def view_patient_disease_groups(patient_id, disease_group_id=None):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
disease_group = None
if disease_group_id is None:
form = AddPatientDiseaseGroupForm()
# TODO permissions
# TODO sort order
form.disease_group_id.choices = [(x.id, x.name) for x in DiseaseGroup.query.all() if not patient.in_disease_group(x)]
# TODO check if already in disease group
if request.method == 'POST':
if not patient.can_edit(current_user):
abort(403)
if form.validate():
disease_group_id = form.disease_group_id.data
disease_group = DiseaseGroup.query.get_or_404(disease_group_id)
try:
add_patient_to_disease_group(patient, disease_group)
db.session.commit()
except IntegrityError:
db.session.rollback()
flash('Saved.', 'success')
return redirect(url_for('patients.view_patient_disease_groups', patient_id=patient.id))
else:
disease_group = DiseaseGroupPatient.query\
.filter(DiseaseGroupPatient.patient == patient)\
.filter(DiseaseGroupPatient.id == disease_group_id)\
.first_or_404()
if not disease_group.can_edit(disease_group):
abort(403)
form = EditPatientDiseaseGroupForm(obj=disease_group)
if form.validate_on_submit():
disease_group.is_active = form.is_active.data
db.session.commit()
flash('Saved.', 'success')
return redirect(url_for('patients.view_patient_disease_groups', patient_id=patient.id))
context = dict(
patient=patient,
patient_data=get_patient_data(patient),
form=form,
disease_group=disease_group,
)
return render_template('patient/disease_groups.html', **context)
def view_pathology_list(patient_id):
patient = Patient.query.get_or_404(patient_id)
context = dict(
patient=patient,
patient_data=get_patient_data(patient),
)
return render_template('patient/pathology.html', **context)
def view_diagnosis(patient_id, disease_group_id):
patient = Patient.query.get_or_404(patient_id)
disease_group = DiseaseGroup.query.get_or_404(disease_group_id)
if not patient.can_view(current_user):
abort(403)
context = dict(patient=patient, patient_data=get_patient_data(patient), disease_group=disease_group)
return render_template("patient/diagnosis.html", **context)
def view_result_graph(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
form = ResultGraphForm()
form.result_code.choices = get_result_code_choices()
context = dict(patient=patient, patient_data=get_patient_data(patient), form=form)
return render_template("patient/results_graph.html", **context)
def view_result_definitions(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
result_group_definitions = ResultGroupDefinition.query.order_by(ResultGroupDefinition.name).all()
context = dict(
patient=patient, patient_data=get_patient_data(patient), result_group_definitions=result_group_definitions
)
return render_template("patient/result_definitions.html", **context)
def view_demographics_list(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
facility_patients = get_facility_patients(patient)
context = dict(
patient=patient,
patient_data=get_patient_data(patient),
facility_patients=facility_patients
)
return render_template('patient/demographics.html', **context)
def view_result_list(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
context = dict(patient=patient, patient_data=get_patient_data(patient))
form = SelectResultGroupForm(formdata=request.args, csrf_enabled=False)
result_group_choices = get_result_group_choices()
result_group_choices.insert(0, ("", "All"))
form.result_group_definition_id.choices = result_group_choices
if form.validate():
result_group_definition_id = form.result_group_definition_id.data
else:
result_group_definition_id = None
query = (
Result.query.join(Result.result_group)
.join(Result.result_definition)
.join(ResultGroup.result_group_definition)
.join(ResultGroup.facility)
.filter(ResultGroup.patient == patient)
)
if result_group_definition_id is not None:
result_group_definition = ResultGroupDefinition.query.get_or_404(result_group_definition_id)
query = query.filter(ResultGroup.result_group_definition == result_group_definition)
context["result_group_definition"] = result_group_definition
query, ordering = order_query(query, LIST_ORDER_BY, "date", DESCENDING)
query = query.order_by(desc(ResultGroup.date), ResultGroupDefinition.name, ResultDefinition.name)
pagination = paginate_query(query, default_per_page=50)
results = pagination.items
context.update(dict(pagination=pagination, ordering=ordering, results=results, form=form))
return render_template("patient/results_list.html", **context)
def delete_patient(patient_id):
patient = Patient.query.get_or_404(patient_id)
# TODO probably shouldn't be able to delete a patient who belongs to non-editable units
if not patient.can_edit(current_user):
abort(403)
form = DeleteForm()
if form.validate_on_submit():
db.session.delete(patient)
db.session.commit()
flash('Patient deleted.', 'success')
return redirect(url_for('patients.view_patient_list'))
else:
context = dict(
patient=patient,
patient_data=get_patient_data(patient)
)
return render_template('patient/delete.html', **context)
def view_patient_units(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
form = PatientUnitForm()
# TODO permissions
# TODO sort order
form.unit_id.choices = [(x.id, x.name) for x in Unit.query.all() if not patient.in_unit(x)]
# TODO check if already in unit
if request.method == 'POST':
if not patient.can_edit(current_user):
abort(403)
if form.validate():
unit_id = form.unit_id.data
unit = Unit.query.get_or_404(unit_id)
try:
add_patient_to_unit(patient, unit)
db.session.commit()
except IntegrityError:
db.session.rollback()
flash('Saved.', 'success')
return redirect(url_for('patients.view_patient_units', patient_id=patient.id))
context = dict(
patient=patient,
patient_data=get_patient_data(patient),
form=form,
)
return render_template('patient/units.html', **context)
def view_patient_list():
if not current_user.has_view_patient_permission:
abort(403)
form = get_patient_search_form(current_user)
query = build_patient_search_query(current_user, form)
ordering = Ordering(form.order_by.data, form.order_direction.data)
pagination = paginate_query(query, default_per_page=PER_PAGE_DEFAULT)
patients = pagination.items
patients = [(x, get_patient_data(x)) for x in patients]
context = dict(
patients=patients,
form=form,
pagination=pagination,
ordering=ordering,
per_page_choices=PER_PAGE_CHOICES,
)
return render_template('patients.html', **context)
def view_result_table(patient_id):
patient = Patient.query.get_or_404(patient_id)
if not patient.can_view(current_user):
abort(403)
form = ResultTableForm(formdata=request.args, csrf_enabled=False)
form.result_codes.choices = get_result_code_choices()
result_codes = form.result_codes.data
# Default result codes
if not result_codes:
result_codes = ["CREATININE"]
result_definitions = ResultDefinition.query.filter(ResultDefinition.code.in_(result_codes)).all()
result_definition_dict = {x.code: x for x in result_definitions}
# Remove invalid result codes
result_codes = [x for x in result_codes if x in result_definition_dict]
form.result_codes.data = result_codes
if result_codes:
# Sorting is done later to keep item grouping consistent
results = (
Result.query.join(Result.result_definition)
.join(Result.result_group)
.filter(ResultDefinition.code.in_(result_codes))
.filter(ResultGroup.patient == patient)
.order_by(ResultGroup.id)
.order_by(Result.id)
.all()
)
else:
results = []
table = ResultTable(result_codes)
table.add_all(results)
# Build list of sortable columns
sort_columns = ["date", "source"]
sort_columns.extend([RESULT_CODE_SORT_PREFIX + x for x in result_codes])
ordering = ordering_from_request(sort_columns, "date", DESCENDING)
sort_column = ordering.column
reverse = ordering.direction == DESCENDING
if sort_column.startswith(RESULT_CODE_SORT_PREFIX):
sort_result_code = sort_column.split(RESULT_CODE_SORT_PREFIX)[1]
table.sort_by_result_code(sort_result_code, reverse)
elif sort_column == "source":
table.sort_by_facility(reverse)
else:
table.sort_by_date(reverse)
result_columns = [(result_definition_dict[x], RESULT_CODE_SORT_PREFIX + x) for x in result_codes]
context = dict(
patient=patient,
patient_data=get_patient_data(patient),
table=table,
ordering=ordering,
form=form,
result_columns=result_columns,
)
return render_template("patient/results_table.html", **context)