3163 refactor some base mdm stuff (#3166)

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IAnyResource.java

@@ -31,7 +31,7 @@ public interface IAnyResource extends IBaseResource {
 	/**
 	 * Search parameter constant for <b>_id</b>
 	 */
-	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="token"  )
+	@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="token")
 	String SP_RES_ID = "_id";
 
 	/**

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java

@@ -257,8 +257,16 @@ public class MdmConsumerConfig {
 	}
 
 	@Bean
-	MdmControllerHelper mdmProviderHelper(FhirContext theFhirContext, IResourceLoader theResourceLoader, IMdmSettings theMdmSettings, MessageHelper messageHelper) {
+	MdmControllerHelper mdmProviderHelper(FhirContext theFhirContext,
-		return new MdmControllerHelper(theFhirContext, theResourceLoader, theMdmSettings, messageHelper);
+													  IResourceLoader theResourceLoader,
+													  IMdmSettings theMdmSettings,
+													  IMdmMatchFinderSvc theMdmMatchFinderSvc,
+													  MessageHelper messageHelper) {
+		return new MdmControllerHelper(theFhirContext,
+			theResourceLoader,
+			theMdmMatchFinderSvc,
+			theMdmSettings,
+			messageHelper);
 	}
 
 	@Bean

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
 import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
 import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
 import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
+import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
 import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
 import ca.uhn.fhir.mdm.util.MessageHelper;
@@ -29,8 +30,6 @@ import java.util.List;
 public abstract class BaseProviderR4Test extends BaseMdmR4Test {
 	MdmProviderDstu3Plus myMdmProvider;
 	@Autowired
-	private IMdmMatchFinderSvc myMdmMatchFinderSvc;
-	@Autowired
 	private IMdmControllerSvc myMdmControllerSvc;
 	@Autowired
 	private IMdmClearJobSubmitter myMdmClearJobSubmitter;
@@ -39,6 +38,8 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
 	@Autowired
 	private MdmSettings myMdmSettings;
 	@Autowired
+	private MdmControllerHelper myMdmHelper;
+	@Autowired
 	BatchJobHelper myBatchJobHelper;
 	@Autowired
 	MessageHelper myMessageHelper;
@@ -55,7 +56,7 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
 
 	@BeforeEach
 	public void before() {
-		myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmSubmitSvc, myMdmSettings);
+		myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmHelper, myMdmSubmitSvc, myMdmSettings);
 		defaultScript = myMdmSettings.getScriptText();
 	}
 

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmControllerHelper.java

@@ -21,20 +21,36 @@ package ca.uhn.fhir.mdm.provider;
  */
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
+import ca.uhn.fhir.mdm.api.MatchedTarget;
+import ca.uhn.fhir.mdm.api.MdmConstants;
 import ca.uhn.fhir.mdm.util.MdmResourceUtil;
 import ca.uhn.fhir.mdm.util.MessageHelper;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.provider.ProviderConstants;
+import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.validation.IResourceLoader;
 import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import javax.annotation.Nonnull;
+import java.math.BigDecimal;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
 @Service
 public class MdmControllerHelper {
 
@@ -42,12 +58,18 @@ public class MdmControllerHelper {
 	private final IResourceLoader myResourceLoader;
 	private final IMdmSettings myMdmSettings;
 	private final MessageHelper myMessageHelper;
+	private final IMdmMatchFinderSvc myMdmMatchFinderSvc;
 
 	@Autowired
-	public MdmControllerHelper(FhirContext theFhirContext, IResourceLoader theResourceLoader, IMdmSettings theMdmSettings, MessageHelper theMessageHelper) {
+	public MdmControllerHelper(FhirContext theFhirContext,
+										IResourceLoader theResourceLoader,
+										IMdmMatchFinderSvc theMdmMatchFinderSvc,
+										IMdmSettings theMdmSettings,
+										MessageHelper theMessageHelper) {
 		myFhirContext = theFhirContext;
 		myResourceLoader = theResourceLoader;
 		myMdmSettings = theMdmSettings;
+		myMdmMatchFinderSvc = theMdmMatchFinderSvc;
 		myMessageHelper = theMessageHelper;
 	}
 
@@ -104,4 +126,58 @@ public class MdmControllerHelper {
 			throw new InvalidRequestException(myMessageHelper.getMessageForUnmanagedResource());
 		}
 	}
+
+	/**
+	 * Helper method which will return a bundle of all Matches and Possible Matches.
+	 */
+	public IBaseBundle getMatchesAndPossibleMatchesForResource(IAnyResource theResource, String theResourceType) {
+		List<MatchedTarget> matches = myMdmMatchFinderSvc.getMatchedTargets(theResourceType, theResource);
+		matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
+
+		BundleBuilder builder = new BundleBuilder(myFhirContext);
+		builder.setBundleField("type", "searchset");
+		builder.setBundleField("id", UUID.randomUUID().toString());
+		builder.setMetaField("lastUpdated", builder.newPrimitive("instant", new Date()));
+
+		IBaseBundle retVal = builder.getBundle();
+		for (MatchedTarget next : matches) {
+			boolean shouldKeepThisEntry = next.isMatch() || next.isPossibleMatch();
+			if (!shouldKeepThisEntry) {
+				continue;
+			}
+
+			IBase entry = builder.addEntry();
+			builder.addToEntry(entry, "resource", next.getTarget());
+
+			IBaseBackboneElement search = builder.addSearch(entry);
+			toBundleEntrySearchComponent(builder, search, next);
+		}
+		return retVal;
+	}
+
+	public IBaseBackboneElement toBundleEntrySearchComponent(BundleBuilder theBuilder, IBaseBackboneElement theSearch, MatchedTarget theMatchedTarget) {
+		theBuilder.setSearchField(theSearch, "mode", "match");
+		double score = theMatchedTarget.getMatchResult().getNormalizedScore();
+		theBuilder.setSearchField(theSearch, "score",
+			theBuilder.newPrimitive("decimal", BigDecimal.valueOf(score)));
+
+		String matchGrade = getMatchGrade(theMatchedTarget);
+		IBaseDatatype codeType = (IBaseDatatype) myFhirContext.getElementDefinition("code").newInstance(matchGrade);
+		IBaseExtension searchExtension = theSearch.addExtension();
+		searchExtension.setUrl(MdmConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE);
+		searchExtension.setValue(codeType);
+
+		return theSearch;
+	}
+
+	@Nonnull
+	protected String getMatchGrade(MatchedTarget theTheMatchedTarget) {
+		String retVal = "probable";
+		if (theTheMatchedTarget.isMatch()) {
+			retVal = "certain";
+		} else if (theTheMatchedTarget.isPossibleMatch()) {
+			retVal = "possible";
+		}
+		return retVal;
+	}
 }

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java

@@ -72,9 +72,9 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
 	private static final Logger ourLog = getLogger(MdmProviderDstu3Plus.class);
 
 	private final IMdmControllerSvc myMdmControllerSvc;
-	private final IMdmMatchFinderSvc myMdmMatchFinderSvc;
 	private final IMdmSubmitSvc myMdmSubmitSvc;
 	private final IMdmSettings myMdmSettings;
+	private final MdmControllerHelper myMdmControllerHelper;
 
 	public static final int DEFAULT_PAGE_SIZE = 20;
 	public static final int MAX_PAGE_SIZE = 100;
@@ -85,10 +85,14 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
 	 * Note that this is not a spring bean. Any necessary injections should
 	 * happen in the constructor
 	 */
-	public MdmProviderDstu3Plus(FhirContext theFhirContext, IMdmControllerSvc theMdmControllerSvc, IMdmMatchFinderSvc theMdmMatchFinderSvc, IMdmSubmitSvc theMdmSubmitSvc, IMdmSettings theIMdmSettings) {
+	public MdmProviderDstu3Plus(FhirContext theFhirContext,
+										 IMdmControllerSvc theMdmControllerSvc,
+										 MdmControllerHelper theMdmHelper,
+										 IMdmSubmitSvc theMdmSubmitSvc,
+										 IMdmSettings theIMdmSettings) {
 		super(theFhirContext);
 		myMdmControllerSvc = theMdmControllerSvc;
-		myMdmMatchFinderSvc = theMdmMatchFinderSvc;
+		myMdmControllerHelper = theMdmHelper;
 		myMdmSubmitSvc = theMdmSubmitSvc;
 		myMdmSettings = theIMdmSettings;
 	}
@@ -98,7 +102,7 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
 		if (thePatient == null) {
 			throw new InvalidRequestException("resource may not be null");
 		}
-		return getMatchesAndPossibleMatchesForResource(thePatient, "Patient");
+		return myMdmControllerHelper.getMatchesAndPossibleMatchesForResource(thePatient, "Patient");
 	}
 
 	@Operation(name = ProviderConstants.MDM_MATCH)
@@ -108,51 +112,7 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
 		if (theResource == null) {
 			throw new InvalidRequestException("resource may not be null");
 		}
-		return getMatchesAndPossibleMatchesForResource(theResource, theResourceType.getValueAsString());
+		return myMdmControllerHelper.getMatchesAndPossibleMatchesForResource(theResource, theResourceType.getValueAsString());
-	}
-
-	/**
-	 * Helper method which will return a bundle of all Matches and Possible Matches.
-	 */
-	private IBaseBundle getMatchesAndPossibleMatchesForResource(IAnyResource theResource, String theResourceType) {
-		List<MatchedTarget> matches = myMdmMatchFinderSvc.getMatchedTargets(theResourceType, theResource);
-		matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
-
-		BundleBuilder builder = new BundleBuilder(myFhirContext);
-		builder.setBundleField("type", "searchset");
-		builder.setBundleField("id", UUID.randomUUID().toString());
-		builder.setMetaField("lastUpdated", builder.newPrimitive("instant", new Date()));
-
-		IBaseBundle retVal = builder.getBundle();
-		for (MatchedTarget next : matches) {
-			boolean shouldKeepThisEntry = next.isMatch() || next.isPossibleMatch();
-			if (!shouldKeepThisEntry) {
-				continue;
-			}
-
-			IBase entry = builder.addEntry();
-			builder.addToEntry(entry, "resource", next.getTarget());
-
-			IBaseBackboneElement search = builder.addSearch(entry);
-			toBundleEntrySearchComponent(builder, search, next);
-		}
-		return retVal;
-	}
-
-
-	public IBaseBackboneElement toBundleEntrySearchComponent(BundleBuilder theBuilder, IBaseBackboneElement theSearch, MatchedTarget theMatchedTarget) {
-		theBuilder.setSearchField(theSearch, "mode", "match");
-		double score = theMatchedTarget.getMatchResult().getNormalizedScore();
-		theBuilder.setSearchField(theSearch, "score",
-			theBuilder.newPrimitive("decimal", BigDecimal.valueOf(score)));
-
-		String matchGrade = getMatchGrade(theMatchedTarget);
-		IBaseDatatype codeType = (IBaseDatatype) myFhirContext.getElementDefinition("code").newInstance(matchGrade);
-		IBaseExtension searchExtension = theSearch.addExtension();
-		searchExtension.setUrl(MdmConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE);
-		searchExtension.setValue(codeType);
-
-		return theSearch;
 	}
 
 	@Operation(name = ProviderConstants.MDM_MERGE_GOLDEN_RESOURCES)
@@ -353,17 +313,6 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
 		return retval;
 	}
 
-	@Nonnull
-	protected String getMatchGrade(MatchedTarget theTheMatchedTarget) {
-		String retVal = "probable";
-		if (theTheMatchedTarget.isMatch()) {
-			retVal = "certain";
-		} else if (theTheMatchedTarget.isPossibleMatch()) {
-			retVal = "possible";
-		}
-		return retVal;
-	}
-
 	private String getResourceType(String theParamName, IPrimitiveType<String> theResourceId) {
 		if (theResourceId != null) {
 			return getResourceType(theParamName, theResourceId.getValueAsString());

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderLoader.java

@@ -39,7 +39,7 @@ public class MdmProviderLoader {
 	@Autowired
 	private ResourceProviderFactory myResourceProviderFactory;
 	@Autowired
-	private IMdmMatchFinderSvc myMdmMatchFinderSvc;
+	private MdmControllerHelper myMdmControllerHelper;
 	@Autowired
 	private IMdmControllerSvc myMdmControllerSvc;
 	@Autowired
@@ -54,7 +54,11 @@ public class MdmProviderLoader {
 			case DSTU3:
 			case R4:
 				myResourceProviderFactory.addSupplier(() -> {
-					myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmSubmitSvc, myMdmSettings);
+					myMdmProvider = new MdmProviderDstu3Plus(myFhirContext,
+						myMdmControllerSvc,
+						myMdmControllerHelper,
+						myMdmSubmitSvc,
+						myMdmSettings);
 					return myMdmProvider;
 				});
 				break;