Work on migrator

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -34,10 +34,14 @@ public enum ResourceEncodingEnum {
 	 * See ResourceHistoryTable RES_ENCODING column
 	 */
 
-	/** Json */
+	/**
+	 * Json
+	 */
 	JSON,
-	
+
-	/** Json Compressed */
+	/**
+	 * Json Compressed
+	 */
 	JSONC,
 
 	/**
@@ -48,5 +52,5 @@ public enum ResourceEncodingEnum {
 	public IParser newParser(FhirContext theContext) {
 		return theContext.newJsonParser();
 	}
-	
+
 }

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -32,7 +32,7 @@ import javax.persistence.*;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_COORDS", indexes = {
-	@Index(name = "IDX_SP_COORDS_HASH", columnList = "HASH_IDENTITY,SP_VALUE,SP_LATITUDE,SP_LONGITUDE"),
+	@Index(name = "IDX_SP_COORDS_HASH", columnList = "HASH_IDENTITY,SP_LATITUDE,SP_LONGITUDE"),
 	@Index(name = "IDX_SP_COORDS_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_COORDS_RESID", columnList = "RES_ID")
 })

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -37,7 +37,7 @@ import java.util.Date;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_DATE", indexes = {
-//	@Index(name = "IDX_SP_DATE", columnList = "RES_TYPE,SP_NAME,SP_VALUE_LOW,SP_VALUE_HIGH"),
+	// We previously had an index called IDX_SP_DATE - Dont reuse
 	@Index(name = "IDX_SP_DATE_HASH", columnList = "HASH_IDENTITY,SP_VALUE_LOW,SP_VALUE_HIGH"),
 	@Index(name = "IDX_SP_DATE_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_DATE_RESID", columnList = "RES_ID")

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -37,7 +37,7 @@ import java.math.BigDecimal;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_NUMBER", indexes = {
-//	@Index(name = "IDX_SP_NUMBER", columnList = "RES_TYPE,SP_NAME,SP_VALUE"),
+//	We used to have an index with name IDX_SP_NUMBER - Dont reuse
 	@Index(name = "IDX_SP_NUMBER_HASH_VAL", columnList = "HASH_IDENTITY,SP_VALUE"),
 	@Index(name = "IDX_SP_NUMBER_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_NUMBER_RESID", columnList = "RES_ID")

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -38,9 +38,10 @@ import java.math.BigDecimal;
 @Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_QUANTITY", indexes = {
-//	@Index(name = "IDX_SP_QUANTITY", columnList = "RES_TYPE,SP_NAME,SP_SYSTEM,SP_UNITS,SP_VALUE"),
+//	We used to have an index named IDX_SP_QUANTITY - Dont reuse
 	@Index(name = "IDX_SP_QUANTITY_HASH", columnList = "HASH_IDENTITY,SP_VALUE"),
 	@Index(name = "IDX_SP_QUANTITY_HASH_UN", columnList = "HASH_IDENTITY_AND_UNITS,SP_VALUE"),
+	@Index(name = "IDX_SP_QUANTITY_HASH_SYSUN", columnList = "HASH_IDENTITY_SYS_UNITS,SP_VALUE"),
 	@Index(name = "IDX_SP_QUANTITY_UPDATED", columnList = "SP_UPDATED"),
 	@Index(name = "IDX_SP_QUANTITY_RESID", columnList = "RES_ID")
 })

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -20,36 +20,21 @@ package ca.uhn.fhir.jpa.entity;
  * #L%
  */
 
-import java.io.Serializable;
-import java.util.Date;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ForeignKey;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.hibernate.annotations.ColumnDefault;
 import org.hibernate.search.annotations.Field;
 import org.hl7.fhir.instance.model.api.IIdType;
 
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.Date;
+
 @Entity
-@Table(name = "HFJ_RES_LINK" , indexes= {
+@Table(name = "HFJ_RES_LINK", indexes = {
-	@Index(name="IDX_RL_TPATHRES", columnList= "SRC_PATH,TARGET_RESOURCE_ID"), 
+	@Index(name = "IDX_RL_TPATHRES", columnList = "SRC_PATH,TARGET_RESOURCE_ID"),
-	@Index(name="IDX_RL_SRC", columnList= "SRC_RESOURCE_ID"), 
+	@Index(name = "IDX_RL_SRC", columnList = "SRC_RESOURCE_ID"),
-	@Index(name="IDX_RL_DEST", columnList= "TARGET_RESOURCE_ID")
+	@Index(name = "IDX_RL_DEST", columnList = "TARGET_RESOURCE_ID")
 })
 public class ResourceLink implements Serializable {
 
@@ -64,30 +49,30 @@ public class ResourceLink implements Serializable {
 	@Column(name = "SRC_PATH", length = 100, nullable = false)
 	private String mySourcePath;
 
-	@ManyToOne(optional = false, fetch=FetchType.LAZY)
+	@ManyToOne(optional = false, fetch = FetchType.LAZY)
-	@JoinColumn(name = "SRC_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = false, foreignKey=@ForeignKey(name="FK_RESLINK_SOURCE"))
+	@JoinColumn(name = "SRC_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = false, foreignKey = @ForeignKey(name = "FK_RESLINK_SOURCE"))
 	private ResourceTable mySourceResource;
 
 	@Column(name = "SRC_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
 	private Long mySourceResourcePid;
 
-	@Column(name = "SOURCE_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@Column(name = "SOURCE_RESOURCE_TYPE", nullable = false, length = ResourceTable.RESTYPE_LEN)
 	@Field()
 	private String mySourceResourceType;
 
-	@ManyToOne(optional = true, fetch=FetchType.LAZY)
+	@ManyToOne(optional = true, fetch = FetchType.LAZY)
-	@JoinColumn(name = "TARGET_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = true, foreignKey=@ForeignKey(name="FK_RESLINK_TARGET"))
+	@JoinColumn(name = "TARGET_RESOURCE_ID", referencedColumnName = "RES_ID", nullable = true, foreignKey = @ForeignKey(name = "FK_RESLINK_TARGET"))
 	private ResourceTable myTargetResource;
 
 	@Column(name = "TARGET_RESOURCE_ID", insertable = false, updatable = false, nullable = true)
 	@Field()
 	private Long myTargetResourcePid;
 
-	@Column(name = "TARGET_RESOURCE_TYPE", nullable=false, length=ResourceTable.RESTYPE_LEN)
+	@Column(name = "TARGET_RESOURCE_TYPE", nullable = false, length = ResourceTable.RESTYPE_LEN)
 	@Field()
 	private String myTargetResourceType;
 
-	@Column(name = "TARGET_RESOURCE_URL", length=200, nullable = true)
+	@Column(name = "TARGET_RESOURCE_URL", length = 200, nullable = true)
 	@Field()
 	private String myTargetResourceUrl;
 

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -19,44 +19,36 @@ package ca.uhn.fhir.jpa.entity;
  * limitations under the License.
  * #L%
  */
-import java.io.Serializable;
-import java.util.Date;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.Id;
-import javax.persistence.Lob;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-
-import org.hibernate.annotations.Immutable;
-import org.hibernate.annotations.Subselect;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.primitive.InstantDt;
 import ca.uhn.fhir.rest.api.Constants;
+import org.hibernate.annotations.Immutable;
+import org.hibernate.annotations.Subselect;
+
+import javax.persistence.*;
+import java.io.Serializable;
+import java.util.Date;
 
 //@formatter:off
 @Entity
 @Immutable
-@Subselect("SELECT h.pid        as pid            " + 
+@Subselect("SELECT h.pid        as pid            " +
-		",  h.res_id            as res_id         "	+ 
+	",  h.res_id            as res_id         " +
-		",  h.res_type          as res_type       " + 
+	",  h.res_type          as res_type       " +
-		",  h.res_version       as res_version    " + // FHIR version
+	",  h.res_version       as res_version    " + // FHIR version
-		",  h.res_ver           as res_ver        " + // resource version
+	",  h.res_ver           as res_ver        " + // resource version
-		",  h.has_tags          as has_tags       " + 
+	",  h.has_tags          as has_tags       " +
-		",  h.res_deleted_at    as res_deleted_at "	+ 
+	",  h.res_deleted_at    as res_deleted_at " +
-		",  h.res_published     as res_published  " + 
+	",  h.res_published     as res_published  " +
-		",  h.res_updated       as res_updated    "	+ 
+	",  h.res_updated       as res_updated    " +
-		",  h.res_text          as res_text       " + 
+	",  h.res_text          as res_text       " +
-		",  h.res_encoding      as res_encoding   "	+ 
+	",  h.res_encoding      as res_encoding   " +
-		",  f.forced_id         as forced_pid      " + 
+	",  f.forced_id         as forced_pid      " +
-		"FROM HFJ_RES_VER h "
+	"FROM HFJ_RES_VER h "
-		+ "    LEFT OUTER JOIN HFJ_FORCED_ID f ON f.resource_pid = h.res_id "
+	+ "    LEFT OUTER JOIN HFJ_FORCED_ID f ON f.resource_pid = h.res_id "
-		+ "    INNER JOIN HFJ_RESOURCE r       ON r.res_id = h.res_id and r.res_ver = h.res_ver")
+	+ "    INNER JOIN HFJ_RESOURCE r       ON r.res_id = h.res_id and r.res_ver = h.res_ver")
 // @formatter:on
 public class ResourceSearchView implements IBaseResourceEntity, Serializable {
 
@@ -142,7 +134,7 @@ public class ResourceSearchView implements IBaseResourceEntity, Serializable {
 			return new IdDt(myResourceType + '/' + id + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
 		} else {
 			return new IdDt(
-					getResourceType() + '/' + getForcedId() + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
+				getResourceType() + '/' + getForcedId() + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
 		}
 	}
 

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

@@ -19,9 +19,9 @@ import static org.apache.commons.lang3.StringUtils.left;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -28,6 +28,7 @@ import java.io.Serializable;
 
 @Entity
 @Table(name = "HFJ_RES_PARAM_PRESENT", indexes = {
+	// We used to have a constraint named IDX_RESPARMPRESENT_SPID_RESID - Don't reuse
 	@Index(name = "IDX_RESPARMPRESENT_RESID", columnList = "RES_ID"),
 	@Index(name = "IDX_RESPARMPRESENT_HASHPRES", columnList = "HASH_PRESENCE")
 })

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

@@ -29,9 +29,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  * 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.
@@ -93,15 +93,17 @@ public class TermConcept implements Serializable {
 	private Long myIndexStatus;
 	@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "conceptParentPidsAnalyzer"))
 	@Lob
-	@Column(name="PARENT_PIDS", nullable = true)
+	@Column(name = "PARENT_PIDS", nullable = true)
 	private String myParentPids;
 	@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
 	private Collection<TermConceptParentChildLink> myParents;
 	@Column(name = "CODE_SEQUENCE", nullable = true)
 	private Integer mySequence;
+
 	public TermConcept() {
 		super();
 	}
+
 	public TermConcept(TermCodeSystemVersion theCs, String theCode) {
 		setCodeSystemVersion(theCs);
 		setCode(theCode);

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -38,7 +38,7 @@ public class TermConceptMapGroup implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGROUP_CONCEPTMAP"))
+	@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGROUP_CONCEPTMAP"))
 	private TermConceptMap myConceptMap;
 
 	@Column(name = "SOURCE_URL", nullable = false, length = 200)

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -42,7 +42,7 @@ public class TermConceptMapGroupElement implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGELEMENT_GROUP"))
+	@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGELEMENT_GROUP"))
 	private TermConceptMapGroup myConceptMapGroup;
 
 	@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.
@@ -41,7 +41,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
 	private Long myId;
 
 	@ManyToOne()
-	@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey=@ForeignKey(name="FK_TCMGETARGET_ELEMENT"))
+	@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
 	private TermConceptMapGroupElement myConceptMapGroupElement;
 
 	@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
  * 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.

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -105,7 +105,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 		DataSource dataSource = ProxyDataSourceBuilder
 			.create(retVal)
-//			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
+			.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
 			.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
 			.countQuery(new ThreadQueryCountHolder())
 			.build();

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java

@@ -1,17 +1,22 @@
 package ca.uhn.fhir.jpa.migrate;
 
+import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+import org.thymeleaf.util.StringUtils;
 
 import javax.sql.DataSource;
-import java.sql.Connection;
+import java.sql.*;
-import java.sql.DatabaseMetaData;
-import java.sql.ResultSet;
-import java.sql.SQLException;
 import java.util.HashSet;
+import java.util.Locale;
 import java.util.Objects;
 import java.util.Set;
 
 public class JdbcUtils {
+	private static final Logger ourLog = LoggerFactory.getLogger(JdbcUtils.class);
+
 	/**
 	 * Retrieve all index names
 	 */
@@ -19,14 +24,18 @@ public class JdbcUtils {
 		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
 		Connection connection = dataSource.getConnection();
 		return theConnectionProperties.getTxTemplate().execute(t -> {
-			DatabaseMetaData metadata = null;
+			DatabaseMetaData metadata;
 			try {
 				metadata = connection.getMetaData();
 				ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, false);
 
 				Set<String> indexNames = new HashSet<>();
 				while (indexes.next()) {
+
+					ourLog.debug("*** Next index: {}", new ColumnMapRowMapper().mapRow(indexes, 0));
+
 					String indexName = indexes.getString("INDEX_NAME");
+					indexName = StringUtils.toUpperCase(indexName, Locale.US);
 					indexNames.add(indexName);
 				}
 
@@ -37,4 +46,92 @@ public class JdbcUtils {
 		});
 
 	}
+
+	@SuppressWarnings("ConstantConditions")
+	public static boolean isIndexUnique(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theIndexName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, false);
+
+				while (indexes.next()) {
+					String indexName = indexes.getString("INDEX_NAME");
+					if (indexName.equalsIgnoreCase(theIndexName)) {
+						boolean nonUnique = indexes.getBoolean("NON_UNIQUE");
+						return !nonUnique;
+					}
+				}
+
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+
+			throw new InternalErrorException("Can't find index: " + theIndexName + " on table " + theTableName);
+		});
+
+	}
+
+	/**
+	 * Retrieve all index names
+	 */
+	public static String getColumnType(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theColumnName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		try (Connection connection = dataSource.getConnection()) {
+			return theConnectionProperties.getTxTemplate().execute(t -> {
+				DatabaseMetaData metadata;
+				try {
+					metadata = connection.getMetaData();
+					ResultSet indexes = metadata.getColumns(null, null, theTableName, theColumnName);
+
+					indexes.next();
+
+					int dataType = indexes.getInt("DATA_TYPE");
+					Long length = indexes.getLong("COLUMN_SIZE");
+					switch (dataType) {
+						case Types.VARCHAR:
+							return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
+						case Types.BIGINT:
+							return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(length);
+						default:
+							throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
+					}
+
+				} catch (SQLException e) {
+					throw new InternalErrorException(e);
+				}
+
+			});
+		}
+	}
+
+	/**
+	 * Retrieve all index names
+	 */
+	public static Set<String> getColumnNames(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getColumns(null, null, theTableName, null);
+
+				Set<String> columnNames = new HashSet<>();
+				while (indexes.next()) {
+					String columnName = indexes.getString("COLUMN_NAME");
+					columnName = StringUtils.toUpperCase(columnName, Locale.US);
+					columnNames.add(columnName);
+				}
+
+				return columnNames;
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+
+	}
+
 }

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTask.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.Set;
+
+public class AddColumnTask extends BaseTableColumnTypeTask<AddColumnTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(AddColumnTask.class);
+
+
+	@Override
+	public void execute() throws SQLException {
+		Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
+		if (columnNames.contains(getColumnName())) {
+			ourLog.info("Column {} already exists on table {} - No action performed", getColumnName(), getTableName());
+			return;
+		}
+
+		String type = getSqlType();
+		String nullable = getSqlNotNull();
+		String sql = "alter table " + getTableName() + " add column " + getColumnName() + " " + type + " " + nullable;
+		ourLog.info("Adding column {} of type {} to table {}", getColumnName(), type, getTableName());
+		executeSql(sql);
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java

@@ -4,26 +4,23 @@ import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.thymeleaf.util.StringUtils;
 
 import java.sql.SQLException;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Locale;
 import java.util.Set;
 
-public class AddIndexTask extends BaseTask<AddIndexTask> {
+public class AddIndexTask extends BaseTableTask<AddIndexTask> {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(AddIndexTask.class);
-	private String myTableName;
 	private String myIndexName;
 	private List<String> myColumns;
 	private Boolean myUnique;
 
-	public void setTableName(String theTableName) {
-		myTableName = theTableName;
-	}
-
 	public void setIndexName(String theIndexName) {
-		myIndexName = theIndexName;
+		myIndexName = StringUtils.toUpperCase(theIndexName, Locale.US);
 	}
 
 	public void setColumns(List<String> theColumns) {
@@ -36,23 +33,23 @@ public class AddIndexTask extends BaseTask<AddIndexTask> {
 
 	@Override
 	public void validate() {
+		super.validate();
 		Validate.notBlank(myIndexName, "Index name not specified");
-		Validate.notBlank(myTableName, "Table name not specified");
 		Validate.isTrue(myColumns.size() > 0, "Columns not specified");
 		Validate.notNull(myUnique, "Uniqueness not specified");
 	}
 
 	@Override
 	public void execute() throws SQLException {
-		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), myTableName);
+		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), getTableName());
 		if (indexNames.contains(myIndexName)) {
-			ourLog.info("Index {} already exists on table {} - No action performed", myIndexName, myTableName);
+			ourLog.info("Index {} already exists on table {} - No action performed", myIndexName, getTableName());
 			return;
 		}
 
 		String unique = myUnique ? "UNIQUE " : "";
 		String columns = String.join(", ", myColumns);
-		String sql = "CREATE " + unique + " INDEX " + myIndexName + " ON " + myTableName + "(" + columns + ")";
+		String sql = "CREATE " + unique + " INDEX " + myIndexName + " ON " + getTableName() + "(" + columns + ")";
 		executeSql(sql);
 	}
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTask.java

@@ -0,0 +1,90 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Consumer;
+
+public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ArbitrarySqlTask.class);
+	private final String myDescription;
+	private List<Task> myTask = new ArrayList<>();
+	private int myBatchSize = 1000;
+
+	public ArbitrarySqlTask(String theDescription) {
+		myDescription = theDescription;
+	}
+
+	public void addQuery(String theSql, QueryModeEnum theMode, Consumer<Map<String, Object>> theConsumer) {
+		myTask.add(new QueryTask(theSql, theMode, theConsumer));
+	}
+
+	@Override
+	public void validate() {
+		// nothing
+	}
+
+	@Override
+	public void execute() throws SQLException {
+		ourLog.info("Starting: {}", myDescription);
+
+		for (Task next : myTask) {
+			next.execute();
+		}
+
+	}
+
+	public void setBatchSize(int theBatchSize) {
+		myBatchSize = theBatchSize;
+	}
+
+	public enum QueryModeEnum {
+		BATCH_UNTIL_NO_MORE
+	}
+
+	private abstract class Task {
+		public abstract void execute();
+	}
+
+	private class QueryTask extends Task {
+		private final String mySql;
+		private final QueryModeEnum myMode;
+		private final Consumer<Map<String, Object>> myConsumer;
+
+		public QueryTask(String theSql, QueryModeEnum theMode, Consumer<Map<String, Object>> theConsumer) {
+			mySql = theSql;
+			myMode = theMode;
+			myConsumer = theConsumer;
+		}
+
+
+		@Override
+		public void execute() {
+			List<Map<String, Object>> rows;
+			do {
+				ourLog.info("Querying for up to {} rows", myBatchSize);
+				rows = getTxTemplate().execute(t -> {
+					JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+					jdbcTemplate.setMaxRows(myBatchSize);
+					return jdbcTemplate.query(mySql, new ColumnMapRowMapper());
+				});
+
+				ourLog.info("Processing {} rows", rows.size());
+				List<Map<String, Object>> finalRows = rows;
+				getTxTemplate().execute(t -> {
+					for (Map<String, Object> nextRow : finalRows) {
+						myConsumer.accept(nextRow);
+					}
+					return null;
+				});
+			} while (rows.size() > 0);
+		}
+	}
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTask.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.apache.commons.lang3.Validate;
+import org.thymeleaf.util.StringUtils;
+
+import java.util.Locale;
+
+public abstract class BaseTableColumnTask<T extends BaseTableTask> extends BaseTableTask<T> {
+
+	private String myColumnName;
+
+	@SuppressWarnings("unchecked")
+	public T setColumnName(String theColumnName) {
+		myColumnName = StringUtils.toUpperCase(theColumnName, Locale.US);
+		return (T) this;
+	}
+
+
+	public String getColumnName() {
+		return myColumnName;
+	}
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notBlank(myColumnName, "Column name not specified");
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java

@@ -0,0 +1,122 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import org.apache.commons.lang3.Validate;
+import org.springframework.util.Assert;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Objects;
+
+public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends BaseTableColumnTask<T> {
+
+	private ColumnTypeEnum myColumnType;
+	private Map<ColumnTypeEnum, Map<DriverTypeEnum, String>> myColumnTypeToDriverTypeToSqlType = new HashMap<>();
+	private Boolean myNullable;
+	private Long myColumnLength;
+
+	/**
+	 * Constructor
+	 */
+	BaseTableColumnTypeTask() {
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.DERBY_EMBEDDED, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MARIADB_10_1, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MYSQL_5_7, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.MSSQL_2012, "bigint");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.ORACLE_12C, "number(19,0)");
+		setColumnType(ColumnTypeEnum.LONG, DriverTypeEnum.POSTGRES_9_4, "int8");
+
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.DERBY_EMBEDDED, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MARIADB_10_1, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MYSQL_5_7, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.MSSQL_2012, "varchar(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.ORACLE_12C, "varchar2(?)");
+		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.POSTGRES_9_4, "varchar(?)");
+	}
+
+	public ColumnTypeEnum getColumnType() {
+		return myColumnType;
+	}
+
+	private void setColumnType(ColumnTypeEnum theColumnType, DriverTypeEnum theDriverType, String theColumnTypeSql) {
+		Map<DriverTypeEnum, String> columnSqlType = myColumnTypeToDriverTypeToSqlType.computeIfAbsent(theColumnType, k -> new HashMap<>());
+		if (columnSqlType.containsKey(theDriverType)) {
+			throw new IllegalStateException("Duplicate key: " + theDriverType);
+		}
+		columnSqlType.put(theDriverType, theColumnTypeSql);
+	}
+
+
+	@Override
+	public void validate() {
+		super.validate();
+		Validate.notNull(myColumnType);
+		Validate.notNull(myNullable);
+
+		if (myColumnType == ColumnTypeEnum.STRING) {
+			Validate.notNull(myColumnLength);
+		} else {
+			Validate.isTrue(myColumnLength == null);
+		}
+	}
+
+	@SuppressWarnings("unchecked")
+	public T setColumnType(ColumnTypeEnum theColumnType) {
+		myColumnType = theColumnType;
+		return (T) this;
+	}
+
+	protected String getSqlType() {
+		String retVal = myColumnTypeToDriverTypeToSqlType.get(myColumnType).get(getDriverType());
+		Objects.requireNonNull(retVal);
+
+		if (myColumnType == ColumnTypeEnum.STRING) {
+			retVal = retVal.replace("?", Long.toString(getColumnLength()));
+		}
+
+		return retVal;
+	}
+
+	public boolean isNullable() {
+		return myNullable;
+	}
+
+	public void setNullable(boolean theNullable) {
+		myNullable = theNullable;
+	}
+
+	protected String getSqlNotNull() {
+		return isNullable() ? "" : " not null";
+	}
+
+	public Long getColumnLength() {
+		return myColumnLength;
+	}
+
+	public void setColumnLength(int theColumnLength) {
+		myColumnLength = (long) theColumnLength;
+	}
+
+
+	public enum ColumnTypeEnum {
+
+		LONG {
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength == null, "Must not supply a column length");
+				return "bigint";
+			}
+		},
+		STRING {
+			@Override
+			public String getDescriptor(Long theColumnLength) {
+				Assert.isTrue(theColumnLength != null, "Must supply a column length");
+				return "varchar(" + theColumnLength + ")";
+			}
+		};
+
+		public abstract String getDescriptor(Long theColumnLength);
+
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableTask.java

@@ -0,0 +1,21 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import org.apache.commons.lang3.Validate;
+
+public abstract class BaseTableTask<T extends BaseTableTask> extends BaseTask {
+	private String myTableName;
+
+	public String getTableName() {
+		return myTableName;
+	}
+
+	public T setTableName(String theTableName) {
+		myTableName = theTableName;
+		return (T) this;
+	}
+
+	@Override
+	public void validate() {
+		Validate.notBlank(myTableName);
+	}
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java

@@ -34,7 +34,7 @@ public abstract class BaseTask<T extends BaseTask> {
 		Integer changes = getConnectionProperties().getTxTemplate().execute(t -> {
 			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
 			int changesCount = jdbcTemplate.update(theSql, theArguments);
-			ourLog.info("SQL {} returned {}", theSql, changesCount);
+			ourLog.info("SQL \"{}\" returned {}", theSql, changesCount);
 			return changesCount;
 		});
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java

@@ -1,57 +1,129 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+import ca.uhn.fhir.util.StopWatch;
+import com.google.common.collect.ForwardingMap;
 import org.apache.commons.lang3.Validate;
+import org.checkerframework.checker.nullness.compatqual.NullableDecl;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.core.ResultSetExtractor;
-import org.springframework.jdbc.core.RowMapper;
 
-import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.function.Consumer;
 import java.util.function.Function;
 
-public class CalculateHashesTask extends BaseTask {
+public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask> {
 
-	private String myTableName;
+	private static final Logger ourLog = LoggerFactory.getLogger(CalculateHashesTask.class);
-	private String myColumnName;
+	private int myBatchSize = 10000;
+	private Map<String, Function<MandatoryKeyMap<String, Object>, Long>> myCalculators = new HashMap<>();
 
-	public void setTableName(String theTableName) {
+	public void setBatchSize(int theBatchSize) {
-		myTableName = theTableName;
+		myBatchSize = theBatchSize;
 	}
 
-	public void setColumnName(String theColumnName) {
-		myColumnName = theColumnName;
-	}
-
-	@Override
-	public void validate() {
-		Validate.notBlank(myTableName);
-		Validate.notBlank(myColumnName);
-	}
 
 	@Override
 	public void execute() {
-		List<Map<String, Object>> rows = getTxTemplate().execute(t->{
+		List<Map<String, Object>> rows;
-			JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+		do {
-			int batchSize = 10000;
+			rows = getTxTemplate().execute(t -> {
-			jdbcTemplate.setMaxRows(batchSize);
+				JdbcTemplate jdbcTemplate = newJdbcTemnplate();
-			String sql = "SELECT * FROM " + myTableName + " WHERE " + myColumnName + " IS NULL";
+				jdbcTemplate.setMaxRows(myBatchSize);
-			ourLog.info("Loading up to {} rows in {} with no hashes", batchSize, myTableName);
+				String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
-			return jdbcTemplate.queryForList(sql);
+				ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
+				return jdbcTemplate.queryForList(sql);
+			});
+
+			updateRows(rows);
+		} while (rows.size() > 0);
+	}
+
+	private void updateRows(List<Map<String, Object>> theRows) {
+		StopWatch sw = new StopWatch();
+		getTxTemplate().execute(t -> {
+
+			// Loop through rows
+			assert theRows != null;
+			for (Map<String, Object> nextRow : theRows) {
+
+				Map<String, Long> newValues = new HashMap<>();
+				MandatoryKeyMap<String, Object> nextRowMandatoryKeyMap = new MandatoryKeyMap<>(nextRow);
+
+				// Apply calculators
+				for (Map.Entry<String, Function<MandatoryKeyMap<String, Object>, Long>> nextCalculatorEntry : myCalculators.entrySet()) {
+					String nextColumn = nextCalculatorEntry.getKey();
+					Function<MandatoryKeyMap<String, Object>, Long> nextCalculator = nextCalculatorEntry.getValue();
+					Long value = nextCalculator.apply(nextRowMandatoryKeyMap);
+					newValues.put(nextColumn, value);
+				}
+
+				// Generate update SQL
+				StringBuilder sqlBuilder = new StringBuilder();
+				List<Long> arguments = new ArrayList<>();
+				sqlBuilder.append("UPDATE ");
+				sqlBuilder.append(getTableName());
+				sqlBuilder.append(" SET ");
+				for (Map.Entry<String, Long> nextNewValueEntry : newValues.entrySet()) {
+					if (arguments.size() > 0) {
+						sqlBuilder.append(", ");
+					}
+					sqlBuilder.append(nextNewValueEntry.getKey()).append(" = ?");
+					arguments.add(nextNewValueEntry.getValue());
+				}
+				sqlBuilder.append(" WHERE SP_ID = ?");
+				arguments.add((Long) nextRow.get("SP_ID"));
+
+				// Apply update SQL
+				newJdbcTemnplate().update(sqlBuilder.toString(), arguments.toArray());
+
+			}
+
+			return theRows.size();
 		});
+		ourLog.info("Updated {} rows on {} in {}", theRows.size(), getTableName(), sw.toString());
+	}
 
-
+	public CalculateHashesTask addCalculator(String theColumnName, Function<MandatoryKeyMap<String, Object>, Long> theConsumer) {
+		Validate.isTrue(myCalculators.containsKey(theColumnName) == false);
+		myCalculators.put(theColumnName, theConsumer);
+		return this;
 	}
 
 
-	private Map<String, Function<Map<String, Object>, Long>> myColumnMappers;
+	public static class MandatoryKeyMap<K, V> extends ForwardingMap<K, V> {
 
-	public void addCalculator(String theColumnName, Function<Map<String, Object>, Long> theConsumer) {
+		private final Map<K, V> myWrap;
 
+		public MandatoryKeyMap(Map<K, V> theWrap) {
+			myWrap = theWrap;
+		}
+
+		@Override
+		public V get(@NullableDecl Object theKey) {
+			if (!containsKey(theKey)) {
+				throw new IllegalArgumentException("No key: " + theKey);
+			}
+			return super.get(theKey);
+		}
+
+		public String getString(String theKey) {
+			return (String) get(theKey);
+		}
+
+		@Override
+		protected Map<K, V> delegate() {
+			return myWrap;
+		}
+
+		public String getResourceType() {
+			return getString("RES_TYPE");
+		}
+
+		public String getParamName() {
+			return getString("SP_NAME");
+		}
 	}
-
-	private static final Logger ourLog = LoggerFactory.getLogger(CalculateHashesTask.class);
 }

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java

@@ -8,58 +8,74 @@ import org.slf4j.LoggerFactory;
 import java.sql.SQLException;
 import java.util.Set;
 
-public class DropIndexTask extends BaseTask<DropIndexTask> {
+public class DropIndexTask extends BaseTableTask<DropIndexTask> {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(DropIndexTask.class);
 	private String myIndexName;
-	private String myTableName;
 
 	@Override
 	public void validate() {
+		super.validate();
 		Validate.notBlank(myIndexName, "The index name must not be blank");
-		Validate.notBlank(myTableName, "The table name must not be blank");
 
 		if (getDescription() == null) {
-			setDescription("Drop index " + myIndexName + " on table " + myTableName);
+			setDescription("Drop index " + myIndexName + " on table " + getTableName());
 		}
 	}
 
 	@Override
 	public void execute() throws SQLException {
-		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), myTableName);
+		Set<String> indexNames = JdbcUtils.getIndexNames(getConnectionProperties(), getTableName());
 
 		if (!indexNames.contains(myIndexName)) {
-			ourLog.info("Index {} does not exist on table {} - No action needed", myIndexName, myTableName);
+			ourLog.info("Index {} does not exist on table {} - No action needed", myIndexName, getTableName());
 			return;
 		}
 
-		ourLog.info("Dropping index {} on table {}", myIndexName, myTableName);
+		boolean isUnique = JdbcUtils.isIndexUnique(getConnectionProperties(), getTableName(), myIndexName);
+		String uniquenessString = isUnique ? "unique" : "non-unique";
+		ourLog.info("Dropping {} index {} on table {}", uniquenessString, myIndexName, getTableName());
 
 		String sql = null;
-		switch (getDriverType()) {
+
-			case MYSQL_5_7:
+		if (isUnique) {
-			case MARIADB_10_1:
+			// Drop constraint
-				sql = "ALTER TABLE " + myTableName + " DROP INDEX " + myIndexName;
+			switch (getDriverType()) {
-				break;
+				case MYSQL_5_7:
-			case POSTGRES_9_4:
+				case MARIADB_10_1:
-			case DERBY_EMBEDDED:
+					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
-			case ORACLE_12C:
+					break;
-				sql = "DROP INDEX " + myIndexName;
+				case DERBY_EMBEDDED:
-				break;
+					sql = "DROP INDEX " + myIndexName;
-			case MSSQL_2012:
+					break;
-				sql = "DROP INDEX " + myTableName + "." + myIndexName;
+				case POSTGRES_9_4:
-				break;
+				case ORACLE_12C:
+				case MSSQL_2012:
+					sql = "ALTER TABLE " + getTableName() + " DROP CONSTRAINT " + myIndexName;
+					break;
+			}
+		} else {
+			// Drop index
+			switch (getDriverType()) {
+				case MYSQL_5_7:
+				case MARIADB_10_1:
+					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
+					break;
+				case POSTGRES_9_4:
+				case DERBY_EMBEDDED:
+				case ORACLE_12C:
+					sql = "DROP INDEX " + myIndexName;
+					break;
+				case MSSQL_2012:
+					sql = "DROP INDEX " + getTableName() + "." + myIndexName;
+					break;
+			}
 		}
 		executeSql(sql);
 
 	}
 
 
-	public DropIndexTask setTableName(String theTableName) {
-		myTableName = theTableName;
-		return this;
-	}
-
 	public DropIndexTask setIndexName(String theIndexName) {
 		myIndexName = theIndexName;
 		return this;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ModifyColumnTask.java

@@ -0,0 +1,69 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+
+public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ModifyColumnTask.class);
+
+
+	@Override
+	public void execute() {
+
+		String existingType;
+		try {
+			existingType = JdbcUtils.getColumnType(getConnectionProperties(), getTableName(), getColumnName());
+		} catch (SQLException e) {
+			throw new InternalErrorException(e);
+		}
+
+		String wantedType = getColumnType().getDescriptor(getColumnLength());
+		if (existingType.equals(wantedType)) {
+			ourLog.info("Column {} on table {} is already of type {} - No action performed", getColumnName(), getTableName(), wantedType);
+			return;
+		}
+
+		String type = getSqlType();
+		String notNull = getSqlNotNull();
+
+		String sql;
+		String sqlNotNull = null;
+		switch (getDriverType()) {
+			case DERBY_EMBEDDED:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " set data type " + type;
+				break;
+			case MARIADB_10_1:
+			case MYSQL_5_7:
+				sql = "alter table " + getTableName() + " modify column " + getColumnName() + " " + type + notNull;
+				break;
+			case POSTGRES_9_4:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " type " + type;
+				if (isNullable() == false) {
+					sqlNotNull = "alter table " + getTableName() + " alter column " + getColumnName() + " set not null";
+				}
+				break;
+			case ORACLE_12C:
+				sql = "alter table " + getTableName() + " modify " + getColumnName() + " " + type + notNull;
+				break;
+			case MSSQL_2012:
+				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " " + type + notNull;
+				break;
+			default:
+				throw new IllegalStateException("Dont know how to handle " + getDriverType());
+		}
+
+		ourLog.info("Updating column {} on table {} to type {}", getColumnName(), getTableName(), type);
+		executeSql(sql);
+
+		if (sqlNotNull != null) {
+			ourLog.info("Updating column {} on table {} to not null", getColumnName(), getTableName());
+			executeSql(sqlNotNull);
+		}
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -1,10 +1,8 @@
 package ca.uhn.fhir.jpa.migrate.tasks;
 
-import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.migrate.taskdef.AddIndexTask;
+import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
+import ca.uhn.fhir.jpa.migrate.taskdef.*;
-import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask;
-import ca.uhn.fhir.jpa.migrate.taskdef.DropIndexTask;
 import ca.uhn.fhir.util.VersionEnum;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.MultimapBuilder;
@@ -20,31 +18,240 @@ public class HapiFhirJpaMigrationTasks {
 	public HapiFhirJpaMigrationTasks() {
 
 		// Forced ID changes
-		forVersion(VersionEnum.V3_5_0)
+		Builder.BuilderWithTableName forcedId = forVersion(VersionEnum.V3_5_0).onTable("HFJ_FORCED_ID");
-			.onTable("HFJ_FORCED_ID")
+		forcedId
 			.dropIndex("IDX_FORCEDID_TYPE_FORCEDID");
-		forVersion(VersionEnum.V3_5_0)
+		forcedId
-			.onTable("HFJ_FORCED_ID")
 			.dropIndex("IDX_FORCEDID_TYPE_RESID");
-		forVersion(VersionEnum.V3_5_0)
+		forcedId
-			.onTable("HFJ_FORCED_ID")
 			.addIndex("IDX_FORCEDID_TYPE_FID")
 			.unique(true)
 			.withColumns("RESOURCE_TYPE", "FORCED_ID");
 
 		// Indexes - Coords
-		forVersion(VersionEnum.V3_5_0)
+		Builder.BuilderWithTableName spidxCoords = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_COORDS");
-			.onTable("HFJ_SPIDX_COORDS")
+		spidxCoords
 			.dropIndex("IDX_SP_COORDS_HASH");
-		forVersion(VersionEnum.V3_5_0)
+		spidxCoords
-			.onTable("HFJ_SPIDX_COORDS")
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxCoords
 			.addIndex("IDX_SP_COORDS_HASH")
 			.unique(false)
 			.withColumns("HASH_IDENTITY", "SP_VALUE", "SP_LATITUDE", "SP_LONGITUDE");
-		forVersion(VersionEnum.V3_5_0)
+		spidxCoords
-			.addTask(new CalculateHashesTask().calculator(()->{
+			.addTask(new CalculateHashesTask()
-				return ResourceIndexedSearchParamCoords.calculateHashIdentity("resourceType", "paramName");
+				.setColumnName("HASH_IDENTITY")
-			}));
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Date
+		Builder.BuilderWithTableName spidxDate = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_DATE");
+		spidxDate
+			.dropIndex("IDX_SP_TOKEN");
+		spidxDate
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxDate
+			.addIndex("IDX_SP_DATE_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH");
+		spidxDate
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Number
+		Builder.BuilderWithTableName spidxNumber = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_NUMBER");
+		spidxNumber
+			.dropIndex("IDX_SP_NUMBER");
+		spidxNumber
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxNumber
+			.addIndex("IDX_SP_NUMBER_HASH_VAL")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE");
+		spidxNumber
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+			);
+
+		// Indexes - Quantity
+		Builder.BuilderWithTableName spidxQuantity = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_QUANTITY");
+		spidxQuantity
+			.dropIndex("IDX_SP_QUANTITY");
+		spidxQuantity
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addColumn("HASH_IDENTITY_SYS_UNITS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addColumn("HASH_IDENTITY_AND_UNITS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_VALUE");
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH_UN")
+			.unique(false)
+			.withColumns("HASH_IDENTITY_AND_UNITS", "SP_VALUE");
+		spidxQuantity
+			.addIndex("IDX_SP_QUANTITY_HASH_SYSUN")
+			.unique(false)
+			.withColumns("HASH_IDENTITY_SYS_UNITS", "SP_VALUE");
+		spidxQuantity
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_IDENTITY_AND_UNITS", t -> ResourceIndexedSearchParamQuantity.calculateHashUnits(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_UNITS")))
+				.addCalculator("HASH_IDENTITY_SYS_UNITS", t -> ResourceIndexedSearchParamQuantity.calculateHashSystemAndUnits(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_SYSTEM"), t.getString("SP_UNITS")))
+			);
+
+		// Indexes - String
+		Builder.BuilderWithTableName spidxString = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_STRING");
+		spidxString
+			.dropIndex("IDX_SP_STRING");
+		spidxString
+			.addColumn("HASH_NORM_PREFIX")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxString
+			.addColumn("HASH_NORM")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxString
+			.addIndex("IDX_SP_STRING_HASH_NRM")
+			.unique(false)
+			.withColumns("HASH_NORM_PREFIX", "SP_VALUE_NORMALIZED");
+		spidxString
+			.addIndex("IDX_SP_STRING_HASH_EXCT")
+			.unique(false)
+			.withColumns("HASH_EXACT");
+		spidxString
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("IDX_SP_STRING_HASH_NRM", t -> ResourceIndexedSearchParamString.calculateHashNormalized(new DaoConfig(), t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_VALUE_NORMALIZED")))
+				.addCalculator("IDX_SP_STRING_HASH_EXCT", t -> ResourceIndexedSearchParamString.calculateHashExact(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE_EXACT")))
+			);
+
+		// Indexes - Token
+		Builder.BuilderWithTableName spidxToken = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_TOKEN");
+		spidxToken
+			.dropIndex("IDX_SP_TOKEN");
+		spidxToken
+			.dropIndex("IDX_SP_TOKEN_UNQUAL");
+		spidxToken
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_SYS")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_SYS_AND_VALUE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addColumn("HASH_VALUE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH")
+			.unique(false)
+			.withColumns("HASH_IDENTITY");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_S")
+			.unique(false)
+			.withColumns("HASH_SYS");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_SV")
+			.unique(false)
+			.withColumns("HASH_SYS_AND_VALUE");
+		spidxToken
+			.addIndex("IDX_SP_TOKEN_HASH_V")
+			.unique(false)
+			.withColumns("HASH_VALUE");
+		spidxToken
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_SYS", t -> ResourceIndexedSearchParamToken.calculateHashSystem(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM")))
+				.addCalculator("HASH_SYS_AND_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashSystemAndValue(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM"), t.getString("SP_VALUE")))
+				.addCalculator("HASH_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashValue(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE")))
+			);
+
+		// Indexes - URI
+		Builder.BuilderWithTableName spidxUri = forVersion(VersionEnum.V3_5_0).onTable("HFJ_SPIDX_URI");
+		spidxUri
+			.addColumn("HASH_IDENTITY")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spidxUri
+			.addIndex("IDX_SP_URI_HASH_IDENTITY")
+			.unique(false)
+			.withColumns("HASH_IDENTITY", "SP_URI");
+		spidxUri
+			.addIndex("IDX_SP_URI_HASH_URI")
+			.unique(false)
+			.withColumns("HASH_URI");
+		spidxUri
+			.addTask(new CalculateHashesTask()
+				.setColumnName("HASH_IDENTITY")
+				.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")))
+				.addCalculator("HASH_URI", t -> ResourceIndexedSearchParamUri.calculateHashUri(t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_URI")))
+			);
+
+		// Search Parameter Presence
+		Builder.BuilderWithTableName spp = forVersion(VersionEnum.V3_5_0).onTable("HFJ_RES_PARAM_PRESENT");
+		spp.dropIndex("IDX_RESPARMPRESENT_SPID_RESID");
+		spp
+			.addColumn("HASH_PRESENCE")
+			.nullable()
+			.type(AddColumnTask.ColumnTypeEnum.LONG);
+		spp
+			.addIndex("IDX_RESPARMPRESENT_HASHPRES")
+			.unique(false)
+			.withColumns("HASH_PRESENCE");
+		ArbitrarySqlTask consolidateSearchParamPresenceIndexesTask = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		consolidateSearchParamPresenceIndexesTask.setBatchSize(1);
+		String sql = "SELECT " +
+			"HFJ_SEARCH_PARM.RES_TYPE RES_TYPE, HFJ_SEARCH_PARM.PARAM_NAME PARAM_NAME, " +
+			"HFJ_RES_PARAM_PRESENT.PID PID, HFJ_RES_PARAM_PRESENT.SP_ID SP_ID, HFJ_RES_PARAM_PRESENT.SP_PRESENT SP_PRESENT, HFJ_RES_PARAM_PRESENT.HASH_PRESENT HASH_PRESENT " +
+			"from HFJ_RES_PARAM_PRESENT " +
+			"join HFJ_SEARCH_PARM ON (HFJ_SEARCH_PARM.PID = HFJ_RES_PARAM_PRESENT.SP_ID) " +
+			"where HFJ_RES_PARAM_PRESENT.HASH_PRESENT is null";
+		consolidateSearchParamPresenceIndexesTask.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
+			Long pid = (Long) t.get("PID");
+			Boolean present = (Boolean) t.get("SP_PRESENT");
+			String resType = (String) t.get("RES_TYPE");
+			String paramName = (String) t.get("PARAM_NAME");
+			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
+			consolidateSearchParamPresenceIndexesTask.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENCE = ? where PID = ?", hash, pid);
+		});
+		forVersion(VersionEnum.V3_5_0).addTask(consolidateSearchParamPresenceIndexesTask);
+
+		// Concept
+		Builder.BuilderWithTableName trmConcept = forVersion(VersionEnum.V3_5_0).onTable("TRM_CONCEPT");
+		trmConcept
+			.addIndex("IDX_CONCEPT_UPDATED")
+			.unique(false)
+			.withColumns("CONCEPT_UPDATED");
+		trmConcept
+			.modifyColumn("CODE")
+			.nonNullable()
+			.withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 500);
 
 	}
 
@@ -74,6 +281,7 @@ public class HapiFhirJpaMigrationTasks {
 
 		private class BuilderWithTableName {
 			private String myIndexName;
+			private String myColumnName;
 
 			void dropIndex(String theIndexName) {
 				DropIndexTask task = new DropIndexTask();
@@ -87,6 +295,21 @@ public class HapiFhirJpaMigrationTasks {
 				return new BuilderAddIndexWithName();
 			}
 
+			public BuilderAddColumnWithName addColumn(String theColumnName) {
+				myColumnName = theColumnName;
+				return new BuilderAddColumnWithName();
+			}
+
+			public void addTask(BaseTableTask<?> theTask) {
+				theTask.setTableName(myTableName);
+				Builder.this.addTask(theTask);
+			}
+
+			public BuilderModifyColumnWithName modifyColumn(String theColumnName) {
+				myColumnName = theColumnName;
+				return new BuilderModifyColumnWithName();
+			}
+
 			private class BuilderAddIndexWithName {
 				private boolean myUnique;
 
@@ -106,6 +329,57 @@ public class HapiFhirJpaMigrationTasks {
 					}
 				}
 			}
+
+			private class BuilderAddColumnWithName {
+				private boolean myNullable;
+
+				public BuilderAddColumnWithNameNullable nullable() {
+					myNullable = true;
+					return new BuilderAddColumnWithNameNullable();
+				}
+
+				private class BuilderAddColumnWithNameNullable {
+					public void type(AddColumnTask.ColumnTypeEnum theColumnType) {
+						AddColumnTask task = new AddColumnTask();
+						task.setColumnName(myColumnName);
+						task.setNullable(myNullable);
+						task.setColumnType(theColumnType);
+						addTask(task);
+					}
+				}
+			}
+
+			private class BuilderModifyColumnWithName {
+
+				private boolean myNullable;
+
+				public BuilderModifyColumnWithNameAndNullable nullable() {
+					myNullable = true;
+					return new BuilderModifyColumnWithNameAndNullable();
+				}
+
+				public BuilderModifyColumnWithNameAndNullable nonNullable() {
+					myNullable = false;
+					return new BuilderModifyColumnWithNameAndNullable();
+				}
+
+				private class BuilderModifyColumnWithNameAndNullable {
+
+					public void withType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, int theLength) {
+						if (theColumnType == BaseTableColumnTypeTask.ColumnTypeEnum.STRING) {
+							ModifyColumnTask task = new ModifyColumnTask();
+							task.setColumnName(myColumnName);
+							task.setTableName(myTableName);
+							task.setColumnLength(theLength);
+							task.setNullable(myNullable);
+							addTask(task);
+						} else {
+							throw new IllegalArgumentException("Can not specify length for column of type " + theColumnType);
+						}
+					}
+
+				}
+			}
 		}
 	}
 

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTest.java

@@ -0,0 +1,44 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
+
+public class AddColumnTest extends BaseTest {
+
+	@Test
+	public void testColumnDoesntAlreadyExist() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
+
+		AddColumnTask task = new AddColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("newcol");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		task.setNullable(true);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL", "NEWCOL"));
+	}
+
+	@Test
+	public void testColumnAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");
+
+		AddColumnTask task = new AddColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("newcol");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getColumnNames(getConnectionProperties(), "SOMETABLE"), containsInAnyOrder("PID", "TEXTCOL", "NEWCOL"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTest.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.entity.SearchParamPresent;
+import org.junit.Test;
+
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class ArbitrarySqlTest extends BaseTest {
+
+	@Test
+	public void test350MigrateSearchParams() {
+		executeSql("create table HFJ_SEARCH_PARM (PID bigint not null, RES_TYPE varchar(255), PARAM_NAME varchar(255))");
+		executeSql("insert into HFJ_SEARCH_PARM (PID, RES_TYPE, PARAM_NAME) values (1, 'Patient', 'identifier')");
+		executeSql("insert into HFJ_SEARCH_PARM (PID, RES_TYPE, PARAM_NAME) values (2, 'Patient', 'family')");
+		executeSql("create table HFJ_RES_PARAM_PRESENT (PID bigint, SP_ID bigint, SP_PRESENT boolean, HASH_PRESENT bigint)");
+		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (100, 1, true, null)");
+		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (101, 2, true, null)");
+
+		ArbitrarySqlTask task = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		task.setBatchSize(1);
+		String sql = "SELECT " +
+			"HFJ_SEARCH_PARM.RES_TYPE RES_TYPE, HFJ_SEARCH_PARM.PARAM_NAME PARAM_NAME, " +
+			"HFJ_RES_PARAM_PRESENT.PID PID, HFJ_RES_PARAM_PRESENT.SP_ID SP_ID, HFJ_RES_PARAM_PRESENT.SP_PRESENT SP_PRESENT, HFJ_RES_PARAM_PRESENT.HASH_PRESENT HASH_PRESENT " +
+			"from HFJ_RES_PARAM_PRESENT " +
+			"join HFJ_SEARCH_PARM ON (HFJ_SEARCH_PARM.PID = HFJ_RES_PARAM_PRESENT.SP_ID) " +
+			"where HFJ_RES_PARAM_PRESENT.HASH_PRESENT is null";
+		task.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
+			Long pid = (Long) t.get("PID");
+			Boolean present = (Boolean) t.get("SP_PRESENT");
+			String resType = (String) t.get("RES_TYPE");
+			String paramName = (String) t.get("PARAM_NAME");
+			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
+			task.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENT = ? where PID = ?", hash, pid);
+		});
+
+		getMigrator().addTask(task);
+		getMigrator().migrate();
+
+
+		List<Map<String, Object>> rows = executeQuery("select * from HFJ_RES_PARAM_PRESENT order by PID asc");
+		assertEquals(2, rows.size());
+		assertEquals(100L, rows.get(0).get("PID"));
+		assertEquals(-1100208805056022671L, rows.get(0).get("HASH_PRESENT"));
+		assertEquals(101L, rows.get(1).get("PID"));
+		assertEquals(-756348509333838170L, rows.get(1).get("HASH_PRESENT"));
+
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTest.java

@@ -5,6 +5,10 @@ import ca.uhn.fhir.jpa.migrate.Migrator;
 import org.intellij.lang.annotations.Language;
 import org.junit.After;
 import org.junit.Before;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
+
+import java.util.List;
+import java.util.Map;
 
 public class BaseTest {
 
@@ -22,13 +26,19 @@ public class BaseTest {
 	}
 
 
-	protected void executeSql(@Language("SQL") String theSql) {
+	protected void executeSql(@Language("SQL") String theSql, Object... theArgs) {
 		myConnectionProperties.getTxTemplate().execute(t -> {
-			myConnectionProperties.newJdbcTemplate().execute(theSql);
+			myConnectionProperties.newJdbcTemplate().update(theSql, theArgs);
 			return null;
 		});
 	}
 
+	protected List<Map<String, Object>> executeQuery(@Language("SQL") String theSql, Object... theArgs) {
+		return myConnectionProperties.getTxTemplate().execute(t -> {
+			return myConnectionProperties.newJdbcTemplate().query(theSql, theArgs, new ColumnMapRowMapper());
+		});
+	}
+
 	public Migrator getMigrator() {
 		return myMigrator;
 	}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/CreateHashesTest.java

@@ -0,0 +1,53 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
+import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
+import org.junit.Test;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class CreateHashesTest extends BaseTest {
+
+	@Test
+	public void testCreateHashes() {
+		executeSql("create table HFJ_SPIDX_TOKEN (SP_ID bigint not null, SP_MISSING boolean, SP_NAME varchar(100) not null, RES_ID bigint, RES_TYPE varchar(255) not null, SP_UPDATED timestamp, HASH_IDENTITY bigint, HASH_SYS bigint, HASH_SYS_AND_VALUE bigint, HASH_VALUE bigint, SP_SYSTEM varchar(200), SP_VALUE varchar(200), primary key (SP_ID))");
+		executeSql("insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (false, 'identifier', 999, 'Patient', '2018-09-03 07:44:49.196', 'urn:oid:1.2.410.100110.10.41308301', '88888888', 1)");
+		executeSql("insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (false, 'identifier', 999, 'Patient', '2018-09-03 07:44:49.196', 'urn:oid:1.2.410.100110.10.41308301', '99999999', 2)");
+
+		CalculateHashesTask task = new CalculateHashesTask();
+		task.setTableName("HFJ_SPIDX_TOKEN");
+		task.setColumnName("HASH_IDENTITY");
+		task.addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME")));
+		task.addCalculator("HASH_SYS", t -> ResourceIndexedSearchParamToken.calculateHashSystem(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM")));
+		task.addCalculator("HASH_SYS_AND_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashSystemAndValue(t.getResourceType(), t.getParamName(), t.getString("SP_SYSTEM"), t.getString("SP_VALUE")));
+		task.addCalculator("HASH_VALUE", t -> ResourceIndexedSearchParamToken.calculateHashValue(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE")));
+		task.setBatchSize(1);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+
+		getConnectionProperties().getTxTemplate().execute(t -> {
+			Map<String, Object> map;
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+
+			map = jdbcTemplate.queryForMap("select * from HFJ_SPIDX_TOKEN where SP_ID = 1");
+			assertEquals(7001889285610424179L, map.get("HASH_IDENTITY"));
+			assertEquals(2686400398917843456L, map.get("HASH_SYS"));
+			assertEquals(-3943098850992523411L, map.get("HASH_SYS_AND_VALUE"));
+			assertEquals(845040519142030272L, map.get("HASH_VALUE"));
+
+			map = jdbcTemplate.queryForMap("select * from HFJ_SPIDX_TOKEN where SP_ID = 2");
+			assertEquals(7001889285610424179L, map.get("HASH_IDENTITY"));
+			assertEquals(2686400398917843456L, map.get("HASH_SYS"));
+			assertEquals(-6583685191951870327L, map.get("HASH_SYS_AND_VALUE"));
+			assertEquals(8271382783311609619L, map.get("HASH_VALUE"));
+
+			return null;
+		});
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ModifyColumnTest.java

@@ -0,0 +1,32 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+public class ModifyColumnTest extends BaseTest {
+
+
+	@Test
+	public void testColumnAlreadyExists() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");
+
+		ModifyColumnTask task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("TEXTCOL");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.STRING);
+		task.setNullable(true);
+		task.setColumnLength(300);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertEquals("varchar(300)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java

@@ -9,5 +9,4 @@ public class HapiFhirJpaMigrationTasksTest {
 		new HapiFhirJpaMigrationTasks();
 	}
 
-
 }

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/DefaultProfileValidationSupport.java

@@ -1,8 +1,8 @@
 package org.hl7.fhir.r4.hapi.ctx;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.api.Constants;
 import org.apache.commons.io.Charsets;
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -15,6 +15,7 @@ import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.*;
@@ -169,7 +170,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     InputStreamReader reader = null;
     if (inputStream != null) {
       try {
-        reader = new InputStreamReader(inputStream, Charsets.UTF_8);
+        reader = new InputStreamReader(inputStream, Constants.CHARSET_UTF8);
 
         Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
         for (BundleEntryComponent next : bundle.getEntry()) {
@@ -190,8 +191,14 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
           }
         }
       } finally {
-        IOUtils.closeQuietly(reader);
+        try {
-        IOUtils.closeQuietly(inputStream);
+          if (reader != null) {
+            reader.close();
+          }
+          inputStream.close();
+        } catch (IOException e) {
+          ourLog.warn("Failure closing stream", e);
+        }
       }
     } else {
       ourLog.warn("Unable to load resource: {}", theClasspath);
@@ -202,7 +209,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
     ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
     InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
     if (valuesetText != null) {
-      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+      InputStreamReader reader = new InputStreamReader(valuesetText, Constants.CHARSET_UTF8);
 
       Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
       for (BundleEntryComponent next : bundle.getEntry()) {