More work on terminology service
This commit is contained in:
parent
a2954ef181
commit
1b8843aa5e
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@ -22,15 +22,12 @@ package ca.uhn.fhir.rest.server;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.rest.annotation.GetPage;
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import ca.uhn.fhir.rest.annotation.GetPage;
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import ca.uhn.fhir.util.CoverageIgnore;
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public class PageProvider {
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public class PageProvider {
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// @GetPage(dstu1=true)
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// public Bundle getPageDstu1() {
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// return null;
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// }
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@GetPage()
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@GetPage()
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@CoverageIgnore
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public IResource getPage() {
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public IResource getPage() {
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return null;
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return null;
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}
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}
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@ -124,8 +124,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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private boolean myUseBrowserFriendlyContentTypes;
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private boolean myUseBrowserFriendlyContentTypes;
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/**
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/**
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* Constructor. Note that if no {@link FhirContext} is passed in to the server (either through the constructor, or through {@link #setFhirContext(FhirContext)}) the server will determine which
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* Constructor. Note that if no {@link FhirContext} is passed in to the server (either through the constructor, or
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* version of FHIR to support through classpath scanning. This is brittle, and it is highly recommended to explicitly specify a FHIR version.
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* through {@link #setFhirContext(FhirContext)}) the server will determine which
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* version of FHIR to support through classpath scanning. This is brittle, and it is highly recommended to explicitly
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* specify a FHIR version.
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*/
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*/
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public RestfulServer() {
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public RestfulServer() {
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this(null);
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this(null);
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@ -148,7 +150,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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/**
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/**
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* This method is called prior to sending a response to incoming requests. It is used to add custom headers.
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* This method is called prior to sending a response to incoming requests. It is used to add custom headers.
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* <p>
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* <p>
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* Use caution if overriding this method: it is recommended to call <code>super.addHeadersToResponse</code> to avoid inadvertantly disabling functionality.
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* Use caution if overriding this method: it is recommended to call <code>super.addHeadersToResponse</code> to avoid
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* inadvertantly disabling functionality.
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* </p>
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* </p>
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*/
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*/
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public void addHeadersToResponse(HttpServletResponse theHttpResponse) {
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public void addHeadersToResponse(HttpServletResponse theHttpResponse) {
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@ -383,7 +386,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* @deprecated As of HAPI FHIR 1.5, this property has been moved to {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
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* @deprecated As of HAPI FHIR 1.5, this property has been moved to
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* {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
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*/
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*/
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@Override
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@Override
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@Deprecated
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@Deprecated
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@ -397,7 +401,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Returns the default encoding to return (XML/JSON) if an incoming request does not specify a preference (either with the <code>_format</code> URL parameter, or with an <code>Accept</code> header
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* Returns the default encoding to return (XML/JSON) if an incoming request does not specify a preference (either
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* with the <code>_format</code> URL parameter, or with an <code>Accept</code> header
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* in the request. The default is {@link EncodingEnum#XML}. Will not return null.
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* in the request. The default is {@link EncodingEnum#XML}. Will not return null.
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*/
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*/
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@Override
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@Override
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@ -411,7 +416,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Gets the {@link FhirContext} associated with this server. For efficient processing, resource providers and plain providers should generally use this context if one is needed, as opposed to
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* Gets the {@link FhirContext} associated with this server. For efficient processing, resource providers and plain
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* providers should generally use this context if one is needed, as opposed to
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* creating their own.
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* creating their own.
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*/
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*/
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@Override
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@Override
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@ -449,7 +455,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Allows users of RestfulServer to override the getRequestPath method to let them build their custom request path implementation
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* Allows users of RestfulServer to override the getRequestPath method to let them build their custom request path
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* implementation
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*
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*
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* @param requestFullPath
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* @param requestFullPath
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* the full request path
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* the full request path
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@ -475,7 +482,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Get the server address strategy, which is used to determine what base URL to provide clients to refer to this server. Defaults to an instance of {@link IncomingRequestAddressStrategy}
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* Get the server address strategy, which is used to determine what base URL to provide clients to refer to this
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* server. Defaults to an instance of {@link IncomingRequestAddressStrategy}
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*/
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*/
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public IServerAddressStrategy getServerAddressStrategy() {
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public IServerAddressStrategy getServerAddressStrategy() {
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return myServerAddressStrategy;
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return myServerAddressStrategy;
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@ -495,7 +503,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Returns the method bindings for this server which are not specific to any particular resource type. This method is internal to HAPI and developers generally do not need to interact with it. Use
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* Returns the method bindings for this server which are not specific to any particular resource type. This method is
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* internal to HAPI and developers generally do not need to interact with it. Use
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* with caution, as it may change.
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* with caution, as it may change.
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*/
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*/
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public List<BaseMethodBinding<?>> getServerBindings() {
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public List<BaseMethodBinding<?>> getServerBindings() {
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@ -503,9 +512,11 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Returns the server conformance provider, which is the provider that is used to generate the server's conformance (metadata) statement if one has been explicitly defined.
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* Returns the server conformance provider, which is the provider that is used to generate the server's conformance
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* (metadata) statement if one has been explicitly defined.
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* <p>
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* <p>
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* By default, the ServerConformanceProvider for the declared version of FHIR is used, but this can be changed, or set to <code>null</code> to use the appropriate one for the given FHIR version.
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* By default, the ServerConformanceProvider for the declared version of FHIR is used, but this can be changed, or
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* set to <code>null</code> to use the appropriate one for the given FHIR version.
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* </p>
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* </p>
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*/
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*/
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public Object getServerConformanceProvider() {
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public Object getServerConformanceProvider() {
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@ -513,7 +524,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Gets the server's name, as exported in conformance profiles exported by the server. This is informational only, but can be helpful to set with something appropriate.
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* Gets the server's name, as exported in conformance profiles exported by the server. This is informational only,
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* but can be helpful to set with something appropriate.
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*
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*
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* @see RestfulServer#setServerName(String)
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* @see RestfulServer#setServerName(String)
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*/
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*/
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@ -526,7 +538,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Gets the server's version, as exported in conformance profiles exported by the server. This is informational only, but can be helpful to set with something appropriate.
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* Gets the server's version, as exported in conformance profiles exported by the server. This is informational only,
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* but can be helpful to set with something appropriate.
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*/
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*/
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public String getServerVersion() {
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public String getServerVersion() {
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return myServerVersion;
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return myServerVersion;
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@ -696,10 +709,12 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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} catch (Throwable e) {
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} catch (Throwable e) {
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/*
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/*
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* We have caught an exception during request processing. This might be because a handling method threw something they wanted to throw (e.g. UnprocessableEntityException because the request
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* We have caught an exception during request processing. This might be because a handling method threw
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* something they wanted to throw (e.g. UnprocessableEntityException because the request
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* had business requirement problems) or it could be due to bugs (e.g. NullPointerException).
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* had business requirement problems) or it could be due to bugs (e.g. NullPointerException).
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*
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*
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* First we let the interceptors have a crack at converting the exception into something HAPI can use (BaseServerResponseException)
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* First we let the interceptors have a crack at converting the exception into something HAPI can use
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* (BaseServerResponseException)
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*/
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*/
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BaseServerResponseException exception = null;
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BaseServerResponseException exception = null;
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for (int i = getInterceptors().size() - 1; i >= 0; i--) {
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for (int i = getInterceptors().size() - 1; i >= 0; i--) {
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}
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}
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/*
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/*
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* If none of the interceptors converted the exception, default behaviour is to keep the exception as-is if it extends BaseServerResponseException, otherwise wrap it in an
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* If none of the interceptors converted the exception, default behaviour is to keep the exception as-is if it
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* extends BaseServerResponseException, otherwise wrap it in an
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* InternalErrorException.
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* InternalErrorException.
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*/
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*/
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if (exception == null) {
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if (exception == null) {
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}
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}
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/**
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/**
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* Initializes the server. Note that this method is final to avoid accidentally introducing bugs in implementations, but subclasses may put initialization code in {@link #initialize()}, which is
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* Initializes the server. Note that this method is final to avoid accidentally introducing bugs in implementations,
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* but subclasses may put initialization code in {@link #initialize()}, which is
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* called immediately before beginning initialization of the restful server's internal init.
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* called immediately before beginning initialization of the restful server's internal init.
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*/
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*/
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@Override
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@Override
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@ -780,11 +797,6 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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// findSystemMethods(confProvider);
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// findSystemMethods(confProvider);
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findResourceMethods(confProvider);
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findResourceMethods(confProvider);
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} catch (Exception ex) {
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ourLog.error("An error occurred while loading request handlers!", ex);
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throw new ServletException("Failed to initialize FHIR Restful server", ex);
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}
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ourLog.trace("Invoking provider initialize methods");
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ourLog.trace("Invoking provider initialize methods");
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if (getResourceProviders() != null) {
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if (getResourceProviders() != null) {
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for (IResourceProvider iResourceProvider : getResourceProviders()) {
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for (IResourceProvider iResourceProvider : getResourceProviders()) {
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}
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}
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}
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}
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try {
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/*
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* This is a bit odd, but we have a placeholder @GetPage method for now
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* that gets the server to bind for the paging request. At some point
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* it would be nice to set things up so that client code could provide
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* an alternate implementation, but this isn't currently possible..
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*/
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findResourceMethods(new PageProvider());
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findResourceMethods(new PageProvider());
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} catch (Exception ex) {
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} catch (Exception ex) {
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ourLog.error("An error occurred while loading request handlers!", ex);
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ourLog.error("An error occurred while loading request handlers!", ex);
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throw new ServletException("Failed to initialize FHIR Restful server", ex);
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throw new ServletException("Failed to initialize FHIR Restful server", ex);
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}
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}
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/**
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/**
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* This method may be overridden by subclasses to do perform initialization that needs to be performed prior to the server being used.
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* This method may be overridden by subclasses to do perform initialization that needs to be performed prior to the
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* server being used.
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*
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*
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* @throws ServletException
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* @throws ServletException
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* If the initialization failed. Note that you should consider throwing {@link UnavailableException} (which extends {@link ServletException}), as this is a flag to the servlet container
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* If the initialization failed. Note that you should consider throwing {@link UnavailableException}
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* (which extends {@link ServletException}), as this is a flag to the servlet container
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* that the servlet is not usable.
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* that the servlet is not usable.
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*/
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*/
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protected void initialize() throws ServletException {
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protected void initialize() throws ServletException {
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}
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}
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/**
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/**
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* Should the server "pretty print" responses by default (requesting clients can always override this default by supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
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* Should the server "pretty print" responses by default (requesting clients can always override this default by
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* supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
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* parameter in the request URL.
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* parameter in the request URL.
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* <p>
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* <p>
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* The default is <code>false</code>
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* The default is <code>false</code>
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}
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}
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/**
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/**
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* Should the server attempt to decompress incoming request contents (default is <code>true</code>). Typically this should be set to <code>true</code> unless the server has other configuration to
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* Should the server attempt to decompress incoming request contents (default is <code>true</code>). Typically this
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* should be set to <code>true</code> unless the server has other configuration to
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* deal with decompressing request bodies (e.g. a filter applied to the whole server).
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* deal with decompressing request bodies (e.g. a filter applied to the whole server).
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*/
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*/
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public boolean isUncompressIncomingContents() {
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public boolean isUncompressIncomingContents() {
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}
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}
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/**
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/**
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* @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor} instead as an interceptor on your server and it will provide more useful syntax
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* @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
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* instead as an interceptor on your server and it will provide more useful syntax
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* highlighting. Deprocated in 1.4
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* highlighting. Deprocated in 1.4
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*/
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*/
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@Deprecated
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@Deprecated
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}
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}
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/**
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/**
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* Register a single provider. This could be a Resource Provider or a "plain" provider not associated with any resource.
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* Register a single provider. This could be a Resource Provider or a "plain" provider not associated with any
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* resource.
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*
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*
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* @param provider
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* @param provider
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* @throws Exception
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* @throws Exception
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@ -1053,8 +1077,7 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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String resourceName = getFhirContext().getResourceDefinition(resourceType).getName();
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String resourceName = getFhirContext().getResourceDefinition(resourceType).getName();
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if (myTypeToProvider.containsKey(resourceName)) {
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if (myTypeToProvider.containsKey(resourceName)) {
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throw new ServletException("Multiple resource providers return resource type[" + resourceName + "]: First[" + myTypeToProvider.get(resourceName).getClass().getCanonicalName()
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throw new ServletException("Multiple resource providers return resource type[" + resourceName + "]: First[" + myTypeToProvider.get(resourceName).getClass().getCanonicalName() + "] and Second[" + rsrcProvider.getClass().getCanonicalName() + "]");
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+ "] and Second[" + rsrcProvider.getClass().getCanonicalName() + "]");
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}
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}
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if (!inInit) {
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if (!inInit) {
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myResourceProviders.add(rsrcProvider);
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myResourceProviders.add(rsrcProvider);
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}
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}
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/**
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/**
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* Sets the profile tagging behaviour for the server. When set to a value other than {@link AddProfileTagEnum#NEVER} (which is the default), the server will automatically add a profile tag based on
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* Sets the profile tagging behaviour for the server. When set to a value other than {@link AddProfileTagEnum#NEVER}
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* (which is the default), the server will automatically add a profile tag based on
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* the class of the resource(s) being returned.
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* the class of the resource(s) being returned.
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*
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*
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* @param theAddProfileTag
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* @param theAddProfileTag
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* The behaviour enum (must not be null)
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* The behaviour enum (must not be null)
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* @deprecated As of HAPI FHIR 1.5, this property has been moved to {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
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* @deprecated As of HAPI FHIR 1.5, this property has been moved to
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* {@link FhirContext#setAddProfileTagWhenEncoding(AddProfileTagEnum)}
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*/
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*/
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@Deprecated
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@Deprecated
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@CoverageIgnore
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@CoverageIgnore
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@ -1192,7 +1217,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Should the server "pretty print" responses by default (requesting clients can always override this default by supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
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* Should the server "pretty print" responses by default (requesting clients can always override this default by
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* supplying an <code>Accept</code> header in the request, or a <code>_pretty</code>
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* parameter in the request URL.
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* parameter in the request URL.
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* <p>
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* <p>
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* The default is <code>false</code>
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* The default is <code>false</code>
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@ -1206,10 +1232,12 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
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}
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}
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/**
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/**
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* Sets the default encoding to return (XML/JSON) if an incoming request does not specify a preference (either with the <code>_format</code> URL parameter, or with an <code>Accept</code> header in
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* Sets the default encoding to return (XML/JSON) if an incoming request does not specify a preference (either with
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* the <code>_format</code> URL parameter, or with an <code>Accept</code> header in
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* the request. The default is {@link EncodingEnum#XML}.
|
* the request. The default is {@link EncodingEnum#XML}.
|
||||||
* <p>
|
* <p>
|
||||||
* Note when testing this feature: Some browsers will include "application/xml" in their Accept header, which means that the
|
* Note when testing this feature: Some browsers will include "application/xml" in their Accept header, which means
|
||||||
|
* that the
|
||||||
* </p>
|
* </p>
|
||||||
*/
|
*/
|
||||||
public void setDefaultResponseEncoding(EncodingEnum theDefaultResponseEncoding) {
|
public void setDefaultResponseEncoding(EncodingEnum theDefaultResponseEncoding) {
|
||||||
|
@ -1218,7 +1246,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Sets (enables/disables) the server support for ETags. Must not be <code>null</code>. Default is {@link #DEFAULT_ETAG_SUPPORT}
|
* Sets (enables/disables) the server support for ETags. Must not be <code>null</code>. Default is
|
||||||
|
* {@link #DEFAULT_ETAG_SUPPORT}
|
||||||
*
|
*
|
||||||
* @param theETagSupport
|
* @param theETagSupport
|
||||||
* The ETag support mode
|
* The ETag support mode
|
||||||
|
@ -1340,7 +1369,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Provide a server address strategy, which is used to determine what base URL to provide clients to refer to this server. Defaults to an instance of {@link IncomingRequestAddressStrategy}
|
* Provide a server address strategy, which is used to determine what base URL to provide clients to refer to this
|
||||||
|
* server. Defaults to an instance of {@link IncomingRequestAddressStrategy}
|
||||||
*/
|
*/
|
||||||
public void setServerAddressStrategy(IServerAddressStrategy theServerAddressStrategy) {
|
public void setServerAddressStrategy(IServerAddressStrategy theServerAddressStrategy) {
|
||||||
Validate.notNull(theServerAddressStrategy, "Server address strategy can not be null");
|
Validate.notNull(theServerAddressStrategy, "Server address strategy can not be null");
|
||||||
|
@ -1348,15 +1378,18 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Returns the server conformance provider, which is the provider that is used to generate the server's conformance (metadata) statement.
|
* Returns the server conformance provider, which is the provider that is used to generate the server's conformance
|
||||||
|
* (metadata) statement.
|
||||||
* <p>
|
* <p>
|
||||||
* By default, the ServerConformanceProvider implementation for the declared version of FHIR is used, but this can be changed, or set to <code>null</code> if you do not wish to export a conformance
|
* By default, the ServerConformanceProvider implementation for the declared version of FHIR is used, but this can be
|
||||||
|
* changed, or set to <code>null</code> if you do not wish to export a conformance
|
||||||
* statement.
|
* statement.
|
||||||
* </p>
|
* </p>
|
||||||
* Note that this method can only be called before the server is initialized.
|
* Note that this method can only be called before the server is initialized.
|
||||||
*
|
*
|
||||||
* @throws IllegalStateException
|
* @throws IllegalStateException
|
||||||
* Note that this method can only be called prior to {@link #init() initialization} and will throw an {@link IllegalStateException} if called after that.
|
* Note that this method can only be called prior to {@link #init() initialization} and will throw an
|
||||||
|
* {@link IllegalStateException} if called after that.
|
||||||
*/
|
*/
|
||||||
public void setServerConformanceProvider(Object theServerConformanceProvider) {
|
public void setServerConformanceProvider(Object theServerConformanceProvider) {
|
||||||
if (myStarted) {
|
if (myStarted) {
|
||||||
|
@ -1379,21 +1412,24 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Sets the server's name, as exported in conformance profiles exported by the server. This is informational only, but can be helpful to set with something appropriate.
|
* Sets the server's name, as exported in conformance profiles exported by the server. This is informational only,
|
||||||
|
* but can be helpful to set with something appropriate.
|
||||||
*/
|
*/
|
||||||
public void setServerName(String theServerName) {
|
public void setServerName(String theServerName) {
|
||||||
myServerName = theServerName;
|
myServerName = theServerName;
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Gets the server's version, as exported in conformance profiles exported by the server. This is informational only, but can be helpful to set with something appropriate.
|
* Gets the server's version, as exported in conformance profiles exported by the server. This is informational only,
|
||||||
|
* but can be helpful to set with something appropriate.
|
||||||
*/
|
*/
|
||||||
public void setServerVersion(String theServerVersion) {
|
public void setServerVersion(String theServerVersion) {
|
||||||
myServerVersion = theServerVersion;
|
myServerVersion = theServerVersion;
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Should the server attempt to decompress incoming request contents (default is <code>true</code>). Typically this should be set to <code>true</code> unless the server has other configuration to
|
* Should the server attempt to decompress incoming request contents (default is <code>true</code>). Typically this
|
||||||
|
* should be set to <code>true</code> unless the server has other configuration to
|
||||||
* deal with decompressing request bodies (e.g. a filter applied to the whole server).
|
* deal with decompressing request bodies (e.g. a filter applied to the whole server).
|
||||||
*/
|
*/
|
||||||
public void setUncompressIncomingContents(boolean theUncompressIncomingContents) {
|
public void setUncompressIncomingContents(boolean theUncompressIncomingContents) {
|
||||||
|
@ -1401,7 +1437,8 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor} instead as an interceptor on your server and it will provide more useful syntax
|
* @deprecated This feature did not work well, and will be removed. Use {@link ResponseHighlighterInterceptor}
|
||||||
|
* instead as an interceptor on your server and it will provide more useful syntax
|
||||||
* highlighting. Deprocated in 1.4
|
* highlighting. Deprocated in 1.4
|
||||||
*/
|
*/
|
||||||
@Deprecated
|
@Deprecated
|
||||||
|
|
Binary file not shown.
|
@ -25,68 +25,43 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||||
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Collections;
|
import java.util.Collections;
|
||||||
import java.util.Date;
|
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
|
|
||||||
import javax.annotation.PostConstruct;
|
|
||||||
import javax.annotation.PreDestroy;
|
|
||||||
|
|
||||||
import org.apache.commons.codec.binary.StringUtils;
|
import org.apache.commons.codec.binary.StringUtils;
|
||||||
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
|
|
||||||
import org.hl7.fhir.dstu3.hapi.validation.HapiWorkerContext;
|
import org.hl7.fhir.dstu3.hapi.validation.HapiWorkerContext;
|
||||||
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
|
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
|
||||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||||
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
||||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||||
import org.hl7.fhir.dstu3.model.Coding;
|
import org.hl7.fhir.dstu3.model.Coding;
|
||||||
import org.hl7.fhir.dstu3.model.IdType;
|
import org.hl7.fhir.dstu3.model.IdType;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet;
|
import org.hl7.fhir.dstu3.model.ValueSet;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
|
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
|
||||||
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
|
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
|
||||||
import org.hl7.fhir.instance.model.api.IIdType;
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
|
import org.springframework.beans.factory.annotation.Qualifier;
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
|
||||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
|
||||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
|
||||||
import ca.uhn.fhir.jpa.util.LogicUtil;
|
import ca.uhn.fhir.jpa.util.LogicUtil;
|
||||||
import ca.uhn.fhir.rest.param.TokenParam;
|
import ca.uhn.fhir.rest.param.TokenParam;
|
||||||
import ca.uhn.fhir.rest.param.UriParam;
|
|
||||||
import ca.uhn.fhir.rest.server.IBundleProvider;
|
|
||||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||||
|
|
||||||
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
|
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
private IJpaValidationSupportDstu3 myJpaValidationSupport;
|
@Qualifier("myJpaValidationSupportChainDstu3")
|
||||||
|
private IValidationSupport myValidationSupport;
|
||||||
private ValidationSupportChain myValidationSupport;
|
|
||||||
|
|
||||||
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
|
|
||||||
|
|
||||||
@Autowired
|
@Autowired
|
||||||
private IFhirResourceDaoCodeSystem<CodeSystem, CodeableConcept, Coding> myCodeSystemDao;
|
private IFhirResourceDaoCodeSystem<CodeSystem, CodeableConcept, Coding> myCodeSystemDao;
|
||||||
|
|
||||||
@Override
|
|
||||||
@PostConstruct
|
|
||||||
public void postConstruct() {
|
|
||||||
super.postConstruct();
|
|
||||||
myDefaultProfileValidationSupport = new DefaultProfileValidationSupport();
|
|
||||||
myValidationSupport = new ValidationSupportChain(myDefaultProfileValidationSupport, myJpaValidationSupport);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
@PreDestroy
|
|
||||||
public void purgeCaches() {
|
|
||||||
myDefaultProfileValidationSupport.flush();
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public ValueSet expand(IIdType theId, String theFilter) {
|
public ValueSet expand(IIdType theId, String theFilter) {
|
||||||
ValueSet source = myValidationSupport.fetchResource(getContext(), ValueSet.class, theId.getValue());
|
ValueSet source = myValidationSupport.fetchResource(getContext(), ValueSet.class, theId.getValue());
|
||||||
|
@ -301,4 +276,9 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
|
||||||
return null;
|
return null;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void purgeCaches() {
|
||||||
|
// nothing
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -119,7 +119,11 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||||
tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
|
tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
|
||||||
filters = {
|
filters = {
|
||||||
@TokenFilterDef(factory = LowerCaseFilterFactory.class),
|
@TokenFilterDef(factory = LowerCaseFilterFactory.class),
|
||||||
}) // Def
|
}),
|
||||||
|
@AnalyzerDef(name = "exactAnalyzer",
|
||||||
|
tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
|
||||||
|
filters = {
|
||||||
|
})
|
||||||
}
|
}
|
||||||
)
|
)
|
||||||
//@formatter:on
|
//@formatter:on
|
||||||
|
|
|
@ -26,6 +26,7 @@ import java.io.Serializable;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Collection;
|
import java.util.Collection;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
import javax.persistence.CascadeType;
|
import javax.persistence.CascadeType;
|
||||||
import javax.persistence.Column;
|
import javax.persistence.Column;
|
||||||
|
@ -40,6 +41,7 @@ import javax.persistence.ManyToOne;
|
||||||
import javax.persistence.OneToMany;
|
import javax.persistence.OneToMany;
|
||||||
import javax.persistence.SequenceGenerator;
|
import javax.persistence.SequenceGenerator;
|
||||||
import javax.persistence.Table;
|
import javax.persistence.Table;
|
||||||
|
import javax.persistence.Transient;
|
||||||
import javax.persistence.UniqueConstraint;
|
import javax.persistence.UniqueConstraint;
|
||||||
|
|
||||||
import org.apache.commons.lang3.Validate;
|
import org.apache.commons.lang3.Validate;
|
||||||
|
@ -47,13 +49,22 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
|
||||||
import org.apache.commons.lang3.builder.HashCodeBuilder;
|
import org.apache.commons.lang3.builder.HashCodeBuilder;
|
||||||
import org.apache.commons.lang3.builder.ToStringBuilder;
|
import org.apache.commons.lang3.builder.ToStringBuilder;
|
||||||
import org.apache.commons.lang3.builder.ToStringStyle;
|
import org.apache.commons.lang3.builder.ToStringStyle;
|
||||||
|
import org.hibernate.search.annotations.Analyze;
|
||||||
|
import org.hibernate.search.annotations.Analyzer;
|
||||||
|
import org.hibernate.search.annotations.Field;
|
||||||
|
import org.hibernate.search.annotations.Fields;
|
||||||
|
import org.hibernate.search.annotations.Indexed;
|
||||||
|
import org.hibernate.search.annotations.Store;
|
||||||
|
|
||||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
||||||
|
|
||||||
|
//@formatter:off
|
||||||
@Entity
|
@Entity
|
||||||
|
@Indexed()
|
||||||
@Table(name="TRM_CONCEPT", uniqueConstraints= {
|
@Table(name="TRM_CONCEPT", uniqueConstraints= {
|
||||||
@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
|
@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
|
||||||
})
|
})
|
||||||
|
//@formatter:on
|
||||||
public class TermConcept implements Serializable {
|
public class TermConcept implements Serializable {
|
||||||
private static final int MAX_DESC_LENGTH = 400;
|
private static final int MAX_DESC_LENGTH = 400;
|
||||||
|
|
||||||
|
@ -63,23 +74,46 @@ public class TermConcept implements Serializable {
|
||||||
private Collection<TermConceptParentChildLink> myChildren;
|
private Collection<TermConceptParentChildLink> myChildren;
|
||||||
|
|
||||||
@Column(name="CODE", length=100, nullable=false)
|
@Column(name="CODE", length=100, nullable=false)
|
||||||
|
@Fields({
|
||||||
|
@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),
|
||||||
|
})
|
||||||
private String myCode;
|
private String myCode;
|
||||||
|
|
||||||
@ManyToOne()
|
@ManyToOne()
|
||||||
@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
|
@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
|
||||||
private TermCodeSystemVersion myCodeSystem;
|
private TermCodeSystemVersion myCodeSystem;
|
||||||
|
|
||||||
|
//@formatter:off
|
||||||
@Column(name="DISPLAY", length=MAX_DESC_LENGTH, nullable=true)
|
@Column(name="DISPLAY", length=MAX_DESC_LENGTH, nullable=true)
|
||||||
|
@Fields({
|
||||||
|
@Field(name = "myDisplay", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
|
||||||
|
@Field(name = "myDisplayEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
|
||||||
|
@Field(name = "myDisplayNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
|
||||||
|
@Field(name = "myDisplayPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
|
||||||
|
})
|
||||||
private String myDisplay;
|
private String myDisplay;
|
||||||
|
//@formatter:on
|
||||||
@OneToMany(cascade=CascadeType.ALL, fetch=FetchType.LAZY, mappedBy="myChild")
|
|
||||||
private Collection<TermConceptParentChildLink> myParents;
|
|
||||||
|
|
||||||
@Id()
|
@Id()
|
||||||
@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
|
@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
|
||||||
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PID")
|
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PID")
|
||||||
@Column(name="PID")
|
@Column(name="PID")
|
||||||
private Long myPid;
|
private Long myId;
|
||||||
|
|
||||||
|
@Transient
|
||||||
|
@Fields({
|
||||||
|
@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
|
||||||
|
})
|
||||||
|
private String myParentPids;
|
||||||
|
|
||||||
|
@OneToMany(cascade=CascadeType.ALL, fetch=FetchType.LAZY, mappedBy="myChild")
|
||||||
|
private Collection<TermConceptParentChildLink> myParents;
|
||||||
|
|
||||||
|
@Column(name="CODESYSTEM_PID", insertable=false, updatable=false)
|
||||||
|
@Fields({
|
||||||
|
@Field(name="myCodeSystemVersionPid")
|
||||||
|
})
|
||||||
|
private long myCodeSystemVersionPid;
|
||||||
|
|
||||||
public TermConcept() {
|
public TermConcept() {
|
||||||
super();
|
super();
|
||||||
|
@ -100,6 +134,12 @@ public class TermConcept implements Serializable {
|
||||||
return this;
|
return this;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public void addChildren(List<TermConcept> theChildren, RelationshipTypeEnum theRelationshipType) {
|
||||||
|
for (TermConcept next : theChildren) {
|
||||||
|
addChild(next, theRelationshipType);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public boolean equals(Object theObj) {
|
public boolean equals(Object theObj) {
|
||||||
if (!(theObj instanceof TermConcept)) {
|
if (!(theObj instanceof TermConcept)) {
|
||||||
|
@ -110,20 +150,15 @@ public class TermConcept implements Serializable {
|
||||||
}
|
}
|
||||||
|
|
||||||
TermConcept obj = (TermConcept)theObj;
|
TermConcept obj = (TermConcept)theObj;
|
||||||
if (obj.myPid == null) {
|
if (obj.myId == null) {
|
||||||
return false;
|
return false;
|
||||||
}
|
}
|
||||||
|
|
||||||
EqualsBuilder b = new EqualsBuilder();
|
EqualsBuilder b = new EqualsBuilder();
|
||||||
b.append(myPid, obj.myPid);
|
b.append(myId, obj.myId);
|
||||||
return b.isEquals();
|
return b.isEquals();
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
|
||||||
public String toString() {
|
|
||||||
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();
|
|
||||||
}
|
|
||||||
|
|
||||||
public Collection<TermConceptParentChildLink> getChildren() {
|
public Collection<TermConceptParentChildLink> getChildren() {
|
||||||
if (myChildren == null) {
|
if (myChildren == null) {
|
||||||
myChildren = new ArrayList<TermConceptParentChildLink>();
|
myChildren = new ArrayList<TermConceptParentChildLink>();
|
||||||
|
@ -143,6 +178,10 @@ public class TermConcept implements Serializable {
|
||||||
return myDisplay;
|
return myDisplay;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public Long getId() {
|
||||||
|
return myId;
|
||||||
|
}
|
||||||
|
|
||||||
public Collection<TermConceptParentChildLink> getParents() {
|
public Collection<TermConceptParentChildLink> getParents() {
|
||||||
if (myParents == null) {
|
if (myParents == null) {
|
||||||
myParents = new ArrayList<TermConceptParentChildLink>();
|
myParents = new ArrayList<TermConceptParentChildLink>();
|
||||||
|
@ -153,7 +192,7 @@ public class TermConcept implements Serializable {
|
||||||
@Override
|
@Override
|
||||||
public int hashCode() {
|
public int hashCode() {
|
||||||
HashCodeBuilder b = new HashCodeBuilder();
|
HashCodeBuilder b = new HashCodeBuilder();
|
||||||
b.append(myPid);
|
b.append(myId);
|
||||||
return b.toHashCode();
|
return b.toHashCode();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -163,6 +202,9 @@ public class TermConcept implements Serializable {
|
||||||
|
|
||||||
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
|
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
|
||||||
myCodeSystem = theCodeSystem;
|
myCodeSystem = theCodeSystem;
|
||||||
|
if (theCodeSystem.getPid() != null) {
|
||||||
|
myCodeSystemVersionPid = theCodeSystem.getPid();
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
public void setDisplay(String theDisplay) {
|
public void setDisplay(String theDisplay) {
|
||||||
|
@ -172,10 +214,21 @@ public class TermConcept implements Serializable {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
public void addChildren(List<TermConcept> theChildren, RelationshipTypeEnum theRelationshipType) {
|
public void setParentPids(Set<Long> theParentPids) {
|
||||||
for (TermConcept next : theChildren) {
|
StringBuilder b = new StringBuilder();
|
||||||
addChild(next, theRelationshipType);
|
for (Long next : theParentPids) {
|
||||||
|
if (b.length() > 0) {
|
||||||
|
b.append(' ');
|
||||||
}
|
}
|
||||||
|
b.append(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
myParentPids = b.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String toString() {
|
||||||
|
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -28,6 +28,10 @@ import java.util.List;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
import java.util.concurrent.TimeUnit;
|
import java.util.concurrent.TimeUnit;
|
||||||
|
|
||||||
|
import javax.persistence.EntityManager;
|
||||||
|
import javax.persistence.PersistenceContext;
|
||||||
|
import javax.persistence.PersistenceContextType;
|
||||||
|
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
import org.springframework.transaction.annotation.Propagation;
|
import org.springframework.transaction.annotation.Propagation;
|
||||||
import org.springframework.transaction.annotation.Transactional;
|
import org.springframework.transaction.annotation.Transactional;
|
||||||
|
@ -71,6 +75,9 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
@Autowired
|
@Autowired
|
||||||
protected FhirContext myContext;
|
protected FhirContext myContext;
|
||||||
|
|
||||||
|
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
|
||||||
|
protected EntityManager myEntityManager;
|
||||||
|
|
||||||
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
|
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
|
||||||
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
|
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
|
||||||
TermConcept nextChild = nextChildLink.getChild();
|
TermConcept nextChild = nextChildLink.getChild();
|
||||||
|
@ -170,32 +177,39 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
return retVal;
|
return retVal;
|
||||||
}
|
}
|
||||||
|
|
||||||
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack) {
|
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, HashSet<Long> thePidsInHierarchy) {
|
||||||
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
|
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (theConceptsStack.size() % 10000 == 0) {
|
if (theConceptsStack.size() % 10000 == 0) {
|
||||||
ourLog.info("Have saved {} concepts",theConceptsStack.size());
|
ourLog.info("Have saved {} concepts", theConceptsStack.size());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
theConcept.setParentPids(thePidsInHierarchy);
|
||||||
|
theConcept.setCodeSystem(theCodeSystem);
|
||||||
|
|
||||||
|
TermConcept flushedConcept = myConceptDao.saveAndFlush(theConcept);
|
||||||
|
thePidsInHierarchy.add(flushedConcept.getId());
|
||||||
|
try {
|
||||||
for (TermConceptParentChildLink next : theConcept.getChildren()) {
|
for (TermConceptParentChildLink next : theConcept.getChildren()) {
|
||||||
persistChildren(next.getChild(), theCodeSystem, theConceptsStack);
|
persistChildren(next.getChild(), theCodeSystem, theConceptsStack, thePidsInHierarchy);
|
||||||
}
|
}
|
||||||
|
|
||||||
myConceptDao.save(theConcept);
|
|
||||||
|
|
||||||
for (TermConceptParentChildLink next : theConcept.getChildren()) {
|
for (TermConceptParentChildLink next : theConcept.getChildren()) {
|
||||||
myConceptParentChildLinkDao.save(next);
|
myConceptParentChildLinkDao.save(next);
|
||||||
}
|
}
|
||||||
|
} finally {
|
||||||
|
thePidsInHierarchy.remove(flushedConcept.getId());
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
@Transactional(propagation = Propagation.REQUIRED)
|
@Transactional(propagation = Propagation.REQUIRED)
|
||||||
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, TermCodeSystemVersion theCodeSystem) {
|
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, TermCodeSystemVersion theCodeSystemVersion) {
|
||||||
ourLog.info("Storing code system");
|
ourLog.info("Storing code system");
|
||||||
|
|
||||||
ValidateUtil.isNotNullOrThrowInvalidRequest(theCodeSystem.getResource() != null, "No resource supplied");
|
ValidateUtil.isNotNullOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
|
||||||
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
|
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
|
||||||
|
|
||||||
// Grab the existing versions so we can delete them later
|
// Grab the existing versions so we can delete them later
|
||||||
|
@ -207,11 +221,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
if (codeSystem == null) {
|
if (codeSystem == null) {
|
||||||
codeSystem = new TermCodeSystem();
|
codeSystem = new TermCodeSystem();
|
||||||
}
|
}
|
||||||
codeSystem.setResource(theCodeSystem.getResource());
|
codeSystem.setResource(theCodeSystemVersion.getResource());
|
||||||
codeSystem.setCodeSystemUri(theSystemUri);
|
codeSystem.setCodeSystemUri(theSystemUri);
|
||||||
myCodeSystemDao.save(codeSystem);
|
myCodeSystemDao.save(codeSystem);
|
||||||
} else {
|
} else {
|
||||||
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystem.getResource().getId())) {
|
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
|
||||||
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvc.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri, codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvc.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri, codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||||
throw new UnprocessableEntityException(msg);
|
throw new UnprocessableEntityException(msg);
|
||||||
}
|
}
|
||||||
|
@ -222,24 +236,24 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
// Validate the code system
|
// Validate the code system
|
||||||
IdentityHashMap<TermConcept, Object> conceptsStack = new IdentityHashMap<TermConcept, Object>();
|
IdentityHashMap<TermConcept, Object> conceptsStack = new IdentityHashMap<TermConcept, Object>();
|
||||||
int totalCodeCount = 0;
|
int totalCodeCount = 0;
|
||||||
for (TermConcept next : theCodeSystem.getConcepts()) {
|
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
|
||||||
totalCodeCount += validateConceptForStorage(next, theCodeSystem, conceptsStack);
|
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack);
|
||||||
}
|
}
|
||||||
|
|
||||||
ourLog.info("Saving version");
|
ourLog.info("Saving version");
|
||||||
|
|
||||||
myCodeSystemVersionDao.save(theCodeSystem);
|
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
|
||||||
|
|
||||||
ourLog.info("Saving code system");
|
ourLog.info("Saving code system");
|
||||||
|
|
||||||
codeSystem.setCurrentVersion(theCodeSystem);
|
codeSystem.setCurrentVersion(theCodeSystemVersion);
|
||||||
myCodeSystemDao.save(codeSystem);
|
codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
|
||||||
|
|
||||||
ourLog.info("Saving {} concepts...", totalCodeCount);
|
ourLog.info("Saving {} concepts...", totalCodeCount);
|
||||||
|
|
||||||
conceptsStack = new IdentityHashMap<TermConcept, Object>();
|
conceptsStack = new IdentityHashMap<TermConcept, Object>();
|
||||||
for (TermConcept next : theCodeSystem.getConcepts()) {
|
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
|
||||||
persistChildren(next, theCodeSystem, conceptsStack);
|
persistChildren(next, codeSystemVersion, conceptsStack, new HashSet<Long>());
|
||||||
}
|
}
|
||||||
|
|
||||||
/*
|
/*
|
||||||
|
@ -280,7 +294,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
ValidateUtil.isNotNullOrThrowInvalidRequest(theConcept.getCodeSystem() == theCodeSystem, "Codesystem contains a code which does not reference the codesystem");
|
ValidateUtil.isNotNullOrThrowInvalidRequest(theConcept.getCodeSystem() == theCodeSystem, "Codesystem contains a code which does not reference the codesystem");
|
||||||
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code which does not reference the codesystem");
|
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code which does not reference the codesystem");
|
||||||
|
|
||||||
|
|
||||||
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
|
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
|
||||||
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
|
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
|
||||||
}
|
}
|
||||||
|
@ -306,5 +319,4 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
|
||||||
return myConceptDao.findByCodeSystemAndCode(csv, theCode);
|
return myConceptDao.findByCodeSystemAndCode(csv, theCode);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -24,8 +24,18 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||||
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.Collections;
|
import java.util.Collections;
|
||||||
|
import java.util.HashSet;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
import org.apache.lucene.search.BooleanQuery;
|
||||||
|
import org.apache.lucene.search.BooleanQuery.Builder;
|
||||||
|
import org.apache.lucene.search.Filter;
|
||||||
|
import org.apache.lucene.search.Query;
|
||||||
|
import org.hibernate.search.jpa.FullTextEntityManager;
|
||||||
|
import org.hibernate.search.jpa.FullTextQuery;
|
||||||
|
import org.hibernate.search.query.dsl.BooleanJunction;
|
||||||
|
import org.hibernate.search.query.dsl.QueryBuilder;
|
||||||
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
|
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
|
||||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||||
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
|
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
|
||||||
|
@ -38,6 +48,7 @@ import org.hl7.fhir.dstu3.model.ValueSet;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
|
||||||
|
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
|
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
|
||||||
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander;
|
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander;
|
||||||
|
@ -54,6 +65,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||||
import ca.uhn.fhir.rest.method.RequestDetails;
|
import ca.uhn.fhir.rest.method.RequestDetails;
|
||||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||||
|
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||||
import ca.uhn.fhir.util.CoverageIgnore;
|
import ca.uhn.fhir.util.CoverageIgnore;
|
||||||
import ca.uhn.fhir.util.UrlUtil;
|
import ca.uhn.fhir.util.UrlUtil;
|
||||||
|
|
||||||
|
@ -109,24 +121,50 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
|
||||||
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
|
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
|
||||||
TermCodeSystemVersion csv = cs.getCurrentVersion();
|
TermCodeSystemVersion csv = cs.getCurrentVersion();
|
||||||
|
|
||||||
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
|
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
|
||||||
|
QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
|
||||||
|
BooleanJunction<?> bool = qb.bool();
|
||||||
|
|
||||||
boolean haveSpecificWantedCode = false;
|
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
|
||||||
|
|
||||||
|
Set<String> wantCodes = new HashSet<String>();
|
||||||
for (ConceptReferenceComponent next : theInclude.getConcept()) {
|
for (ConceptReferenceComponent next : theInclude.getConcept()) {
|
||||||
String nextCode = next.getCode();
|
String nextCode = next.getCode();
|
||||||
if (isNotBlank(nextCode)) {
|
if (isNotBlank(nextCode)) {
|
||||||
haveSpecificWantedCode = true;
|
wantCodes.add(nextCode);
|
||||||
TermConcept termCode = myConceptDao.findByCodeSystemAndCode(csv, nextCode);
|
bool.should(qb.keyword().onField("myCode").matching(nextCode).createQuery());
|
||||||
if (termCode != null) {
|
|
||||||
addCodeIfFilterMatches(retVal, termCode, theInclude.getFilter(), nextCode);
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (!haveSpecificWantedCode) {
|
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
|
||||||
for(TermConcept next : myConceptDao.findByCodeSystemVersion(csv)) {
|
if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
|
||||||
addCodeIfFilterMatches(retVal, next, theInclude.getFilter(), system);
|
if (isNotBlank(nextFilter.getValue())) {
|
||||||
|
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
|
||||||
}
|
}
|
||||||
|
} else if (nextFilter.getOp() == FilterOperator.ISA) {
|
||||||
|
if (isNotBlank(nextFilter.getValue())) {
|
||||||
|
TermConcept code = super.findCode(system, nextFilter.getValue());
|
||||||
|
bool.must(qb.keyword().onField("myParentPids").matching(code.getId()).createQuery());
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
|
||||||
|
|
||||||
|
Query luceneQuery = bool.createQuery();
|
||||||
|
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
|
||||||
|
@SuppressWarnings("unchecked")
|
||||||
|
List<TermConcept> result = jpaQuery.getResultList();
|
||||||
|
for (TermConcept nextConcept : result) {
|
||||||
|
if (!wantCodes.isEmpty() && !wantCodes.contains(nextConcept.getCode())) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
ValueSetExpansionContainsComponent contains = retVal.addContains();
|
||||||
|
contains.setCode(nextConcept.getCode());
|
||||||
|
contains.setSystem(system);
|
||||||
|
contains.setDisplay(nextConcept.getDisplay());
|
||||||
}
|
}
|
||||||
|
|
||||||
return retVal;
|
return retVal;
|
||||||
|
@ -177,7 +215,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
|
||||||
return new CodeValidationResult(def);
|
return new CodeValidationResult(def);
|
||||||
}
|
}
|
||||||
|
|
||||||
return new CodeValidationResult(IssueSeverity.ERROR, "Unkonwn code {" + theCodeSystem +"}" + theCode);
|
return new CodeValidationResult(IssueSeverity.ERROR, "Unkonwn code {" + theCodeSystem + "}" + theCode);
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
@ -6,7 +6,10 @@ import static org.junit.Assert.assertEquals;
|
||||||
import static org.junit.Assert.assertThat;
|
import static org.junit.Assert.assertThat;
|
||||||
import static org.junit.Assert.fail;
|
import static org.junit.Assert.fail;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.List;
|
||||||
import java.util.Set;
|
import java.util.Set;
|
||||||
|
import java.util.TreeSet;
|
||||||
|
|
||||||
import org.hl7.fhir.dstu3.model.AuditEvent;
|
import org.hl7.fhir.dstu3.model.AuditEvent;
|
||||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||||
|
@ -15,6 +18,9 @@ import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
||||||
import org.hl7.fhir.dstu3.model.Observation;
|
import org.hl7.fhir.dstu3.model.Observation;
|
||||||
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
|
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
|
||||||
import org.hl7.fhir.dstu3.model.ValueSet;
|
import org.hl7.fhir.dstu3.model.ValueSet;
|
||||||
|
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||||
|
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
|
||||||
|
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
|
||||||
import org.hl7.fhir.instance.model.api.IIdType;
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
import org.junit.AfterClass;
|
import org.junit.AfterClass;
|
||||||
import org.junit.Before;
|
import org.junit.Before;
|
||||||
|
@ -264,6 +270,74 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testExpandWithSystemAndCodesInLocalValueSet() {
|
||||||
|
createLocalCsAndVs();
|
||||||
|
|
||||||
|
ValueSet vs = new ValueSet();
|
||||||
|
ConceptSetComponent include = vs.getCompose().addInclude();
|
||||||
|
include.setSystem(URL_MY_CODE_SYSTEM);
|
||||||
|
include.addConcept().setCode("A");
|
||||||
|
include.addConcept().setCode("AA");
|
||||||
|
include.addConcept().setCode("AAA");
|
||||||
|
include.addConcept().setCode("AB");
|
||||||
|
|
||||||
|
ValueSet result = myValueSetDao.expand(vs, null);
|
||||||
|
|
||||||
|
String encoded = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
|
||||||
|
ourLog.info(encoded);
|
||||||
|
|
||||||
|
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
|
||||||
|
assertThat(codes, containsInAnyOrder("A", "AA", "AAA", "AB"));
|
||||||
|
|
||||||
|
int idx = codes.indexOf("AAA");
|
||||||
|
assertEquals("AAA", result.getExpansion().getContains().get(idx).getCode());
|
||||||
|
assertEquals("Code AAA", result.getExpansion().getContains().get(idx).getDisplay());
|
||||||
|
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(idx).getSystem());
|
||||||
|
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
|
||||||
|
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
|
||||||
|
//
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testExpandWithSystemAndCodesAndFilterInLocalValueSet() {
|
||||||
|
createLocalCsAndVs();
|
||||||
|
|
||||||
|
ValueSet vs = new ValueSet();
|
||||||
|
ConceptSetComponent include = vs.getCompose().addInclude();
|
||||||
|
include.setSystem(URL_MY_CODE_SYSTEM);
|
||||||
|
include.addConcept().setCode("A");
|
||||||
|
include.addConcept().setCode("AA");
|
||||||
|
include.addConcept().setCode("AAA");
|
||||||
|
include.addConcept().setCode("AB");
|
||||||
|
|
||||||
|
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue("Code AAA");
|
||||||
|
|
||||||
|
ValueSet result = myValueSetDao.expand(vs, null);
|
||||||
|
|
||||||
|
String encoded = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
|
||||||
|
ourLog.info(encoded);
|
||||||
|
|
||||||
|
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
|
||||||
|
assertThat(codes, containsInAnyOrder("AAA"));
|
||||||
|
|
||||||
|
assertEquals("AAA", result.getExpansion().getContains().get(0).getCode());
|
||||||
|
assertEquals("Code AAA", result.getExpansion().getContains().get(0).getDisplay());
|
||||||
|
assertEquals(URL_MY_CODE_SYSTEM, result.getExpansion().getContains().get(0).getSystem());
|
||||||
|
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
|
||||||
|
// ValueSet expansion = myValueSetDao.expandByIdentifier(URL_MY_VALUE_SET, "cervical");
|
||||||
|
//
|
||||||
|
}
|
||||||
|
|
||||||
|
private ArrayList<String> toCodesContains(List<ValueSetExpansionContainsComponent> theContains) {
|
||||||
|
ArrayList<String> retVal = new ArrayList<String>();
|
||||||
|
for (ValueSetExpansionContainsComponent next : theContains) {
|
||||||
|
retVal.add(next.getCode());
|
||||||
|
}
|
||||||
|
return retVal;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
public void testSearchCodeAboveLocalCodesystem() {
|
public void testSearchCodeAboveLocalCodesystem() {
|
||||||
createLocalCsAndVs();
|
createLocalCsAndVs();
|
||||||
|
|
Loading…
Reference in New Issue