原文链接:Processing FHIR Bundles using HAPI
另外一篇文章:FHIR transactions: the Search functionality
FHIR中是通过transaction来实现资源批量处理的.服务器对每个资源都单独处理,看起来就像是每个资源都是单独发送/提交的(除了批量更新的情况之外 要么都成功 要么都失败). 对于服务器而言,要处理bundle中每个资源的引用是很困难的,不论是新添加的资源或者是已经存在的. 其中有一点,服务器首先要判断这个资源服务器上存在不存在. 用例描述: 通过FHIR标准将某个可穿戴式设备(家用血糖仪)采集的血糖数据导入到数据仓库当中去. 血糖仪能够采集血糖数据,通过USB接口,利用桌面应用程序把数据取出来,发送给数据仓库.数据仓库期望 所存储的是结构化数据,这样子便于展示和临床决策支持之用. 思路: 大体上可以有多次操作和单次操作.
The application constructing a bundle may not be sure whether a particular resource will already exist at the time that the transaction is executed; this is typically the case with reference resources such as patient and provider. In this case, the bundle should contain a candidate resource with a cid: identifier, and an additional search parameter using an Atom link:
<link href="http://localhost/Patient?[parameters]" rel="search"/>
<entry>
<title>Patient details</title>
<id>cid:patient@bundle</id>
<updated>2014-05-28T22:12:21Z</updated>
<link href="http://localhost/Patient?identifier=PRP1660" rel="search"/>
<content type="text/xml">
<Patient xmlns="http://hl7.org/fhir">
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">Joe Bloggs</div>
</text>
<identifier>
<value value="PRP1660"/>
</identifier>
<name>
<text value="Joe Bloggs"/>
</name>
</Patient>
</content>
</entry>
方法2是一种自定义方法,需要发送方接受方的协调,FHIR中暂时没有定义和描述此类服务的方式. 方法3 你要定义消息事件类型,添加消息头资源,发送方和接受方需要协调 方法4POSTing to the root (#4) is attractive –provided that the server knows how to perform the ‘search processing’ (i.e. recognize the search link for a resource in the bundle and process accordingly. We could possibly use a profile so that the server can validate the bundle first. 通用型的事务处理过程是很复杂的,一方面包括了ID的重写操作,另一方面也要照顾bundle中需要删除操作的资源.通过profle资源来约束限制事务的处理过程的行为,比方说,服务器识别出profile,将其作为某次transaction的基准,而不需要实现所有功能.
不论选取那种方式,都需要在响应时返回一个bundle,包含了各个资源,每个资源都会分配一个ID. 下面的代码是方式2的范例,仅供参考.
类的示例：
public class GlucoseBundleProcessor {
private MyMongo _myMongo; //the database helper class
public GlucoseBundleProcessor(MyMongo myMongo){
_myMongo = myMongo;
}
//process with a Bundle...
public List<IResource> processGlucoseBundle(Bundle bundle) {
//generate a list of resources...
List<IResource> theResources = new ArrayList<IResource>(); //list of resources in bundle
for (BundleEntry entry : bundle.getEntries()) {
theResources.add(entry.getResource());
}
return this.process(theResources);
}
//process with a List of resources
public List<IResource> processGlucoseUploads(List<IResource> theResources) {
return this.process(theResources);
}
//process a bundle of glucose results, adding them to the repository...
private List<IResource> process(List<IResource> theResources) {
Patient patient = null; //this will be the patient resource. There should only be one....
Device device = null; //this will be the device resource. There should only be one....
List<IResource> insertList = new ArrayList<IResource>(); //list of resource to insert...
//First pass: assign all the CID:'s to a new ID. For more complex scenarios, we'd keep track of
//the changes, but for this profile, we don't need to...
//Note that this processing is highly specific to this profile !!! (For example, we ignore resources we don't expect to see)
for (IResource resource : theResources) {
String currentID = resource.getId().getValue();
if (currentID.substring(0,4).equals("cid:")) {
//Obviouslym the base URL should not be hard coded...
String newID = "http://myUrl/" + java.util.UUID.randomUUID().toString();
resource.setId(new IdDt(newID)); //and here's the new URL
}
//if this resource is a patient or device, then set the appropriate objects. We'll use these to set
// the references in the Observations in the second pass. In real life we'd want to be sure there is only one of each...
if (resource instanceof Patient) {
patient = (Patient) resource;
//we need to see if there's already a patient with this identifier. If there is - and there is one,
//then we use that Patient rather than adding a new one.
// This could be triggered by a 'rel=search' link on the bundle entry in a generic routine...
IdentifierDt identifier = patient.getIdentifier().size() >0 ? patient.getIdentifier().get(0) : null;
if (identifier != null) {
List<IResource> lst = _myMongo.findResourcesByIdentifier("Patient",identifier);
if (lst.size() == 1) {
//there is a single patient with that identifier...
patient = (Patient) lst.get(0);
resource.setId(patient.getId()); //set the identifier in the list. We need to return this...
} else if (lst.size() > 1) {
//here is where we ought to raise an error - we cannot know which one to use.
} else {
//if there isn't a single resource with this identifier, we need to add a new one
insertList.add(patient);
}
} else {
insertList.add(patient);
}
}
//look up a Device in the same way as as for a Patient
if (resource instanceof Device) {
device = (Device) resource;
IdentifierDt identifier = device.getIdentifier().size() >0 ? device.getIdentifier().get(0) : null;
if (identifier != null) {
List<IResource> lst = _myMongo.findResourcesByIdentifier("Device", identifier);
if (lst.size() == 1) {
device = (Device) lst.get(0);
resource.setId(device.getId()); //set the identifier in the list. We need to retuen this...
} else {
insertList.add(device);
}
} else {
insertList.add(device);
}
}
if (resource instanceof Observation) {
//we always add observations...
insertList.add(resource);
}
}
//Second Pass: Now we re-set all the resource references. This is very crude, and rather manual.
// We also really ought to make sure that the patient and the device have been set.....
for (IResource resource : theResources) {
if (resource instanceof Observation) {
Observation obs = (Observation) resource;
//this will be the correct ID - either a new one from the bundle, or a pre-existing one...
obs.setSubject(new ResourceReferenceDt(patient.getId()));
//set the performer - there can be more than one in the spec, hence a list...
List<ResourceReferenceDt> lstReferences = new ArrayList<ResourceReferenceDt>();
lstReferences.add(new ResourceReferenceDt(device.getId()));
obs.setPerformer(lstReferences);
}
}
//Last pass - write out the resources
for (IResource resource : insertList) {
_myMongo.saveResource(resource);
}
//we return the bundle with the updated resourceID's - as per the spec...
return theResources;
}
}
代码示例
@WebServlet(urlPatterns= {"/fhir/service/glucoseprocessor"}, displayName="Process Glucose bundle")
public class GlucoseResultServlet extends HttpServlet {
private MyMongo _myMongo;
private FhirContext _fhirContext;
@Override
public void init(ServletConfig config) throws ServletException {
//get the 'global' resources from the servlet context
ServletContext ctx = config.getServletContext();
_myMongo = (MyMongo) ctx.getAttribute("mymongo");
_fhirContext = (FhirContext) ctx.getAttribute("fhircontext");
}
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
PrintWriter out = response.getWriter();
//first parse into a fhir bundle (need to check the mime type here. Should also check for _format paramters as well)
//if we have to to this a lot, then a separate utility class would be good...
Bundle bundle = null;
IParser parser = null;
String ct = request.getHeader("content-type");
if (ct.equals("application/xml+fhir")){
parser = _fhirContext.newXmlParser();
bundle = parser.parseBundle(request.getReader());
} else if (ct.equals("application/json+fhir")){
parser = _fhirContext.newJsonParser();
bundle = parser.parseBundle(request.getReader());
} else {
OperationOutcome operationOutcome = new OperationOutcome();
operationOutcome.getText().setDiv("Invalid content-type header: " + ct);
parser = _fhirContext.newXmlParser();
response.setStatus(415); //unsupported media type
out.println(parser.encodeResourceToString(operationOutcome));
return;
}
//now we have a bundle we can process it...
GlucoseBundleProcessor glucoseBundleProcessor = new GlucoseBundleProcessor(_myMongo);
//process the bundle, and get back the list of resources with updated ID's...
List<IResource> resources = glucoseBundleProcessor.processGlucoseBundle(bundle);
Bundle newBundle = new Bundle();
newBundle.getTitle().setValue("Processed Glucose results");
newBundle.setId(new IdDt(java.util.UUID.randomUUID().toString()));
newBundle.setPublished(new InstantDt());
for (IResource resource : resources) {
newBundle.addResource(resource,_fhirContext,"http://localServer/fhir");
}
response.setStatus(201); //created
out.println(parser.encodeBundleToString(newBundle));
}
}