Merge branch 'philips-3.6.0' of github.com:jamesagnew/hapi-fhir into philips-3.6.0

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchTotalModeEnum.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.api;
 
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * 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%
+ */
+
 import java.util.HashMap;
 import java.util.Map;
 

hapi-fhir-jpaserver-migrate/pom.xml

@@ -31,6 +31,10 @@
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-jdbc</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-dbcp2</artifactId>
+		</dependency>
 
 		<!-- This dependency includes the core HAPI-FHIR classes -->
 		<dependency>
@@ -45,11 +49,6 @@
 			<artifactId>derby</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-dbcp2</artifactId>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.migrate;
 
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -76,20 +77,13 @@ public enum DriverTypeEnum {
 			throw new InternalErrorException("Unable to find driver class: " + myDriverClassName, e);
 		}
 
-		SingleConnectionDataSource dataSource = new SingleConnectionDataSource(){
+		BasicDataSource dataSource = new BasicDataSource();
-			@Override
+//		dataSource.setAutoCommit(false);
-			protected Connection getConnectionFromDriver(Properties props) throws SQLException {
-				Connection connect = driver.connect(theUrl, props);
-				assert connect != null;
-				return connect;
-			}
-		};
-		dataSource.setAutoCommit(false);
 		dataSource.setDriverClassName(myDriverClassName);
 		dataSource.setUrl(theUrl);
 		dataSource.setUsername(theUsername);
 		dataSource.setPassword(thePassword);
-		dataSource.setSuppressClose(true);
+//		dataSource.setSuppressClose(true);
 
 		DataSourceTransactionManager transactionManager = new DataSourceTransactionManager();
 		transactionManager.setDataSource(dataSource);

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

@@ -23,15 +23,21 @@ 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.apache.commons.lang3.concurrent.BasicThreadFactory;
 import org.checkerframework.checker.nullness.compatqual.NullableDecl;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.jdbc.core.ColumnMapRowMapper;
 import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.RowCallbackHandler;
 
+import java.sql.ResultSet;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.*;
 import java.util.function.Function;
 
 public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask> {
@@ -39,75 +45,147 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 	private static final Logger ourLog = LoggerFactory.getLogger(CalculateHashesTask.class);
 	private int myBatchSize = 10000;
 	private Map<String, Function<MandatoryKeyMap<String, Object>, Long>> myCalculators = new HashMap<>();
+	private ThreadPoolExecutor myExecutor;
 
 	public void setBatchSize(int theBatchSize) {
 		myBatchSize = theBatchSize;
 	}
 
+	/**
+	 * Constructor
+	 */
+	public CalculateHashesTask() {
+		super();
+	}
 
 	@Override
-	public void execute() {
+	public synchronized void execute() throws SQLException {
 		if (isDryRun()) {
 			return;
 		}
 
-		List<Map<String, Object>> rows;
+		initializeExecutor();
-		do {
+		try {
-			rows = getTxTemplate().execute(t -> {
-				JdbcTemplate jdbcTemplate = newJdbcTemnplate();
-				jdbcTemplate.setMaxRows(myBatchSize);
-				String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
-				ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
-				return jdbcTemplate.queryForList(sql);
-			});
 
-			updateRows(rows);
+			while(true) {
-		} while (rows.size() > 0);
+				MyRowCallbackHandler rch = new MyRowCallbackHandler();
-	}
+				getTxTemplate().execute(t -> {
+					JdbcTemplate jdbcTemplate = newJdbcTemnplate();
+					jdbcTemplate.setMaxRows(100000);
+					String sql = "SELECT * FROM " + getTableName() + " WHERE " + getColumnName() + " IS NULL";
+					ourLog.info("Finding up to {} rows in {} that requires hashes", myBatchSize, getTableName());
 
-	private void updateRows(List<Map<String, Object>> theRows) {
+					jdbcTemplate.query(sql, rch);
-		StopWatch sw = new StopWatch();
+					rch.done();
-		getTxTemplate().execute(t -> {
 
-			// Loop through rows
+					return null;
-			assert theRows != null;
+				});
-			for (Map<String, Object> nextRow : theRows) {
 
-				Map<String, Long> newValues = new HashMap<>();
+				rch.submitNext();
-				MandatoryKeyMap<String, Object> nextRowMandatoryKeyMap = new MandatoryKeyMap<>(nextRow);
+				List<Future<?>> futures = rch.getFutures();
-
+				if (futures.isEmpty()) {
-				// Apply calculators
+					break;
-				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
+				ourLog.info("Waiting for {} tasks to complete", futures.size());
-				StringBuilder sqlBuilder = new StringBuilder();
+				for (Future<?> next : futures) {
-				List<Long> arguments = new ArrayList<>();
+					try {
-				sqlBuilder.append("UPDATE ");
+						next.get();
-				sqlBuilder.append(getTableName());
+					} catch (Exception e) {
-				sqlBuilder.append(" SET ");
+						throw new SQLException(e);
-				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();
+		} finally {
-		});
+			destroyExecutor();
-		ourLog.info("Updated {} rows on {} in {}", theRows.size(), getTableName(), sw.toString());
+		}
+	}
+
+	private void destroyExecutor() {
+		myExecutor.shutdownNow();
+	}
+
+	private void initializeExecutor() {
+		int maximumPoolSize = Runtime.getRuntime().availableProcessors();
+
+		LinkedBlockingQueue<Runnable> executorQueue = new LinkedBlockingQueue<>(maximumPoolSize);
+		BasicThreadFactory threadFactory = new BasicThreadFactory.Builder()
+			.namingPattern("worker-" + "-%d")
+			.daemon(false)
+			.priority(Thread.NORM_PRIORITY)
+			.build();
+		RejectedExecutionHandler rejectedExecutionHandler = new RejectedExecutionHandler() {
+			@Override
+			public void rejectedExecution(Runnable theRunnable, ThreadPoolExecutor theExecutor) {
+				ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", executorQueue.size());
+				StopWatch sw = new StopWatch();
+				try {
+					executorQueue.put(theRunnable);
+				} catch (InterruptedException theE) {
+					throw new RejectedExecutionException("Task " + theRunnable.toString() +
+						" rejected from " + theE.toString());
+				}
+				ourLog.info("Slot become available after {}ms", sw.getMillis());
+			}
+		};
+		myExecutor = new ThreadPoolExecutor(
+			1,
+			maximumPoolSize,
+			0L,
+			TimeUnit.MILLISECONDS,
+			executorQueue,
+			threadFactory,
+			rejectedExecutionHandler);
+	}
+
+	private Future<?> updateRows(List<Map<String, Object>> theRows) {
+		Runnable task = () -> {
+			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());
+		};
+		return myExecutor.submit(task);
 	}
 
 	public CalculateHashesTask addCalculator(String theColumnName, Function<MandatoryKeyMap<String, Object>, Long> theConsumer) {
@@ -116,6 +194,39 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 		return this;
 	}
 
+	private class MyRowCallbackHandler implements RowCallbackHandler {
+
+		private List<Map<String, Object>> myRows = new ArrayList<>();
+		private List<Future<?>> myFutures = new ArrayList<>();
+
+		@Override
+		public void processRow(ResultSet rs) throws SQLException {
+			Map<String, Object> row = new ColumnMapRowMapper().mapRow(rs, 0);
+			myRows.add(row);
+
+			if (myRows.size() >= myBatchSize) {
+				submitNext();
+			}
+		}
+
+		private void submitNext() {
+			if (myRows.size() > 0) {
+				myFutures.add(updateRows(myRows));
+				myRows = new ArrayList<>();
+			}
+		}
+
+		public List<Future<?>> getFutures() {
+			return myFutures;
+		}
+
+		public void done() {
+			if (myRows.size() > 0) {
+				submitNext();
+			}
+		}
+	}
+
 
 	public static class MandatoryKeyMap<K, V> extends ForwardingMap<K, V> {
 

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

@@ -9,7 +9,7 @@ import java.util.Map;
 
 import static org.junit.Assert.assertEquals;
 
-public class CreateHashesTest extends BaseTest {
+public class CalculateHashesTest extends BaseTest {
 
 	@Test
 	public void testCreateHashes() {
@@ -50,4 +50,36 @@ public class CreateHashesTest extends BaseTest {
 		});
 	}
 
+	@Test
+	public void testCreateHashesLargeNumber() {
+		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))");
+
+		for (int i = 0; i < 777; i++) {
+			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', '8888888" + i + "', " + i + ")");
+		}
+
+		Long count = getConnectionProperties().getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			return jdbcTemplate.queryForObject("SELECT count(*) FROM HFJ_SPIDX_TOKEN WHERE HASH_VALUE IS NULL", Long.class);
+		});
+		assertEquals(777L, count.longValue());
+
+		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(3);
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		count = getConnectionProperties().getTxTemplate().execute(t -> {
+			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+			return jdbcTemplate.queryForObject("SELECT count(*) FROM HFJ_SPIDX_TOKEN WHERE HASH_VALUE IS NULL", Long.class);
+		});
+		assertEquals(0L, count.longValue());
+	}
 }

pom.xml

@@ -1727,6 +1727,12 @@
 								<copy todir="target/site/apidocs-jpaserver">
 									<fileset dir="hapi-fhir-jpaserver-base/target/site/apidocs"/>
 								</copy>
+								<copy todir="target/site/apidocs-client">
+									<fileset dir="hapi-fhir-client/target/site/apidocs"/>
+								</copy>
+								<copy todir="target/site/apidocs-server">
+									<fileset dir="hapi-fhir-server/target/site/apidocs"/>
+								</copy>
 								<copy todir="target/site/xref-jpaserver">
 									<fileset dir="hapi-fhir-jpaserver-base/target/site/xref"/>
 								</copy>
@@ -2131,6 +2137,8 @@
 				<module>hapi-fhir-structures-dstu2</module>
 				<module>hapi-fhir-structures-dstu3</module>
 				<module>hapi-fhir-structures-r4</module>
+				<module>hapi-fhir-client</module>
+				<module>hapi-fhir-server</module>
 				<module>hapi-fhir-jpaserver-base</module>
 				<module>hapi-fhir-jaxrsserver-base</module>
 				<!-- <module>hapi-fhir-cobertura</module> -->

src/changes/changes.xml

@@ -100,6 +100,10 @@
 				permission is granted. This has been corrected so that transaction() allows both
 				batch and transaction requests to proceed.
 			</action>
+			<action type="add">
+				The JPA server version migrator tool now runs in a multithreaded way, allowing it to
+				upgrade th database faster when migration tasks require data updates.
+			</action>
 		</release>
 
 		<release version="3.5.0" date="2018-09-17">

src/site/site.xml

@@ -115,6 +115,8 @@
 				<item name="Model API (DSTU2)" href="./apidocs-dstu2/index.html" />
 				<item name="Model API (DSTU3)" href="./apidocs-dstu3/index.html" />
 				<item name="Model API (R4)" href="./apidocs-r4/index.html" />
+				<item name="Client API" href="./apidocs-client/index.html" />
+				<item name="Server API" href="./apidocs-server/index.html" />
 				<item name="JPA Server API" href="./apidocs-jpaserver/index.html" />
 			</item>
 			<item name="Command Line Tool (hapi-fhir-cli)" href="./doc_cli.html" />

src/site/xdoc/docindex.xml

@@ -70,6 +70,8 @@
 				<li><a href="./apidocs-dstu/index.html">Model API (DSTU1)</a></li>
 				<li><a href="./apidocs-dstu2/index.html" >Model API (DSTU2)</a></li>
 				<li><a href="./apidocs-dstu3/index.html" >Model API (STU3)</a></li>
+				<li><a href="./apidocs-client/index.html" >Client API</a></li>
+				<li><a href="./apidocs-server/index.html" >Server API</a></li>
 				<li><a href="./apidocs-jpaserver/index.html">JPA Server API</a></li>
 			</ul>