func (s *ServiceSuite) TestBundleToEventStreamUnsupportedEvent(c *C) {
data, err := ioutil.ReadFile("fixtures/brad_bradworth_event_source_bundle.json")
util.CheckErr(err)
bundle := new(models.Bundle)
json.Unmarshal(data, bundle)
bundle.Entry = append(bundle.Entry, models.BundleEntryComponent{
Resource: &models.Encounter{},
Search: &models.BundleEntrySearchComponent{
Mode: "include",
},
})
_, err = BundleToEventStream(bundle)
c.Assert(err, NotNil)
c.Assert(err.Error(), Equals, "Unsupported: Converting Encounter to Event")
}
func (dal *mongoDataAccessLayer) Search(baseURL url.URL, searchQuery search.Query) (*models.Bundle, error) {
searcher := search.NewMongoSearcher(dal.Database)
var result interface{}
var err error
usesIncludes := len(searchQuery.Options().Include) > 0
usesRevIncludes := len(searchQuery.Options().RevInclude) > 0
// Only use (slower) pipeline if it is needed
if usesIncludes || usesRevIncludes {
result = models.NewSlicePlusForResourceName(searchQuery.Resource, 0, 0)
err = searcher.CreatePipeline(searchQuery).All(result)
} else {
result = models.NewSliceForResourceName(searchQuery.Resource, 0, 0)
err = searcher.CreateQuery(searchQuery).All(result)
}
if err != nil {
return nil, convertMongoErr(err)
}
includesMap := make(map[string]interface{})
var entryList []models.BundleEntryComponent
resultVal := reflect.ValueOf(result).Elem()
for i := 0; i < resultVal.Len(); i++ {
var entry models.BundleEntryComponent
entry.Resource = resultVal.Index(i).Addr().Interface()
entry.Search = &models.BundleEntrySearchComponent{Mode: "match"}
entryList = append(entryList, entry)
if usesIncludes || usesRevIncludes {
rpi, ok := entry.Resource.(ResourcePlusRelatedResources)
if ok {
for k, v := range rpi.GetIncludedAndRevIncludedResources() {
includesMap[k] = v
}
}
}
}
for _, v := range includesMap {
var entry models.BundleEntryComponent
entry.Resource = v
entry.Search = &models.BundleEntrySearchComponent{Mode: "include"}
entryList = append(entryList, entry)
}
var bundle models.Bundle
bundle.Id = bson.NewObjectId().Hex()
bundle.Type = "searchset"
bundle.Entry = entryList
options := searchQuery.Options()
// Need to get the true total (not just how many were returned in this response)
var total uint32
if resultVal.Len() == options.Count || resultVal.Len() == 0 {
// Need to get total count from the server, since there may be more or the offset was too high
intTotal, err := searcher.CreateQueryWithoutOptions(searchQuery).Count()
if err != nil {
return nil, convertMongoErr(err)
}
total = uint32(intTotal)
} else {
// We can figure out the total by adding the offset and # results returned
total = uint32(options.Offset + resultVal.Len())
}
bundle.Total = &total
// Add links for paging
bundle.Link = generatePagingLinks(baseURL, searchQuery, total)
return &bundle, nil
}
func (s *ServiceSuite) TestEndToEndCalculationsWithNACHADS(c *C) {
// Get the test data for Chad Chadworth (for the CHADS test -- get it?)
data, err := os.Open("fixtures/chad_chadworth_bundle.json")
util.CheckErr(err)
defer data.Close()
// Remove the AFib entry (index 5) so he is Not Applicable
bundle := new(models.Bundle)
decoder := json.NewDecoder(data)
err = decoder.Decode(bundle)
util.CheckErr(err)
bundle.Entry = append(bundle.Entry[:5], bundle.Entry[6:]...)
b, err := json.Marshal(bundle)
util.CheckErr(err)
// Store Chad Chadworth's modified information to Mongo
res, err := http.Post(s.Server.URL+"/", "application/json", bytes.NewBuffer(b))
util.CheckErr(err)
defer res.Body.Close()
// Get the response so we can pull out the patient ID
decoder = json.NewDecoder(res.Body)
responseBundle := new(models.Bundle)
err = decoder.Decode(responseBundle)
util.CheckErr(err)
patientID := responseBundle.Entry[0].Resource.(*models.Patient).Id
// Confirm there are no risk assessments or pies
raCollection := s.Database.C("riskassessments")
count, err := raCollection.Count()
util.CheckErr(err)
c.Assert(count, Equals, 0)
piesCollection := s.Database.C("pies")
count, err = piesCollection.Count()
util.CheckErr(err)
c.Assert(count, Equals, 0)
// Now register the plugins and request the calculation!
s.Service.RegisterPlugin(assessments.NewCHA2DS2VAScPlugin())
s.Service.RegisterPlugin(assessments.NewSimplePlugin())
err = s.Service.Calculate(patientID, s.Server.URL, s.Server.URL+"/pies")
util.CheckErr(err)
count, err = raCollection.Find(bson.M{"method.coding.code": "CHADS"}).Count()
util.CheckErr(err)
c.Assert(count, Equals, 1)
count, err = raCollection.Find(bson.M{"method.coding.code": "Simple"}).Count()
util.CheckErr(err)
c.Assert(count, Equals, 4)
count, err = piesCollection.Count()
util.CheckErr(err)
c.Assert(count, Equals, 4)
var ras []models.RiskAssessment
err = raCollection.Find(bson.M{"method.coding.code": "CHADS"}).All(&ras)
util.CheckErr(err)
// Check that the CHADS is not applicable
c.Assert(ras, HasLen, 1)
ra := ras[0]
c.Assert(ra.Subject.Reference, Equals, "Patient/"+patientID)
c.Assert(ra.Method.MatchesCode("http://interventionengine.org/risk-assessments", "CHADS"), Equals, true)
c.Assert(time.Now().Sub(ra.Date.Time) < time.Minute, Equals, true)
c.Assert(ra.Prediction, HasLen, 1)
c.Assert(ra.Prediction[0].Outcome.Text, Equals, "Stroke")
c.Assert(ra.Prediction[0].ProbabilityCodeableConcept.Coding, HasLen, 1)
c.Assert(ra.Prediction[0].ProbabilityCodeableConcept.Coding[0].System, Equals, "http://snomed.info/sct")
c.Assert(ra.Prediction[0].ProbabilityCodeableConcept.Coding[0].Code, Equals, "385432009")
c.Assert(ra.Prediction[0].ProbabilityCodeableConcept.Text, Equals, "Not applicable")
c.Assert(ra.Basis, HasLen, 0)
c.Assert(ra.Meta.Tag, HasLen, 1)
c.Assert(ra.Meta.Tag[0], DeepEquals, models.Coding{System: "http://interventionengine.org/tags/", Code: "MOST_RECENT"})
// Simple should still be good
ras = nil
err = raCollection.Find(bson.M{"method.coding.code": "Simple"}).Sort("date.time").All(&ras)
util.CheckErr(err)
loc := time.FixedZone("-0500", -5*60*60)
s.checkSimpleRiskAssessment(c, &ras[0], patientID, time.Date(2012, time.September, 20, 8, 0, 0, 0, loc), 1, false)
s.checkSimplePie(c, &ras[0], patientID, 1, 0)
s.checkSimpleRiskAssessment(c, &ras[1], patientID, time.Date(2013, time.September, 2, 10, 0, 0, 0, loc), 3, false)
s.checkSimplePie(c, &ras[1], patientID, 2, 1)
s.checkSimpleRiskAssessment(c, &ras[2], patientID, time.Date(2014, time.January, 17, 20, 35, 0, 0, loc), 4, false)
s.checkSimplePie(c, &ras[2], patientID, 3, 1)
s.checkSimpleRiskAssessment(c, &ras[3], patientID, time.Date(2014, time.January, 17, 20, 40, 0, 0, loc), 3, true)
s.checkSimplePie(c, &ras[3], patientID, 2, 1)
}
func (rc *ResourceController) IndexHandler(rw http.ResponseWriter, r *http.Request, next http.HandlerFunc) {
defer func() {
if r := recover(); r != nil {
rw.Header().Set("Content-Type", "application/json; charset=utf-8")
switch x := r.(type) {
case search.Error:
rw.WriteHeader(x.HTTPStatus)
json.NewEncoder(rw).Encode(x.OperationOutcome)
return
default:
outcome := &models.OperationOutcome{
Issue: []models.OperationOutcomeIssueComponent{
models.OperationOutcomeIssueComponent{
Severity: "fatal",
Code: "exception",
},
},
}
rw.WriteHeader(http.StatusInternalServerError)
json.NewEncoder(rw).Encode(outcome)
}
}
}()
result := models.NewSliceForResourceName(rc.Name, 0, 0)
// Create and execute the Mongo query based on the http query params
searcher := search.NewMongoSearcher(Database)
searchQuery := search.Query{Resource: rc.Name, Query: r.URL.RawQuery}
mgoQuery := searcher.CreateQuery(searchQuery)
// Horrible, horrible hack (for now) to ensure patients are sorted by name. This is needed by
// the frontend, else paging won't work correctly. This should be removed when the general
// sorting feature is implemented.
if rc.Name == "Patient" {
// To add insult to injury, mongo will not let us sort by family *and* given name:
// Executor error: BadValue cannot sort with keys that are parallel arrays
mgoQuery = mgoQuery.Sort("name.0.family.0" /*", name.0.given.0"*/, "_id")
}
err := mgoQuery.All(result)
if err != nil {
http.Error(rw, err.Error(), http.StatusInternalServerError)
}
var entryList []models.BundleEntryComponent
resultVal := reflect.ValueOf(result).Elem()
for i := 0; i < resultVal.Len(); i++ {
var entry models.BundleEntryComponent
entry.Resource = resultVal.Index(i).Addr().Interface()
entryList = append(entryList, entry)
}
var bundle models.Bundle
bundle.Id = bson.NewObjectId().Hex()
bundle.Type = "searchset"
bundle.Entry = entryList
options := searchQuery.Options()
// Need to get the true total (not just how many were returned in this response)
var total uint32
if resultVal.Len() == options.Count || resultVal.Len() == 0 {
// Need to get total count from the server, since there may be more or the offset was too high
intTotal, err := searcher.CreateQueryWithoutOptions(searchQuery).Count()
if err != nil {
http.Error(rw, err.Error(), http.StatusInternalServerError)
}
total = uint32(intTotal)
} else {
// We can figure out the total by adding the offset and # results returned
total = uint32(options.Offset + resultVal.Len())
}
bundle.Total = &total
// Add links for paging
bundle.Link = generatePagingLinks(r, searchQuery, total)
context.Set(r, rc.Name, reflect.ValueOf(result).Elem().Interface())
context.Set(r, "Resource", rc.Name)
context.Set(r, "Action", "search")
rw.Header().Set("Content-Type", "application/json; charset=utf-8")
rw.Header().Set("Access-Control-Allow-Origin", "*")
json.NewEncoder(rw).Encode(&bundle)
}