Syntax fixes for the JPA migrator

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.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/search/StaleSearchDeletingSvcImpl.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search;
  * 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/search/reindex/IResourceReindexingSvc.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search.reindex;
  * 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/search/reindex/ResourceReindexingSvcImpl.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search.reindex;
  * 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/subscription/BaseSubscriptionInterceptor.java

@@ -68,9 +68,9 @@ import java.util.concurrent.*;
  * 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/subscription/ResourceModifiedMessage.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.subscription;
  * 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-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java

@@ -127,7 +127,9 @@ public class JdbcUtils {
 						switch (dataType) {
 							case Types.VARCHAR:
 								return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
+							case Types.NUMERIC:
 							case Types.BIGINT:
+							case Types.DECIMAL:
 								return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(null);
 							case Types.INTEGER:
 								return BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null);
@@ -135,7 +137,7 @@ public class JdbcUtils {
 							case Types.TIMESTAMP_WITH_TIMEZONE:
 								return BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP.getDescriptor(null);
 							default:
-								throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
+								throw new IllegalArgumentException("Don't know how to handle datatype " + dataType + " for column " + theColumnName + " on table " + theTableName);
 						}
 
 					}

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate;
  * 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-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTask.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * 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.
@@ -42,6 +42,7 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 	private List<Task> myTask = new ArrayList<>();
 	private int myBatchSize = 1000;
 	private String myExecuteOnlyIfTableExists;
+	private List<TableAndColumn> myConditionalOnExistenceOf = new ArrayList<>();
 
 	public ArbitrarySqlTask(String theTableName, String theDescription) {
 		myTableName = theTableName;
@@ -69,6 +70,14 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 			}
 		}
 
+		for (TableAndColumn next : myConditionalOnExistenceOf) {
+			String columnType = JdbcUtils.getColumnType(getConnectionProperties(), next.getTable(), next.getColumn());
+			if (columnType == null) {
+				ourLog.info("Table {} does not have column {} - No action performed", next.getTable(), next.getColumn());
+				return;
+			}
+		}
+
 		for (Task next : myTask) {
 			next.execute();
 		}
@@ -83,6 +92,13 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 		myExecuteOnlyIfTableExists = theExecuteOnlyIfTableExists;
 	}
 
+	/**
+	 * This task will only execute if the following column exists
+	 */
+	public void addExecuteOnlyIfColumnExists(String theTableName, String theColumnName) {
+		myConditionalOnExistenceOf.add(new TableAndColumn(theTableName, theColumnName));
+	}
+
 	public enum QueryModeEnum {
 		BATCH_UNTIL_NO_MORE
 	}
@@ -129,4 +145,22 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 			} while (rows.size() > 0);
 		}
 	}
+
+	private static class TableAndColumn {
+		private final String myTable;
+		private final String myColumn;
+
+		private TableAndColumn(String theTable, String theColumn) {
+			myTable = theTable;
+			myColumn = theColumn;
+		}
+
+		public String getTable() {
+			return myTable;
+		}
+
+		public String getColumn() {
+			return myColumn;
+		}
+	}
 }

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * 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-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -36,7 +36,7 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-@SuppressWarnings({"UnstableApiUsage", "SqlNoDataSourceInspection", "SpellCheckingInspection"})
+@SuppressWarnings({"SqlNoDataSourceInspection", "SpellCheckingInspection"})
 public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 
 	private final Set<FlagEnum> myFlags;
@@ -90,10 +90,12 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 		// Forced ID changes
 		Builder.BuilderWithTableName forcedId = version.onTable("HFJ_FORCED_ID");
 		version.startSectionWithMessage("Starting work on table: " + forcedId.getTableName());
+
 		forcedId
 			.dropIndex("IDX_FORCEDID_TYPE_FORCEDID");
 		forcedId
 			.dropIndex("IDX_FORCEDID_TYPE_RESID");
+
 		forcedId
 			.addIndex("IDX_FORCEDID_TYPE_FID")
 			.unique(true)
@@ -332,9 +334,10 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			"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_PRESENCE is null";
+		consolidateSearchParamPresenceIndexesTask.addExecuteOnlyIfColumnExists("HFJ_RES_PARAM_PRESENT", "SP_ID");
 		consolidateSearchParamPresenceIndexesTask.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
-			Long pid = (Long) t.get("PID");
+			Number pid = (Number) t.get("PID");
-			Boolean present = (Boolean) t.get("SP_PRESENT");
+			Boolean present = columnToBoolean(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);
@@ -494,6 +497,18 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.addSql(DriverTypeEnum.MSSQL_2012, "alter table TRM_CONCEPT_MAP_GRP_ELM_TGT add constraint FK_TCMGETARGET_ELEMENT foreign key (CONCEPT_MAP_GRP_ELM_PID) references TRM_CONCEPT_MAP_GRP_ELEMENT");
 	}
 
+	private Boolean columnToBoolean(Object theValue) {
+		if (theValue == null) {
+			return null;
+		}
+		if (theValue instanceof Boolean) {
+			return (Boolean) theValue;
+		}
+
+		long longValue = ((Number) theValue).longValue();
+		return longValue == 1L;
+	}
+
 	private void init340() {
 		Builder version = forVersion(VersionEnum.V3_4_0);
 
@@ -537,10 +552,6 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			myCommandLineValue = theCommandLineValue;
 		}
 
-		public String getCommandLineValue() {
-			return myCommandLineValue;
-		}
-
 		public static FlagEnum fromCommandLineValue(String theCommandLineValue) {
 			Optional<FlagEnum> retVal = Arrays.stream(values()).filter(t -> t.myCommandLineValue.equals(theCommandLineValue)).findFirst();
 			return retVal.orElseThrow(() -> {

hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt

@@ -121,6 +121,9 @@ drop table hfj_search_result cascade constraints;
 drop table hfj_search_include cascade constraints;
 drop table hfj_search cascade constraints;
 drop table hfj_res_param_present cascade constraints;
+DROP TABLE HFJ_RES_REINDEX_JOB cascade constraints;
+DROP TABLE HFJ_SEARCH_PARM cascade constraints;
+DROP TABLE HFJ_TAG_DEF cascade CONSTRAINTS;
 drop table hfj_idx_cmp_string_uniq cascade constraints;
 drop table hfj_subscription_stats cascade constraints;
 drop table trm_concept_property cascade constraints;
@@ -130,11 +133,11 @@ drop table trm_codesystem_ver cascade constraints;
 drop table trm_codesystem cascade constraints;
 DROP TABLE hfj_resource CASCADE CONSTRAINTS;
 DROP TABLE hfj_res_ver CASCADE CONSTRAINTS;
-drop table cdr_audit_evt_target_module cascade constraints;
+DROP TABLE TRM_CONCEPT_DESIG CASCADE CONSTRAINTS;
-drop table cdr_audit_evt_target_res cascade constraints;
+DROP TABLE TRM_CONCEPT_MAP CASCADE CONSTRAINTS;
-drop table cdr_audit_evt_target_user cascade constraints;
+DROP TABLE TRM_CONCEPT_MAP_GROUP CASCADE CONSTRAINTS;
-drop table cdr_xact_log_step cascade constraints;
+DROP TABLE TRM_CONCEPT_MAP_GRP_ELEMENT CASCADE CONSTRAINTS;
-drop table cdr_xact_log cascade constraints;
+DROP TABLE TRM_CONCEPT_MAP_GRP_ELM_TGT CASCADE CONSTRAINTS;
 
 
 

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server;
  * 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-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/BaseRule.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
  * 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-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamed.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
  * 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-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamedAndScoped.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.server.interceptor.auth;
 
+/*-
+ * #%L
+ * HAPI FHIR - Server Framework
+ * %%
+ * Copyright (C) 2014 - 2018 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%
+ */
+
 public interface IAuthRuleBuilderOperationNamedAndScoped {
 
 	/**

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/OperationRule.java

@@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
  * 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.