func (m *MongoSearchSuite) SetUpSuite(c *C) {
m.EST = time.FixedZone("EST", -5*60*60)
m.Local, _ = time.LoadLocation("Local")
//turnOnDebugLog()
// Set up the database
m.DBServer = &dbtest.DBServer{}
m.DBServer.SetPath(c.MkDir())
m.Session = m.DBServer.Session()
db := m.Session.DB("fhir-test")
m.MongoSearcher = &MongoSearcher{db}
// Read in the data in FHIR format
data, err := ioutil.ReadFile("../fixtures/search_test_data.json")
util.CheckErr(err)
maps := make([]interface{}, 19)
err = json.Unmarshal(data, &maps)
util.CheckErr(err)
for _, resourceMap := range maps {
r := models.MapToResource(resourceMap, true)
collection := models.PluralizeLowerResourceName(reflect.TypeOf(r).Elem().Name())
util.CheckErr(db.C(collection).Insert(r))
}
}
func (m *MongoSearchSuite) TestEncounterTypeQueryWithCountAndOffset(c *C) {
// First do with an offset of 1
q := Query{"Encounter", "type=http://www.ama-assn.org/go/cpt|99201&_offset=1&_count=1"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
offset1 := &models.Encounter{}
err = mq.One(offset1)
util.CheckErr(err)
// Now do an offset of 2
q = Query{"Encounter", "type=http://www.ama-assn.org/go/cpt|99201&_offset=2&_count=1"}
mq = m.MongoSearcher.CreateQuery(q)
num, err = mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
offset2 := &models.Encounter{}
err = mq.One(offset2)
util.CheckErr(err)
// Now make sure they are not the same
c.Assert(offset1.Id, Not(Equals), offset2.Id)
}
func (s *ServiceSuite) TestUnconfirmedResourcesDontGenerateEvents(c *C) {
data, err := ioutil.ReadFile("fixtures/brad_bradworth_event_source_bundle.json")
util.CheckErr(err)
bundle := new(models.Bundle)
json.Unmarshal(data, bundle)
// Switch a few resources to be unconfirmed
bundle.Entry[2].Resource.(*models.Condition).VerificationStatus = "refuted"
bundle.Entry[4].Resource.(*models.MedicationStatement).Status = "entered-in-error"
es, err := BundleToEventStream(bundle)
util.CheckErr(err)
c.Assert(es.Patient, NotNil)
c.Assert(es.Patient.Id, Equals, "507f1f77bcf86cd799439001")
c.Assert(es.Events, HasLen, 3)
loc := time.FixedZone("-0500", -5*60*60)
// Event 0 (Condition: Atrial Fibrillation)
c.Assert(es.Events[0].Date.Equal(time.Date(2012, time.September, 20, 8, 0, 0, 0, loc)), Equals, true)
c.Assert(es.Events[0].Type, Equals, "Condition")
c.Assert(es.Events[0].End, Equals, false)
c.Assert(es.Events[0].Value, DeepEquals, bundle.Entry[1].Resource)
// Event 1 (Condition: Cerebral infarction due to cerebral artery occlusion)
c.Assert(es.Events[1].Date.Equal(time.Date(2014, time.January, 17, 20, 35, 0, 0, loc)), Equals, true)
c.Assert(es.Events[1].Type, Equals, "Condition")
c.Assert(es.Events[1].End, Equals, false)
c.Assert(es.Events[1].Value, DeepEquals, bundle.Entry[3].Resource)
// Event 2 (Condition END: Cerebral infarction due to cerebral artery occlusion)
c.Assert(es.Events[2].Date.Equal(time.Date(2014, time.January, 17, 20, 40, 0, 0, loc)), Equals, true)
c.Assert(es.Events[2].Type, Equals, "Condition")
c.Assert(es.Events[2].End, Equals, true)
c.Assert(es.Events[2].Value, DeepEquals, bundle.Entry[3].Resource)
}
func performSearch(c *C, url string) *models.Bundle {
res, err := http.Get(url)
util.CheckErr(err)
decoder := json.NewDecoder(res.Body)
bundle := &models.Bundle{}
err = decoder.Decode(bundle)
util.CheckErr(err)
return bundle
}
func (s *ServerSuite) TestGetPatient(c *C) {
res, err := http.Get(s.Server.URL + "/Patient/" + s.FixtureId)
util.CheckErr(err)
decoder := json.NewDecoder(res.Body)
patient := &models.Patient{}
err = decoder.Decode(patient)
util.CheckErr(err)
c.Assert(patient.Name[0].Family[0], Equals, "Donald")
}
func LoadBundleFromFixture(fileName string) *Bundle {
data, err := os.Open(fileName)
defer data.Close()
util.CheckErr(err)
decoder := json.NewDecoder(data)
bundle := &Bundle{}
err = decoder.Decode(bundle)
util.CheckErr(err)
return bundle
}
func loadPatientFromFixture(fileName string) *models.Patient {
data, err := os.Open(fileName)
defer data.Close()
util.CheckErr(err)
decoder := json.NewDecoder(data)
patient := &models.Patient{}
err = decoder.Decode(patient)
util.CheckErr(err)
return patient
}
func LoadMapFromFixture(fileName string) interface{} {
data, err := os.Open(fileName)
defer data.Close()
util.CheckErr(err)
decoder := json.NewDecoder(data)
i := make(map[string]interface{})
err = decoder.Decode(&i)
util.CheckErr(err)
return i
}
func (r *RecordMatchRunSuite) SetUpSuite(c *C) {
data, err := os.Open("../fixtures/record-match-run-responses.json")
util.CheckErr(err)
defer data.Close()
decoder := json.NewDecoder(data)
rmr := &RecordMatchRun{}
err = decoder.Decode(rmr)
util.CheckErr(err)
r.Run = rmr
}
func do_dact(filename string) {
reader, err := dbxml.Open(filename)
util.CheckErr(err)
fmt.Println(">>>", filename)
docs, err := reader.All()
util.CheckErr(err)
for docs.Next() {
do_data(filename, docs.Name(), []byte(docs.Content()))
}
showmemstats()
reader.Close()
}
func (m *MongoSearchSuite) TestConditionReferenceQueryByPatientGender(c *C) {
q := Query{"Condition", "patient.gender=male"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 5)
q = Query{"Condition", "patient.gender=female"}
mq = m.MongoSearcher.CreateQuery(q)
num, err = mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
}
func (m *MongoSearchSuite) TestPatientNameStringQuery(c *C) {
q := Query{"Patient", "name=Peters"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 2)
q = Query{"Patient", "name=John"}
mq = m.MongoSearcher.CreateQuery(q)
num, err = mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
}
func (m *MongoSearchSuite) TestImmunizationDoseSequenceWrongNumberQuery(c *C) {
q := Query{"Immunization", "dose-sequence=0"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
q = Query{"Immunization", "dose-sequence=2"}
mq = m.MongoSearcher.CreateQuery(q)
num, err = mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func main() {
data, err := ioutil.ReadFile("xpath.xml")
util.CheckErr(err)
doc, err := xml.Parse(data, nil, nil, 0, xml.DefaultEncodingBytes)
util.CheckErr(err)
defer doc.Free()
n, err := doc.Root().Search(`/probe/header/@vendor`)
fmt.Println("Vendor:")
fmt.Println(n)
util.CheckErr(err)
}
func (i *IndividualResultSuite) TestFindResultsForMeasurePopulation(c *C) {
pq := PopulationQuery{MeasureID: "efgh", EffectiveDate: 1234, Population: InitialPatientPopulation}
pr, err := FindResultsForMeasurePopulation(i.Database, pq)
util.CheckErr(err)
c.Assert(pr.Total, Equals, 2)
pt := pr.Patients[0]
c.Assert(pt.Last, Equals, "A")
pq.Population = Denominator
pr, err = FindResultsForMeasurePopulation(i.Database, pq)
util.CheckErr(err)
c.Assert(pr.Total, Equals, 1)
pt = pr.Patients[0]
c.Assert(pt.Last, Equals, "A")
}
func (q *QualityReportSuite) TestFindOrCreateQualityReport(c *C) {
qr := &QualityReport{MeasureID: "abcd", EffectiveDate: 1234, NPI: "efg"}
id := bson.NewObjectId()
qr.ID = id
q.Database.C("query_cache").Insert(qr)
qrToFind := &QualityReport{MeasureID: "abcd", EffectiveDate: 1234}
err := FindOrCreateQualityReport(q.Database, qrToFind)
util.CheckErr(err)
c.Assert(qrToFind.NPI, Equals, "efg")
qrDoesntExist := &QualityReport{MeasureID: "foobar", EffectiveDate: 1234}
err = FindOrCreateQualityReport(q.Database, qrDoesntExist)
util.CheckErr(err)
count, _ := q.Database.C("query_cache").Count()
c.Assert(count, Equals, 2)
}
func (q *QualityReportSuite) TestFindQualityAndPopulateQualityReport(c *C) {
qr := &QualityReport{MeasureID: "abcd", EffectiveDate: 1234, NPI: "efg"}
id := bson.NewObjectId()
qr.ID = id
q.Database.C("query_cache").Insert(qr)
qrToFind := &QualityReport{MeasureID: "abcd", EffectiveDate: 1234}
exists, err := FindQualityAndPopulateQualityReport(q.Database, qrToFind)
util.CheckErr(err)
c.Assert(exists, Equals, true)
c.Assert(qrToFind.NPI, Equals, "efg")
qrDoesntExist := &QualityReport{MeasureID: "foobar", EffectiveDate: 1234}
exists, err = FindQualityAndPopulateQualityReport(q.Database, qrDoesntExist)
util.CheckErr(err)
c.Assert(exists, Equals, false)
}
func (s *ServerSuite) TestUpdatePatient(c *C) {
data, err := os.Open("../fixtures/patient-example-c.json")
util.CheckErr(err)
defer data.Close()
client := &http.Client{}
req, err := http.NewRequest("PUT", s.Server.URL+"/Patient/"+s.FixtureId, data)
util.CheckErr(err)
_, err = client.Do(req)
patientCollection := Database.C("patients")
patient := models.Patient{}
err = patientCollection.Find(bson.M{"_id": s.FixtureId}).One(&patient)
util.CheckErr(err)
c.Assert(patient.Name[0].Family[0], Equals, "Darkwing")
}
func (m *MongoSearchSuite) TestNonMatchingDeviceStringQuery(c *C) {
q := Query{"Device", "manufacturer=Zinc"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func main() {
doUtf8 := true
doRaw := true
if util.IsTerminal(os.Stdin) {
syntax()
return
}
for _, arg := range os.Args[1:] {
switch arg {
case "-r":
doUtf8 = false
case "-u":
doRaw = false
default:
syntax()
return
}
}
if !doUtf8 && !doRaw {
syntax()
return
}
data, err := ioutil.ReadAll(os.Stdin)
util.CheckErr(err)
str := string(data)
if doRaw {
fmt.Println("[[[RAW]]]")
n := 0
for i, p := range textcat.GetPatterns(str, false) {
if i == textcat.MaxPatterns {
break
}
n += 1
fmt.Printf("%s\t%d\n", p.S, p.I)
}
if n < textcat.MaxPatterns {
fmt.Fprintf(os.Stderr, "Warning: there are less than %d raw patterns\n", textcat.MaxPatterns)
}
}
if doUtf8 {
fmt.Println("[[[UTF8]]]")
n := 0
for i, p := range textcat.GetPatterns(str, true) {
if i == textcat.MaxPatterns {
break
}
n += 1
fmt.Printf("%s\t%d\n", p.S, p.I)
}
if n < textcat.MaxPatterns {
fmt.Fprintf(os.Stderr, "Warning: there are less than %d utf8 patterns\n", textcat.MaxPatterns)
}
}
}
func (m *MongoSearchSuite) TestSubscriptionURLQuery(c *C) {
q := Query{"Subscription", "url=https://biliwatch.com/customers/mount-auburn-miu/on-result"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
}
func (m *MongoSearchSuite) TestValueQuantityQueryByValueAndWrongUnit(c *C) {
q := Query{"Observation", "value-quantity=185||pounds"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func (m *MongoSearchSuite) TestNonMatchingPatientAddressStringQuery(c *C) {
q := Query{"Patient", "address=CA"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func (m *MongoSearchSuite) TestNonMatchingPatientNameStringQuery(c *C) {
q := Query{"Patient", "name=Peterson"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func (s *UploadSuite) TestUnorderedDependencies(c *C) {
// Setup the mock server
resourceCount := 0
ts := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
output := "Created"
decoder := json.NewDecoder(r.Body)
switch {
case strings.Contains(r.RequestURI, "Patient"):
if isValid(decoder, &models.Patient{}) {
w.Header().Add("Location", "http://localhost/Patient/1/_history/1")
}
case strings.Contains(r.RequestURI, "Condition"):
if isValid(decoder, &models.Condition{}) {
w.Header().Add("Location", "http://localhost/Condition/1") // Purposefully no _history to test this use case
}
}
fmt.Fprintln(w, output)
resourceCount++
}))
defer ts.Close()
patient := &models.Patient{Id: "a1"}
condition := &models.Condition{Id: "b2"}
condition.Patient = &models.Reference{Reference: "cid:a1"}
// Upload the resources in the wrong order
refMap, err := UploadResources([]interface{}{condition, patient}, ts.URL)
util.CheckErr(err)
// Assert that it processed all resources and correctly mapped refs
c.Assert(len(refMap), Equals, 2)
c.Assert(refMap["a1"], Equals, "Patient/1")
c.Assert(refMap["b2"], Equals, "Condition/1")
}
func (m *MongoSearchSuite) TestConditionIdQuery(c *C) {
q := Query{"Condition", "_id=8664777288161060797"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
cond := &models.Condition{}
err = mq.One(cond)
util.CheckErr(err)
cond2 := &models.Condition{}
err = m.Session.DB("fhir-test").C("conditions").FindId("8664777288161060797").One(cond2)
c.Assert(cond, DeepEquals, cond2)
}
func InsertResourceFromFile(db *mgo.Database, resourceType string, filePath string) interface{} {
collection := db.C(GetCollectionName(resourceType))
resource := NewStructForResourceName(resourceType)
LoadResourceFromFile(filePath, resource)
// Set a unique identifier to this resource
rptr := reflect.ValueOf(resource)
r := rptr.Elem()
logger.Log.WithFields(logrus.Fields{"kind": r.Kind()}).Debug("InsertResourceFromFile")
if r.Kind() == reflect.Struct {
logger.Log.WithFields(logrus.Fields{"method": "InsertResourceFromFile"}).Debug("Recognize struct")
f := r.FieldByName("ID")
if f.IsValid() {
logger.Log.WithFields(logrus.Fields{"method": "InsertResourceFromFile"}).Debug("Id field is valid")
if f.CanSet() {
objID := bson.NewObjectId()
logger.Log.WithFields(
logrus.Fields{"method": "InsertResourceFromFile", "obj id": objID}).Debug("ID field can be set")
f.Set(reflect.ValueOf(objID))
}
}
}
//logger.Log.WithFields(logrus.Fields{"resource": resource}).Info("InsertResourceFromFile")
err := collection.Insert(resource)
util.CheckErr(err)
return resource
}
func (m *MongoSearchSuite) TestConditionMultipleCodesWrongICD10Query(c *C) {
q := Query{"Condition", "code=http://hl7.org/fhir/sid/icd-9|428.0,http://snomed.info/sct|981000124106,http://hl7.org/fhir/sid/icd-10|I21.0"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 2)
}
func (m *MongoSearchSuite) TestValueQuantityQueryByValueAndSystemAndWrongCode(c *C) {
q := Query{"Observation", "value-quantity=185|http://unitsofmeasure.org|lbs"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 0)
}
func (m *MongoSearchSuite) TestDeviceStringQuery(c *C) {
q := Query{"Device", "manufacturer=Acme"}
mq := m.MongoSearcher.CreateQuery(q)
num, err := mq.Count()
util.CheckErr(err)
c.Assert(num, Equals, 1)
dev := &models.Device{}
err = mq.One(dev)
util.CheckErr(err)
dev2 := &models.Device{}
err = m.Session.DB("fhir-test").C("devices").FindId("7045606679745526995").One(dev2)
c.Assert(dev, DeepEquals, dev2)
}