// This application will create a new record set in the patient matching test
// harness. This record set will be associated with a FHIR resource tag.
// It will generate a pair of matching patient records, apply the tag, and
// then upload them to the FHIR server. It will also upload an answer key.
func main() {
fhirURL := flag.String("fhirURL", "", "URL for the patient matching test harness server")
recordSetName := flag.String("name", "", "Name of the record set")
flag.Parse()
trimmedFhirURL := strings.TrimRight(*fhirURL, "/")
recordSet := &ptm_models.RecordSet{Name: *recordSetName}
recordSet.ResourceType = "Patient"
recordSet.Parameters = generateRecordSetParameters(trimmedFhirURL, *recordSetName)
recordSetURL := trimmedFhirURL + "/RecordSet"
rsj, err := json.Marshal(recordSet)
if err != nil {
return
}
body := bytes.NewReader(rsj)
resp, err := http.Post(recordSetURL, "application/json", body)
if err != nil {
fmt.Printf("Couldn't upload the resource: %s\n", err.Error())
return
}
decoder := json.NewDecoder(resp.Body)
decoder.Decode(recordSet)
fuzzers := []PatientFuzzer{AbbreviateFirstName, TransposeBirthDayMonth, ShuffleLastName}
tagCoding := models.Coding{System: tagURL, Code: tagValue(*recordSetName)}
meta := &models.Meta{Tag: []models.Coding{tagCoding}}
patientURL := trimmedFhirURL + "/Patient"
var matches []Match
for i := 0; i < 300; i++ {
patient := ptgen.GenerateDemographics()
patient.Meta = meta
source, err := PostAndGetLocation(patient, patientURL)
if err != nil {
return
}
fuzzer := fuzzers[rand.Intn(3)]
copy := CopyPatient(&patient)
fuzzer(copy)
target, err := PostAndGetLocation(copy, patientURL)
if err != nil {
return
}
matches = append(matches, Match{source, target})
}
bundle := &models.Bundle{}
bundle.Type = "document"
bundle.Id = bson.NewObjectId().Hex()
comp := models.Composition{}
comp.Date = &models.FHIRDateTime{Time: time.Now(), Precision: models.Timestamp}
comp.Type = &models.CodeableConcept{Coding: []models.Coding{models.Coding{System: "http://loinc.org", Code: "11503-0"}}}
comp.Title = "Answer Key for " + *recordSetName
comp.Status = "final"
comp.Subject = &models.Reference{Reference: fmt.Sprintf("%s/RecordSet/%s", trimmedFhirURL, recordSet.ID.Hex())}
compEntry := models.BundleEntryComponent{}
compEntry.Resource = &comp
bundle.Entry = append(bundle.Entry, compEntry)
for _, match := range matches {
entry := models.BundleEntryComponent{}
entry.FullUrl = match.Source
linkType := models.BundleLinkComponent{Relation: "type", Url: "http://hl7.org/fhir/Patient"}
linkRelated := models.BundleLinkComponent{Relation: "related", Url: match.Target}
entry.Link = []models.BundleLinkComponent{linkType, linkRelated}
score := 1.0
entry.Search = &models.BundleEntrySearchComponent{Score: &score}
bundle.Entry = append(bundle.Entry, entry)
}
PostAnswerKey(bundle, recordSet.ID.Hex(), trimmedFhirURL+"/AnswerKey")
}
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 (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)
}
