsession=dbsession,
recipient_name=recipient.recipient_name,
basetable=task.tablename,
task_pk=task.get_pk()):
log.info(
"Task {!r} already exported to recipient {!r}; "
"ignoring", task, recipient)
# Not a warning; it's normal to see these because it allows the
# client API to skip some checks for speed.
return
# OK; safe to export now.
et = ExportedTask(recipient, task)
dbsession.add(et)
et.export(req)
dbsession.commit() # so the ExportedTask is visible to others ASAP
except lockfile.AlreadyLocked:
log.warning(
"Export logfile {!r} already locked by another process; "
"aborting", lockfilename)
def task_classes(self) -> List[Type[Task]]:
"""
Return a list of task classes permitted by the filter.
Uses caching, since the filter will be called repeatedly.
"""
if self._task_classes is None:
self._task_classes = [] # type: List[Type[Task]]
if self.task_types:
starting_classes = task_classes_from_table_names(
self.task_types)
else:
starting_classes = Task.all_subclasses_by_shortname()
skip_anonymous_tasks = self.skip_anonymous_tasks()
for cls in starting_classes:
if (self.tasks_offering_trackers_only
and not cls.provides_trackers):
# Class doesn't provide trackers; skip
continue
if skip_anonymous_tasks and not cls.has_patient:
# Anonymous task; skip
continue
if self.text_contents and not cls.get_text_filter_columns():
# Text filter and task has no text columns; skip
continue
self._task_classes.append(cls)
sort_task_classes_in_place(self._task_classes, self.sort_method)
return self._task_classes
def rebuild_entire_task_index(
cls,
session: SqlASession,
indexed_at_utc: Pendulum,
skip_tasks_with_missing_tables: bool = False,
) -> None:
"""
Rebuilds the entire index.
Args:
session: an SQLAlchemy Session
indexed_at_utc: current time in UTC
skip_tasks_with_missing_tables: should we skip over tasks if their
tables are not in the database? (This is so we can rebuild an
index from a database upgrade, but not crash because newer
tasks haven't had their tables created yet.)
"""
log.info("Rebuilding entire task index")
# noinspection PyUnresolvedReferences
idxtable = cls.__table__ # type: Table
# Delete all entries
with if_sqlserver_disable_constraints_triggers(session, idxtable.name):
session.execute(idxtable.delete())
# Now rebuild:
for taskclass in Task.all_subclasses_by_tablename():
if skip_tasks_with_missing_tables:
basetable = taskclass.tablename
engine = get_engine_from_session(session)
if not table_exists(engine, basetable):
continue
cls.rebuild_index_for_task_type(
session, taskclass, indexed_at_utc, delete_first=False
)
def apply_standard_task_fields(self, task: Task) -> None:
"""
Writes some default values to an SQLAlchemy ORM object representing
a task.
"""
self.apply_standard_db_fields(task)
task.when_created = self.era_time
def all_tracker_task_classes() -> List[Type[Task]]:
"""
Returns a list of all task classes that provide tracker information.
"""
return [
cls for cls in Task.all_subclasses_by_shortname()
if cls.provides_trackers
]
def add_tasks(self, patient_id: int):
for cls in Task.all_subclasses_by_tablename():
task = cls()
task.id = self.next_id(cls.id)
self.apply_standard_task_fields(task)
if task.has_patient:
task.patient_id = patient_id
self.fill_in_task_fields(task)
self.dbsession.add(task)
self.dbsession.commit()
def offers_all_non_anonymous_task_types(self) -> bool:
"""
Does this filter offer every single non-anonymous task class? Used for
efficiency when using indexes.
"""
offered_task_classes = self.task_classes
for taskclass in Task.all_subclasses_by_shortname():
if taskclass.is_anonymous:
continue
if taskclass not in offered_task_classes:
return False
return True
def _task_matches_python_parts_of_filter(self, task: Task) -> bool:
"""
Does the task pass the Python parts of the filter?
Only applicable to the direct (not "via index") route.
"""
assert not self._via_index
# "Is task complete" filter
if self._filter.complete_only:
if not task.is_complete():
return False
return True
def make_from_task(
cls, task: Task, indexed_at_utc: Pendulum
) -> "TaskIndexEntry":
"""
Returns a task index entry for the specified
:class:`camcops_server.cc_modules.cc_task.Task`. The
returned index requires inserting into a database session.
Args:
task:
a :class:`camcops_server.cc_modules.cc_task.Task`
indexed_at_utc:
current time in UTC
"""
assert indexed_at_utc is not None, "Missing indexed_at_utc"
index = cls()
index.indexed_at_utc = indexed_at_utc
index.task_table_name = task.tablename
index.task_pk = task.pk
patient = task.patient
index.patient_pk = patient.pk if patient else None
index.device_id = task.device_id
index.era = task.era
index.when_created_utc = task.get_creation_datetime_utc()
index.when_created_iso = task.when_created
# noinspection PyProtectedMember
index.when_added_batch_utc = task._when_added_batch_utc
index.adding_user_id = task.get_adding_user_id()
index.group_id = task.group_id
index.task_is_complete = task.is_complete()
return index
def rebuild_entire_task_index(cls, session: SqlASession,
indexed_at_utc: Pendulum) -> None:
"""
Rebuilds the entire index.
Args:
session: an SQLAlchemy Session
indexed_at_utc: current time in UTC
"""
log.info("Rebuilding entire task index")
# noinspection PyUnresolvedReferences
idxtable = cls.__table__ # type: Table
# Delete all entries
session.execute(
idxtable.delete()
)
# Now rebuild:
for taskclass in Task.all_subclasses_by_tablename():
cls.rebuild_index_for_task_type(session, taskclass,
indexed_at_utc,
delete_first=False)
def create_tasks(self) -> None:
from camcops_server.cc_modules.cc_blob import Blob
from camcops_server.tasks.photo import Photo
from camcops_server.cc_modules.cc_task import Task
patient_with_two_idnums = self.create_patient_with_two_idnums()
patient_with_one_idnum = self.create_patient_with_one_idnum()
for cls in Task.all_subclasses_by_tablename():
t1 = cls()
t1.id = 1
self.apply_standard_task_fields(t1)
if t1.has_patient:
t1.patient_id = patient_with_two_idnums.id
if isinstance(t1, Photo):
b = Blob()
b.id = 1
self.apply_standard_db_fields(b)
b.tablename = t1.tablename
b.tablepk = t1.id
b.fieldname = "photo_blobid"
b.filename = "some_picture.png"
b.mimetype = MimeType.PNG
b.image_rotation_deg_cw = 0
b.theblob = DEMO_PNG_BYTES
self.dbsession.add(b)
t1.photo_blobid = b.id
self.dbsession.add(t1)
t2 = cls()
t2.id = 2
self.apply_standard_task_fields(t2)
if t2.has_patient:
t2.patient_id = patient_with_one_idnum.id
self.dbsession.add(t2)
self.dbsession.commit()
DemoDatabaseTestCase,
DemoRequestTestCase,
ExtendedTestCase,
) # nopep8
from camcops_server.cc_modules.cc_user import (
SecurityLoginFailure,
set_password_directly,
User,
) # nopep8
from camcops_server.cc_modules.celery import (
CELERY_APP_NAME,
CELERY_SOFT_TIME_LIMIT_SEC,
) # nopep8
log.info("Imports complete")
log.info("Using {} tasks", len(Task.all_subclasses_by_tablename()))
if TYPE_CHECKING:
from pyramid.router import Router # nopep8
# =============================================================================
# Other constants
# =============================================================================
WINDOWS = platform.system() == "Windows"
# =============================================================================
# Helper functions for web server launcher
# =============================================================================
def setUp(self) -> None:
super().setUp()
from cardinal_pythonlib.datetimefunc import (
convert_datetime_to_utc,
format_datetime,
)
from camcops_server.cc_modules.cc_blob import Blob
from camcops_server.cc_modules.cc_constants import DateFormat
from camcops_server.cc_modules.cc_device import Device
from camcops_server.cc_modules.cc_group import Group
from camcops_server.cc_modules.cc_patient import Patient
from camcops_server.cc_modules.cc_patientidnum import PatientIdNum
from camcops_server.cc_modules.cc_task import Task
from camcops_server.cc_modules.cc_user import User
from camcops_server.tasks.photo import Photo
Base.metadata.create_all(self.engine)
self.era_time = pendulum.parse("2010-07-07T13:40+0100")
self.era_time_utc = convert_datetime_to_utc(self.era_time)
self.era = format_datetime(self.era_time, DateFormat.ISO8601)
# Set up groups, users, etc.
# ... ID number definitions
iddef1 = IdNumDefinition(which_idnum=1,
description="NHS number",
short_description="NHS#",
hl7_assigning_authority="NHS",
hl7_id_type="NHSN")
self.dbsession.add(iddef1)
iddef2 = IdNumDefinition(which_idnum=2,
description="RiO number",
short_description="RiO",
hl7_assigning_authority="CPFT",
hl7_id_type="CPFT_RiO")
self.dbsession.add(iddef2)
# ... group
self.group = Group()
self.group.name = "testgroup"
self.group.description = "Test group"
self.group.upload_policy = "sex AND anyidnum"
self.group.finalize_policy = "sex AND idnum1"
self.dbsession.add(self.group)
self.dbsession.flush() # sets PK fields
# ... users
self.user = User.get_system_user(self.dbsession)
self.user.upload_group_id = self.group.id
self.req._debugging_user = self.user # improve our debugging user
# ... devices
self.server_device = Device.get_server_device(self.dbsession)
self.other_device = Device()
self.other_device.name = "other_device"
self.other_device.friendly_name = "Test device that may upload"
self.other_device.registered_by_user = self.user
self.other_device.when_registered_utc = self.era_time_utc
self.other_device.camcops_version = CAMCOPS_SERVER_VERSION
self.dbsession.add(self.other_device)
self.dbsession.flush() # sets PK fields
# Populate database with two of everything
p1 = Patient()
p1.id = 1
self._apply_standard_db_fields(p1)
p1.forename = "Forename1"
p1.surname = "Surname1"
p1.dob = pendulum.parse("1950-01-01")
self.dbsession.add(p1)
p1_idnum1 = PatientIdNum()
p1_idnum1.id = 1
self._apply_standard_db_fields(p1_idnum1)
p1_idnum1.patient_id = p1.id
p1_idnum1.which_idnum = iddef1.which_idnum
p1_idnum1.idnum_value = 333
self.dbsession.add(p1_idnum1)
p1_idnum2 = PatientIdNum()
p1_idnum2.id = 2
self._apply_standard_db_fields(p1_idnum2)
p1_idnum2.patient_id = p1.id
p1_idnum2.which_idnum = iddef2.which_idnum
p1_idnum2.idnum_value = 444
self.dbsession.add(p1_idnum2)
p2 = Patient()
p2.id = 2
self._apply_standard_db_fields(p2)
p2.forename = "Forename2"
p2.surname = "Surname2"
p2.dob = pendulum.parse("1975-12-12")
self.dbsession.add(p2)
p2_idnum1 = PatientIdNum()
p2_idnum1.id = 3
self._apply_standard_db_fields(p2_idnum1)
p2_idnum1.patient_id = p2.id
p2_idnum1.which_idnum = iddef1.which_idnum
p2_idnum1.idnum_value = 555
self.dbsession.add(p2_idnum1)
self.dbsession.flush()
for cls in Task.all_subclasses_by_tablename():
t1 = cls()
t1.id = 1
self._apply_standard_task_fields(t1)
if t1.has_patient:
t1.patient_id = p1.id
if isinstance(t1, Photo):
b = Blob()
b.id = 1
self._apply_standard_db_fields(b)
b.tablename = t1.tablename
b.tablepk = t1.id
b.fieldname = 'photo_blobid'
b.filename = "some_picture.png"
b.mimetype = MimeType.PNG
b.image_rotation_deg_cw = 0
b.theblob = DEMO_PNG_BYTES
self.dbsession.add(b)
t1.photo_blobid = b.id
self.dbsession.add(t1)
t2 = cls()
t2.id = 2
self._apply_standard_task_fields(t2)
if t2.has_patient:
t2.patient_id = p2.id
self.dbsession.add(t2)
self.dbsession.commit()
class Mfi20(TaskHasPatientMixin, Task, metaclass=Mfi20Metaclass):
__tablename__ = "mfi20"
shortname = "MFI-20"
prohibits_clinical = True
prohibits_commercial = True
N_QUESTIONS = 20
MIN_SCORE_PER_Q = 1
MAX_SCORE_PER_Q = 5
MIN_SCORE = MIN_SCORE_PER_Q * N_QUESTIONS
MAX_SCORE = MAX_SCORE_PER_Q * N_QUESTIONS
N_Q_PER_SUBSCALE = 4 # always
MIN_SUBSCALE = MIN_SCORE_PER_Q * N_Q_PER_SUBSCALE
MAX_SUBSCALE = MAX_SCORE_PER_Q * N_Q_PER_SUBSCALE
ALL_QUESTIONS = strseq("q", 1, N_QUESTIONS)
REVERSE_QUESTIONS = Task.fieldnames_from_list(
"q", {2, 5, 9, 10, 13, 14, 16, 17, 18, 19}
)
GENERAL_FATIGUE_QUESTIONS = Task.fieldnames_from_list("q", {1, 5, 12, 16})
PHYSICAL_FATIGUE_QUESTIONS = Task.fieldnames_from_list("q", {2, 8, 14, 20})
REDUCED_ACTIVITY_QUESTIONS = Task.fieldnames_from_list("q", {3, 6, 10, 17})
REDUCED_MOTIVATION_QUESTIONS = Task.fieldnames_from_list(
"q", {4, 9, 15, 18}
)
MENTAL_FATIGUE_QUESTIONS = Task.fieldnames_from_list("q", {7, 11, 13, 19})
@staticmethod
def longname(req: "CamcopsRequest") -> str:
_ = req.gettext
return _("Multidimensional Fatigue Inventory")
def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]:
subscale_range = f"[{self.MIN_SUBSCALE}–{self.MAX_SUBSCALE}]"
return self.standard_task_summary_fields() + [
SummaryElement(
name="total",
coltype=Integer(),
value=self.total_score(),
comment=f"Total score [{self.MIN_SCORE}–{self.MAX_SCORE}]",
),
SummaryElement(
name="general_fatigue",
coltype=Integer(),
value=self.general_fatigue_score(),
comment=f"General fatigue {subscale_range}",
),
SummaryElement(
name="physical_fatigue",
coltype=Integer(),
value=self.physical_fatigue_score(),
comment=f"Physical fatigue {subscale_range}",
),
SummaryElement(
name="reduced_activity",
coltype=Integer(),
value=self.reduced_activity_score(),
comment=f"Reduced activity {subscale_range}",
),
SummaryElement(
name="reduced_motivation",
coltype=Integer(),
value=self.reduced_motivation_score(),
comment=f"Reduced motivation {subscale_range}",
),
SummaryElement(
name="mental_fatigue",
coltype=Integer(),
value=self.mental_fatigue_score(),
comment=f"Mental fatigue {subscale_range}",
),
]
def is_complete(self) -> bool:
if self.any_fields_none(self.ALL_QUESTIONS):
return False
if not self.field_contents_valid():
return False
return True
def score_fields(self, fields: List[str]) -> int:
total = 0
for f in fields:
value = getattr(self, f)
if value is not None:
if f in self.REVERSE_QUESTIONS:
value = self.MAX_SCORE_PER_Q + 1 - value
total += value if value is not None else 0
return total
def total_score(self) -> int:
return self.score_fields(self.ALL_QUESTIONS)
def general_fatigue_score(self) -> int:
return self.score_fields(self.GENERAL_FATIGUE_QUESTIONS)
def physical_fatigue_score(self) -> int:
return self.score_fields(self.PHYSICAL_FATIGUE_QUESTIONS)
def reduced_activity_score(self) -> int:
return self.score_fields(self.REDUCED_ACTIVITY_QUESTIONS)
def reduced_motivation_score(self) -> int:
return self.score_fields(self.REDUCED_MOTIVATION_QUESTIONS)
def mental_fatigue_score(self) -> int:
return self.score_fields(self.MENTAL_FATIGUE_QUESTIONS)
def get_task_html(self, req: CamcopsRequest) -> str:
fullscale_range = f"[{self.MIN_SCORE}–{self.MAX_SCORE}]"
subscale_range = f"[{self.MIN_SUBSCALE}–{self.MAX_SUBSCALE}]"
rows = ""
for q_num in range(1, self.N_QUESTIONS + 1):
q_field = "q" + str(q_num)
question_cell = "{}. {}".format(q_num, self.wxstring(req, q_field))
score = getattr(self, q_field)
rows += tr_qa(question_cell, score)
html = """
<div class="{CssClass.SUMMARY}">
<table class="{CssClass.SUMMARY}">
{tr_is_complete}
{total_score}
{general_fatigue_score}
{physical_fatigue_score}
{reduced_activity_score}
{reduced_motivation_score}
{mental_fatigue_score}
</table>
</div>
<table class="{CssClass.TASKDETAIL}">
<tr>
<th width="60%">Question</th>
<th width="40%">Answer <sup>[8]</sup></th>
</tr>
{rows}
</table>
<div class="{CssClass.FOOTNOTES}">
[1] Questions 2, 5, 9, 10, 13, 14, 16, 17, 18, 19
reverse-scored when summing.
[2] Sum for questions 1–20.
[3] General fatigue: Sum for questions 1, 5, 12, 16.
[4] Physical fatigue: Sum for questions 2, 8, 14, 20.
[5] Reduced activity: Sum for questions 3, 6, 10, 17.
[6] Reduced motivation: Sum for questions 4, 9, 15, 18.
[7] Mental fatigue: Sum for questions 7, 11, 13, 19.
[8] All questions are rated from “1 – yes, that is true” to
“5 – no, that is not true”.
</div>
""".format(
CssClass=CssClass,
tr_is_complete=self.get_is_complete_tr(req),
total_score=tr(
req.sstring(SS.TOTAL_SCORE) + " <sup>[1][2]</sup>",
f"{answer(self.total_score())} {fullscale_range}",
),
general_fatigue_score=tr(
self.wxstring(req, "general_fatigue") + " <sup>[1][3]</sup>",
f"{answer(self.general_fatigue_score())} {subscale_range}",
),
physical_fatigue_score=tr(
self.wxstring(req, "physical_fatigue") + " <sup>[1][4]</sup>",
f"{answer(self.physical_fatigue_score())} {subscale_range}",
),
reduced_activity_score=tr(
self.wxstring(req, "reduced_activity") + " <sup>[1][5]</sup>",
f"{answer(self.reduced_activity_score())} {subscale_range}",
),
reduced_motivation_score=tr(
self.wxstring(req, "reduced_motivation")
+ " <sup>[1][6]</sup>",
f"{answer(self.reduced_motivation_score())} {subscale_range}",
),
mental_fatigue_score=tr(
self.wxstring(req, "mental_fatigue") + " <sup>[1][7]</sup>",
f"{answer(self.mental_fatigue_score())} {subscale_range}",
),
rows=rows,
)
return html
SCALE_BDI_I = "BDI-I" # must match client
SCALE_BDI_IA = "BDI-IA" # must match client
SCALE_BDI_II = "BDI-II" # must match client
TOPICS_BY_SCALE = {
SCALE_BDI_I: BDI_I_QUESTION_TOPICS,
SCALE_BDI_IA: BDI_IA_QUESTION_TOPICS,
SCALE_BDI_II: BDI_II_QUESTION_TOPICS,
}
NQUESTIONS = 21
TASK_SCORED_FIELDS = strseq("q", 1, NQUESTIONS)
MAX_SCORE = NQUESTIONS * 3
SUICIDALITY_QNUM = 9 # Q9 in all versions of the BDI (I, IA, II)
SUICIDALITY_FN = "q9" # fieldname
CUSTOM_SOMATIC_KHANDAKER_BDI_II_QNUMS = [4, 15, 16, 18, 19, 20, 21]
CUSTOM_SOMATIC_KHANDAKER_BDI_II_FIELDS = Task.fieldnames_from_list(
"q", CUSTOM_SOMATIC_KHANDAKER_BDI_II_QNUMS)
# =============================================================================
# BDI (crippled)
# =============================================================================
class BdiMetaclass(DeclarativeMeta):
# noinspection PyInitNewSignature
def __init__(
cls: Type["Bdi"],
name: str,
bases: Tuple[Type, ...],
classdict: Dict[str, Any],
) -> None:
add_multiple_columns(
def get_rows_colnames(self, req: "CamcopsRequest") -> PlainReportType:
final_rows = [] # type: List[Sequence[Sequence[Any]]]
colnames = [] # type: List[str]
dbsession = req.dbsession
group_ids = req.user.ids_of_groups_user_may_report_on
superuser = req.user.superuser
via_index = req.get_bool_param(ViewParam.VIA_INDEX, True)
if via_index:
# noinspection PyUnresolvedReferences
query = (
select([
TaskIndexEntry.task_table_name.label("task"),
extract_year(
TaskIndexEntry.when_created_utc).label("year"), # noqa
extract_month(TaskIndexEntry.when_created_utc).label(
"month"), # noqa
func.count().label("num_tasks_added"),
]).select_from(TaskIndexEntry.__table__).group_by(
"task", "year", "month").order_by("task", desc("year"),
desc("month")))
if not superuser:
# Restrict to accessible groups
# noinspection PyProtectedMember
query = query.where(TaskIndexEntry.group_id.in_(group_ids))
rows, colnames = get_rows_fieldnames_from_query(dbsession, query)
final_rows.extend(rows)
else:
classes = Task.all_subclasses_by_tablename()
for cls in classes:
# noinspection PyProtectedMember
select_fields = [
literal(cls.__tablename__).label("task"),
# func.year() is specific to some DBs, e.g. MySQL
# so is func.extract();
# http://modern-sql.com/feature/extract
extract_year(isotzdatetime_to_utcdatetime(cls.when_created)
).label("year"),
extract_month(
isotzdatetime_to_utcdatetime(
cls.when_created)).label("month"),
func.count().label("num_tasks_added"),
]
# noinspection PyUnresolvedReferences
select_from = cls.__table__
# noinspection PyProtectedMember
wheres = [cls._current == True] # nopep8
if not superuser:
# Restrict to accessible groups
# noinspection PyProtectedMember
wheres.append(cls._group_id.in_(group_ids))
group_by = ["year", "month"]
order_by = [desc("year"), desc("month")]
# ... http://docs.sqlalchemy.org/en/latest/core/tutorial.html#ordering-or-grouping-by-a-label # noqa
query = select(select_fields) \
.select_from(select_from) \
.where(and_(*wheres)) \
.group_by(*group_by) \
.order_by(*order_by)
rows, colnames = get_rows_fieldnames_from_query(
dbsession, query)
final_rows.extend(rows)
return PlainReportType(rows=final_rows, column_names=colnames)
class Sfmpq2(TaskHasPatientMixin, Task, metaclass=Sfmpq2Metaclass):
__tablename__ = "sfmpq2"
shortname = "SF-MPQ2"
N_QUESTIONS = 22
MAX_SCORE_PER_Q = 10
ALL_QUESTIONS = strseq("q", 1, N_QUESTIONS)
CONTINUOUS_PAIN_QUESTIONS = Task.fieldnames_from_list(
"q", {1, 5, 6, 8, 9, 10})
INTERMITTENT_PAIN_QUESTIONS = Task.fieldnames_from_list(
"q", {2, 3, 4, 11, 16, 18})
NEUROPATHIC_PAIN_QUESTIONS = Task.fieldnames_from_list(
"q", {7, 17, 19, 20, 21, 22})
AFFECTIVE_PAIN_QUESTIONS = Task.fieldnames_from_list("q", {12, 13, 14, 15})
@staticmethod
def longname(req: CamcopsRequest) -> str:
_ = req.gettext
return _("Short-Form McGill Pain Questionnaire 2")
def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]:
return self.standard_task_summary_fields() + [
SummaryElement(
name="total_pain",
coltype=Float(),
value=self.total_pain(),
comment=f"Total pain (/{self.MAX_SCORE_PER_Q})",
),
SummaryElement(
name="continuous_pain",
coltype=Float(),
value=self.continuous_pain(),
comment=f"Continuous pain (/{self.MAX_SCORE_PER_Q})",
),
SummaryElement(
name="intermittent_pain",
coltype=Float(),
value=self.intermittent_pain(),
comment=f"Intermittent pain (/{self.MAX_SCORE_PER_Q})",
),
SummaryElement(
name="neuropathic_pain",
coltype=Float(),
value=self.neuropathic_pain(),
comment=f"Neuropathic pain (/{self.MAX_SCORE_PER_Q})",
),
SummaryElement(
name="affective_pain",
coltype=Float(),
value=self.affective_pain(),
comment=f"Affective pain (/{self.MAX_SCORE_PER_Q})",
),
]
def is_complete(self) -> bool:
if self.any_fields_none(self.ALL_QUESTIONS):
return False
if not self.field_contents_valid():
return False
return True
def total_pain(self) -> float:
return self.mean_fields(self.ALL_QUESTIONS)
def continuous_pain(self) -> float:
return self.mean_fields(self.CONTINUOUS_PAIN_QUESTIONS)
def intermittent_pain(self) -> float:
return self.mean_fields(self.INTERMITTENT_PAIN_QUESTIONS)
def neuropathic_pain(self) -> float:
return self.mean_fields(self.NEUROPATHIC_PAIN_QUESTIONS)
def affective_pain(self) -> float:
return self.mean_fields(self.AFFECTIVE_PAIN_QUESTIONS)
def format_average(self, value) -> str:
return "{} / {}".format(
answer(ws.number_to_dp(value, 3, default="?")),
self.MAX_SCORE_PER_Q,
)
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)
question_cell = "{}. {}".format(q_num, self.wxstring(req, q_field))
score = getattr(self, q_field)
rows += tr_qa(question_cell, score)
html = """
<div class="{CssClass.SUMMARY}">
<table class="{CssClass.SUMMARY}">
{tr_is_complete}
{total_pain}
{continuous_pain}
{intermittent_pain}
{neuropathic_pain}
{affective_pain}
</table>
</div>
<table class="{CssClass.TASKDETAIL}">
<tr>
<th width="60%">Question</th>
<th width="40%">Answer <sup>[6]</sup></th>
</tr>
{rows}
</table>
<div class="{CssClass.FOOTNOTES}">
[1] Average of items 1–22.
[2] Average of items 1, 5, 6, 8, 9, 10.
[3] Average of items 2, 3, 4, 11, 16, 18.
[4] Average of items 7, 17, 19, 20, 21, 22.
[5] Average of items 12, 13, 14, 15.
[6] All items are rated from “0 – none” to
“10 – worst possible”.
</div>
""".format(
CssClass=CssClass,
tr_is_complete=self.get_is_complete_tr(req),
total_pain=tr(
self.wxstring(req, "total_pain") + " <sup>[1]</sup>",
self.format_average(self.total_pain()),
),
continuous_pain=tr(
self.wxstring(req, "continuous_pain") + " <sup>[2]</sup>",
self.format_average(self.continuous_pain()),
),
intermittent_pain=tr(
self.wxstring(req, "intermittent_pain") + " <sup>[3]</sup>",
self.format_average(self.intermittent_pain()),
),
neuropathic_pain=tr(
self.wxstring(req, "neuropathic_pain") + " <sup>[4]</sup>",
self.format_average(self.neuropathic_pain()),
),
affective_pain=tr(
self.wxstring(req, "affective_pain") + " <sup>[5]</sup>",
self.format_average(self.affective_pain()),
),
rows=rows,
)
return html
def check_index(
cls, session: SqlASession, show_all_bad: bool = False
) -> bool:
"""
Checks the index.
Args:
session:
an SQLAlchemy Session
show_all_bad:
show all bad entries? (If false, return upon the first)
Returns:
bool: is the index OK?
"""
ok = True
log.info("Checking all task indexes represent valid entries")
for taskclass in Task.all_subclasses_by_tablename():
tasktablename = taskclass.tablename
log.debug("Checking {}", tasktablename)
# noinspection PyUnresolvedReferences,PyProtectedMember
q_idx_without_original = session.query(TaskIndexEntry).filter(
TaskIndexEntry.task_table_name == tasktablename,
~exists()
.select_from(taskclass.__table__)
.where(
and_(
TaskIndexEntry.task_pk == taskclass._pk,
taskclass._current == True, # noqa: E712
)
),
)
# No check for a valid patient at this time.
for index in q_idx_without_original:
log.error("Task index without matching original: {!r}", index)
ok = False
if not show_all_bad:
return ok
log.info("Checking all tasks have an index")
for taskclass in Task.all_subclasses_by_tablename():
tasktablename = taskclass.tablename
log.debug("Checking {}", tasktablename)
# noinspection PyUnresolvedReferences,PyProtectedMember
q_original_with_idx = session.query(taskclass).filter(
taskclass._current == True, # noqa: E712
~exists()
.select_from(TaskIndexEntry.__table__)
.where(
and_(
TaskIndexEntry.task_pk == taskclass._pk,
TaskIndexEntry.task_table_name == tasktablename,
)
),
)
for orig in q_original_with_idx:
log.error("Task without index entry: {!r}", orig)
ok = False
if not show_all_bad:
return ok
return ok
def test_all_tasks(self) -> None:
self.announce("test_all_tasks")
from datetime import date
import hl7
from sqlalchemy.sql.schema import Column
from camcops_server.cc_modules.cc_ctvinfo import CtvInfo # noqa: F811
from camcops_server.cc_modules.cc_patient import Patient # noqa: F811
from camcops_server.cc_modules.cc_simpleobjects import IdNumReference
from camcops_server.cc_modules.cc_snomed import ( # noqa: F811
SnomedExpression, )
from camcops_server.cc_modules.cc_string import APPSTRING_TASKNAME
from camcops_server.cc_modules.cc_summaryelement import SummaryElement
from camcops_server.cc_modules.cc_trackerhelpers import ( # noqa: F811
TrackerInfo, )
from camcops_server.cc_modules.cc_spreadsheet import ( # noqa: F811
SpreadsheetPage, )
from camcops_server.cc_modules.cc_xml import XmlElement
subclasses = Task.all_subclasses_by_tablename()
tables = [cls.tablename for cls in subclasses]
log.info("Actual task table names: {!r} (n={})", tables, len(tables))
req = self.req
recipdef = self.recipdef
dummy_data_factory = DummyDataInserter()
for cls in subclasses:
log.info("Testing {}", cls)
assert cls.extrastring_taskname != APPSTRING_TASKNAME
q = self.dbsession.query(cls)
t = q.first() # type: Task
self.assertIsNotNone(t, "Missing task!")
# Name validity
validate_task_tablename(t.tablename)
# Core functions
self.assertIsInstance(t.is_complete(), bool)
self.assertIsInstance(t.get_task_html(req), str)
for trackerinfo in t.get_trackers(req):
self.assertIsInstance(trackerinfo, TrackerInfo)
ctvlist = t.get_clinical_text(req)
if ctvlist is not None:
for ctvinfo in ctvlist:
self.assertIsInstance(ctvinfo, CtvInfo)
for est in t.get_all_summary_tables(req):
self.assertIsInstance(est.get_spreadsheet_page(),
SpreadsheetPage)
self.assertIsInstance(est.get_xml_element(), XmlElement)
self.assertIsInstance(t.has_patient, bool)
self.assertIsInstance(t.is_anonymous, bool)
self.assertIsInstance(t.has_clinician, bool)
self.assertIsInstance(t.has_respondent, bool)
self.assertIsInstance(t.tablename, str)
for fn in t.get_fieldnames():
self.assertIsInstance(fn, str)
self.assertIsInstance(t.field_contents_valid(), bool)
for msg in t.field_contents_invalid_because():
self.assertIsInstance(msg, str)
for fn in t.get_blob_fields():
self.assertIsInstance(fn, str)
self.assertIsInstance(t.pk,
int) # all our examples do have PKs # noqa
self.assertIsInstance(t.is_preserved(), bool)
self.assertIsInstance(t.was_forcibly_preserved(), bool)
self.assertIsInstanceOrNone(t.get_creation_datetime(), Pendulum)
self.assertIsInstanceOrNone(t.get_creation_datetime_utc(),
Pendulum)
self.assertIsInstanceOrNone(
t.get_seconds_from_creation_to_first_finish(), float)
self.assertIsInstance(t.get_adding_user_id(), int)
self.assertIsInstance(t.get_adding_user_username(), str)
self.assertIsInstance(t.get_removing_user_username(), str)
self.assertIsInstance(t.get_preserving_user_username(), str)
self.assertIsInstance(t.get_manually_erasing_user_username(), str)
# Summaries
for se in t.standard_task_summary_fields():
self.assertIsInstance(se, SummaryElement)
# SNOMED-CT
if req.snomed_supported:
for snomed_code in t.get_snomed_codes(req):
self.assertIsInstance(snomed_code, SnomedExpression)
# Clinician
self.assertIsInstance(t.get_clinician_name(), str)
# Respondent
self.assertIsInstance(t.is_respondent_complete(), bool)
# Patient
self.assertIsInstanceOrNone(t.patient, Patient)
self.assertIsInstance(t.is_female(), bool)
self.assertIsInstance(t.is_male(), bool)
self.assertIsInstanceOrNone(t.get_patient_server_pk(), int)
self.assertIsInstance(t.get_patient_forename(), str)
self.assertIsInstance(t.get_patient_surname(), str)
dob = t.get_patient_dob()
assert (dob is None or isinstance(dob, date)
or isinstance(dob, Date))
self.assertIsInstanceOrNone(t.get_patient_dob_first11chars(), str)
self.assertIsInstance(t.get_patient_sex(), str)
self.assertIsInstance(t.get_patient_address(), str)
for idnum in t.get_patient_idnum_objects():
self.assertIsInstance(idnum.get_idnum_reference(),
IdNumReference)
self.assertIsInstance(idnum.is_superficially_valid(), bool)
self.assertIsInstance(idnum.description(req), str)
self.assertIsInstance(idnum.short_description(req), str)
self.assertIsInstance(idnum.get_filename_component(req), str)
# HL7 v2
pidseg = t.get_patient_hl7_pid_segment(req, recipdef)
assert isinstance(pidseg, str) or isinstance(pidseg, hl7.Segment)
for dataseg in t.get_hl7_data_segments(req, recipdef):
self.assertIsInstance(dataseg, hl7.Segment)
for dataseg in t.get_hl7_extra_data_segments(recipdef):
self.assertIsInstance(dataseg, hl7.Segment)
# FHIR
self.assertIsInstance(
t.get_fhir_bundle(req, recipdef).as_json(),
dict) # the main test is not crashing!
# Other properties
self.assertIsInstance(t.is_erased(), bool)
self.assertIsInstance(t.is_live_on_tablet(), bool)
for attrname, col in t.gen_text_filter_columns():
self.assertIsInstance(attrname, str)
self.assertIsInstance(col, Column)
# Views
for page in t.get_spreadsheet_pages(req):
self.assertIsInstance(page.get_tsv(), str)
self.assertIsInstance(t.get_xml(req), str)
self.assertIsInstance(t.get_html(req), str)
self.assertIsInstance(t.get_pdf(req), bytes)
self.assertIsInstance(t.get_pdf_html(req), str)
self.assertIsInstance(t.suggested_pdf_filename(req), str)
self.assertIsInstance(
t.get_rio_metadata(
req,
which_idnum=1,
uploading_user_id=self.user.id,
document_type="some_doc_type",
),
str,
)
# Help
help_url = t.help_url()
self.assertEqual(
urllib.request.urlopen(help_url).getcode(),
HttpStatus.OK,
msg=f"Task help not found at {help_url}",
)
# Special operations
t.apply_special_note(req,
"Debug: Special note! (1)",
from_console=True)
t.apply_special_note(req,
"Debug: Special note! (2)",
from_console=False)
self.assertIsInstance(t.special_notes, list)
t.cancel_from_export_log(req, from_console=True)
t.cancel_from_export_log(req, from_console=False)
# Insert random data and check it doesn't crash.
dummy_data_factory.fill_in_task_fields(t)
self.assertIsInstance(t.get_html(req), str)
# Destructive special operations
self.assertFalse(t.is_erased())
t.manually_erase(req)
self.assertTrue(t.is_erased())
t.delete_entirely(req)
def get_rows_colnames(self, req: "CamcopsRequest") -> PlainReportType:
dbsession = req.dbsession
group_ids = req.user.ids_of_groups_user_may_report_on
superuser = req.user.superuser
by_year = req.get_bool_param(ViewParam.BY_YEAR, DEFAULT_BY_YEAR)
by_month = req.get_bool_param(ViewParam.BY_MONTH, DEFAULT_BY_MONTH)
by_task = req.get_bool_param(ViewParam.BY_TASK, DEFAULT_BY_TASK)
by_user = req.get_bool_param(ViewParam.BY_USER, DEFAULT_BY_USER)
via_index = req.get_bool_param(ViewParam.VIA_INDEX, True)
label_year = "year"
label_month = "month"
label_task = "task"
label_user = "******"
label_n = "num_tasks_added"
final_rows = [] # type: List[Sequence[Sequence[Any]]]
colnames = [] # type: List[str] # for type checker
if via_index:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Indexed method (preferable)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
selectors = [] # type: List[FunctionElement]
groupers = [] # type: List[str]
sorters = [] # type: List[Union[str, UnaryExpression]]
if by_year:
selectors.append(
extract_year(
TaskIndexEntry.when_created_utc).label(label_year))
groupers.append(label_year)
sorters.append(desc(label_year))
if by_month:
selectors.append(
extract_month(
TaskIndexEntry.when_created_utc).label(label_month))
groupers.append(label_month)
sorters.append(desc(label_month))
if by_task:
selectors.append(
TaskIndexEntry.task_table_name.label(label_task))
groupers.append(label_task)
sorters.append(label_task)
if by_user:
selectors.append(User.username.label(label_user))
groupers.append(label_user)
sorters.append(label_user)
# Regardless:
selectors.append(func.count().label(label_n))
# noinspection PyUnresolvedReferences
query = (
select(selectors).select_from(
TaskIndexEntry.__table__).group_by(*groupers).order_by(
*sorters)
# ... https://docs.sqlalchemy.org/en/latest/core/tutorial.html#ordering-or-grouping-by-a-label # noqa
)
if by_user:
# noinspection PyUnresolvedReferences
query = query.select_from(User.__table__).where(
TaskIndexEntry.adding_user_id == User.id)
if not superuser:
# Restrict to accessible groups
# noinspection PyProtectedMember
query = query.where(TaskIndexEntry.group_id.in_(group_ids))
rows, colnames = get_rows_fieldnames_from_query(dbsession, query)
# noinspection PyTypeChecker
final_rows = rows
else:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Without using the server method (worse)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
groupers = [] # type: List[str]
sorters = [] # type: List[Tuple[str, bool]]
# ... (key, reversed/descending)
if by_year:
groupers.append(label_year)
sorters.append((label_year, True))
if by_month:
groupers.append(label_month)
sorters.append((label_month, True))
if by_task:
groupers.append(label_task)
# ... redundant in the SQL, which involves multiple queries
# (one per task type), but useful for the Python
# aggregation.
sorters.append((label_task, False))
if by_user:
groupers.append(label_user)
sorters.append((label_user, False))
classes = Task.all_subclasses_by_tablename()
counter = Counter()
for cls in classes:
selectors = [] # type: List[FunctionElement]
if by_year:
selectors.append(
# func.year() is specific to some DBs, e.g. MySQL
# so is func.extract();
# http://modern-sql.com/feature/extract
extract_year(
isotzdatetime_to_utcdatetime(cls.when_created)
).label(label_year))
if by_month:
selectors.append(
extract_month(
isotzdatetime_to_utcdatetime(
cls.when_created)).label(label_month))
if by_task:
selectors.append(
literal(cls.__tablename__).label(label_task))
if by_user:
selectors.append(User.username.label(label_user))
# Regardless:
selectors.append(func.count().label(label_n))
# noinspection PyUnresolvedReferences
query = (
select(selectors).select_from(cls.__table__).where(
cls._current == True) # noqa: E712
.group_by(*groupers))
if by_user:
# noinspection PyUnresolvedReferences
query = query.select_from(
User.__table__).where(cls._adding_user_id == User.id)
if not superuser:
# Restrict to accessible groups
# noinspection PyProtectedMember
query = query.where(cls._group_id.in_(group_ids))
rows, colnames = get_rows_fieldnames_from_query(
dbsession, query)
if by_task:
final_rows.extend(rows)
else:
for row in rows: # type: RowProxy
key = tuple(row[keyname] for keyname in groupers)
count = row[label_n]
counter.update({key: count})
if not by_task:
PseudoRow = namedtuple("PseudoRow", groupers + [label_n])
for key, total in counter.items():
values = list(key) + [total]
final_rows.append(PseudoRow(*values))
# Complex sorting:
# https://docs.python.org/3/howto/sorting.html#sort-stability-and-complex-sorts # noqa
for key, descending in reversed(sorters):
final_rows.sort(key=attrgetter(key), reverse=descending)
return PlainReportType(rows=final_rows, column_names=colnames)
class Iesr(TaskHasPatientMixin, Task, metaclass=IesrMetaclass):
"""
Server implementation of the IES-R task.
"""
__tablename__ = "iesr"
shortname = "IES-R"
provides_trackers = True
event = Column("event", UnicodeText, comment="Relevant event")
NQUESTIONS = 22
MIN_SCORE = 0 # per question
MAX_SCORE = 4 # per question
MAX_TOTAL = 88
MAX_AVOIDANCE = 32
MAX_INTRUSION = 28
MAX_HYPERAROUSAL = 28
QUESTION_FIELDS = strseq("q", 1, NQUESTIONS)
AVOIDANCE_QUESTIONS = [5, 7, 8, 11, 12, 13, 17, 22]
AVOIDANCE_FIELDS = Task.fieldnames_from_list("q", AVOIDANCE_QUESTIONS)
INTRUSION_QUESTIONS = [1, 2, 3, 6, 9, 16, 20]
INTRUSION_FIELDS = Task.fieldnames_from_list("q", INTRUSION_QUESTIONS)
HYPERAROUSAL_QUESTIONS = [4, 10, 14, 15, 18, 19, 21]
HYPERAROUSAL_FIELDS = Task.fieldnames_from_list("q",
HYPERAROUSAL_QUESTIONS)
@staticmethod
def longname(req: "CamcopsRequest") -> str:
_ = req.gettext
return _("Impact of Events Scale – Revised")
def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]:
return [
TrackerInfo(
value=self.total_score(),
plot_label="IES-R total score (lower is better)",
axis_label=f"Total score (out of {self.MAX_TOTAL})",
axis_min=-0.5,
axis_max=self.MAX_TOTAL + 0.5,
),
TrackerInfo(
value=self.avoidance_score(),
plot_label="IES-R avoidance score",
axis_label=f"Avoidance score (out of {self.MAX_AVOIDANCE})",
axis_min=-0.5,
axis_max=self.MAX_AVOIDANCE + 0.5,
),
TrackerInfo(
value=self.intrusion_score(),
plot_label="IES-R intrusion score",
axis_label=f"Intrusion score (out of {self.MAX_INTRUSION})",
axis_min=-0.5,
axis_max=self.MAX_INTRUSION + 0.5,
),
TrackerInfo(
value=self.hyperarousal_score(),
plot_label="IES-R hyperarousal score",
axis_label=
f"Hyperarousal score (out of {self.MAX_HYPERAROUSAL})", # noqa
axis_min=-0.5,
axis_max=self.MAX_HYPERAROUSAL + 0.5,
),
]
def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]:
return self.standard_task_summary_fields() + [
SummaryElement(
name="total_score",
coltype=Integer(),
value=self.total_score(),
comment=f"Total score (/ {self.MAX_TOTAL})",
),
SummaryElement(
name="avoidance_score",
coltype=Integer(),
value=self.avoidance_score(),
comment=f"Avoidance score (/ {self.MAX_AVOIDANCE})",
),
SummaryElement(
name="intrusion_score",
coltype=Integer(),
value=self.intrusion_score(),
comment=f"Intrusion score (/ {self.MAX_INTRUSION})",
),
SummaryElement(
name="hyperarousal_score",
coltype=Integer(),
value=self.hyperarousal_score(),
comment=f"Hyperarousal score (/ {self.MAX_HYPERAROUSAL})",
),
]
def get_clinical_text(self, req: CamcopsRequest) -> List[CtvInfo]:
if not self.is_complete():
return CTV_INCOMPLETE
t = self.total_score()
a = self.avoidance_score()
i = self.intrusion_score()
h = self.hyperarousal_score()
return [
CtvInfo(content=(f"IES-R total score {t}/{self.MAX_TOTAL} "
f"(avoidance {a}/{self.MAX_AVOIDANCE} "
f"intrusion {i}/{self.MAX_INTRUSION}, "
f"hyperarousal {h}/{self.MAX_HYPERAROUSAL})"))
]
def total_score(self) -> int:
return self.sum_fields(self.QUESTION_FIELDS)
def avoidance_score(self) -> int:
return self.sum_fields(self.AVOIDANCE_FIELDS)
def intrusion_score(self) -> int:
return self.sum_fields(self.INTRUSION_FIELDS)
def hyperarousal_score(self) -> int:
return self.sum_fields(self.HYPERAROUSAL_FIELDS)
def is_complete(self) -> bool:
return bool(self.field_contents_valid() and self.event
and self.all_fields_not_none(self.QUESTION_FIELDS))
def get_task_html(self, req: CamcopsRequest) -> str:
option_dict = {None: None}
for a in range(self.MIN_SCORE, self.MAX_SCORE + 1):
option_dict[a] = req.wappstring(AS.IESR_A_PREFIX + str(a))
h = f"""
<div class="{CssClass.SUMMARY}">
<table class="{CssClass.SUMMARY}">
{self.get_is_complete_tr(req)}
<tr>
<td>Total score</td>
<td>{answer(self.total_score())} / {self.MAX_TOTAL}</td>
</td>
<tr>
<td>Avoidance score</td>
<td>{answer(self.avoidance_score())} / {self.MAX_AVOIDANCE}</td>
</td>
<tr>
<td>Intrusion score</td>
<td>{answer(self.intrusion_score())} / {self.MAX_INTRUSION}</td>
</td>
<tr>
<td>Hyperarousal score</td>
<td>{answer(self.hyperarousal_score())} / {self.MAX_HYPERAROUSAL}</td>
</td>
</table>
</div>
<table class="{CssClass.TASKDETAIL}">
{tr_qa(req.sstring(SS.EVENT), self.event)}
</table>
<table class="{CssClass.TASKDETAIL}">
<tr>
<th width="75%">Question</th>
<th width="25%">Answer (0–4)</th>
</tr>
""" # noqa
for q in range(1, self.NQUESTIONS + 1):
a = getattr(self, "q" + str(q))
fa = (f"{a}: {get_from_dict(option_dict, a)}"
if a is not None else None)
h += tr(self.wxstring(req, "q" + str(q)), answer(fa))
h += ("""
</table>
""" + DATA_COLLECTION_UNLESS_UPGRADED_DIV)
return h
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(req.snomed(
SnomedLookup.IESR_PROCEDURE_ASSESSMENT))
]
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.IESR_SCALE),
{req.snomed(SnomedLookup.IESR_SCORE): self.total_score()},
))
return codes
class Suppsp(TaskHasPatientMixin, Task, metaclass=SuppspMetaclass):
__tablename__ = "suppsp"
shortname = "SUPPS-P"
N_QUESTIONS = 20
MIN_SCORE_PER_Q = 1
MAX_SCORE_PER_Q = 4
MIN_SCORE = MIN_SCORE_PER_Q * N_QUESTIONS
MAX_SCORE = MAX_SCORE_PER_Q * N_QUESTIONS
N_Q_PER_SUBSCALE = 4 # always
MIN_SUBSCALE = MIN_SCORE_PER_Q * N_Q_PER_SUBSCALE
MAX_SUBSCALE = MAX_SCORE_PER_Q * N_Q_PER_SUBSCALE
ALL_QUESTIONS = strseq("q", 1, N_QUESTIONS)
NEGATIVE_URGENCY_QUESTIONS = Task.fieldnames_from_list("q", {6, 8, 13, 15})
LACK_OF_PERSEVERANCE_QUESTIONS = Task.fieldnames_from_list(
"q", {1, 4, 7, 11})
LACK_OF_PREMEDITATION_QUESTIONS = Task.fieldnames_from_list(
"q", {2, 5, 12, 19})
SENSATION_SEEKING_QUESTIONS = Task.fieldnames_from_list(
"q", {9, 14, 16, 18})
POSITIVE_URGENCY_QUESTIONS = Task.fieldnames_from_list(
"q", {3, 10, 17, 20})
@staticmethod
def longname(req: "CamcopsRequest") -> str:
_ = req.gettext
return _("Short UPPS-P Impulsive Behaviour Scale")
def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]:
subscale_range = f"[{self.MIN_SUBSCALE}–{self.MAX_SUBSCALE}]"
return self.standard_task_summary_fields() + [
SummaryElement(
name="total",
coltype=Integer(),
value=self.total_score(),
comment=f"Total score [{self.MIN_SCORE}–{self.MAX_SCORE}]",
),
SummaryElement(
name="negative_urgency",
coltype=Integer(),
value=self.negative_urgency_score(),
comment=f"Negative urgency {subscale_range}",
),
SummaryElement(
name="lack_of_perseverance",
coltype=Integer(),
value=self.lack_of_perseverance_score(),
comment=f"Lack of perseverance {subscale_range}",
),
SummaryElement(
name="lack_of_premeditation",
coltype=Integer(),
value=self.lack_of_premeditation_score(),
comment=f"Lack of premeditation {subscale_range}",
),
SummaryElement(
name="sensation_seeking",
coltype=Integer(),
value=self.sensation_seeking_score(),
comment=f"Sensation seeking {subscale_range}",
),
SummaryElement(
name="positive_urgency",
coltype=Integer(),
value=self.positive_urgency_score(),
comment=f"Positive urgency {subscale_range}",
),
]
def is_complete(self) -> bool:
if self.any_fields_none(self.ALL_QUESTIONS):
return False
if not self.field_contents_valid():
return False
return True
def total_score(self) -> int:
return self.sum_fields(self.ALL_QUESTIONS)
def negative_urgency_score(self) -> int:
return self.sum_fields(self.NEGATIVE_URGENCY_QUESTIONS)
def lack_of_perseverance_score(self) -> int:
return self.sum_fields(self.LACK_OF_PERSEVERANCE_QUESTIONS)
def lack_of_premeditation_score(self) -> int:
return self.sum_fields(self.LACK_OF_PREMEDITATION_QUESTIONS)
def sensation_seeking_score(self) -> int:
return self.sum_fields(self.SENSATION_SEEKING_QUESTIONS)
def positive_urgency_score(self) -> int:
return self.sum_fields(self.POSITIVE_URGENCY_QUESTIONS)
def get_task_html(self, req: CamcopsRequest) -> str:
normal_score_dict = {
None: None,
1: "1 — " + self.wxstring(req, "a0"),
2: "2 — " + self.wxstring(req, "a1"),
3: "3 — " + self.wxstring(req, "a2"),
4: "4 — " + self.wxstring(req, "a3"),
}
reverse_score_dict = {
None: None,
4: "4 — " + self.wxstring(req, "a0"),
3: "3 — " + self.wxstring(req, "a1"),
2: "2 — " + self.wxstring(req, "a2"),
1: "1 — " + self.wxstring(req, "a3"),
}
reverse_q_nums = {3, 6, 8, 9, 10, 13, 14, 15, 16, 17, 18, 20}
fullscale_range = f"[{self.MIN_SCORE}–{self.MAX_SCORE}]"
subscale_range = f"[{self.MIN_SUBSCALE}–{self.MAX_SUBSCALE}]"
rows = ""
for q_num in range(1, self.N_QUESTIONS + 1):
q_field = "q" + str(q_num)
question_cell = "{}. {}".format(q_num, self.wxstring(req, q_field))
score = getattr(self, q_field)
score_dict = normal_score_dict
if q_num in reverse_q_nums:
score_dict = reverse_score_dict
answer_cell = get_from_dict(score_dict, score)
rows += tr_qa(question_cell, answer_cell)
html = """
<div class="{CssClass.SUMMARY}">
<table class="{CssClass.SUMMARY}">
{tr_is_complete}
{total_score}
{negative_urgency_score}
{lack_of_perseverance_score}
{lack_of_premeditation_score}
{sensation_seeking_score}
{positive_urgency_score}
</table>
</div>
<table class="{CssClass.TASKDETAIL}">
<tr>
<th width="60%">Question</th>
<th width="40%">Score</th>
</tr>
{rows}
</table>
<div class="{CssClass.FOOTNOTES}">
[1] Sum for questions 1–20.
[2] Sum for questions 6, 8, 13, 15.
[3] Sum for questions 1, 4, 7, 11.
[4] Sum for questions 2, 5, 12, 19.
[5] Sum for questions 9, 14, 16, 18.
[6] Sum for questions 3, 10, 17, 20.
</div>
""".format(
CssClass=CssClass,
tr_is_complete=self.get_is_complete_tr(req),
total_score=tr(
req.sstring(SS.TOTAL_SCORE) + " <sup>[1]</sup>",
f"{answer(self.total_score())} {fullscale_range}",
),
negative_urgency_score=tr(
self.wxstring(req, "negative_urgency") + " <sup>[2]</sup>",
f"{answer(self.negative_urgency_score())} {subscale_range}",
),
lack_of_perseverance_score=tr(
self.wxstring(req, "lack_of_perseverance") + " <sup>[3]</sup>",
f"{answer(self.lack_of_perseverance_score())} {subscale_range}", # noqa: E501
),
lack_of_premeditation_score=tr(
self.wxstring(req, "lack_of_premeditation") +
" <sup>[4]</sup>",
f"{answer(self.lack_of_premeditation_score())} {subscale_range}", # noqa: E501
),
sensation_seeking_score=tr(
self.wxstring(req, "sensation_seeking") + " <sup>[5]</sup>",
f"{answer(self.sensation_seeking_score())} {subscale_range}",
),
positive_urgency_score=tr(
self.wxstring(req, "positive_urgency") + " <sup>[6]</sup>",
f"{answer(self.positive_urgency_score())} {subscale_range}",
),
rows=rows,
)
return html