func (r *RoutesSuite) TestPieRoute(c *C) {
// Insert the pie in the database
patientURL := "http://testurl.org"
pie := plugin.NewPie(patientURL)
r.Database.C("pies").Insert(pie)
// Now get the pie from the server
pieURL := fmt.Sprintf("%s/pies/%s", r.Server.URL, pie.Id.Hex())
resp, err := http.Get(pieURL)
util.CheckErr(err)
c.Assert(resp.StatusCode, Equals, http.StatusOK)
// Does the pie data contain the patient URL?
defer resp.Body.Close()
buf := new(bytes.Buffer)
buf.ReadFrom(resp.Body)
responseBody := buf.String()
c.Assert(strings.Contains(responseBody, patientURL), Equals, true)
}
// Calculate takes a stream of events and returns a slice of corresponding risk calculation results
func (c *SimplePlugin) Calculate(es *plugin.EventStream, fhirEndpointURL string) ([]plugin.RiskServiceCalculationResult, error) {
var results []plugin.RiskServiceCalculationResult
// Keep a map of active conditions and medications -- so we don't double-count duplicates in the record.
cMap := make(map[string]int)
mMap := make(map[string]int)
// Create the initial pie
pie := plugin.NewPie(fhirEndpointURL + "/Patient/" + es.Patient.Id)
pie.Slices = c.Config().DefaultPieSlices
// Now go through the event stream, updating the pie
for _, event := range es.Events {
// NOTE: guard against future dates (for example, our patient generator can create future events)
if event.Date.Local().After(time.Now()) {
continue
}
var isFactor bool
pie = pie.Clone(true)
switch r := event.Value.(type) {
case *models.Condition:
if r.Code == nil || len(r.Code.Coding) == 0 {
continue
}
isFactor = true
key := r.Code.Coding[0].System + "|" + r.Code.Coding[0].Code
count := cMap[key]
if !event.End {
cMap[key] = count + 1
} else if count > 0 {
cMap[key] = count - 1
}
pie.UpdateSliceValue("Conditions", calculateCount(cMap))
case *models.MedicationStatement:
if r.MedicationCodeableConcept == nil || len(r.MedicationCodeableConcept.Coding) == 0 {
continue
}
isFactor = true
key := r.MedicationCodeableConcept.Coding[0].System + "|" + r.MedicationCodeableConcept.Coding[0].Code
count := mMap[key]
if !event.End {
mMap[key] = count + 1
} else if count > 0 {
mMap[key] = count - 1
}
pie.UpdateSliceValue("Medications", calculateCount(mMap))
}
if isFactor {
score := pie.TotalValues()
results = append(results, plugin.RiskServiceCalculationResult{
AsOf: event.Date,
Score: &score,
ProbabilityDecimal: nil,
Pie: pie,
})
}
}
// If there are no results, provide a 0 score for the current time
if len(results) == 0 {
zero := 0
results = append(results, plugin.RiskServiceCalculationResult{
AsOf: time.Now(),
Score: &zero,
ProbabilityDecimal: nil,
Pie: pie,
})
}
return results, nil
}
// Calculate takes a stream of events and returns a slice of corresponding risk calculation results
func (c *CHA2DS2VAScPlugin) Calculate(es *plugin.EventStream, fhirEndpointURL string) ([]plugin.RiskServiceCalculationResult, error) {
var results []plugin.RiskServiceCalculationResult
// First make sure there is AFIB in the history, since this score is only valid for patients with AFIB
var hasAFib bool
for i := 0; !hasAFib && i < len(es.Events); i++ {
if es.Events[i].Type == "Condition" && !es.Events[i].End {
if cond, ok := es.Events[i].Value.(*models.Condition); ok {
hasAFib = fuzzyFindCondition("427.31", "http://hl7.org/fhir/sid/icd-9", cond)
}
}
}
if !hasAFib {
return nil, plugin.NewNotApplicableError("CHA2DS2-VASc is only applicable to patients with Atrial Fibrillation")
}
// Create the initial pie based on gender
pie := plugin.NewPie(fhirEndpointURL + "/Patient/" + es.Patient.Id)
pie.Slices = c.Config().DefaultPieSlices
if es.Patient.Gender == "female" {
pie.UpdateSliceValue("Gender", 1)
} else if es.Patient.Gender == "male" {
pie.UpdateSliceValue("Gender", 0)
}
// Now go through the event stream, updating the pie
var hasAfib bool
for _, event := range es.Events {
// NOTE: We are not paying attention to end times -- if it's in the patient history, we count it.
// Also guard against future dates (for example, our patient generator can create future events)
if event.End || event.Date.Local().After(time.Now()) {
continue
}
var isFactor bool
pie = pie.Clone(true)
switch event.Type {
case "Condition":
r := event.Value.(*models.Condition)
if fuzzyFindCondition("427.31", "http://hl7.org/fhir/sid/icd-9", r) {
// Found atrial fibrillation, so all events from here on should produce scores
hasAfib = true
isFactor = true
} else if fuzzyFindCondition("428", "http://hl7.org/fhir/sid/icd-9", r) {
pie.UpdateSliceValue("Congestive Heart Failure", 1)
isFactor = true
} else if fuzzyFindCondition("401", "http://hl7.org/fhir/sid/icd-9", r) {
pie.UpdateSliceValue("Hypertension", 1)
isFactor = true
} else if fuzzyFindCondition("250", "http://hl7.org/fhir/sid/icd-9", r) {
pie.UpdateSliceValue("Diabetes", 1)
isFactor = true
} else if fuzzyFindCondition("434", "http://hl7.org/fhir/sid/icd-9", r) {
pie.UpdateSliceValue("Stroke", 2)
isFactor = true
} else if fuzzyFindCondition("443", "http://hl7.org/fhir/sid/icd-9", r) {
pie.UpdateSliceValue("Vascular Disease", 1)
isFactor = true
}
case "Age":
age := event.Value.(int)
if age >= 65 && age < 75 {
pie.UpdateSliceValue("Age", 1)
isFactor = true
} else if age >= 75 {
pie.UpdateSliceValue("Age", 2)
isFactor = true
}
}
if hasAfib && isFactor {
score := pie.TotalValues()
percent := ScoreToStrokeRisk[score]
results = append(results, plugin.RiskServiceCalculationResult{
AsOf: event.Date,
Score: &score,
ProbabilityDecimal: &percent,
Pie: pie,
})
}
}
return results, nil
}
func (s *ServiceSuite) TestBuildRiskAssessmentBundle(c *C) {
one, two, three, four := 1, 2, 3, 4
results := []plugin.RiskServiceCalculationResult{
{
AsOf: time.Date(2000, 7, 14, 15, 59, 59, 999, time.UTC),
Score: &one,
Pie: plugin.NewPie(s.Server.URL + "/Patient/12345"),
}, {
AsOf: time.Date(2000, 7, 14, 16, 0, 0, 0, time.UTC),
Score: &one,
Pie: plugin.NewPie(s.Server.URL + "/Patient/12345"),
}, {
AsOf: time.Date(2012, 1, 1, 11, 0, 0, 0, time.UTC),
Score: &three,
Pie: plugin.NewPie(s.Server.URL + "/Patient/12345"),
}, {
AsOf: time.Date(2013, 1, 1, 11, 0, 0, 0, time.UTC),
Score: &four,
Pie: plugin.NewPie(s.Server.URL + "/Patient/12345"),
}, {
AsOf: time.Date(2014, 2, 3, 10, 0, 0, 0, time.UTC),
Score: &two,
Pie: plugin.NewPie(s.Server.URL + "/Patient/12345"),
},
}
pieBasisURL := "http://example.org/Pie"
simplePlugin := assessments.NewSimplePlugin()
bundle := buildRiskAssessmentBundle("12345", results, pieBasisURL, simplePlugin.Config())
c.Assert(bundle, NotNil)
c.Assert(bundle.Type, Equals, "transaction")
c.Assert(bundle.Entry, HasLen, 6)
// First check the delete entry
c.Assert(bundle.Entry[0].FullUrl, Equals, "")
c.Assert(bundle.Entry[0].Link, HasLen, 0)
c.Assert(bundle.Entry[0].Resource, IsNil)
c.Assert(bundle.Entry[0].Response, IsNil)
c.Assert(bundle.Entry[0].Search, IsNil)
c.Assert(bundle.Entry[0].Request.Method, Equals, "DELETE")
delURL := bundle.Entry[0].Request.Url
c.Assert(strings.HasPrefix(delURL, "RiskAssessment?"), Equals, true)
delValues, err := url.ParseQuery(strings.TrimPrefix(delURL, "RiskAssessment?"))
util.CheckErr(err)
c.Assert(delValues, HasLen, 2)
c.Assert(delValues.Get("patient"), Equals, "12345")
c.Assert(delValues.Get("method"), Equals, "http://interventionengine.org/risk-assessments|Simple")
// Now check the post entries
for i := 1; i < len(bundle.Entry); i++ {
entry := bundle.Entry[i]
result := results[i-1]
c.Assert(entry.FullUrl, Equals, "")
c.Assert(entry.Link, HasLen, 0)
c.Assert(entry.Response, IsNil)
c.Assert(entry.Search, IsNil)
c.Assert(entry.Request.Method, Equals, "POST")
c.Assert(entry.Request.Url, Equals, "RiskAssessment")
c.Assert(entry.Resource, NotNil)
ra, ok := entry.Resource.(*models.RiskAssessment)
c.Assert(ok, Equals, true)
c.Assert(ra.Id, Equals, "")
c.Assert(ra.Basis, HasLen, 1)
c.Assert(ra.Basis[0].Reference, Equals, pieBasisURL+"/"+result.Pie.Id.Hex())
c.Assert(ra.Date.Time, DeepEquals, result.AsOf)
c.Assert(ra.Date.Precision, Equals, models.Precision(models.Timestamp))
c.Assert(*ra.Method, DeepEquals, simplePlugin.Config().Method)
c.Assert(ra.Prediction, HasLen, 1)
c.Assert(*ra.Prediction[0].Outcome, DeepEquals, simplePlugin.Config().PredictedOutcome)
c.Assert(*ra.Prediction[0].ProbabilityDecimal, Equals, float64(*result.Score))
c.Assert(ra.Subject.Reference, Equals, "Patient/12345")
}
}