def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(
req.snomed(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT))
] # noqa
# add(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_ATTENTION_ORIENTATION) # noqa
# add(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_MEMORY)
# add(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_FLUENCY)
# add(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_LANGUAGE)
# add(SnomedLookup.ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_VISUOSPATIAL)
if self.is_complete(): # could refine: is each subscale complete?
a = self.attn_score()
m = self.mem_score()
f = self.fluency_score()
lang = self.lang_score()
v = self.vsp_score()
t = a + m + f + lang + v
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.ACE_R_SCALE),
{
req.snomed(SnomedLookup.ACE_R_SCORE):
t,
req.snomed(SnomedLookup.ACE_R_SUBSCORE_ATTENTION_ORIENTATION):
a, # noqa
req.snomed(SnomedLookup.ACE_R_SUBSCORE_MEMORY):
m,
req.snomed(SnomedLookup.ACE_R_SUBSCORE_FLUENCY):
f,
req.snomed(SnomedLookup.ACE_R_SUBSCORE_LANGUAGE):
lang,
req.snomed(SnomedLookup.ACE_R_SUBSCORE_VISUOSPATIAL):
v,
}))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
procedure = req.snomed(SnomedLookup.BMI_PROCEDURE_MEASUREMENT)
if self.is_complete():
unit = req.snomed(SnomedLookup.UNIT_OF_MEASURE)
kg = req.snomed(SnomedLookup.KILOGRAM)
m = req.snomed(SnomedLookup.METRE)
kg_per_sq_m = req.snomed(SnomedLookup.KG_PER_SQ_M)
qty_bmi = req.snomed(SnomedLookup.BMI_OBSERVABLE)
qty_height = req.snomed(SnomedLookup.BODY_HEIGHT_OBSERVABLE)
qty_weight = req.snomed(SnomedLookup.BODY_WEIGHT_OBSERVABLE)
return [
SnomedExpression(procedure, [
SnomedAttributeGroup({
qty_bmi: self.bmi(),
unit: kg_per_sq_m,
}),
SnomedAttributeGroup({
qty_weight: self.mass_kg,
unit: kg,
}),
SnomedAttributeGroup({
qty_height: self.height_m,
unit: m,
}),
])
]
else:
return [SnomedExpression(procedure)]
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
if not self.is_complete():
return []
return [
SnomedExpression(req.snomed(SnomedLookup.PHOTOGRAPH_PROCEDURE)),
SnomedExpression(
req.snomed(SnomedLookup.PHOTOGRAPH_PHYSICAL_OBJECT)),
]
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
procedure = req.snomed(SnomedLookup.PHQ15_PROCEDURE)
codes = [SnomedExpression(procedure)]
if self.is_complete():
scale = req.snomed(SnomedLookup.PHQ15_SCALE)
score = req.snomed(SnomedLookup.PHQ15_SCORE)
codes.append(SnomedExpression(scale, {score: self.total_score()}))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [SnomedExpression(req.snomed(SnomedLookup.GAD7_PROCEDURE_ASSESSMENT))] # noqa
if self.is_complete():
codes.append(SnomedExpression(
req.snomed(SnomedLookup.GAD7_SCALE),
{
req.snomed(SnomedLookup.GAD7_SCORE): self.total_score(),
}
))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
# The BADLS is ALWAYS carer-rated, so it's appropriate to put the
# SNOMED-CT codes in.
codes = [
SnomedExpression(
req.snomed(SnomedLookup.BADLS_PROCEDURE_ASSESSMENT))
]
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.BADLS_SCALE),
{req.snomed(SnomedLookup.BADLS_SCORE): self.total_score()},
))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(req.snomed(
SnomedLookup.NART_PROCEDURE_ASSESSMENT))
] # noqa
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.NART_SCALE),
{
# Best value debatable:
req.snomed(SnomedLookup.NART_SCORE):
self.nelson_full_scale_iq(), # noqa
}))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
expressions = [] # type: List[SnomedExpression]
procedure_bmi = req.snomed(SnomedLookup.BMI_PROCEDURE_MEASUREMENT)
unit = req.snomed(SnomedLookup.UNIT_OF_MEASURE)
if self.is_complete():
kg = req.snomed(SnomedLookup.KILOGRAM)
m = req.snomed(SnomedLookup.METRE)
kg_per_sq_m = req.snomed(SnomedLookup.KG_PER_SQ_M)
qty_bmi = req.snomed(SnomedLookup.BMI_OBSERVABLE)
qty_height = req.snomed(SnomedLookup.BODY_HEIGHT_OBSERVABLE)
qty_weight = req.snomed(SnomedLookup.BODY_WEIGHT_OBSERVABLE)
expressions.append(
SnomedExpression(
procedure_bmi,
[
SnomedAttributeGroup(
{qty_bmi: self.bmi(), unit: kg_per_sq_m}
),
SnomedAttributeGroup(
{qty_weight: self.mass_kg, unit: kg}
),
SnomedAttributeGroup(
{qty_height: self.height_m, unit: m}
),
],
)
)
else:
expressions.append(SnomedExpression(procedure_bmi))
if self.waist_cm is not None:
procedure_waist = req.snomed(
SnomedLookup.WAIST_CIRCUMFERENCE_PROCEDURE_MEASUREMENT
)
cm = req.snomed(SnomedLookup.CENTIMETRE)
qty_waist_circum = req.snomed(
SnomedLookup.WAIST_CIRCUMFERENCE_OBSERVABLE
)
expressions.append(
SnomedExpression(
procedure_waist,
[
SnomedAttributeGroup(
{qty_waist_circum: self.waist_cm, unit: cm}
)
],
)
)
return expressions
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(req.snomed(
SnomedLookup.HADS_PROCEDURE_ASSESSMENT))
] # noqa
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.HADS_SCALE),
{
req.snomed(SnomedLookup.HADS_ANXIETY_SCORE):
self.anxiety_score(), # noqa
req.snomed(SnomedLookup.HADS_DEPRESSION_SCORE):
self.depression_score(), # noqa
}))
return codes
def get_snomed_codes(self,
req: CamcopsRequest,
fallback: bool = True) -> List[SnomedExpression]:
"""
Returns all SNOMED-CT codes for this task.
Args:
req: the
:class:`camcops_server.cc_modules.cc_request.CamcopsRequest`
fallback: for example, if F32.10 is unknown, should we fall back to
F32.1?
Returns:
a list of
:class:`camcops_server.cc_modules.cc_snomed.SnomedExpression`
objects
"""
if not req.icd10_snomed_supported:
return []
snomed_codes = [] # type: List[SnomedExpression]
# noinspection PyTypeChecker
for item in self.items:
concepts = self._get_snomed_concepts(item.code, req, fallback)
if not concepts:
continue
focusconcept = SnomedFocusConcept(concepts)
snomed_codes.append(SnomedExpression(focusconcept))
return snomed_codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(req.snomed(
SnomedLookup.WSAS_PROCEDURE_ASSESSMENT))
]
if self.is_complete():
d = {
req.snomed(SnomedLookup.WSAS_SCORE): self.total_score(),
req.snomed(SnomedLookup.WSAS_HOME_MANAGEMENT_SCORE): self.q2,
req.snomed(SnomedLookup.WSAS_SOCIAL_LEISURE_SCORE): self.q3,
req.snomed(SnomedLookup.WSAS_PRIVATE_LEISURE_SCORE): self.q4,
req.snomed(SnomedLookup.WSAS_RELATIONSHIPS_SCORE): self.q5,
}
if not self.retired_etc:
d[req.snomed(SnomedLookup.WSAS_WORK_SCORE)] = self.q1
codes.append(
SnomedExpression(req.snomed(SnomedLookup.WSAS_SCALE), d))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
if not self.is_complete():
return []
return [
SnomedExpression(
req.snomed(SnomedLookup.PDSS_SCALE), {
req.snomed(SnomedLookup.PDSS_SCORE): self.total_score(),
})
]
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
scale_lookup = SnomedLookup.BDI_SCALE
if self.bdi_scale in (SCALE_BDI_I, SCALE_BDI_IA):
score_lookup = SnomedLookup.BDI_SCORE
proc_lookup = SnomedLookup.BDI_PROCEDURE_ASSESSMENT
elif self.bdi_scale == SCALE_BDI_II:
score_lookup = SnomedLookup.BDI_II_SCORE
proc_lookup = SnomedLookup.BDI_II_PROCEDURE_ASSESSMENT
else:
return []
codes = [SnomedExpression(req.snomed(proc_lookup))]
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(scale_lookup),
{req.snomed(score_lookup): self.total_score()},
))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
refinement = {} # type: Dict[SnomedConcept, str]
if self.note:
refinement[req.snomed(SnomedLookup.CLINICAL_NOTE)] = self.note
codes = [
SnomedExpression(
req.snomed(SnomedLookup.PROGRESS_NOTE_PROCEDURE),
refinement=refinement or None,
)
]
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
procedure = req.snomed(
SnomedLookup.PHQ9_PROCEDURE_DEPRESSION_SCREENING)
codes = [SnomedExpression(procedure)]
if self.is_complete():
scale = req.snomed(SnomedLookup.PHQ9_SCALE)
score = req.snomed(SnomedLookup.PHQ9_SCORE)
screen_negative = req.snomed(
SnomedLookup.PHQ9_FINDING_NEGATIVE_SCREENING_FOR_DEPRESSION)
screen_positive = req.snomed(
SnomedLookup.PHQ9_FINDING_POSITIVE_SCREENING_FOR_DEPRESSION)
if self.is_mds() or self.is_ods():
# Threshold debatable, but if you have "other depressive
# syndrome", it seems wrong to say you've screened negative for
# depression.
procedure_result = screen_positive
else:
procedure_result = screen_negative
codes.append(SnomedExpression(scale, {score: self.total_score()}))
codes.append(SnomedExpression(procedure_result))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(
req.snomed(SnomedLookup.HONOSWA_PROCEDURE_ASSESSMENT))
]
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.HONOSWA_SCALE),
{
req.snomed(SnomedLookup.HONOSWA_SCORE):
self.total_score(),
req.snomed(SnomedLookup.HONOSWA_1_OVERACTIVE_SCORE):
self.q1, # noqa
req.snomed(SnomedLookup.HONOSWA_2_SELFINJURY_SCORE):
self.q2, # noqa
req.snomed(SnomedLookup.HONOSWA_3_SUBSTANCE_SCORE):
self.q3, # noqa
req.snomed(SnomedLookup.HONOSWA_4_COGNITIVE_SCORE):
self.q4, # noqa
req.snomed(SnomedLookup.HONOSWA_5_PHYSICAL_SCORE):
self.q5,
req.snomed(SnomedLookup.HONOSWA_6_PSYCHOSIS_SCORE):
self.q6, # noqa
req.snomed(SnomedLookup.HONOSWA_7_DEPRESSION_SCORE):
self.q7, # noqa
req.snomed(SnomedLookup.HONOSWA_8_OTHERMENTAL_SCORE):
self.q8, # noqa
req.snomed(SnomedLookup.HONOSWA_9_RELATIONSHIPS_SCORE):
self.q9, # noqa
req.snomed(SnomedLookup.HONOSWA_10_ADL_SCORE):
self.q10,
req.snomed(SnomedLookup.HONOSWA_11_LIVINGCONDITIONS_SCORE):
self.q11, # noqa
req.snomed(SnomedLookup.HONOSWA_12_OCCUPATION_SCORE):
self.q12, # noqa
},
))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(
req.snomed(SnomedLookup.EQ5D5L_PROCEDURE_ASSESSMENT))
] # noqa
if self.is_complete():
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.EQ5D5L_SCALE),
{
# SnomedLookup.EQ5D5L_INDEX_VALUE: not used; see docstring above # noqa
req.snomed(SnomedLookup.EQ5D5L_MOBILITY_SCORE):
self.q1,
req.snomed(SnomedLookup.EQ5D5L_SELF_CARE_SCORE):
self.q2,
req.snomed(SnomedLookup.EQ5D5L_USUAL_ACTIVITIES_SCORE):
self.q3, # noqa
req.snomed(SnomedLookup.EQ5D5L_PAIN_DISCOMFORT_SCORE):
self.q4, # noqa
req.snomed(SnomedLookup.EQ5D5L_ANXIETY_DEPRESSION_SCORE):
self.q5, # noqa
}))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(
req.snomed(SnomedLookup.HONOSCA_PROCEDURE_ASSESSMENT))
] # noqa
if self.is_complete():
a = self.section_a_score()
b = self.section_b_score()
total = a + b
codes.append(
SnomedExpression(
req.snomed(SnomedLookup.HONOSCA_SCALE),
{
req.snomed(SnomedLookup.HONOSCA_SCORE):
total,
req.snomed(SnomedLookup.HONOSCA_SECTION_A_SCORE):
a,
req.snomed(SnomedLookup.HONOSCA_SECTION_B_SCORE):
b,
req.snomed(SnomedLookup.HONOSCA_SECTION_A_PLUS_B_SCORE):
total, # noqa
}))
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
if not req.icd9cm_snomed_supported:
return []
snomed_codes = [] # type: List[SnomedExpression]
# noinspection PyTypeChecker
for item in self.items:
try:
concepts = req.icd9cm_snomed(item.code)
except KeyError: # no known code
continue
if not concepts:
continue
focusconcept = SnomedFocusConcept(concepts)
snomed_codes.append(SnomedExpression(focusconcept))
return snomed_codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
if not self.is_complete():
return []
return [SnomedExpression(req.snomed(SnomedLookup.QOL_SCALE))]
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
refinement = {} # type: Dict[SnomedConcept, str]
def add(snomed_lookup: str, contents: Optional[str]) -> None:
if not contents:
return
nonlocal refinement
concept = req.snomed(snomed_lookup)
refinement[concept] = contents
# not location
# not contact type
add(SnomedLookup.PSYCLERK_REASON_FOR_REFERRAL, self.reason_for_contact)
add(SnomedLookup.PSYCLERK_PRESENTING_ISSUE, self.presenting_issue)
add(SnomedLookup.PSYCLERK_SYSTEMS_REVIEW, self.systems_review)
add(SnomedLookup.PSYCLERK_COLLATERAL_HISTORY, self.collateral_history)
add(
SnomedLookup.PSYCLERK_PAST_MEDICAL_SURGICAL_MENTAL_HEALTH_HISTORY,
self.diagnoses_medical,
)
add(
SnomedLookup.PSYCLERK_PAST_MEDICAL_SURGICAL_MENTAL_HEALTH_HISTORY,
self.diagnoses_psychiatric,
)
add(SnomedLookup.PSYCLERK_PROCEDURES, self.operations_procedures)
add(
SnomedLookup.PSYCLERK_ALLERGIES_ADVERSE_REACTIONS,
self.allergies_adverse_reactions,
)
add(SnomedLookup.PSYCLERK_MEDICATIONS_MEDICAL_DEVICES,
self.medications)
add(
SnomedLookup.PSYCLERK_DRUG_SUBSTANCE_USE,
self.recreational_drug_use,
)
add(SnomedLookup.PSYCLERK_FAMILY_HISTORY, self.family_history)
add(
SnomedLookup.PSYCLERK_DEVELOPMENTAL_HISTORY,
self.developmental_history,
)
add(
SnomedLookup.PSYCLERK_SOCIAL_PERSONAL_HISTORY,
self.personal_history,
)
add(SnomedLookup.PSYCLERK_PERSONALITY, self.premorbid_personality)
add(
SnomedLookup.PSYCLERK_PRISON_RECORD_CRIMINAL_ACTIVITY,
self.forensic_history,
)
add(
SnomedLookup.PSYCLERK_SOCIAL_HISTORY_BASELINE,
self.current_social_situation,
)
add(SnomedLookup.PSYCLERK_MSE_APPEARANCE,
self.mse_appearance_behaviour) # duplication
add(SnomedLookup.PSYCLERK_MSE_BEHAVIOUR,
self.mse_appearance_behaviour) # duplication
add(SnomedLookup.PSYCLERK_MSE_MOOD, self.mse_mood_subjective) # close
add(SnomedLookup.PSYCLERK_MSE_AFFECT, self.mse_mood_objective)
# ... Logic here: "objective mood" is certainly affect (emotional
# weather). "Subjective mood" is both mood (emotional climate) and
# affect. Not perfect, but reasonable.
add(SnomedLookup.PSYCLERK_MSE_THOUGHT, self.mse_thought_form)
add(SnomedLookup.PSYCLERK_MSE_THOUGHT, self.mse_thought_content)
# ... No way of disambiguating the two in SNOMED-CT.
add(SnomedLookup.PSYCLERK_MSE_PERCEPTION, self.mse_perception)
add(SnomedLookup.PSYCLERK_MSE_COGNITION, self.mse_cognition)
add(SnomedLookup.PSYCLERK_MSE_INSIGHT, self.mse_insight)
add(
SnomedLookup.PSYCLERK_PHYSEXAM_GENERAL,
self.physical_examination_general,
)
add(
SnomedLookup.PSYCLERK_PHYSEXAM_CARDIOVASCULAR,
self.physical_examination_cardiovascular,
)
add(
SnomedLookup.PSYCLERK_PHYSEXAM_RESPIRATORY,
self.physical_examination_respiratory,
)
add(
SnomedLookup.PSYCLERK_PHYSEXAM_ABDOMINAL,
self.physical_examination_abdominal,
)
add(
SnomedLookup.PSYCLERK_PHYSEXAM_NEUROLOGICAL,
self.physical_examination_neurological,
)
add(SnomedLookup.PSYCLERK_ASSESSMENT_SCALES, self.assessment_scales)
add(
SnomedLookup.PSYCLERK_INVESTIGATIONS_RESULTS,
self.investigations_results,
)
add(SnomedLookup.PSYCLERK_SAFETY_ALERTS, self.safety_alerts)
add(SnomedLookup.PSYCLERK_RISK_ASSESSMENT, self.risk_assessment)
add(
SnomedLookup.PSYCLERK_RELEVANT_LEGAL_INFORMATION,
self.relevant_legal_information,
)
add(SnomedLookup.PSYCLERK_CURRENT_PROBLEMS, self.current_problems)
add(
SnomedLookup.PSYCLERK_PATIENT_CARER_CONCERNS,
self.patient_carer_concerns,
)
add(SnomedLookup.PSYCLERK_CLINICAL_NARRATIVE, self.impression)
add(SnomedLookup.PSYCLERK_MANAGEMENT_PLAN, self.management_plan)
add(SnomedLookup.PSYCLERK_INFORMATION_GIVEN, self.information_given)
codes = [
SnomedExpression(
req.snomed(
SnomedLookup.DIAGNOSTIC_PSYCHIATRIC_INTERVIEW_PROCEDURE),
refinement=refinement or None,
)
]
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(req.snomed(SnomedLookup.PROGRESS_NOTE_PROCEDURE))
] # noqa
return codes
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [
SnomedExpression(
req.snomed(SnomedLookup.PSYCHIATRIC_ASSESSMENT_PROCEDURE))
] # noqa
return codes
def fhir_observation_component_from_snomed(req: "CamcopsRequest",
expr: SnomedExpression) -> Dict:
"""
Returns a FHIR ObservationComponent (as a dict in JSON format) for a SNOMED
CT expression.
"""
observable_entity = req.snomed(SnomedLookup.OBSERVABLE_ENTITY)
expr_longform = expr.as_string(longform=True)
# For SNOMED, we are providing an observation where the "value" is a code
# -- thus, we use "valueCodeableConcept" as the specific value (the generic
# being "value<something>" or what FHIR calls "value[x]"). But there also
# needs to be a coding system, specified via "code".
return ObservationComponent(
jsondict={
# code = "the type of thing reported here"
# Per https://www.hl7.org/fhir/observation.html#code-interop, we
# use SNOMED 363787002 = Observable entity.
Fc.CODE:
CodeableConcept(
jsondict={
Fc.CODING: [
Coding(
jsondict={
Fc.SYSTEM:
Fc.CODE_SYSTEM_SNOMED_CT,
Fc.CODE:
str(observable_entity.identifier),
Fc.DISPLAY:
observable_entity.as_string(longform=True),
Fc.USER_SELECTED:
False,
}).as_json()
],
Fc.TEXT:
observable_entity.term,
}).as_json(),
# value = "the value of the thing"; the actual SNOMED code of
# interest:
Fc.VALUE_CODEABLE_CONCEPT:
CodeableConcept(
jsondict={
Fc.CODING: [
Coding(
jsondict={
# http://www.hl7.org/fhir/snomedct.html
Fc.SYSTEM:
Fc.CODE_SYSTEM_SNOMED_CT,
Fc.CODE:
expr.as_string(longform=False),
Fc.DISPLAY:
expr_longform,
Fc.USER_SELECTED:
False,
# ... means "did the user choose it themselves?" # noqa: E501
# version: not used
}).as_json()
],
Fc.TEXT:
expr_longform,
}).as_json(),
}).as_json()
def get_snomed_codes(self, req: CamcopsRequest) -> List[SnomedExpression]:
codes = [SnomedExpression(req.snomed(SnomedLookup.BPRS1962_SCALE))]
return codes
