Use separate index columns

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -1225,15 +1225,22 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					for (IBaseReference nextRef : allRefs) {
 						IIdType nextId = nextRef.getReferenceElement();
 						String nextIdText = nextId.getValue();
+						if (nextIdText == null) {
+							continue;
+						}
 						int qmIndex = nextIdText.indexOf('?');
 						if (qmIndex != -1) {
 							for (int i = qmIndex - 1; i >= 0; i--) {
 								if (nextIdText.charAt(i) == '/') {
+									if (i < nextIdText.length() - 1 && nextIdText.charAt(i + 1) == '?') {
+										// Just in case the URL is in the form Patient/?foo=bar
+										continue;
+									}
 									nextIdText = nextIdText.substring(i + 1);
 									break;
 								}
 							}
-							String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?'));
+							String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?')).replace("/", "");
 							RuntimeResourceDefinition matchResourceDef = getContext().getResourceDefinition(resourceTypeString);
 							if (matchResourceDef == null) {
 								String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java

@@ -1,25 +1,5 @@
 package ca.uhn.fhir.jpa.dao;
 
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2016 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseResourceIndexedSearchParam.java

@@ -40,11 +40,6 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
 
 	private static final long serialVersionUID = 1L;
 
-	@Id
-	@GeneratedValue(strategy = GenerationType.AUTO)
-	@Column(name = "SP_ID")
-	private Long myId;
-
 	@Field
 	@Column(name = "SP_NAME", length = MAX_SP_NAME, nullable = false)
 	private String myParamName;
@@ -61,9 +56,7 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
 	@Column(name = "RES_TYPE", nullable = false)
 	private String myResourceType;
 
-	protected Long getId() {
+	protected abstract Long getId();
-		return myId;
-	}
 
 	public String getParamName() {
 		return myParamName;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java

@@ -55,8 +55,8 @@ public class ResourceHistoryTable extends BaseHasResource implements Serializabl
 	private static final long serialVersionUID = 1L;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.AUTO)
+	@SequenceGenerator(name = "SEQ_RESOURCE_HISTORY_ID", sequenceName = "SEQ_RESOURCE_HISTORY_ID")
-	@SequenceGenerator(name = "RES_HISTORY_PID", sequenceName = "RES_HISTORY_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_RESOURCE_HISTORY_ID")
 	@Column(name = "PID")
 	private Long myId;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamCoords.java

@@ -23,7 +23,11 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
 import javax.persistence.Index;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -45,6 +49,12 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
 
 	private static final long serialVersionUID = 1L;
 
+	@Id
+	@SequenceGenerator(name = "SEQ_SPIDX_COORDS", sequenceName = "SEQ_SPIDX_COORDS")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_COORDS")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Column(name = "SP_LATITUDE")
 	@Field
 	public double myLatitude;
@@ -82,6 +92,11 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public double getLatitude() {
 		return myLatitude;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamDate.java

@@ -25,6 +25,10 @@ import java.util.Date;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
@@ -47,6 +51,12 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
 
 	private static final long serialVersionUID = 1L;
 
+	@Id
+	@SequenceGenerator(name = "SEQ_SPIDX_DATE", sequenceName = "SEQ_SPIDX_DATE")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_DATE")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Column(name = "SP_VALUE_HIGH", nullable = true)
 	@Temporal(TemporalType.TIMESTAMP)
 	@Field
@@ -92,6 +102,11 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public Date getValueHigh() {
 		return myValueHigh;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamNumber.java

@@ -25,6 +25,10 @@ import java.math.BigDecimal;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -49,6 +53,12 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
 
 	private static final long serialVersionUID = 1L;
 	
+	@Id
+	@SequenceGenerator(name = "SEQ_SPIDX_NUMBER", sequenceName = "SEQ_SPIDX_NUMBER")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_NUMBER")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Column(name = "SP_VALUE", nullable = true)
 	@Field
 	@NumericField
@@ -82,6 +92,11 @@ public class ResourceIndexedSearchParamNumber extends BaseResourceIndexedSearchP
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public BigDecimal getValue() {
 		return myValue;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamQuantity.java

@@ -25,6 +25,10 @@ import java.math.BigDecimal;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -51,6 +55,12 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
 
 	private static final long serialVersionUID = 1L;
 
+	@Id
+	@SequenceGenerator(name = "SEQ_SPIDX_QUANTITY", sequenceName = "SEQ_SPIDX_QUANTITY")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_QUANTITY")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Column(name = "SP_SYSTEM", nullable = true, length = MAX_LENGTH)
 	@Field
 	public String mySystem;
@@ -97,6 +107,11 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public String getSystem() {
 		return mySystem;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamString.java

@@ -23,8 +23,12 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.StringUtils;
@@ -101,6 +105,17 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 
 	private static final long serialVersionUID = 1L;
 
+	@Id
+	@SequenceGenerator(name="SEQ_SPIDX_STRING", sequenceName="SEQ_SPIDX_STRING")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_STRING")
+	@Column(name = "SP_ID")
+	private Long myId;
+
+	@ManyToOne(optional = false)
+	@JoinColumn(name = "RES_ID", referencedColumnName="RES_ID", insertable=false, updatable=false)
+	@ContainedIn
+	private ResourceTable myResourceTable;
+
 	@Column(name = "SP_VALUE_EXACT", length = MAX_LENGTH, nullable = true)
 	@Fields({
 		@Field(name = "myValueText", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
@@ -113,15 +128,10 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	@Column(name = "SP_VALUE_NORMALIZED", length = MAX_LENGTH, nullable = true)
 	private String myValueNormalized;
 
-	@ManyToOne(optional = false)
-	@JoinColumn(name = "RES_ID", referencedColumnName="RES_ID", insertable=false, updatable=false)
-	@ContainedIn
-	private ResourceTable myResourceTable;
-
-
 	public ResourceIndexedSearchParamString() {
 	}
 
+
 	public ResourceIndexedSearchParamString(String theName, String theValueNormalized, String theValueExact) {
 		setParamName(theName);
 		setValueNormalized(theValueNormalized);
@@ -147,6 +157,11 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public String getValueExact() {
 		return myValueExact;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamToken.java

@@ -23,6 +23,10 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.StringUtils;
@@ -43,6 +47,12 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 
 	private static final long serialVersionUID = 1L;
 	
+	@Id
+	@SequenceGenerator(name = "SEQ_SPIDX_TOKEN", sequenceName = "SEQ_SPIDX_TOKEN")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_TOKEN")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Field()
 	@Column(name = "SP_SYSTEM", nullable = true, length = MAX_LENGTH)
 	public String mySystem;
@@ -80,6 +90,11 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public String getSystem() {
 		return mySystem;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamUri.java

@@ -23,7 +23,11 @@ package ca.uhn.fhir.jpa.entity;
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
 import javax.persistence.Index;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.StringUtils;
@@ -49,6 +53,12 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
 
 	private static final long serialVersionUID = 1L;
 
+	@Id
+	@SequenceGenerator(name="SEQ_SPIDX_URI", sequenceName="SEQ_SPIDX_URI")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator="SEQ_SPIDX_URI")
+	@Column(name = "SP_ID")
+	private Long myId;
+
 	@Column(name = "SP_URI", nullable = true, length = MAX_LENGTH)
 	@Field()
 	public String myUri;
@@ -80,6 +90,11 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
 		return b.isEquals();
 	}
 
+	@Override
+	protected Long getId() {
+		return myId;
+	}
+
 	public String getUri() {
 		return myUri;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -36,6 +36,7 @@ import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.Index;
 import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
@@ -144,14 +145,12 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	//@formatter:on
 	private String myContentText;
 
-	@Column(name = "HAS_CONTAINED", nullable = true)
-	private boolean myHasContainedResource;
-
 	@Column(name = "SP_HAS_LINKS")
 	private boolean myHasLinks;
 
 	@Id
-	@GeneratedValue(strategy = GenerationType.AUTO)
+	@SequenceGenerator(name="SEQ_RESOURCE_ID", sequenceName="SEQ_RESOURCE_ID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator="SEQ_RESOURCE_ID")
 	@Column(name = "RES_ID")
 	private Long myId;
 
@@ -346,10 +345,6 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		return false;
 	}
 
-	public boolean isHasContainedResource() {
-		return myHasContainedResource;
-	}
-
 	public boolean isHasLinks() {
 		return myHasLinks;
 	}
@@ -390,10 +385,6 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myContentText = theContentText;
 	}
 
-	public void setHasContainedResource(boolean theHasContainedResource) {
-		myHasContainedResource = theHasContainedResource;
-	}
-
 	public void setHasLinks(boolean theHasLinks) {
 		myHasLinks = theHasLinks;
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java

@@ -345,6 +345,40 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
 
 	}
 
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithOneMatch2() {
+		String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch2";
+		Bundle request = new Bundle();
+
+		myDaoConfig.setAllowInlineMatchUrlReferences(true);
+		
+		Patient p = new Patient();
+		p.addName().addGiven("Heute");
+		p.addIdentifier().setSystem("urn:system").setValue(methodName);
+		p.setId("Patient/" + methodName);
+		IIdType id = myPatientDao.update(p, mySrd).getId();
+		ourLog.info("Created patient, got it: {}", id);
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient/?given=heute");
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		Bundle resp = mySystemDao.transaction(myRequestDetails, request);
+		assertEquals(1, resp.getEntry().size());
+
+		BundleEntryComponent respEntry = resp.getEntry().get(0);
+		assertEquals(Constants.STATUS_HTTP_201_CREATED + " Created", respEntry.getResponse().getStatus());
+		assertThat(respEntry.getResponse().getLocation(), containsString("Observation/"));
+		assertThat(respEntry.getResponse().getLocation(), endsWith("/_history/1"));
+		assertEquals("1", respEntry.getResponse().getEtag());
+
+		o = myObservationDao.read(new IdType(respEntry.getResponse().getLocationElement()), mySrd);
+		assertEquals(id.toVersionless().getValue(), o.getSubject().getReference());
+		assertEquals("1", o.getIdElement().getVersionIdPart());
+
+	}
+
 	@Test
 	public void testTransactionCreateInlineMatchUrlWithNoMatches() {
 		String methodName = "testTransactionCreateInlineMatchUrlWithNoMatches";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java

@@ -116,6 +116,32 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
 		myDaoConfig.setAllowMultipleDelete(true);
 	}
 
+	
+	@Test
+	public void testCreateConditional() {
+		Patient patient = new Patient();
+		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
+		patient.addName().addFamily("Tester").addGiven("Raghad");
+		
+		MethodOutcome output1 = ourClient
+			.update()
+			.resource(patient)
+			.conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100")
+			.execute();
+
+		patient = new Patient();
+		patient.addIdentifier().setSystem("http://uhn.ca/mrns").setValue("100");
+		patient.addName().addFamily("Tester").addGiven("Raghad");
+
+		MethodOutcome output2 = ourClient
+				.update()
+				.resource(patient)
+				.conditionalByUrl("Patient?identifier=http://uhn.ca/mrns|100")
+				.execute();
+
+		assertEquals(output1.getId().getIdPart(), output2.getId().getIdPart());
+	}
+	
 	private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
 		HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
 		CloseableHttpResponse resp = ourHttpClient.execute(get);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplTest.java

@@ -136,7 +136,7 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
 		Set<TermConcept> concepts;
 		Set<String> codes;
 
-		concepts = myTermSvc.findCodesAbove(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "ChildAA");
+		concepts = myTermSvc.findCodesAbove(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "childAA");
 		codes = toCodes(concepts);
 		assertThat(codes, containsInAnyOrder("ParentA", "childAA"));
 

src/changes/changes.xml

@@ -241,6 +241,12 @@
 				first query. This should improve performance when searching against large
 				datasets.
 			</action>
+			<action type="add">
+				JPA server database design has been adjusted
+				so that different tables use different sequences
+				to generate their indexes, resulting in more sequential
+				resource IDs being assigned by the server
+			<action>
 		</release>
 		<release version="1.4" date="2016-02-04">
 			<action type="add">