Partitioninf fix, code cleaning, docker config change

docker-compose.yml

@@ -9,10 +9,10 @@ services:
       POSTGRES_USER: "hapi_iis_web"
       POSTGRES_PASSWORD: "SicMundusCreatusEst"
     healthcheck:
-      test: pg_isready -d hapi_fhir_iis -U $$POSTGRES_USER
+      test: pg_isready -d $$POSTGRES_DB -U $$POSTGRES_USER
       interval: 8s
       timeout: 10s
-      retries: 15
+      retries: 10
       start_period: 5s
 #    volumes:
 #      - ./database/create-postgresql-for-hapi-fhir.sql:/docker-entrypoint-initdb.d/3.sql

pom.xml

@@ -82,6 +82,13 @@
 <!--            <groupId>org.springframework.security.oauth.boot</groupId>-->
 <!--            <artifactId>spring-security-oauth2-autoconfigure</artifactId>-->
 <!--            <version>2.6.8</version>-->
+<!--        </dependency>-->
+
+<!--        <dependency>-->
+<!--&lt;!&ndash;            https://github.com/usnistgov/fhirAdapter &ndash;&gt;-->
+<!--            <groupId>gov.nist.fhir.adapter</groupId>-->
+<!--            <artifactId>fhirAdapter</artifactId>-->
+<!--            <version>1.0-SNAPSHOT</version>-->
 <!--        </dependency>-->
 
         <dependency>

src/main/java/org/immregistries/iis/kernal/fhir/bulkQuery/BulkQueryGroupProviderR5.java

@@ -322,10 +322,11 @@ public Group groupInstanceMemberAdd(
 		if (memberId != null) {
 			logger.info("PATIENT ADD identifier {}", memberId.getValue());
 //			String patientId = identifierSolverInterceptor.solvePatientIdentifier(ServletHelper.requestDetailsWithPartitionName(), memberId);
-			String patientId = patientIFhirResourceDao.search(new SearchParameterMap("identifier", new TokenParam(memberId.getValue())),theRequestDetails).getAllResourceIds().get(0);
-			if (StringUtils.isBlank(patientId)) {
-				throw new InvalidRequestException("Patient with identifier " + memberId.getValue() + " is unknown");
-			}
+			IBundleProvider iBundleProvider = patientIFhirResourceDao.search(new SearchParameterMap("identifier", new TokenParam(memberId.getValue())),theRequestDetails);
+			if (iBundleProvider.isEmpty()) {
+				throw new InvalidRequestException("Patient with identifier " + memberId.getValue() + " is unknown"); // TODO proper exception
+ 			}
+			String patientId = iBundleProvider.getAllResourceIds().get(0);
 			Reference reference = new Reference("Patient/" + patientId).setIdentifier(memberId);
 			memberComponent = group.getMember().stream()
 				.filter(member -> reference.getReference().equals(member.getEntity().getReference()) || (memberId.getValue().equals(member.getEntity().getIdentifier().getValue()) && memberId.getSystem().equals(member.getEntity().getIdentifier().getSystem())))

src/main/java/org/immregistries/iis/kernal/fhir/interceptors/GroupAuthorityInterceptor.java

@@ -4,16 +4,11 @@
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.mdm.util.IdentifierUtil;
-import ca.uhn.fhir.model.base.composite.BaseIdentifierDt;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import com.github.jsonldjava.utils.Obj;
 import org.hl7.fhir.r5.model.Group;
-import org.hl7.fhir.r5.model.Immunization;
 import org.hl7.fhir.r5.model.Organization;
 import org.hl7.fhir.r5.model.Reference;
 import org.immregistries.iis.kernal.InternalClient.FhirRequesterR5;

src/main/java/org/immregistries/iis/kernal/fhir/interceptors/PartitionCreationInterceptor.java

@@ -51,12 +51,18 @@ public class PartitionCreationInterceptor extends RequestTenantPartitionIntercep
 	public static final String PARTITION_NAME_SEPARATOR = "-"; // TEMP TODO find good url structure
 
 
-	@Hook(Pointcut.STORAGE_PARTITION_IDENTIFY_READ)
+	@Hook(value = Pointcut.SERVER_INCOMING_REQUEST_POST_PROCESSED)
+	public boolean partitionIdentifyPostProcessed(RequestDetails theRequestDetails) {
+		extractPartitionIdFromRequest(theRequestDetails);
+		return true;
+	}
+
+	@Hook(value = Pointcut.STORAGE_PARTITION_IDENTIFY_READ, order = -1000)
 	public RequestPartitionId partitionIdentifyRead(RequestDetails theRequestDetails) {
 		return extractPartitionIdFromRequest(theRequestDetails);
 	}
 
-	@Hook(Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE)
+	@Hook(value = Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE, order = -1000)
 	public RequestPartitionId partitionIdentifyCreate(RequestDetails theRequestDetails) {
 		return extractPartitionIdFromRequest(theRequestDetails);
 	}

src/main/java/org/immregistries/iis/kernal/logic/IIncomingMessageHandler.java

@@ -8,7 +8,7 @@
 
 import java.util.*;
 
-public interface IIncomingMessageHandler<Organization extends IBaseResource> {
+public interface IIncomingMessageHandler {
 	public String process(String message, Tenant tenant, String facilityName);
 
 

src/main/java/org/immregistries/iis/kernal/logic/IncomingMessageHandler.java

@@ -32,7 +32,7 @@
 import java.text.SimpleDateFormat;
 import java.util.*;
 
-public abstract class IncomingMessageHandler<Organization extends IBaseResource> implements IIncomingMessageHandler<Organization> {
+public abstract class IncomingMessageHandler implements IIncomingMessageHandler {
 
   	protected final Logger logger = LoggerFactory.getLogger(IncomingMessageHandler.class);
   	@Autowired
@@ -727,16 +727,5 @@ public Date parseDateInternal(String dateString, boolean strict) throws ParseExc
   }
 
   protected static final Random random = new Random();
-  private static final char[] ID_CHARS =
-      {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'J', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T',
-          'U', 'V', 'W', 'X', 'Y', 'Z', '1', '2', '3', '4', '5', '6', '7', '8', '9'};
 
-
-  public String generateId() {
-    StringBuilder patientRegistryId = new StringBuilder();
-    for (int i = 0; i < 12; i++) {
-      patientRegistryId.append(ID_CHARS[random.nextInt(ID_CHARS.length)]);
-    }
-    return patientRegistryId.toString();
-  }
 }

src/main/java/org/immregistries/iis/kernal/logic/IncomingMessageHandlerR4.java

@@ -35,7 +35,7 @@
 
 @org.springframework.stereotype.Service()
 @Conditional(OnR4Condition.class)
-public class IncomingMessageHandlerR4 extends IncomingMessageHandler<Organization> {
+public class IncomingMessageHandlerR4 extends IncomingMessageHandler {
 	private static final double MINIMAL_MATCHING_SCORE = 0.9;
 
 	public String process(String message, Tenant tenant, String sendingFacilityName) {
@@ -1741,30 +1741,6 @@ public List<VaccinationMaster> getVaccinationMasterList(PatientMaster patient) {
 		return vaccinationMasterList;
 	}
 
-	public String generatePatientExternalLink() {
-		IGenericClient fhirClient = getFhirClient();
-		boolean keepLooking = true;
-		int count = 0;
-		while (keepLooking) {
-			count++;
-			if (count > 1000) {
-				throw new RuntimeException("Unable to get a new id, tried 1000 times!");
-			}
-			String patientExternalLink = generateId();
-			try {
-				Bundle bundle = fhirClient.search().forResource(Patient.class)
-					.where(Patient.IDENTIFIER.exactly().code(patientExternalLink)).returnBundle(Bundle.class).execute();
-				if (!bundle.hasEntry()) {
-					return patientExternalLink;
-				}
-			} catch (ResourceNotFoundException e) {
-				return patientExternalLink;
-				// we found a unique id!
-			}
-		}
-		return null;
-	}
-
 	private Organization processSendingOrganization(HL7Reader reader) {
 		String organizationName = reader.getValue(4, 1);
 		Organization sendingOrganization = (Organization) fhirRequester.searchOrganization(