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Merge branch 'master' of https://github.com/srdc/onfhir
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Tuncay NAMLI committed Nov 10, 2021
2 parents a013172 + 2872568 commit 93c21ed
Showing 1 changed file with 33 additions and 102 deletions.
135 changes: 33 additions & 102 deletions onfhir-operations/src/main/scala/io/onfhir/operation/ExpandOperationHandler.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ class ExpandOperationHandler extends FHIROperationHandlerService {
final val SEARCHPARAM_ID: String = "_id"
final val SEARCHPARAM_URL: String = "url"
final val EXPAND_PARAM_FILTER: String = "filter"
final val EXPAND_PARAM_LANGUAGE: String = "displayLanguage"

/**
* Execute the operation and prepare the output parameters for the operation
Expand Down Expand Up @@ -107,89 +108,27 @@ class ExpandOperationHandler extends FHIROperationHandlerService {
fhirResponse.setResponse(resultingResource)
fhirResponse
}
/*
// Build the query from common and resource specific parameters
val query = ResourceQueryBuilder.buildCompleteQuery(RESOURCE_VALUESET, searchParams)
// Search the resources
val searchFuture = ResourceManager.searchDocument(RESOURCE_VALUESET, query, Config.fhirDefaultPageCount.toInt, 1, searchParams)
// Count the resources for the query (without paging)
val countFuture = ResourceManager.resourceCount(RESOURCE_VALUESET, query)
// Run these queries simultaneously
val aggregatedFutures = for {
document <- searchFuture
total <- countFuture
} yield (total, document)
aggregatedFutures map { futures =>
val totalCount = futures._1
val resources = futures._2._1 //actual matched documents
// 1) ValueSet not found - return 404
if (totalCount < 1) {
logger.debug("resource not found, return 404 NotFound...")
throw new NotFoundException(Seq(
OutcomeIssue(
ResultSeverityEnum.INFORMATION.getCode,
FHIRResponse.OUTCOME_CODES.INFORMATIONAL,
None,
if (searchParams.get(SEARCHPARAM_ID).isDefined)
Some(s"Resource with type '${RESOURCE_VALUESET}', id '${searchParams.get(SEARCHPARAM_ID).get.head.value}' not found...")
else
Some(s"Resource with type '${RESOURCE_VALUESET}' not found...")
,
Nil
)
))
}
// 2) ValueSet located
else {
// TODO: In case a ValueSet is queried with 'url', there can be multiple matching ValueSets (there shall not be!). But for the moment, we are just returning the first
val document = resources.head
val currentVersion = FHIRUtil.extractVersionIdFromBson(document)
val id = FHIRUtil.extractIdFromBson(document)
val location = Uri(FHIRUtil.resourceLocationWithVersion(RESOURCE_VALUESET, id, currentVersion))
val lastModified = DateTime(FHIRUtil.extractLastUpdateTimeFromBson(document))
// 2.1) convert bson into regular map format
val resource = FHIRUtil.clearExtraFields(document).fromBson
val resultingResource = buildExpansion(resource, operationRequest)
// 2.2) return the ValueSet
logger.debug("resource found, returning...")
val fhirResponse = new FHIROperationResponse(
StatusCodes.OK, //HTTP Status code
Some(location),
Some(lastModified), //HTTP Last-Modified header
Some(currentVersion)) //HTTP Etag header
fhirResponse.setResponse(resultingResource)
fhirResponse
}
}*/
}

def buildExpansion(valueSet:Resource, operationRequest: FHIROperationRequest):Resource = {
val compose = (valueSet \ VALUESET_COMPOSE).extractOrElse(JObject())

val filterKeys: Seq[String] = operationRequest.extractParamValue[String](EXPAND_PARAM_FILTER).getOrElse("").split(",")

val language: Option[String] = operationRequest.extractParamValue[String](EXPAND_PARAM_LANGUAGE)

// 1) First, filter all the matching concepts
val matchingList:Seq[JObject] = compose \ "include" match {
case includes:JArray => includes.arr.flatMap(include => {
include \ "concept" match {
case concepts:JArray => concepts.arr.flatMap(concept => {
if(containsAll(concept, filterKeys)){
val filteredConcept = filterConcept(concept, filterKeys, language)
if(filteredConcept.nonEmpty){
var matching = JObject()
(include \ "system").extractOpt[String].foreach(s => {matching = matching ~ ("system" -> s)})
(include \ "version").extractOpt[String].foreach(v => {matching = matching ~ ("version" -> v)})
(concept \ "code").extractOpt[String].foreach(c => {matching = matching ~ ("code" -> c)})
(concept \ "display").extractOpt[String].foreach(d => {matching = matching ~ ("display" -> d)})
(concept \ "extension").extractOpt[JArray].foreach(arr => {matching = matching ~ ("extension" -> arr)})
(filteredConcept.get \ "code").extractOpt[String].foreach(c => {matching = matching ~ ("code" -> c)})
(filteredConcept.get \ "display").extractOpt[String].foreach(d => {matching = matching ~ ("display" -> d)})
(filteredConcept.get \ "extension").extractOpt[JArray].foreach(arr => {matching = matching ~ ("extension" -> arr)})
Some(matching)
} else None
})
Expand All @@ -199,32 +138,11 @@ class ExpandOperationHandler extends FHIROperationHandlerService {
case _ => Nil
}

/*val matchingList = ListBuffer[mutable.LinkedHashMap[String, Any]]()
// 1) First, filter all the matching concepts
if(compose.contains("include")) {
compose("include").asInstanceOf[ListBuffer[Resource]] foreach { include =>
if(include.contains("concept")) {
include("concept").asInstanceOf[ListBuffer[Resource]] foreach { concept =>
if (containsAll(concept, filterKeys)) {
val matching = mutable.LinkedHashMap[String, Any]()
if (include.contains("system")) matching("system") = include("system")
if (include.contains("version")) matching("version") = include("version")
if (concept.contains("code")) matching("code") = concept("code")
if (concept.contains("extension")) matching("extension") = concept("extension")
if (concept.contains("display")) matching("display") = concept("display")
matchingList.append(matching)
}
}
}
}
}*/

var resultValueSet = valueSet
// 2) If there is any matching, then create an expansion
if(matchingList.nonEmpty) {
// 2.1) First, remove if any expansion exists in the full ValueSet
resultValueSet = resultValueSet.removeField(_._1 == VALUESET_EXPANSION).asInstanceOf[JObject]
//valueSet.remove(VALUESET_EXPANSION)

// 2.2) Then create the new expansion
val expansion =
Expand All @@ -234,13 +152,6 @@ class ExpandOperationHandler extends FHIROperationHandlerService {
("contains" -> matchingList)

resultValueSet = resultValueSet ~ (VALUESET_EXPANSION -> expansion)

/*val expansion = mutable.LinkedHashMap[String, Any]()
expansion.put("identifier", UUID.randomUUID().toString)
expansion.put("timestamp", DateTime.now.toIsoDateTimeString + "Z")
expansion.put("total", matchingList.size)
expansion.put("contains", matchingList)
valueSet.put(VALUESET_EXPANSION, expansion)*/
}

// In any case, remove the compose element completely
Expand All @@ -249,14 +160,34 @@ class ExpandOperationHandler extends FHIROperationHandlerService {
resultValueSet
}

def containsAll(input:JValue, keys:Seq[String]): Boolean = {
def filterConcept(input:JValue, keys:Seq[String], language: Option[String]): Option[JObject] = {

var output = JObject()
(input \ "code").extractOpt[String].foreach(c => {output = output ~ ("code" -> c)})
(input \ "display").extractOpt[String].foreach(d => {output = output ~ ("display" -> d)})
(input \ "extension").extractOpt[JArray].foreach(arr => {output = output ~ ("extension" -> arr)})

// If there is a language filter, update the display attribute accordingly
if (language.nonEmpty) {
val newDisplay: Option[String] = input \ "designation" match {
case designations: JArray => designations.arr.filter(designation => {
(designation \ "language").extractOpt[String].getOrElse("").equals(language.get)
}).map(designation => (designation \ "value").extractOpt[String].get).headOption
case _ => None
}

if (newDisplay.nonEmpty) {
output = output.removeField(_._1 == "display").asInstanceOf[JObject]
output = output ~ ("display" -> newDisplay.get)
}
}

keys foreach (key =>
if(!((input \ "display").extractOpt[String].getOrElse("").toLowerCase.contains(key.toLowerCase) ||
(input \ "code").extractOpt[String].getOrElse("").toLowerCase.contains(key.toLowerCase)))
return false
if(!((output \ "display").extractOpt[String].getOrElse("").toLowerCase.contains(key.toLowerCase) ||
(output \ "code").extractOpt[String].getOrElse("").toLowerCase.contains(key.toLowerCase)))
return None
)
true
Some(output)
}

}
}

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