diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseMigrateDatabaseCommand.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseMigrateDatabaseCommand.java index f6e9f2569ab..2685989c610 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseMigrateDatabaseCommand.java +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseMigrateDatabaseCommand.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.cli; * 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. @@ -25,15 +25,24 @@ import ca.uhn.fhir.jpa.migrate.Migrator; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; +import org.apache.commons.lang3.StringUtils; import java.util.Arrays; import java.util.Collections; import java.util.List; +import java.util.Set; import java.util.stream.Collectors; +import static org.apache.commons.lang3.StringUtils.defaultString; + public abstract class BaseMigrateDatabaseCommand extends BaseCommand { private static final String MIGRATE_DATABASE = "migrate-database"; + private Set myFlags; + + protected Set getFlags() { + return myFlags; + } @Override public String getCommandDescription() { @@ -68,6 +77,7 @@ public abstract class BaseMigrateDatabaseCommand extends BaseCom addRequiredOption(retVal, "f", "from", "Version", "The database schema version to migrate FROM"); addRequiredOption(retVal, "t", "to", "Version", "The database schema version to migrate TO"); addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")"); + addOptionalOption(retVal, "x", "flags", "Flags", "A comma-separated list of any specific migration flags (these flags are version specific, see migrator documentation for details)"); return retVal; } @@ -97,6 +107,12 @@ public abstract class BaseMigrateDatabaseCommand extends BaseCom boolean dryRun = theCommandLine.hasOption("r"); + String flags = theCommandLine.getOptionValue("x"); + myFlags = Arrays.stream(defaultString(flags).split(",")) + .map(String::trim) + .filter(StringUtils::isNotBlank) + .collect(Collectors.toSet()); + Migrator migrator = new Migrator(); migrator.setConnectionUrl(url); migrator.setDriverType(driverType); diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommand.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommand.java index ff7d39c0fda..6be5b241110 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommand.java +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommand.java @@ -42,7 +42,7 @@ public class HapiMigrateDatabaseCommand extends BaseMigrateDatabaseCommand> tasks = new HapiFhirJpaMigrationTasks().getTasks(theFrom, theTo); + List> tasks = new HapiFhirJpaMigrationTasks(getFlags()).getTasks(theFrom, theTo); tasks.forEach(theMigrator::addTask); } } diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommandTest.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommandTest.java index 7051011ff58..aaee5c3e4aa 100644 --- a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommandTest.java +++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiMigrateDatabaseCommandTest.java @@ -7,14 +7,26 @@ import org.apache.commons.io.IOUtils; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.jdbc.core.support.AbstractLobCreatingPreparedStatementCallback; +import org.springframework.jdbc.support.lob.DefaultLobHandler; +import org.springframework.jdbc.support.lob.LobCreator; import java.io.File; import java.io.IOException; +import java.sql.PreparedStatement; +import java.sql.SQLException; +import java.sql.Timestamp; +import java.sql.Types; import java.util.ArrayList; import java.util.Arrays; import java.util.List; +import java.util.Map; import static org.apache.commons.lang3.StringUtils.isBlank; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; public class HapiMigrateDatabaseCommandTest { @@ -25,39 +37,20 @@ public class HapiMigrateDatabaseCommandTest { } @Test - public void testMigrate() throws IOException { + public void testMigrate_340_350() throws IOException { File directory = new File("target/migrator_derby_test_340_350"); if (directory.exists()) { FileUtils.deleteDirectory(directory); } - String url = "jdbc:derby:directory:target/migrator_derby_test_340_350;create=true"; + String url = "jdbc:derby:directory:" + directory.getAbsolutePath() + ";create=true"; DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(url, "", ""); - String script = IOUtils.toString(HapiMigrateDatabaseCommandTest.class.getResourceAsStream("/persistence_create_derby107_340.sql"), Charsets.UTF_8); - List scriptStatements = new ArrayList<>(Arrays.asList(script.split("\n"))); - for (int i = 0; i < scriptStatements.size(); i++) { - String nextStatement = scriptStatements.get(i); - if (isBlank(nextStatement)) { - scriptStatements.remove(i); - i--; - continue; - } + String initSql = "/persistence_create_derby107_340.sql"; + executeSqlStatements(connectionProperties, initSql); - nextStatement = nextStatement.trim(); - while (nextStatement.endsWith(";")) { - nextStatement = nextStatement.substring(0, nextStatement.length() - 1); - } - scriptStatements.set(i, nextStatement); - } - - connectionProperties.getTxTemplate().execute(t -> { - for (String next : scriptStatements) { - connectionProperties.newJdbcTemplate().execute(next); - } - return null; - }); + seedDatabase340(connectionProperties); ourLog.info("**********************************************"); ourLog.info("Done Setup, Starting Dry Run..."); @@ -75,6 +68,13 @@ public class HapiMigrateDatabaseCommandTest { }; App.main(args); + connectionProperties.getTxTemplate().execute(t -> { + JdbcTemplate jdbcTemplate = connectionProperties.newJdbcTemplate(); + List> values = jdbcTemplate.queryForList("SELECT * FROM hfj_spidx_token"); + assertFalse(values.get(0).keySet().contains("HASH_IDENTITY")); + return null; + }); + ourLog.info("**********************************************"); ourLog.info("Done Setup, Starting Migration..."); ourLog.info("**********************************************"); @@ -89,5 +89,245 @@ public class HapiMigrateDatabaseCommandTest { "-t", "V3_5_0" }; App.main(args); + + connectionProperties.getTxTemplate().execute(t -> { + JdbcTemplate jdbcTemplate = connectionProperties.newJdbcTemplate(); + List> values = jdbcTemplate.queryForList("SELECT * FROM hfj_spidx_token"); + assertEquals(1, values.size()); + assertEquals("identifier", values.get(0).get("SP_NAME")); + assertEquals("12345678", values.get(0).get("SP_VALUE")); + assertTrue(values.get(0).keySet().contains("HASH_IDENTITY")); + assertEquals(7001889285610424179L, values.get(0).get("HASH_IDENTITY")); + return null; + }); } + + @Test + public void testMigrate_340_360() throws IOException { + + File directory = new File("target/migrator_derby_test_340_360"); + if (directory.exists()) { + FileUtils.deleteDirectory(directory); + } + + String url = "jdbc:derby:directory:" + directory.getAbsolutePath() + ";create=true"; + DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(url, "", ""); + + String initSql = "/persistence_create_derby107_340.sql"; + executeSqlStatements(connectionProperties, initSql); + + seedDatabase340(connectionProperties); + + ourLog.info("**********************************************"); + ourLog.info("Done Setup, Starting Migration..."); + ourLog.info("**********************************************"); + + String[] args = new String[]{ + "migrate-database", + "-d", "DERBY_EMBEDDED", + "-u", url, + "-n", "", + "-p", "", + "-f", "V3_4_0", + "-t", "V3_6_0" + }; + App.main(args); + + connectionProperties.getTxTemplate().execute(t -> { + JdbcTemplate jdbcTemplate = connectionProperties.newJdbcTemplate(); + List> values = jdbcTemplate.queryForList("SELECT * FROM hfj_spidx_token"); + assertEquals(1, values.size()); + assertEquals("identifier", values.get(0).get("SP_NAME")); + assertEquals("12345678", values.get(0).get("SP_VALUE")); + assertTrue(values.get(0).keySet().contains("HASH_IDENTITY")); + assertEquals(7001889285610424179L, values.get(0).get("HASH_IDENTITY")); + return null; + }); + } + + private void seedDatabase340(DriverTypeEnum.ConnectionProperties theConnectionProperties) { + theConnectionProperties.getTxTemplate().execute(t -> { + JdbcTemplate jdbcTemplate = theConnectionProperties.newJdbcTemplate(); + + jdbcTemplate.execute( + "insert into HFJ_RESOURCE (RES_DELETED_AT, RES_VERSION, FORCED_ID_PID, HAS_TAGS, RES_PUBLISHED, RES_UPDATED, SP_HAS_LINKS, HASH_SHA256, SP_INDEX_STATUS, RES_LANGUAGE, SP_CMPSTR_UNIQ_PRESENT, SP_COORDS_PRESENT, SP_DATE_PRESENT, SP_NUMBER_PRESENT, SP_QUANTITY_PRESENT, SP_STRING_PRESENT, SP_TOKEN_PRESENT, SP_URI_PRESENT, RES_PROFILE, RES_TYPE, RES_VER, RES_ID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)", + new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) { + @Override + protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException { + thePs.setNull(1, Types.TIMESTAMP); + thePs.setString(2, "R4"); + thePs.setNull(3, Types.BIGINT); + thePs.setBoolean(4, false); + thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis())); + thePs.setTimestamp(6, new Timestamp(System.currentTimeMillis())); + thePs.setBoolean(7, false); + thePs.setNull(8, Types.VARCHAR); + thePs.setLong(9, 1L); + thePs.setNull(10, Types.VARCHAR); + thePs.setBoolean(11, false); + thePs.setBoolean(12, false); + thePs.setBoolean(13, false); + thePs.setBoolean(14, false); + thePs.setBoolean(15, false); + thePs.setBoolean(16, false); + thePs.setBoolean(17, false); + thePs.setBoolean(18, false); + thePs.setNull(19, Types.VARCHAR); + thePs.setString(20, "Patient"); + thePs.setLong(21, 1L); + thePs.setLong(22, 1L); + } + } + ); + + jdbcTemplate.execute( + "insert into HFJ_RES_VER (RES_DELETED_AT, RES_VERSION, FORCED_ID_PID, HAS_TAGS, RES_PUBLISHED, RES_UPDATED, RES_ENCODING, RES_TEXT, RES_ID, RES_TYPE, RES_VER, PID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)", + new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) { + @Override + protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException { + thePs.setNull(1, Types.TIMESTAMP); + thePs.setString(2, "R4"); + thePs.setNull(3, Types.BIGINT); + thePs.setBoolean(4, false); + thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis())); + thePs.setTimestamp(6, new Timestamp(System.currentTimeMillis())); + thePs.setString(7, "JSON"); + theLobCreator.setBlobAsBytes(thePs, 8, "{\"resourceType\":\"Patient\"}".getBytes(Charsets.US_ASCII)); + thePs.setLong(9, 1L); + thePs.setString(10, "Patient"); + thePs.setLong(11, 1L); + thePs.setLong(12, 1L); + } + } + ); + + jdbcTemplate.execute( + "insert into HFJ_SPIDX_STRING (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_VALUE_EXACT, SP_VALUE_NORMALIZED, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)", + new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) { + @Override + protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException { + thePs.setBoolean(1, false); + thePs.setString(2, "given"); + thePs.setLong(3, 1L); // res-id + thePs.setString(4, "Patient"); + thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis())); + thePs.setString(6, "ROBERT"); + thePs.setString(7, "Robert"); + thePs.setLong(8, 1L); + } + } + ); + + jdbcTemplate.execute( + "insert into HFJ_SPIDX_TOKEN (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_SYSTEM, SP_VALUE, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)", + new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) { + @Override + protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException { + thePs.setBoolean(1, false); + thePs.setString(2, "identifier"); + thePs.setLong(3, 1L); // res-id + thePs.setString(4, "Patient"); + thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis())); + thePs.setString(6, "http://foo"); + thePs.setString(7, "12345678"); + thePs.setLong(8, 1L); + } + } + ); + + jdbcTemplate.execute( + "insert into HFJ_SPIDX_DATE (SP_MISSING, SP_NAME, RES_ID, RES_TYPE, SP_UPDATED, SP_VALUE_HIGH, SP_VALUE_LOW, SP_ID) values (?, ?, ?, ?, ?, ?, ?, ?)", + new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) { + @Override + protected void setValues(PreparedStatement thePs, LobCreator theLobCreator) throws SQLException { + thePs.setBoolean(1, false); + thePs.setString(2, "birthdate"); + thePs.setLong(3, 1L); // res-id + thePs.setString(4, "Patient"); + thePs.setTimestamp(5, new Timestamp(System.currentTimeMillis())); + thePs.setTimestamp(6, new Timestamp(1000000000L)); // value high + thePs.setTimestamp(7, new Timestamp(1000000000L)); // value low + thePs.setLong(8, 1L); + } + } + ); + + return null; + }); + + } + + + @Test + public void testMigrate_340_350_NoMigrateHashes() throws IOException { + + File directory = new File("target/migrator_derby_test_340_350_nmh"); + if (directory.exists()) { + FileUtils.deleteDirectory(directory); + } + + String url = "jdbc:derby:directory:" + directory.getAbsolutePath() + ";create=true"; + DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.DERBY_EMBEDDED.newConnectionProperties(url, "", ""); + + String initSql = "/persistence_create_derby107_340.sql"; + executeSqlStatements(connectionProperties, initSql); + + seedDatabase340(connectionProperties); + + ourLog.info("**********************************************"); + ourLog.info("Done Setup, Starting Migration..."); + ourLog.info("**********************************************"); + + String[] args = new String[]{ + "migrate-database", + "-d", "DERBY_EMBEDDED", + "-u", url, + "-n", "", + "-p", "", + "-f", "V3_4_0", + "-t", "V3_5_0", + "-x", "no-migrate-350-hashes" + }; + App.main(args); + + connectionProperties.getTxTemplate().execute(t -> { + JdbcTemplate jdbcTemplate = connectionProperties.newJdbcTemplate(); + List> values = jdbcTemplate.queryForList("SELECT * FROM hfj_spidx_token"); + assertEquals(1, values.size()); + assertEquals("identifier", values.get(0).get("SP_NAME")); + assertEquals("12345678", values.get(0).get("SP_VALUE")); + assertEquals(null, values.get(0).get("HASH_IDENTITY")); + return null; + }); + + } + + private void executeSqlStatements(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theInitSql) throws + IOException { + String script = IOUtils.toString(HapiMigrateDatabaseCommandTest.class.getResourceAsStream(theInitSql), Charsets.UTF_8); + List scriptStatements = new ArrayList<>(Arrays.asList(script.split("\n"))); + for (int i = 0; i < scriptStatements.size(); i++) { + String nextStatement = scriptStatements.get(i); + if (isBlank(nextStatement)) { + scriptStatements.remove(i); + i--; + continue; + } + + nextStatement = nextStatement.trim(); + while (nextStatement.endsWith(";")) { + nextStatement = nextStatement.substring(0, nextStatement.length() - 1); + } + scriptStatements.set(i, nextStatement); + } + + theConnectionProperties.getTxTemplate().execute(t -> { + for (String next : scriptStatements) { + theConnectionProperties.newJdbcTemplate().execute(next); + } + return null; + }); + + } + } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java index 3aa4f830363..b3a7b55eaec 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.config; * 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. @@ -25,6 +25,8 @@ import ca.uhn.fhir.i18n.HapiLocalizer; import ca.uhn.fhir.jpa.dao.DaoRegistry; import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider; import ca.uhn.fhir.jpa.search.*; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; +import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl; import ca.uhn.fhir.jpa.search.warm.CacheWarmingSvcImpl; import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; @@ -32,8 +34,6 @@ import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl; import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor; import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor; import ca.uhn.fhir.jpa.subscription.websocket.SubscriptionWebsocketInterceptor; -import ca.uhn.fhir.jpa.util.IReindexController; -import ca.uhn.fhir.jpa.util.ReindexController; import org.hibernate.cfg.AvailableSettings; import org.hibernate.jpa.HibernatePersistenceProvider; import org.hibernate.query.criteria.LiteralHandlingMode; @@ -60,6 +60,7 @@ import javax.annotation.Nonnull; import java.util.Map; import java.util.concurrent.ScheduledExecutorService; + @Configuration @EnableScheduling @EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data") @@ -150,11 +151,6 @@ public abstract class BaseConfig implements SchedulingConfigurer { return new HibernateJpaDialect(); } - @Bean - public IReindexController reindexController() { - return new ReindexController(); - } - @Bean() public ScheduledExecutorService scheduledExecutorService() { ScheduledExecutorFactoryBean b = new ScheduledExecutorFactoryBean(); @@ -163,7 +159,7 @@ public abstract class BaseConfig implements SchedulingConfigurer { return b.getObject(); } - @Bean(name="mySubscriptionTriggeringProvider") + @Bean(name = "mySubscriptionTriggeringProvider") @Lazy public SubscriptionTriggeringProvider subscriptionTriggeringProvider() { return new SubscriptionTriggeringProvider(); @@ -215,6 +211,11 @@ public abstract class BaseConfig implements SchedulingConfigurer { return retVal; } + @Bean + public IResourceReindexingSvc resourceReindexingSvc() { + return new ResourceReindexingSvcImpl(); + } + public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) { theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer())); theFactory.setPackagesToScan("ca.uhn.fhir.jpa.entity"); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java index d369de228f2..37b46b3fb76 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java @@ -712,20 +712,6 @@ public abstract class BaseHapiFhirDao implements IDao, return dao; } - protected IFhirResourceDao getDaoOrThrowException(Class theClass) { - IFhirResourceDao retVal = getDao(theClass); - if (retVal == null) { - List supportedResourceTypes = getDaos() - .keySet() - .stream() - .map(t -> myContext.getResourceDefinition(t).getName()) - .sorted() - .collect(Collectors.toList()); - throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName() + " - Can handle: " + supportedResourceTypes); - } - return retVal; - } - private Map, IFhirResourceDao> getDaos() { if (myResourceTypeToDao == null) { Map, IFhirResourceDao> resourceTypeToDao = new HashMap<>(); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java index 7d7e65ca449..29ab5fd8d91 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java @@ -29,10 +29,10 @@ import ca.uhn.fhir.jpa.dao.data.ISearchResultDao; import ca.uhn.fhir.jpa.entity.*; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.util.DeleteConflict; import ca.uhn.fhir.jpa.util.ExpungeOptions; import ca.uhn.fhir.jpa.util.ExpungeOutcome; -import ca.uhn.fhir.jpa.util.IReindexController; import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils; import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils; import ca.uhn.fhir.model.api.*; @@ -42,7 +42,6 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.param.ParameterUtil; import ca.uhn.fhir.rest.param.QualifierDetails; -import ca.uhn.fhir.rest.server.RestfulServerUtils; import ca.uhn.fhir.rest.server.exceptions.*; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails; @@ -91,8 +90,6 @@ public abstract class BaseHapiFhirResourceDao extends B private String mySecondaryPrimaryKeyParamName; @Autowired private ISearchParamRegistry mySearchParamRegistry; - @Autowired - private IReindexController myReindexController; @Override public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) { @@ -624,22 +621,21 @@ public abstract class BaseHapiFhirResourceDao extends B TransactionTemplate txTemplate = new TransactionTemplate(myPlatformTransactionManager); txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED); - Integer updatedCount = txTemplate.execute(new TransactionCallback() { - @Override - public @NonNull - Integer doInTransaction(@Nonnull TransactionStatus theStatus) { - return myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType); - } + txTemplate.execute(t->{ + myResourceReindexingSvc.markAllResourcesForReindexing(resourceType); + return null; }); - ourLog.debug("Marked {} resources for reindexing", updatedCount); + ourLog.debug("Marked resources of type {} for reindexing", resourceType); } } mySearchParamRegistry.requestRefresh(); - myReindexController.requestReindex(); } + @Autowired + private IResourceReindexingSvc myResourceReindexingSvc; + @Override public MT metaAddOperation(IIdType theResourceId, MT theMetaAdd, RequestDetails theRequestDetails) { // Notify interceptors @@ -727,6 +723,7 @@ public abstract class BaseHapiFhirResourceDao extends B return retVal; } + @SuppressWarnings("JpaQlInspection") @Override public MT metaGetOperation(Class theType, RequestDetails theRequestDetails) { // Notify interceptors diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java index 70188beca0e..1db7fc848ad 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java @@ -3,42 +3,28 @@ package ca.uhn.fhir.jpa.dao; import ca.uhn.fhir.jpa.dao.data.IForcedIdDao; import ca.uhn.fhir.jpa.dao.data.IResourceTableDao; import ca.uhn.fhir.jpa.dao.data.ITermConceptDao; -import ca.uhn.fhir.jpa.entity.ForcedId; -import ca.uhn.fhir.jpa.entity.ResourceTable; import ca.uhn.fhir.jpa.util.ExpungeOptions; import ca.uhn.fhir.jpa.util.ExpungeOutcome; -import ca.uhn.fhir.jpa.util.ReindexFailureException; import ca.uhn.fhir.jpa.util.ResourceCountCache; import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.api.server.RequestDetails; -import ca.uhn.fhir.rest.server.exceptions.InternalErrorException; -import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails; import ca.uhn.fhir.util.StopWatch; -import org.apache.commons.lang3.concurrent.BasicThreadFactory; -import org.hibernate.search.util.impl.Executors; import org.hl7.fhir.instance.model.api.IBaseResource; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; -import org.springframework.data.domain.PageRequest; import org.springframework.transaction.PlatformTransactionManager; -import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; -import org.springframework.transaction.support.TransactionCallback; -import org.springframework.transaction.support.TransactionCallbackWithoutResult; -import org.springframework.transaction.support.TransactionTemplate; -import javax.annotation.Nonnull; import javax.annotation.Nullable; -import javax.persistence.Query; -import java.util.*; -import java.util.concurrent.*; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import java.util.concurrent.locks.ReentrantLock; -import static org.apache.commons.lang3.StringUtils.isBlank; - /* * #%L * HAPI FHIR JPA Server @@ -48,9 +34,9 @@ import static org.apache.commons.lang3.StringUtils.isBlank; * 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. @@ -76,71 +62,7 @@ public abstract class BaseHapiFhirSystemDao extends BaseHapiFhirDao idsToReindex = txTemplate.execute(theStatus -> { - int maxResult = 500; - if (theCount != null) { - maxResult = Math.min(theCount, 2000); - } - maxResult = Math.max(maxResult, 10); - - ourLog.debug("Beginning indexing query with maximum {}", maxResult); - return myResourceTableDao - .findIdsOfResourcesRequiringReindexing(new PageRequest(0, maxResult)) - .getContent(); - }); - - // If no IDs need reindexing, we're good here - if (idsToReindex.isEmpty()) { - return 0; - } - - // Reindex - StopWatch sw = new StopWatch(); - - // Execute each reindex in a task within a threadpool - int threadCount = getConfig().getReindexThreadCount(); - RejectedExecutionHandler rejectHandler = new Executors.BlockPolicy(); - ThreadPoolExecutor executor = new ThreadPoolExecutor(threadCount, threadCount, - 0L, TimeUnit.MILLISECONDS, - new LinkedBlockingQueue<>(), - myReindexingThreadFactory, - rejectHandler - ); - List> futures = new ArrayList<>(); - for (Long nextId : idsToReindex) { - futures.add(executor.submit(new ResourceReindexingTask(nextId))); - } - for (Future next : futures) { - try { - next.get(); - } catch (Exception e) { - throw new InternalErrorException("Failed to reindex: ", e); - } - } - executor.shutdown(); - - ourLog.info("Reindexed {} resources in {} threads - {}ms/resource", idsToReindex.size(), threadCount, sw.getMillisPerOperation(idsToReindex.size())); - return idsToReindex.size(); - } @Override @Transactional(propagation = Propagation.REQUIRED) @@ -182,165 +104,5 @@ public abstract class BaseHapiFhirSystemDao extends BaseHapiFhirDao() { - @Override - public Void doInTransaction(@Nonnull TransactionStatus theStatus) { - ourLog.info("Marking resource with PID {} as indexing_failed", new Object[] {theId}); - Query q = myEntityManager.createQuery("UPDATE ResourceTable t SET t.myIndexStatus = :status WHERE t.myId = :id"); - q.setParameter("status", INDEX_STATUS_INDEXING_FAILED); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceTag t WHERE t.myResourceId = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamCoords t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamDate t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamNumber t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamQuantity t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamString t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamUri t WHERE t.myResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.mySourceResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.myTargetResourcePid = :id"); - q.setParameter("id", theId); - q.executeUpdate(); - - return null; - } - }); - } - - @Override - @Transactional(propagation = Propagation.NEVER) - public Integer performReindexingPass(final Integer theCount) { - if (getConfig().isStatusBasedReindexingDisabled()) { - return -1; - } - if (!myReindexLock.tryLock()) { - return -1; - } - try { - return doPerformReindexingPass(theCount); - } catch (ReindexFailureException e) { - ourLog.warn("Reindexing failed for resource {}", e.getResourceId()); - markResourceAsIndexingFailed(e.getResourceId()); - return -1; - } finally { - myReindexLock.unlock(); - } - } - - private class ResourceReindexingTask implements Runnable { - private final Long myNextId; - - public ResourceReindexingTask(Long theNextId) { - myNextId = theNextId; - } - - @SuppressWarnings("unchecked") - @Override - public void run() { - TransactionTemplate txTemplate = new TransactionTemplate(myTxManager); - txTemplate.afterPropertiesSet(); - - Throwable reindexFailure; - try { - reindexFailure = txTemplate.execute(new TransactionCallback() { - @Override - public Throwable doInTransaction(TransactionStatus theStatus) { - ResourceTable resourceTable = myResourceTableDao.findById(myNextId).orElseThrow(IllegalStateException::new); - - try { - /* - * This part is because from HAPI 1.5 - 1.6 we changed the format of forced ID to be "type/id" instead of just "id" - */ - ForcedId forcedId = resourceTable.getForcedId(); - if (forcedId != null) { - if (isBlank(forcedId.getResourceType())) { - ourLog.info("Updating resource {} forcedId type to {}", forcedId.getForcedId(), resourceTable.getResourceType()); - forcedId.setResourceType(resourceTable.getResourceType()); - myForcedIdDao.save(forcedId); - } - } - - final IBaseResource resource = toResource(resourceTable, false); - - Class resourceClass = getContext().getResourceDefinition(resourceTable.getResourceType()).getImplementingClass(); - @SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDaoOrThrowException(resourceClass); - dao.reindex(resource, resourceTable); - return null; - - } catch (Exception e) { - ourLog.error("Failed to index resource {}: {}", resourceTable.getIdDt(), e.toString(), e); - theStatus.setRollbackOnly(); - return e; - } - } - }); - } catch (ResourceVersionConflictException e) { - /* - * We reindex in multiple threads, so it's technically possible that two threads try - * to index resources that cause a constraint error now (i.e. because a unique index has been - * added that didn't previously exist). In this case, one of the threads would succeed and - * not get this error, so we'll let the other one fail and try - * again later. - */ - ourLog.info("Failed to reindex {} because of a version conflict. Leaving in unindexed state: {}", e.getMessage()); - reindexFailure = null; - } - - if (reindexFailure != null) { - txTemplate.execute(new TransactionCallbackWithoutResult() { - @Override - protected void doInTransactionWithoutResult(TransactionStatus theStatus) { - ourLog.info("Setting resource PID[{}] status to ERRORED", myNextId); - myResourceTableDao.updateStatusToErrored(myNextId); - } - }); - } - } - } } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoRegistry.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoRegistry.java index 144bbe63353..a8524be8d56 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoRegistry.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoRegistry.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao; * 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. @@ -22,14 +22,17 @@ package ca.uhn.fhir.jpa.dao; import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.RuntimeResourceDefinition; -import org.apache.commons.lang3.Validate; +import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; +import org.hl7.fhir.instance.model.api.IBaseResource; import org.springframework.beans.BeansException; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.ApplicationContext; import org.springframework.context.ApplicationContextAware; import java.util.HashMap; +import java.util.List; import java.util.Map; +import java.util.stream.Collectors; public class DaoRegistry implements ApplicationContextAware { private ApplicationContext myAppCtx; @@ -55,11 +58,23 @@ public class DaoRegistry implements ApplicationContextAware { public IFhirResourceDao getResourceDao(String theResourceName) { IFhirResourceDao retVal = getResourceNameToResourceDao().get(theResourceName); - Validate.notNull(retVal, "No DAO exists for resource type %s - Have: %s", theResourceName, myResourceNameToResourceDao); + if (retVal == null) { + List supportedResourceTypes = getResourceNameToResourceDao() + .keySet() + .stream() + .sorted() + .collect(Collectors.toList()); + throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + theResourceName + " - Can handle: " + supportedResourceTypes); + } return retVal; } + public IFhirResourceDao getResourceDao(Class theResourceType) { + String resourceName = myCtx.getResourceDefinition(theResourceType).getName(); + return (IFhirResourceDao) getResourceDao(resourceName); + } + private Map> getResourceNameToResourceDao() { Map> retVal = myResourceNameToResourceDao; if (retVal == null || retVal.isEmpty()) { diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java index ff8899edf98..4c2dcf968bc 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java @@ -81,6 +81,8 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao { @Autowired private PlatformTransactionManager myTxManager; + @Autowired + private DaoRegistry myDaoRegistry; private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) { ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size()); @@ -363,7 +365,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao { case POST: { // CREATE @SuppressWarnings("rawtypes") - IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass()); + IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(res.getClass()); res.setId((String) null); DaoMethodOutcome outcome; outcome = resourceDao.create(res, nextReqEntry.getRequest().getIfNoneExist(), false, theRequestDetails); @@ -403,7 +405,7 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao { case PUT: { // UPDATE @SuppressWarnings("rawtypes") - IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass()); + IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(res.getClass()); DaoMethodOutcome outcome; diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java index fd47335fb25..81c67874815 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java @@ -1,10 +1,5 @@ package ca.uhn.fhir.jpa.dao; -import java.util.Collection; -import java.util.Set; - -import org.hl7.fhir.instance.model.api.IBaseResource; - import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.RuntimeResourceDefinition; import ca.uhn.fhir.context.RuntimeSearchParam; @@ -13,6 +8,10 @@ import ca.uhn.fhir.jpa.entity.IBaseResourceEntity; import ca.uhn.fhir.jpa.entity.ResourceTable; import ca.uhn.fhir.jpa.entity.ResourceTag; import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider; +import org.hl7.fhir.instance.model.api.IBaseResource; + +import java.util.Collection; +import java.util.Set; /* * #%L diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java index 8d75646bb01..b629dd37992 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirSystemDao.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao; * 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. @@ -53,13 +53,6 @@ public interface IFhirSystemDao extends IDao { IBundleProvider history(Date theDate, Date theUntil, RequestDetails theRequestDetails); - /** - * Marks all indexes as needing fresh indexing - * - * @return Returns the number of affected rows - */ - int markAllResourcesForReindexing(); - /** * Not supported for DSTU1 * @@ -67,8 +60,6 @@ public interface IFhirSystemDao extends IDao { */ MT metaGetOperation(RequestDetails theRequestDetails); - Integer performReindexingPass(Integer theCount); - T transaction(RequestDetails theRequestDetails, T theResources); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ISearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ISearchBuilder.java index 06281a3e022..0857ca7dac7 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ISearchBuilder.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ISearchBuilder.java @@ -43,7 +43,7 @@ public interface ISearchBuilder { FhirContext theContext, IDao theDao); Set loadIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection theMatches, Set theRevIncludes, boolean theReverseMode, - DateRangeParam theLastUpdated); + DateRangeParam theLastUpdated, String theSearchIdOrDescription); /** * How many results may be fetched at once diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java index d798fcd3853..7d457e2b381 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java @@ -1958,7 +1958,7 @@ public class SearchBuilder implements ISearchBuilder { */ @Override public HashSet loadIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection theMatches, Set theRevIncludes, - boolean theReverseMode, DateRangeParam theLastUpdated) { + boolean theReverseMode, DateRangeParam theLastUpdated, String theSearchIdOrDescription) { if (theMatches.size() == 0) { return new HashSet<>(); } @@ -2080,7 +2080,7 @@ public class SearchBuilder implements ISearchBuilder { nextRoundMatches = pidsToInclude; } while (includes.size() > 0 && nextRoundMatches.size() > 0 && addedSomeThisRound); - ourLog.info("Loaded {} {} in {} rounds and {} ms", allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart()); + ourLog.info("Loaded {} {} in {} rounds and {} ms for search {}", allAdded.size(), theReverseMode ? "_revincludes" : "_includes", roundCounts, w.getMillisAndRestart(), theSearchIdOrDescription); return allAdded; } @@ -2316,7 +2316,7 @@ public class SearchBuilder implements ISearchBuilder { myCurrentOffset = end; Collection pidsToScan = myCurrentPids.subList(start, end); Set includes = Collections.singleton(new Include("*", true)); - Set newPids = loadIncludes(myCallingDao, myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated()); + Set newPids = loadIncludes(myCallingDao, myContext, myEntityManager, pidsToScan, includes, false, myParams.getLastUpdated(), mySearchUuid); myCurrentIterator = newPids.iterator(); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java index 554a3e58723..bec7998d5cc 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java @@ -83,6 +83,8 @@ public class TransactionProcessor { private FhirContext myContext; @Autowired private ITransactionProcessorVersionAdapter myVersionAdapter; + @Autowired + private DaoRegistry myDaoRegistry; public static boolean isPlaceholder(IIdType theId) { if (theId != null && theId.getValue() != null) { @@ -749,7 +751,7 @@ public class TransactionProcessor { } private IFhirResourceDao getDaoOrThrowException(Class theClass) { - return myDao.getDaoOrThrowException(theClass); + return myDaoRegistry.getResourceDao(theClass); } protected void flushJpaSession() { diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceReindexJobDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceReindexJobDao.java new file mode 100644 index 00000000000..b1903ece2b9 --- /dev/null +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceReindexJobDao.java @@ -0,0 +1,58 @@ +package ca.uhn.fhir.jpa.dao.data; + +import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity; +import org.springframework.data.domain.Pageable; +import org.springframework.data.jpa.repository.JpaRepository; +import org.springframework.data.jpa.repository.Modifying; +import org.springframework.data.jpa.repository.Query; +import org.springframework.data.repository.query.Param; + +import java.util.Collection; +import java.util.Date; +import java.util.List; + +/* + * #%L + * HAPI FHIR JPA Server + * %% + * 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 IResourceReindexJobDao extends JpaRepository { + + @Modifying + @Query("UPDATE ResourceReindexJobEntity j SET j.myDeleted = true WHERE j.myResourceType = :type") + void markAllOfTypeAsDeleted(@Param("type") String theType); + + @Modifying + @Query("UPDATE ResourceReindexJobEntity j SET j.myDeleted = true") + void markAllOfTypeAsDeleted(); + + @Modifying + @Query("UPDATE ResourceReindexJobEntity j SET j.myDeleted = true WHERE j.myId = :pid") + void markAsDeletedById(@Param("pid") Long theId); + + @Query("SELECT j FROM ResourceReindexJobEntity j WHERE j.myDeleted = :deleted") + List findAll(Pageable thePage, @Param("deleted") boolean theDeleted); + + @Modifying + @Query("UPDATE ResourceReindexJobEntity j SET j.mySuspendedUntil = :suspendedUntil") + void setSuspendedUntil(@Param("suspendedUntil") Date theSuspendedUntil); + + @Modifying + @Query("UPDATE ResourceReindexJobEntity j SET j.myThresholdLow = :low WHERE j.myId = :id") + void setThresholdLow(@Param("id") Long theId, @Param("low") Date theLow); +} diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceTableDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceTableDao.java index 3737cdcbb5d..a5986473d52 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceTableDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceTableDao.java @@ -1,6 +1,5 @@ package ca.uhn.fhir.jpa.dao.data; -import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao; import ca.uhn.fhir.jpa.entity.ResourceTable; import org.springframework.data.domain.Pageable; import org.springframework.data.domain.Slice; @@ -9,6 +8,7 @@ import org.springframework.data.jpa.repository.Modifying; import org.springframework.data.jpa.repository.Query; import org.springframework.data.repository.query.Param; +import java.util.Date; import java.util.List; import java.util.Map; @@ -21,9 +21,9 @@ import java.util.Map; * 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. @@ -43,17 +43,16 @@ public interface IResourceTableDao extends JpaRepository { @Query("SELECT t.myId FROM ResourceTable t WHERE t.myId = :resid AND t.myResourceType = :restype AND t.myDeleted IS NOT NULL") Slice findIdsOfDeletedResourcesOfType(Pageable thePageable, @Param("resid") Long theResourceId, @Param("restype") String theResourceName); - @Query("SELECT t.myId FROM ResourceTable t WHERE t.myIndexStatus IS NULL") - Slice findIdsOfResourcesRequiringReindexing(Pageable thePageable); - - @Query("SELECT t.myResourceType as type, COUNT(*) as count FROM ResourceTable t GROUP BY t.myResourceType") + @Query("SELECT t.myResourceType as type, COUNT(t.myResourceType) as count FROM ResourceTable t GROUP BY t.myResourceType") List> getResourceCounts(); - @Modifying - @Query("UPDATE ResourceTable r SET r.myIndexStatus = null WHERE r.myResourceType = :restype") - int markResourcesOfTypeAsRequiringReindexing(@Param("restype") String theResourceType); + @Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high ORDER BY t.myUpdated ASC") + Slice findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage,@Param("low") Date theLow, @Param("high")Date theHigh); + + @Query("SELECT t.myId FROM ResourceTable t WHERE t.myUpdated >= :low AND t.myUpdated <= :high AND t.myResourceType = :restype ORDER BY t.myUpdated ASC") + Slice findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(Pageable thePage,@Param("restype") String theResourceType, @Param("low") Date theLow, @Param("high")Date theHigh); @Modifying - @Query("UPDATE ResourceTable r SET r.myIndexStatus = " + BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED + " WHERE r.myId = :resid") - void updateStatusToErrored(@Param("resid") Long theId); + @Query("UPDATE ResourceTable t SET t.myIndexStatus = :status WHERE t.myId = :id") + void updateIndexStatus(@Param("id") Long theId, @Param("status") Long theIndexStatus); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IndexingSupport.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IndexingSupport.java index 26a7163758a..4c121819f4c 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IndexingSupport.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IndexingSupport.java @@ -20,11 +20,15 @@ package ca.uhn.fhir.jpa.dao.index; * #L% */ +import java.util.Collection; import java.util.Map; import java.util.Set; import javax.persistence.EntityManager; +import ca.uhn.fhir.jpa.entity.BaseHasResource; +import ca.uhn.fhir.jpa.entity.IBaseResourceEntity; +import ca.uhn.fhir.jpa.entity.ResourceTag; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IIdType; @@ -50,4 +54,5 @@ public interface IndexingSupport { public Long translateForcedIdToPid(String theResourceName, String theResourceId); public String toResourceName(Class theResourceType); public IResourceIndexedCompositeStringUniqueDao getResourceIndexedCompositeStringUniqueDao(); + } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.java new file mode 100644 index 00000000000..cefbd92388b --- /dev/null +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.java @@ -0,0 +1,113 @@ +package ca.uhn.fhir.jpa.entity; + +/* + * #%L + * HAPI FHIR JPA Server + * %% + * 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 com.google.common.annotations.VisibleForTesting; + +import javax.persistence.*; +import java.io.Serializable; +import java.util.Date; + +@Entity +@Table(name = "HFJ_RES_REINDEX_JOB") +public class ResourceReindexJobEntity implements Serializable { + @Id + @SequenceGenerator(name = "SEQ_RES_REINDEX_JOB", sequenceName = "SEQ_RES_REINDEX_JOB") + @GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_RES_REINDEX_JOB") + @Column(name = "PID") + private Long myId; + @Column(name = "RES_TYPE", nullable = true) + private String myResourceType; + /** + * Inclusive + */ + @Column(name = "UPDATE_THRESHOLD_HIGH", nullable = false) + @Temporal(TemporalType.TIMESTAMP) + private Date myThresholdHigh; + @Column(name = "JOB_DELETED", nullable = false) + private boolean myDeleted; + /** + * Inclusive + */ + @Column(name = "UPDATE_THRESHOLD_LOW", nullable = true) + @Temporal(TemporalType.TIMESTAMP) + private Date myThresholdLow; + @Column(name = "SUSPENDED_UNTIL", nullable = true) + @Temporal(TemporalType.TIMESTAMP) + private Date mySuspendedUntil; + + public Date getSuspendedUntil() { + return mySuspendedUntil; + } + + public void setSuspendedUntil(Date theSuspendedUntil) { + mySuspendedUntil = theSuspendedUntil; + } + + /** + * Inclusive + */ + public Date getThresholdLow() { + return myThresholdLow; + } + + /** + * Inclusive + */ + public void setThresholdLow(Date theThresholdLow) { + myThresholdLow = theThresholdLow; + } + + public String getResourceType() { + return myResourceType; + } + + public void setResourceType(String theResourceType) { + myResourceType = theResourceType; + } + + /** + * Inclusive + */ + public Date getThresholdHigh() { + return myThresholdHigh; + } + + /** + * Inclusive + */ + public void setThresholdHigh(Date theThresholdHigh) { + myThresholdHigh = theThresholdHigh; + } + + public Long getId() { + return myId; + } + + @VisibleForTesting + public void setIdForUnitTest(long theId) { + myId = theId; + } + + public void setDeleted(boolean theDeleted) { + myDeleted = theDeleted; + } +} diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java index d8a7645459b..e30a9b83438 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java @@ -564,9 +564,7 @@ public class ResourceTable extends BaseHasResource implements Serializable { retVal.setPublished(getPublished()); retVal.setUpdated(getUpdated()); -// retVal.setEncoding(getEncoding()); retVal.setFhirVersion(getFhirVersion()); -// retVal.setResource(getResource()); retVal.setDeleted(getDeleted()); retVal.setForcedId(getForcedId()); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java index 89483e7ccb1..889bd2099fa 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.provider; * 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. @@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.provider; */ import ca.uhn.fhir.jpa.dao.IFhirSystemDao; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.util.ExpungeOptions; import ca.uhn.fhir.jpa.util.ExpungeOutcome; import ca.uhn.fhir.rest.annotation.At; @@ -31,6 +32,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.param.DateRangeParam; import org.hl7.fhir.instance.model.api.IPrimitiveType; import org.hl7.fhir.r4.model.Parameters; +import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Required; import javax.servlet.http.HttpServletRequest; @@ -42,11 +44,17 @@ public class BaseJpaSystemProvider extends BaseJpaProvider { public static final String PERFORM_REINDEXING_PASS = "$perform-reindexing-pass"; private IFhirSystemDao myDao; + @Autowired + private IResourceReindexingSvc myResourceReindexingSvc; public BaseJpaSystemProvider() { // nothing } + protected IResourceReindexingSvc getResourceReindexingSvc() { + return myResourceReindexingSvc; + } + protected Parameters doExpunge(IPrimitiveType theLimit, IPrimitiveType theExpungeDeletedResources, IPrimitiveType theExpungeOldVersions, IPrimitiveType theExpungeEverything) { ExpungeOptions options = createExpungeOptions(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything); ExpungeOutcome outcome = getDao().expunge(options); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java index 2d0f3e92876..1b6eb10678c 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java @@ -34,11 +34,11 @@ public abstract class BaseJpaSystemProviderDstu2Plus extends BaseJpaSyste @OperationParam(name = "status") }) public IBaseResource markAllResourcesForReindexing() { - Integer count = getDao().markAllResourcesForReindexing(); + getResourceReindexingSvc().markAllResourcesForReindexing(); IBaseParameters retVal = ParametersUtil.newInstance(getContext()); - IPrimitiveType string = ParametersUtil.createString(getContext(), "Marked " + count + " resources"); + IPrimitiveType string = ParametersUtil.createString(getContext(), "Marked resources"); ParametersUtil.addParameterToParameters(getContext(), retVal, "status", string); return retVal; @@ -48,7 +48,7 @@ public abstract class BaseJpaSystemProviderDstu2Plus extends BaseJpaSyste @OperationParam(name = "status") }) public IBaseResource performReindexingPass() { - Integer count = getDao().performReindexingPass(1000); + Integer count = getResourceReindexingSvc().runReindexingPass(); IBaseParameters retVal = ParametersUtil.newInstance(getContext()); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java index 27177cc5c05..83e5268973f 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java @@ -276,8 +276,8 @@ public class PersistedJpaBundleProvider implements IBundleProvider { protected List toResourceList(ISearchBuilder sb, List pidsSubList) { Set includedPids = new HashSet<>(); if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) { - includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated())); - includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated())); + includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated(), myUuid)); + includedPids.addAll(sb.loadIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated(), myUuid)); } // Execute the query and make sure we return distinct results diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java index d546ecc9677..478ad89ef53 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java @@ -313,8 +313,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc { * individually for pages as we return them to clients */ final Set includedPids = new HashSet<>(); - includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated())); - includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated())); + includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getRevIncludes(), true, theParams.getLastUpdated(), "(synchronous)")); + includedPids.addAll(sb.loadIncludes(theCallingDao, myContext, myEntityManager, pids, theParams.getIncludes(), false, theParams.getLastUpdated(), "(synchronous)")); List resources = new ArrayList<>(); sb.loadResourcesByPid(pids, resources, includedPids, false, myEntityManager, myContext, theCallingDao); diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/IResourceReindexingSvc.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/IResourceReindexingSvc.java new file mode 100644 index 00000000000..18d7671bfdc --- /dev/null +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/IResourceReindexingSvc.java @@ -0,0 +1,34 @@ +package ca.uhn.fhir.jpa.search.reindex; + +public interface IResourceReindexingSvc { + + /** + * Marks all indexes as needing fresh indexing + */ + void markAllResourcesForReindexing(); + + /** + * Marks all indexes of the given type as needing fresh indexing + */ + void markAllResourcesForReindexing(String theType); + + /** + * Called automatically by the job scheduler + * + * @return Returns null if the system did not attempt to perform a pass because one was + * already proceeding. Otherwise, returns the number of resources affected. + */ + Integer runReindexingPass(); + + /** + * Does the same thing as {@link #runReindexingPass()} but makes sure to perform at + * least one pass even if one is half finished + */ + Integer forceReindexingPass(); + + /** + * Cancels all running and future reindexing jobs. This is mainly intended + * to be used by unit tests. + */ + void cancelAndPurgeAllJobs(); +} diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java new file mode 100644 index 00000000000..dd09abdab37 --- /dev/null +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java @@ -0,0 +1,450 @@ +package ca.uhn.fhir.jpa.search.reindex; + +import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.context.RuntimeResourceDefinition; +import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao; +import ca.uhn.fhir.jpa.dao.DaoConfig; +import ca.uhn.fhir.jpa.dao.DaoRegistry; +import ca.uhn.fhir.jpa.dao.IFhirResourceDao; +import ca.uhn.fhir.jpa.dao.data.IForcedIdDao; +import ca.uhn.fhir.jpa.dao.data.IResourceReindexJobDao; +import ca.uhn.fhir.jpa.dao.data.IResourceTableDao; +import ca.uhn.fhir.jpa.entity.ForcedId; +import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity; +import ca.uhn.fhir.jpa.entity.ResourceTable; +import ca.uhn.fhir.rest.server.exceptions.InternalErrorException; +import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException; +import ca.uhn.fhir.util.StopWatch; +import com.google.common.annotations.VisibleForTesting; +import org.apache.commons.lang3.Validate; +import org.apache.commons.lang3.concurrent.BasicThreadFactory; +import org.apache.commons.lang3.time.DateUtils; +import org.hibernate.search.util.impl.Executors; +import org.hl7.fhir.instance.model.api.IBaseResource; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.data.domain.PageRequest; +import org.springframework.data.domain.Slice; +import org.springframework.scheduling.annotation.Scheduled; +import org.springframework.transaction.PlatformTransactionManager; +import org.springframework.transaction.TransactionDefinition; +import org.springframework.transaction.support.TransactionCallback; +import org.springframework.transaction.support.TransactionTemplate; + +import javax.annotation.PostConstruct; +import javax.persistence.EntityManager; +import javax.persistence.PersistenceContext; +import javax.persistence.PersistenceContextType; +import javax.persistence.Query; +import javax.transaction.Transactional; +import java.util.Collection; +import java.util.Date; +import java.util.List; +import java.util.concurrent.*; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.concurrent.locks.ReentrantLock; +import java.util.stream.Collectors; + +import static org.apache.commons.lang3.StringUtils.isBlank; +import static org.apache.commons.lang3.StringUtils.isNotBlank; + +public class ResourceReindexingSvcImpl implements IResourceReindexingSvc { + + private static final Date BEGINNING_OF_TIME = new Date(0); + private static final Logger ourLog = LoggerFactory.getLogger(ResourceReindexingSvcImpl.class); + private final ReentrantLock myIndexingLock = new ReentrantLock(); + @Autowired + private IResourceReindexJobDao myReindexJobDao; + @Autowired + private DaoConfig myDaoConfig; + @Autowired + private PlatformTransactionManager myTxManager; + private TransactionTemplate myTxTemplate; + private ThreadFactory myReindexingThreadFactory = new BasicThreadFactory.Builder().namingPattern("ResourceReindex-%d").build(); + private ThreadPoolExecutor myTaskExecutor; + @Autowired + private IResourceTableDao myResourceTableDao; + @Autowired + private DaoRegistry myDaoRegistry; + @Autowired + private IForcedIdDao myForcedIdDao; + @Autowired + private FhirContext myContext; + @PersistenceContext(type = PersistenceContextType.TRANSACTION) + private EntityManager myEntityManager; + + @VisibleForTesting + void setReindexJobDaoForUnitTest(IResourceReindexJobDao theReindexJobDao) { + myReindexJobDao = theReindexJobDao; + } + + @VisibleForTesting + void setDaoConfigForUnitTest(DaoConfig theDaoConfig) { + myDaoConfig = theDaoConfig; + } + + @VisibleForTesting + void setTxManagerForUnitTest(PlatformTransactionManager theTxManager) { + myTxManager = theTxManager; + } + + @VisibleForTesting + void setResourceTableDaoForUnitTest(IResourceTableDao theResourceTableDao) { + myResourceTableDao = theResourceTableDao; + } + + @VisibleForTesting + void setDaoRegistryForUnitTest(DaoRegistry theDaoRegistry) { + myDaoRegistry = theDaoRegistry; + } + + @VisibleForTesting + void setForcedIdDaoForUnitTest(IForcedIdDao theForcedIdDao) { + myForcedIdDao = theForcedIdDao; + } + + @VisibleForTesting + void setContextForUnitTest(FhirContext theContext) { + myContext = theContext; + } + + @PostConstruct + public void start() { + myTxTemplate = new TransactionTemplate(myTxManager); + initExecutor(); + } + + private void initExecutor() { + // Create the threadpool executor used for reindex jobs + int reindexThreadCount = myDaoConfig.getReindexThreadCount(); + RejectedExecutionHandler rejectHandler = new Executors.BlockPolicy(); + myTaskExecutor = new ThreadPoolExecutor(0, reindexThreadCount, + 0L, TimeUnit.MILLISECONDS, + new LinkedBlockingQueue<>(100), + myReindexingThreadFactory, + rejectHandler + ); + } + + @Override + @Transactional(Transactional.TxType.REQUIRED) + public void markAllResourcesForReindexing() { + markAllResourcesForReindexing(null); + } + + @Override + @Transactional(Transactional.TxType.REQUIRED) + public void markAllResourcesForReindexing(String theType) { + String typeDesc; + if (isNotBlank(theType)) { + myReindexJobDao.markAllOfTypeAsDeleted(theType); + typeDesc = theType; + } else { + myReindexJobDao.markAllOfTypeAsDeleted(); + typeDesc = "(any)"; + } + + ResourceReindexJobEntity job = new ResourceReindexJobEntity(); + job.setResourceType(theType); + job.setThresholdHigh(DateUtils.addMinutes(new Date(), 5)); + job = myReindexJobDao.saveAndFlush(job); + + ourLog.info("Marking all resources of type {} for reindexing - Got job ID[{}]", typeDesc, job.getId()); + } + + @Override + @Transactional(Transactional.TxType.NEVER) + @Scheduled(fixedDelay = 10 * DateUtils.MILLIS_PER_SECOND) + public Integer runReindexingPass() { + if (myIndexingLock.tryLock()) { + try { + return doReindexingPassInsideLock(); + } finally { + myIndexingLock.unlock(); + } + } + return null; + } + + private Integer doReindexingPassInsideLock() { + expungeJobsMarkedAsDeleted(); + return runReindexJobs(); + } + + @Override + public Integer forceReindexingPass() { + myIndexingLock.lock(); + try { + return doReindexingPassInsideLock(); + } finally { + myIndexingLock.unlock(); + } + } + + @Override + public void cancelAndPurgeAllJobs() { + ourLog.info("Cancelling and purging all resource reindexing jobs"); + myTxTemplate.execute(t -> { + myReindexJobDao.markAllOfTypeAsDeleted(); + return null; + }); + + myTaskExecutor.shutdown(); + initExecutor(); + + expungeJobsMarkedAsDeleted(); + } + + private Integer runReindexJobs() { + Collection jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false)); + assert jobs != null; + + int count = 0; + for (ResourceReindexJobEntity next : jobs) { + + if (next.getThresholdHigh().getTime() < System.currentTimeMillis()) { + markJobAsDeleted(next); + continue; + } + + count += runReindexJob(next); + } + return count; + } + + private void markJobAsDeleted(ResourceReindexJobEntity next) { + myTxTemplate.execute(t -> { + myReindexJobDao.markAsDeletedById(next.getId()); + return null; + }); + } + + private int runReindexJob(ResourceReindexJobEntity theJob) { + if (theJob.getSuspendedUntil() != null) { + if (theJob.getSuspendedUntil().getTime() > System.currentTimeMillis()) { + return 0; + } + } + + ourLog.info("Performing reindex pass for JOB[{}]", theJob.getId()); + StopWatch sw = new StopWatch(); + AtomicInteger counter = new AtomicInteger(); + + // Calculate range + Date low = theJob.getThresholdLow() != null ? theJob.getThresholdLow() : BEGINNING_OF_TIME; + Date high = theJob.getThresholdHigh(); + + // Query for resources within threshold + Slice range = myTxTemplate.execute(t -> { + PageRequest page = PageRequest.of(0, 10000); + if (isNotBlank(theJob.getResourceType())) { + return myResourceTableDao.findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(page, theJob.getResourceType(), low, high); + } else { + return myResourceTableDao.findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(page, low, high); + } + }); + Validate.notNull(range); + int count = range.getNumberOfElements(); + + // Submit each resource requiring reindexing + List> futures = range + .stream() + .map(t -> myTaskExecutor.submit(new ResourceReindexingTask(t, counter))) + .collect(Collectors.toList()); + + Date latestDate = null; + boolean haveMultipleDates = false; + for (Future next : futures) { + Date nextDate; + try { + nextDate = next.get(); + } catch (Exception e) { + ourLog.error("Failure reindexing", e); + Date suspendedUntil = DateUtils.addMinutes(new Date(), 1); + myTxTemplate.execute(t -> { + myReindexJobDao.setSuspendedUntil(suspendedUntil); + return null; + }); + return counter.get(); + } + + if (nextDate != null) { + if (latestDate != null) { + if (latestDate.getTime() != nextDate.getTime()) { + haveMultipleDates = true; + } + } + if (latestDate == null || latestDate.getTime() < nextDate.getTime()) { + latestDate = new Date(nextDate.getTime()); + } + } + } + + // Just in case we end up in some sort of infinite loop. This shouldn't happen, and couldn't really + // happen unless there were 10000 resources with the exact same update time down to the + // millisecond. + Date newLow; + if (latestDate == null) { + markJobAsDeleted(theJob); + return 0; + } + if (latestDate.getTime() == low.getTime()) { + ourLog.error("Final pass time for reindex JOB[{}] has same ending low value: {}", theJob.getId(), latestDate); + newLow = new Date(latestDate.getTime() + 1); + } else if (!haveMultipleDates) { + newLow = new Date(latestDate.getTime() + 1); + } else { + newLow = latestDate; + } + + myTxTemplate.execute(t -> { + myReindexJobDao.setThresholdLow(theJob.getId(), newLow); + return null; + }); + + ourLog.info("Completed pass of reindex JOB[{}] - Indexed {} resources in {} ({} / sec) - Have indexed until: {}", theJob.getId(), count, sw.toString(), sw.formatThroughput(count, TimeUnit.SECONDS), theJob.getThresholdLow()); + return counter.get(); + } + + private void expungeJobsMarkedAsDeleted() { + myTxTemplate.execute(t -> { + Collection toDelete = myReindexJobDao.findAll(PageRequest.of(0, 10), true); + toDelete.forEach(job -> { + ourLog.info("Purging deleted job[{}]", job.getId()); + myReindexJobDao.deleteById(job.getId()); + }); + return null; + }); + } + + @SuppressWarnings("JpaQlInspection") + private void markResourceAsIndexingFailed(final long theId) { + TransactionTemplate txTemplate = new TransactionTemplate(myTxManager); + txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW); + txTemplate.execute((TransactionCallback) theStatus -> { + ourLog.info("Marking resource with PID {} as indexing_failed", new Object[]{theId}); + + myResourceTableDao.updateIndexStatus(theId, BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED); + + Query q = myEntityManager.createQuery("DELETE FROM ResourceTag t WHERE t.myResourceId = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamCoords t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamDate t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamNumber t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamQuantity t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamString t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceIndexedSearchParamUri t WHERE t.myResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.mySourceResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.myTargetResourcePid = :id"); + q.setParameter("id", theId); + q.executeUpdate(); + + return null; + }); + } + + private class ResourceReindexingTask implements Callable { + private final Long myNextId; + private final AtomicInteger myCounter; + private Date myUpdated; + + ResourceReindexingTask(Long theNextId, AtomicInteger theCounter) { + myNextId = theNextId; + myCounter = theCounter; + } + + + @SuppressWarnings("unchecked") + private void doReindex(ResourceTable theResourceTable, T theResource) { + RuntimeResourceDefinition resourceDefinition = myContext.getResourceDefinition(theResource.getClass()); + Class resourceClass = (Class) resourceDefinition.getImplementingClass(); + final IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceClass); + dao.reindex(theResource, theResourceTable); + + myCounter.incrementAndGet(); + } + + @Override + public Date call() { + Throwable reindexFailure; + try { + reindexFailure = myTxTemplate.execute(t -> { + ResourceTable resourceTable = myResourceTableDao.findById(myNextId).orElseThrow(IllegalStateException::new); + myUpdated = resourceTable.getUpdatedDate(); + + try { + /* + * This part is because from HAPI 1.5 - 1.6 we changed the format of forced ID to be "type/id" instead of just "id" + */ + ForcedId forcedId = resourceTable.getForcedId(); + if (forcedId != null) { + if (isBlank(forcedId.getResourceType())) { + ourLog.info("Updating resource {} forcedId type to {}", forcedId.getForcedId(), resourceTable.getResourceType()); + forcedId.setResourceType(resourceTable.getResourceType()); + myForcedIdDao.save(forcedId); + } + } + + IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceTable.getResourceType()); + IBaseResource resource = dao.toResource(resourceTable, false); + if (resource == null) { + throw new InternalErrorException("Could not find resource version " + resourceTable.getIdDt().toUnqualified().getValue() + " in database"); + } + doReindex(resourceTable, resource); + return null; + + } catch (Exception e) { + ourLog.error("Failed to index resource {}: {}", resourceTable.getIdDt(), e.toString(), e); + t.setRollbackOnly(); + return e; + } + }); + } catch (ResourceVersionConflictException e) { + /* + * We reindex in multiple threads, so it's technically possible that two threads try + * to index resources that cause a constraint error now (i.e. because a unique index has been + * added that didn't previously exist). In this case, one of the threads would succeed and + * not get this error, so we'll let the other one fail and try + * again later. + */ + ourLog.info("Failed to reindex {} because of a version conflict. Leaving in unindexed state: {}", e.getMessage()); + reindexFailure = null; + } + + if (reindexFailure != null) { + ourLog.info("Setting resource PID[{}] status to ERRORED", myNextId); + markResourceAsIndexingFailed(myNextId); + } + + return myUpdated; + } + } +} diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/IReindexController.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/IReindexController.java deleted file mode 100644 index b9935057aef..00000000000 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/IReindexController.java +++ /dev/null @@ -1,34 +0,0 @@ -package ca.uhn.fhir.jpa.util; - -/*- - * #%L - * HAPI FHIR JPA Server - * %% - * 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 IReindexController { - - /** - * This method is called automatically by the scheduler - */ - void performReindexingPass(); - - /** - * This method requests that the reindex process happen as soon as possible - */ - void requestReindex(); -} diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ReindexController.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ReindexController.java deleted file mode 100644 index 1ed136f8791..00000000000 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/ReindexController.java +++ /dev/null @@ -1,119 +0,0 @@ -package ca.uhn.fhir.jpa.util; - -/*- - * #%L - * HAPI FHIR JPA Server - * %% - * 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 ca.uhn.fhir.jpa.dao.DaoConfig; -import ca.uhn.fhir.jpa.dao.IFhirSystemDao; -import org.apache.commons.lang3.time.DateUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.beans.factory.annotation.Autowired; -import org.springframework.scheduling.annotation.Scheduled; -import org.springframework.transaction.annotation.Propagation; -import org.springframework.transaction.annotation.Transactional; - -import java.util.concurrent.Semaphore; - -public class ReindexController implements IReindexController { - - private static final Logger ourLog = LoggerFactory.getLogger(ReindexController.class); - private final Semaphore myReindexingLock = new Semaphore(1); - @Autowired - private DaoConfig myDaoConfig; - @Autowired - private IFhirSystemDao mySystemDao; - private Long myDontReindexUntil; - - /** - * This method is called once per minute to perform any required re-indexing. - *

- * If nothing if found that requires reindexing, the query will not fire again for - * a longer amount of time. - *

- * During most passes this will just check and find that there are no resources - * requiring re-indexing. In that case the method just returns immediately. - * If the search finds that some resources require reindexing, the system will - * do a bunch of reindexing and then return. - */ - @Scheduled(fixedDelay = DateUtils.MILLIS_PER_MINUTE) - @Transactional(propagation = Propagation.NEVER) - @Override - public void performReindexingPass() { - if (myDaoConfig.isSchedulingDisabled() || myDaoConfig.isStatusBasedReindexingDisabled()) { - return; - } - - synchronized (this) { - if (myDontReindexUntil != null && myDontReindexUntil > System.currentTimeMillis()) { - return; - } - } - - if (!myReindexingLock.tryAcquire()) { - ourLog.trace("Not going to reindex in parallel threads"); - return; - } - Integer count; - try { - count = mySystemDao.performReindexingPass(100); - - for (int i = 0; i < 50 && count != null && count != 0; i++) { - count = mySystemDao.performReindexingPass(100); - try { - Thread.sleep(DateUtils.MILLIS_PER_SECOND); - } catch (InterruptedException e) { - break; - } - } - } catch (Exception e) { - ourLog.error("Failure during reindex", e); - count = -1; - } finally { - myReindexingLock.release(); - } - - synchronized (this) { - if (count == null) { - ourLog.info("Reindex pass complete, no remaining resource to index"); - myDontReindexUntil = System.currentTimeMillis() + DateUtils.MILLIS_PER_HOUR; - } else if (count == -1) { - // Reindexing failed - myDontReindexUntil = System.currentTimeMillis() + DateUtils.MILLIS_PER_HOUR; - } else { - ourLog.info("Reindex pass complete, {} remaining resource to index", count); - myDontReindexUntil = null; - } - } - - } - - /** - * Calling this will cause a reindex loop to be triggered sooner that it would otherwise - */ - @Override - public void requestReindex() { - synchronized (this) { - myDontReindexUntil = null; - } - } - - -} diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java index 1d86d6e2070..2b93bbb04bf 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java @@ -4,7 +4,6 @@ import ca.uhn.fhir.jpa.dao.DaoConfig; import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor; import ca.uhn.fhir.validation.ResultSeverityEnum; import net.ttddyy.dsproxy.listener.SingleQueryCountHolder; -import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder; import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel; import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder; import org.apache.commons.dbcp2.BasicDataSource; diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java index 5e7d3cc046c..518aa6bd195 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java @@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.jpa.term.VersionIndependentConcept; import ca.uhn.fhir.jpa.util.ExpungeOptions; @@ -33,7 +34,9 @@ import org.hl7.fhir.instance.model.api.IBaseBundle; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IIdType; import org.junit.*; -import org.mockito.Mockito; +import org.mockito.Answers; +import org.mockito.Mock; +import org.mockito.MockitoAnnotations; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.transaction.PlatformTransactionManager; @@ -75,6 +78,7 @@ public abstract class BaseJpaTest { @Rule public LoggingRule myLoggingRule = new LoggingRule(); + @Mock(answer = Answers.RETURNS_DEEP_STUBS) protected ServletRequestDetails mySrd; protected ArrayList myServerInterceptorList; protected IRequestOperationCallback myRequestOperationCallback = mock(IRequestOperationCallback.class); @@ -89,7 +93,7 @@ public abstract class BaseJpaTest { @After public void afterValidateNoTransaction() { PlatformTransactionManager txManager = getTxManager(); - if (txManager != null) { + if (txManager instanceof JpaTransactionManager) { JpaTransactionManager hibernateTxManager = (JpaTransactionManager) txManager; SessionFactory sessionFactory = (SessionFactory) hibernateTxManager.getEntityManagerFactory(); AtomicBoolean isReadOnly = new AtomicBoolean(); @@ -114,8 +118,9 @@ public abstract class BaseJpaTest { } @Before - public void beforeCreateSrd() { - mySrd = mock(ServletRequestDetails.class, Mockito.RETURNS_DEEP_STUBS); + public void beforeInitMocks() { + MockitoAnnotations.initMocks(this); + when(mySrd.getRequestOperationCallback()).thenReturn(myRequestOperationCallback); myServerInterceptorList = new ArrayList<>(); when(mySrd.getServer().getInterceptors()).thenReturn(myServerInterceptorList); @@ -355,8 +360,9 @@ public abstract class BaseJpaTest { return bundleStr; } - public static void purgeDatabase(DaoConfig theDaoConfig, IFhirSystemDao theSystemDao, ISearchParamPresenceSvc theSearchParamPresenceSvc, ISearchCoordinatorSvc theSearchCoordinatorSvc, ISearchParamRegistry theSearchParamRegistry) { + public static void purgeDatabase(DaoConfig theDaoConfig, IFhirSystemDao theSystemDao, IResourceReindexingSvc theResourceReindexingSvc, ISearchCoordinatorSvc theSearchCoordinatorSvc, ISearchParamRegistry theSearchParamRegistry) { theSearchCoordinatorSvc.cancelAllActiveSearches(); + theResourceReindexingSvc.cancelAndPurgeAllJobs(); boolean expungeEnabled = theDaoConfig.isExpungeEnabled(); theDaoConfig.setExpungeEnabled(true); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java index a1b45f8c4b5..b50ddc44e98 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java @@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.entity.ResourceTable; import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.jpa.util.ResourceCountCache; import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt; @@ -42,7 +43,7 @@ import javax.persistence.EntityManager; import java.io.IOException; import java.io.InputStream; -import static org.junit.Assert.*; +import static org.junit.Assert.fail; import static org.mockito.Mockito.mock; @RunWith(SpringJUnit4ClassRunner.class) @@ -56,6 +57,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest { @Autowired protected ApplicationContext myAppCtx; @Autowired + protected IResourceReindexingSvc myResourceReindexingSvc; + @Autowired @Qualifier("myAppointmentDaoDstu2") protected IFhirResourceDao myAppointmentDao; @Autowired @@ -197,7 +200,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest { @Before @Transactional() public void beforePurgeDatabase() throws InterruptedException { - purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegistry); + purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry); } @Before diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2InterceptorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2InterceptorTest.java index 3f904baf7b8..c9626785a91 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2InterceptorTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2InterceptorTest.java @@ -23,7 +23,7 @@ import org.mockito.stubbing.Answer; import static org.hamcrest.Matchers.containsString; import static org.junit.Assert.*; -import static org.mockito.Matchers.any; +import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.*; public class FhirResourceDaoDstu2InterceptorTest extends BaseJpaDstu2Test { diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java index 152c8edd74a..ecddb19c6f2 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchCustomSearchParamTest.java @@ -988,7 +988,9 @@ public class FhirResourceDaoDstu2SearchCustomSearchParamTest extends BaseJpaDstu mySearchParameterDao.delete(spId, mySrd); mySearchParamRegsitry.forceRefresh(); - mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); // Try with custom gender SP map = new SearchParameterMap(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java index 72d2776a1df..c979ebc840a 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java @@ -3,7 +3,7 @@ package ca.uhn.fhir.jpa.dao.dstu2; import static org.apache.commons.lang3.StringUtils.defaultString; import static org.hamcrest.Matchers.*; import static org.junit.Assert.*; -import static org.mockito.Matchers.eq; +import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.*; import java.io.IOException; diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java index 9737d3593fb..49c587bca56 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java @@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl; import ca.uhn.fhir.jpa.term.IHapiTerminologySvc; @@ -67,6 +68,10 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest { @Qualifier("myResourceCountsCache") protected ResourceCountCache myResourceCountsCache; @Autowired + protected IResourceReindexingSvc myResourceReindexingSvc; + @Autowired + protected IResourceReindexJobDao myResourceReindexJobDao; + @Autowired @Qualifier("myCoverageDaoDstu3") protected IFhirResourceDao myCoverageDao; @Autowired @@ -294,8 +299,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest { @Before @Transactional() - public void beforePurgeDatabase() throws InterruptedException { - purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegsitry); + public void beforePurgeDatabase() { + purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegsitry); } @Before diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java index 36dd96b73d0..1c84d1a3868 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java @@ -30,10 +30,9 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test { CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input); myCodeSystemDao.create(cs, mySrd); - - mySystemDao.markAllResourcesForReindexing(); - int outcome = mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.markAllResourcesForReindexing(); + int outcome= myResourceReindexingSvc.forceReindexingPass(); assertNotEquals(-1, outcome); // -1 means there was a failure myTermSvc.saveDeferred(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3InterceptorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3InterceptorTest.java index 170c6a40dc8..69f72cf4004 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3InterceptorTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3InterceptorTest.java @@ -24,7 +24,7 @@ import org.mockito.stubbing.Answer; import static org.hamcrest.Matchers.containsString; import static org.junit.Assert.*; -import static org.mockito.Matchers.any; +import static org.mockito.ArgumentMatchers.any; import static org.mockito.Mockito.*; public class FhirResourceDaoDstu3InterceptorTest extends BaseJpaDstu3Test { diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java index 7eb293d9418..995189d6b33 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java @@ -994,7 +994,8 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu mySearchParameterDao.delete(spId, mySrd); mySearchParamRegsitry.forceRefresh(); - mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); // Try with custom gender SP map = new SearchParameterMap(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java index f1635fbdb0c..0580a74b70a 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java @@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.config.TestDstu3WithoutLuceneConfig; import ca.uhn.fhir.jpa.dao.*; import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.rest.param.StringParam; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; @@ -144,11 +145,13 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes @Autowired @Qualifier("myJpaValidationSupportChainDstu3") private IValidationSupport myValidationSupport; + @Autowired + private IResourceReindexingSvc myResourceReindexingSvc; @Before public void beforePurgeDatabase() { runInTransaction(() -> { - purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegistry); + purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry); }); } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java index 1355c5ded91..aa5031b91c5 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java @@ -487,10 +487,10 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test { createExternalCsAndLocalVs(); - mySystemDao.markAllResourcesForReindexing(); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); - mySystemDao.performReindexingPass(100); - mySystemDao.performReindexingPass(100); myHapiTerminologySvc.saveDeferred(); myHapiTerminologySvc.saveDeferred(); myHapiTerminologySvc.saveDeferred(); @@ -729,17 +729,17 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test { include.setSystem(URL_MY_CODE_SYSTEM); include.addConcept().setCode("ZZZZ"); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(null); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); myTermSvc.saveDeferred(); - mySystemDao.performReindexingPass(null); myTermSvc.saveDeferred(); // Again - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(null); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); myTermSvc.saveDeferred(); - mySystemDao.performReindexingPass(null); myTermSvc.saveDeferred(); } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java index 7bfd175aec8..f1851844cff 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java @@ -44,7 +44,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString; import static org.hamcrest.Matchers.contains; import static org.hamcrest.Matchers.*; import static org.junit.Assert.*; -import static org.mockito.Matchers.eq; +import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.*; @SuppressWarnings({"unchecked", "deprecation"}) diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java index be99f609aa3..bab9da7fd53 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UniqueSearchParamTest.java @@ -222,8 +222,9 @@ public class FhirResourceDaoDstu3UniqueSearchParamTest extends BaseJpaDstu3Test createUniqueIndexCoverageBeneficiary(); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); List uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java index bbfc58077fd..60303b57138 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java @@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl; @@ -213,6 +214,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest { @Autowired protected ISearchIncludeDao mySearchIncludeDao; @Autowired + protected IResourceReindexJobDao myResourceReindexJobDao; + @Autowired @Qualifier("mySearchParameterDaoR4") protected IFhirResourceDao mySearchParameterDao; @Autowired @@ -237,6 +240,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest { @Qualifier("mySystemDaoR4") protected IFhirSystemDao mySystemDao; @Autowired + protected IResourceReindexingSvc myResourceReindexingSvc; + @Autowired @Qualifier("mySystemProviderR4") protected JpaSystemProviderR4 mySystemProvider; @Autowired @@ -314,7 +319,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest { @Transactional() public void beforePurgeDatabase() throws InterruptedException { final EntityManager entityManager = this.myEntityManager; - purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegsitry); + purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegsitry); } @Before diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java index f334e53d7ac..085decf3de3 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java @@ -30,10 +30,8 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test { CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input); myCodeSystemDao.create(cs, mySrd); - - mySystemDao.markAllResourcesForReindexing(); - - int outcome = mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.markAllResourcesForReindexing(); + int outcome = myResourceReindexingSvc.runReindexingPass(); assertNotEquals(-1, outcome); // -1 means there was a failure myTermSvc.saveDeferred(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java index 4006322d6bc..5abc521dcb6 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java @@ -5,10 +5,7 @@ import ca.uhn.fhir.jpa.dao.SearchParameterMap; import ca.uhn.fhir.rest.param.StringParam; import ca.uhn.fhir.util.TestUtil; import org.hl7.fhir.instance.model.api.IIdType; -import org.hl7.fhir.r4.model.Bundle; -import org.hl7.fhir.r4.model.IdType; -import org.hl7.fhir.r4.model.Organization; -import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.*; import org.junit.After; import org.junit.AfterClass; import org.junit.Test; @@ -83,6 +80,8 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test { Patient p = new Patient(); p.setId(IdType.newRandomUuid()); p.addName().setFamily("FAM"); + p.setActive(true); + p.setBirthDateElement(new DateType("2011-01-01")); p.getManagingOrganization().setReference(org.getId()); Bundle input = new Bundle(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java index 6c988c367e7..07a9514c186 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java @@ -146,8 +146,8 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test mySearchParameterDao.create(fooSp, mySrd); - assertEquals(1, mySystemDao.performReindexingPass(100).intValue()); - assertEquals(0, mySystemDao.performReindexingPass(100).intValue()); + assertEquals(1, myResourceReindexingSvc.forceReindexingPass().intValue()); + assertEquals(0, myResourceReindexingSvc.forceReindexingPass().intValue()); } @@ -1171,7 +1171,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test mySearchParameterDao.delete(spId, mySrd); mySearchParamRegsitry.forceRefresh(); - mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.forceReindexingPass(); // Try with custom gender SP map = new SearchParameterMap(); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java index 650d4f90b11..dedc619d5b2 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java @@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.jpa.config.TestR4WithoutLuceneConfig; import ca.uhn.fhir.jpa.dao.*; import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc; +import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc; import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc; import ca.uhn.fhir.rest.param.StringParam; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; @@ -89,11 +90,13 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest { private IValidationSupport myValidationSupport; @Autowired private IFhirSystemDao mySystemDao; + @Autowired + private IResourceReindexingSvc myResourceReindexingSvc; @Before @Transactional() public void beforePurgeDatabase() { - purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegistry); + purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry); } @Before diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java index c0593617ad9..cd134eeb08c 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java @@ -539,10 +539,9 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test { createExternalCsAndLocalVs(); - mySystemDao.markAllResourcesForReindexing(); - - mySystemDao.performReindexingPass(100); - mySystemDao.performReindexingPass(100); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); myHapiTerminologySvc.saveDeferred(); myHapiTerminologySvc.saveDeferred(); myHapiTerminologySvc.saveDeferred(); @@ -851,17 +850,17 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test { include.setSystem(URL_MY_CODE_SYSTEM); include.addConcept().setCode("ZZZZ"); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(null); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); myTermSvc.saveDeferred(); - mySystemDao.performReindexingPass(null); myTermSvc.saveDeferred(); // Again - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(null); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); myTermSvc.saveDeferred(); - mySystemDao.performReindexingPass(null); myTermSvc.saveDeferred(); } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java index 2b94014d187..e6f1b19f35f 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java @@ -53,7 +53,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString; import static org.hamcrest.Matchers.contains; import static org.hamcrest.Matchers.*; import static org.junit.Assert.*; -import static org.mockito.Matchers.eq; +import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.*; @SuppressWarnings({"unchecked", "deprecation", "Duplicates"}) @@ -162,6 +162,9 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test { runInTransaction(() -> { assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), greaterThan(0)); + Optional tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong()); + assertTrue(tableOpt.isPresent()); + assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue()); }); runInTransaction(() -> { @@ -170,10 +173,16 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test { ResourceTable table = tableOpt.get(); table.setIndexStatus(null); table.setDeleted(new Date()); + table = myResourceTableDao.saveAndFlush(table); + ResourceHistoryTable newHistory = table.toHistory(); + ResourceHistoryTable currentHistory = myResourceHistoryTableDao.findForIdAndVersion(table.getId(), 1L); + newHistory.setEncoding(currentHistory.getEncoding()); + newHistory.setResource(currentHistory.getResource()); + myResourceHistoryTableDao.save(newHistory); }); - mySystemDao.performReindexingPass(1000); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.runReindexingPass(); runInTransaction(() -> { Optional tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong()); @@ -185,6 +194,48 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test { } + @Test + public void testMissingVersionsAreReindexed() { + myDaoConfig.setSchedulingDisabled(true); + + Patient pt1 = new Patient(); + pt1.setActive(true); + pt1.addName().setFamily("FAM"); + IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless(); + + runInTransaction(() -> { + assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), greaterThan(0)); + Optional tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong()); + assertTrue(tableOpt.isPresent()); + assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, tableOpt.get().getIndexStatus().longValue()); + }); + + /* + * This triggers a new version in the HFJ_RESOURCE table, but + * we do not create the corresponding entry in the HFJ_RES_VER + * table. + */ + runInTransaction(() -> { + Optional tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong()); + assertTrue(tableOpt.isPresent()); + ResourceTable table = tableOpt.get(); + table.setIndexStatus(null); + table.setDeleted(new Date()); + myResourceTableDao.saveAndFlush(table); + }); + + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.runReindexingPass(); + + runInTransaction(() -> { + Optional tableOpt = myResourceTableDao.findById(id1.getIdPartAsLong()); + assertTrue(tableOpt.isPresent()); + assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXING_FAILED, tableOpt.get().getIndexStatus().longValue()); + assertThat(myResourceIndexedSearchParamTokenDao.countForResourceId(id1.getIdPartAsLong()), not(greaterThan(0))); + }); + + + } @Test public void testCantSearchForDeletedResourceByLanguageOrTag() { diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java index bd063d48975..96540b89d92 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java @@ -449,9 +449,9 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test { createUniqueObservationSubjectDateCode(); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(1000); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); List uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); @@ -462,9 +462,9 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test { assertEquals(1, mySearchParamRegsitry.getActiveUniqueSearchParams("Observation").size()); - assertEquals(7, mySystemDao.markAllResourcesForReindexing()); - mySystemDao.performReindexingPass(1000); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); @@ -557,8 +557,9 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test { createUniqueIndexCoverageBeneficiary(); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); List uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); @@ -1119,8 +1120,9 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test { pt2.setActive(false); myPatientDao.create(pt1).getId().toUnqualifiedVersionless(); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); List uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); @@ -1129,8 +1131,9 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test { myResourceIndexedCompositeStringUniqueDao.deleteAll(); - mySystemDao.markAllResourcesForReindexing(); - mySystemDao.performReindexingPass(1000); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); + myResourceReindexingSvc.forceReindexingPass(); uniques = myResourceIndexedCompositeStringUniqueDao.findAll(); assertEquals(uniques.toString(), 1, uniques.size()); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTagSnapshotTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTagSnapshotTest.java index 9f727ea1aa4..1d3f9e7f381 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTagSnapshotTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTagSnapshotTest.java @@ -10,7 +10,7 @@ import org.junit.AfterClass; import org.junit.Test; import static org.junit.Assert.*; -import static org.mockito.Matchers.eq; +import static org.mockito.ArgumentMatchers.eq; import static org.mockito.Mockito.when; public class FhirResourceDaoR4UpdateTagSnapshotTest extends BaseJpaR4Test { diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java index 728a75f6950..267eb4aa5ec 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java @@ -1,20 +1,5 @@ package ca.uhn.fhir.jpa.dao.r4; -import static org.hamcrest.Matchers.*; -import static org.junit.Assert.*; -import static org.mockito.Matchers.eq; -import static org.mockito.Mockito.reset; -import static org.mockito.Mockito.verify; - -import java.util.*; - -import net.ttddyy.dsproxy.QueryCountHolder; -import org.hl7.fhir.r4.model.*; -import org.hl7.fhir.instance.model.api.IBaseResource; -import org.hl7.fhir.instance.model.api.IIdType; -import org.junit.*; -import org.mockito.ArgumentCaptor; - import ca.uhn.fhir.jpa.dao.DaoConfig; import ca.uhn.fhir.jpa.dao.SearchParameterMap; import ca.uhn.fhir.model.primitive.InstantDt; @@ -22,11 +7,30 @@ import ca.uhn.fhir.rest.api.MethodOutcome; import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.param.StringParam; -import ca.uhn.fhir.rest.server.exceptions.*; +import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; +import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException; +import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; +import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails; import ca.uhn.fhir.util.TestUtil; +import org.hl7.fhir.instance.model.api.IBaseResource; +import org.hl7.fhir.instance.model.api.IIdType; +import org.hl7.fhir.r4.model.*; +import org.junit.After; +import org.junit.AfterClass; +import org.junit.Ignore; +import org.junit.Test; +import org.mockito.ArgumentCaptor; import org.springframework.test.context.TestPropertySource; +import java.util.*; + +import static org.hamcrest.Matchers.*; +import static org.junit.Assert.*; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.reset; +import static org.mockito.Mockito.verify; + @TestPropertySource(properties = { "scheduling_disabled=true" }) diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java index 5f9770f98b1..4f7378285f9 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java @@ -51,11 +51,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR4Test.class); - @AfterClass - public static void afterClassClearContext() { - TestUtil.clearAllStaticFieldsForUnitTest(); - } - @After public void after() { myDaoConfig.setAllowInlineMatchUrlReferences(false); @@ -175,7 +170,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { fail(); return null; } - + @Test public void testTransactionReSavesPreviouslyDeletedResources() { @@ -238,7 +233,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { myPatientDao.read(new IdType("Patient/pt")); } - @Test public void testResourceCounts() { @@ -534,69 +528,43 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { vs.setUrl("http://foo"); myValueSetDao.create(vs, mySrd); - ResourceTable entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback() { - @Override - public ResourceTable doInTransaction(TransactionStatus theStatus) { - return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong()); - } - }); + ResourceTable entity = new TransactionTemplate(myTxManager).execute(t -> myEntityManager.find(ResourceTable.class, id.getIdPartAsLong())); assertEquals(Long.valueOf(1), entity.getIndexStatus()); - mySystemDao.markAllResourcesForReindexing(); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); - entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback() { - @Override - public ResourceTable doInTransaction(TransactionStatus theStatus) { - return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong()); - } - }); - assertEquals(null, entity.getIndexStatus()); - - mySystemDao.performReindexingPass(null); - - entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback() { - @Override - public ResourceTable doInTransaction(TransactionStatus theStatus) { - return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong()); - } - }); + entity = new TransactionTemplate(myTxManager).execute(t -> myEntityManager.find(ResourceTable.class, id.getIdPartAsLong())); assertEquals(Long.valueOf(1), entity.getIndexStatus()); // Just make sure this doesn't cause a choke - mySystemDao.performReindexingPass(100000); + myResourceReindexingSvc.forceReindexingPass(); // Try making the resource unparseable TransactionTemplate template = new TransactionTemplate(myTxManager); template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW); - template.execute(new TransactionCallback() { - @Override - public ResourceTable doInTransaction(TransactionStatus theStatus) { - ResourceHistoryTable resourceHistoryTable = myResourceHistoryTableDao.findForIdAndVersion(id.getIdPartAsLong(), id.getVersionIdPartAsLong()); - resourceHistoryTable.setEncoding(ResourceEncodingEnum.JSON); - try { - resourceHistoryTable.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8")); - } catch (UnsupportedEncodingException e) { - throw new Error(e); - } - myResourceHistoryTableDao.save(resourceHistoryTable); - - ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new); - table.setIndexStatus(null); - myResourceTableDao.save(table); - - return null; + template.execute((TransactionCallback) t -> { + ResourceHistoryTable resourceHistoryTable = myResourceHistoryTableDao.findForIdAndVersion(id.getIdPartAsLong(), id.getVersionIdPartAsLong()); + resourceHistoryTable.setEncoding(ResourceEncodingEnum.JSON); + try { + resourceHistoryTable.setResource("{\"resourceType\":\"FOO\"}".getBytes("UTF-8")); + } catch (UnsupportedEncodingException e) { + throw new Error(e); } + myResourceHistoryTableDao.save(resourceHistoryTable); + + ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new); + table.setIndexStatus(null); + myResourceTableDao.save(table); + + return null; }); - mySystemDao.performReindexingPass(null); + myResourceReindexingSvc.markAllResourcesForReindexing(); + myResourceReindexingSvc.forceReindexingPass(); - entity = new TransactionTemplate(myTxManager).execute(new TransactionCallback() { - @Override - public ResourceTable doInTransaction(TransactionStatus theStatus) { - return myEntityManager.find(ResourceTable.class, id.getIdPartAsLong()); - } - }); + entity = new TransactionTemplate(myTxManager).execute(theStatus -> myEntityManager.find(ResourceTable.class, id.getIdPartAsLong())); assertEquals(Long.valueOf(2), entity.getIndexStatus()); } @@ -3119,6 +3087,44 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { assertEquals(1, found.size().intValue()); } + @Test + public void testTransactionWithRelativeOidIds() { + Bundle res = new Bundle(); + res.setType(BundleType.TRANSACTION); + + Patient p1 = new Patient(); + p1.setId("urn:oid:0.1.2.3"); + p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01"); + res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient"); + + Observation o1 = new Observation(); + o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02"); + o1.setSubject(new Reference("urn:oid:0.1.2.3")); + res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation"); + + Observation o2 = new Observation(); + o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03"); + o2.setSubject(new Reference("urn:oid:0.1.2.3")); + res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation"); + + Bundle resp = mySystemDao.transaction(mySrd, res); + + ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp)); + + assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue()); + assertEquals(3, resp.getEntry().size()); + + assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdType(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); + assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdType(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); + assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdType(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); + + o1 = myObservationDao.read(new IdType(resp.getEntry().get(1).getResponse().getLocation()), mySrd); + o2 = myObservationDao.read(new IdType(resp.getEntry().get(2).getResponse().getLocation()), mySrd); + assertThat(o1.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart())); + assertThat(o2.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart())); + + } + // // // /** @@ -3221,44 +3227,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { // // } - @Test - public void testTransactionWithRelativeOidIds() { - Bundle res = new Bundle(); - res.setType(BundleType.TRANSACTION); - - Patient p1 = new Patient(); - p1.setId("urn:oid:0.1.2.3"); - p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01"); - res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient"); - - Observation o1 = new Observation(); - o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02"); - o1.setSubject(new Reference("urn:oid:0.1.2.3")); - res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation"); - - Observation o2 = new Observation(); - o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03"); - o2.setSubject(new Reference("urn:oid:0.1.2.3")); - res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation"); - - Bundle resp = mySystemDao.transaction(mySrd, res); - - ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp)); - - assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue()); - assertEquals(3, resp.getEntry().size()); - - assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdType(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); - assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdType(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); - assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdType(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$")); - - o1 = myObservationDao.read(new IdType(resp.getEntry().get(1).getResponse().getLocation()), mySrd); - o2 = myObservationDao.read(new IdType(resp.getEntry().get(2).getResponse().getLocation()), mySrd); - assertThat(o1.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart())); - assertThat(o2.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart())); - - } - /** * This is not the correct way to do it, but we'll allow it to be lenient */ @@ -3471,4 +3439,9 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest { } + @AfterClass + public static void afterClassClearContext() { + TestUtil.clearAllStaticFieldsForUnitTest(); + } + } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java index 1730f0d8523..907792f406e 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java @@ -7,6 +7,7 @@ import static org.junit.Assert.*; import java.io.IOException; import java.util.*; +import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; @@ -236,11 +237,11 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE); mySearchParameterDao.create(fooSp, mySrd); - res = myResourceTableDao.findById(patId.getIdPartAsLong()).orElseThrow(IllegalStateException::new); - assertEquals(null, res.getIndexStatus()); - res = myResourceTableDao.findById(obsId.getIdPartAsLong()).orElseThrow(IllegalStateException::new); - assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, res.getIndexStatus().longValue()); - + runInTransaction(()->{ + List allJobs = myResourceReindexJobDao.findAll(); + assertEquals(1, allJobs.size()); + assertEquals("Patient", allJobs.get(0).getResourceType()); + }); } @Test diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java index 19e36cdb5a3..40e449caec9 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java @@ -7,6 +7,7 @@ import static org.junit.Assert.*; import java.io.IOException; import java.util.*; +import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity; import org.apache.commons.io.IOUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; @@ -236,10 +237,11 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE); mySearchParameterDao.create(fooSp, mySrd); - res = myResourceTableDao.findById(patId.getIdPartAsLong()).orElseThrow(IllegalStateException::new); - assertEquals(null, res.getIndexStatus()); - res = myResourceTableDao.findById(obsId.getIdPartAsLong()).orElseThrow(IllegalStateException::new); - assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, res.getIndexStatus().longValue()); + runInTransaction(()->{ + List allJobs = myResourceReindexJobDao.findAll(); + assertEquals(1, allJobs.size()); + assertEquals("Patient", allJobs.get(0).getResourceType()); + }); } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java index 91d277b53e1..8ed92937952 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java @@ -193,7 +193,7 @@ public class SearchCoordinatorSvcImplTest { }); when(mySearchDao.findByUuid(any())).thenAnswer(t -> myCurrentSearch); IFhirResourceDao dao = myCallingDao; - when(myDaoRegistry.getResourceDao(any())).thenReturn(dao); + when(myDaoRegistry.getResourceDao(any(String.class))).thenReturn(dao); resources = result.getResources(0, 100000); assertEquals(790, resources.size()); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java new file mode 100644 index 00000000000..1549aea1b6a --- /dev/null +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImplTest.java @@ -0,0 +1,262 @@ +package ca.uhn.fhir.jpa.search.reindex; + +import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.jpa.dao.BaseJpaTest; +import ca.uhn.fhir.jpa.dao.DaoConfig; +import ca.uhn.fhir.jpa.dao.DaoRegistry; +import ca.uhn.fhir.jpa.dao.IFhirResourceDao; +import ca.uhn.fhir.jpa.dao.data.IForcedIdDao; +import ca.uhn.fhir.jpa.dao.data.IResourceReindexJobDao; +import ca.uhn.fhir.jpa.dao.data.IResourceTableDao; +import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity; +import ca.uhn.fhir.jpa.entity.ResourceTable; +import org.apache.commons.lang3.time.DateUtils; +import org.hl7.fhir.instance.model.api.IBaseResource; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.junit.Before; +import org.junit.Test; +import org.mockito.ArgumentCaptor; +import org.mockito.Captor; +import org.mockito.Mock; +import org.springframework.data.domain.PageRequest; +import org.springframework.data.domain.SliceImpl; +import org.springframework.transaction.PlatformTransactionManager; + +import java.util.*; + +import static org.junit.Assert.assertEquals; +import static org.mockito.ArgumentMatchers.any; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.*; + + +public class ResourceReindexingSvcImplTest extends BaseJpaTest { + + private static FhirContext ourCtx = FhirContext.forR4(); + + @Mock + private PlatformTransactionManager myTxManager; + + private ResourceReindexingSvcImpl mySvc; + private DaoConfig myDaoConfig; + + @Mock + private DaoRegistry myDaoRegistry; + @Mock + private IForcedIdDao myForcedIdDao; + @Mock + private IResourceReindexJobDao myReindexJobDao; + @Mock + private IResourceTableDao myResourceTableDao; + @Mock + private IFhirResourceDao myResourceDao; + @Captor + private ArgumentCaptor myIdCaptor; + @Captor + private ArgumentCaptor myPageRequestCaptor; + @Captor + private ArgumentCaptor myTypeCaptor; + @Captor + private ArgumentCaptor myLowCaptor; + @Captor + private ArgumentCaptor myHighCaptor; + private ResourceReindexJobEntity mySingleJob; + + @Override + protected FhirContext getContext() { + return ourCtx; + } + + @Override + protected PlatformTransactionManager getTxManager() { + return myTxManager; + } + + @Before + public void before() { + myDaoConfig = new DaoConfig(); + myDaoConfig.setReindexThreadCount(2); + + mySvc = new ResourceReindexingSvcImpl(); + mySvc.setContextForUnitTest(ourCtx); + mySvc.setDaoConfigForUnitTest(myDaoConfig); + mySvc.setDaoRegistryForUnitTest(myDaoRegistry); + mySvc.setForcedIdDaoForUnitTest(myForcedIdDao); + mySvc.setReindexJobDaoForUnitTest(myReindexJobDao); + mySvc.setResourceTableDaoForUnitTest(myResourceTableDao); + mySvc.setTxManagerForUnitTest(myTxManager); + mySvc.start(); + } + + @Test + public void testMarkJobsPastThresholdAsDeleted() { + mockNothingToExpunge(); + mockSingleReindexingJob(null); + mockFourResourcesNeedReindexing(); + mockFetchFourResources(); + + mySingleJob.setThresholdHigh(DateUtils.addMinutes(new Date(), -1)); + + mySvc.forceReindexingPass(); + + verify(myResourceTableDao, never()).findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(any(), any(), any()); + verify(myResourceTableDao, never()).findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(any(), any(), any(), any()); + verify(myReindexJobDao, times(1)).markAsDeletedById(myIdCaptor.capture()); + + assertEquals(123L, myIdCaptor.getValue().longValue()); + } + + @Test + public void testExpungeDeletedJobs() { + ResourceReindexJobEntity job = new ResourceReindexJobEntity(); + job.setIdForUnitTest(123L); + job.setDeleted(true); + when(myReindexJobDao.findAll(any(), eq(true))).thenReturn(Arrays.asList(job)); + + mySvc.forceReindexingPass(); + + verify(myReindexJobDao, times(1)).deleteById(eq(123L)); + } + + @Test + public void testReindexPassAllResources() { + mockNothingToExpunge(); + mockSingleReindexingJob(null); + mockFourResourcesNeedReindexing(); + mockFetchFourResources(); + + int count = mySvc.forceReindexingPass(); + assertEquals(4, count); + + // Make sure we reindexed all 4 resources + verify(myResourceDao, times(4)).reindex(any(), any()); + + // Make sure we updated the low threshold + verify(myReindexJobDao, times(1)).setThresholdLow(myIdCaptor.capture(), myLowCaptor.capture()); + assertEquals(123L, myIdCaptor.getValue().longValue()); + assertEquals(40 * DateUtils.MILLIS_PER_DAY, myLowCaptor.getValue().getTime()); + + // Make sure we didn't do anything unexpected + verify(myReindexJobDao, times(1)).findAll(any(), eq(false)); + verify(myReindexJobDao, times(1)).findAll(any(), eq(true)); + verifyNoMoreInteractions(myReindexJobDao); + } + + @Test + public void testReindexPassPatients() { + mockNothingToExpunge(); + mockSingleReindexingJob("Patient"); + // Mock resource fetch + List values = Arrays.asList(0L, 1L, 2L, 3L); + when(myResourceTableDao.findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(myPageRequestCaptor.capture(), myTypeCaptor.capture(), myLowCaptor.capture(), myHighCaptor.capture())).thenReturn(new SliceImpl<>(values)); + // Mock fetching resources + long[] updatedTimes = new long[]{ + 10 * DateUtils.MILLIS_PER_DAY, + 20 * DateUtils.MILLIS_PER_DAY, + 40 * DateUtils.MILLIS_PER_DAY, + 30 * DateUtils.MILLIS_PER_DAY, + }; + String[] resourceTypes = new String[]{ + "Patient", + "Patient", + "Patient", + "Patient" + }; + List resources = Arrays.asList( + new Patient().setId("Patient/0"), + new Patient().setId("Patient/1"), + new Patient().setId("Patient/2"), + new Patient().setId("Patient/3") + ); + mockWhenResourceTableFindById(updatedTimes, resourceTypes); + when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao); + when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> { + ResourceTable table = (ResourceTable) t.getArguments()[0]; + Long id = table.getId(); + return resources.get(id.intValue()); + }); + + int count = mySvc.forceReindexingPass(); + assertEquals(4, count); + + // Make sure we reindexed all 4 resources + verify(myResourceDao, times(4)).reindex(any(), any()); + + // Make sure we updated the low threshold + verify(myReindexJobDao, times(1)).setThresholdLow(myIdCaptor.capture(), myLowCaptor.capture()); + assertEquals(123L, myIdCaptor.getValue().longValue()); + assertEquals(40 * DateUtils.MILLIS_PER_DAY, myLowCaptor.getValue().getTime()); + + // Make sure we didn't do anything unexpected + verify(myReindexJobDao, times(1)).findAll(any(), eq(false)); + verify(myReindexJobDao, times(1)).findAll(any(), eq(true)); + verifyNoMoreInteractions(myReindexJobDao); + } + + private void mockWhenResourceTableFindById(long[] theUpdatedTimes, String[] theResourceTypes) { + when(myResourceTableDao.findById(any())).thenAnswer(t -> { + ResourceTable retVal = new ResourceTable(); + Long id = (Long) t.getArguments()[0]; + retVal.setId(id); + retVal.setResourceType(theResourceTypes[id.intValue()]); + retVal.setUpdated(new Date(theUpdatedTimes[id.intValue()])); + return Optional.of(retVal); + }); + } + + private void mockFetchFourResources() { + // Mock fetching resources + long[] updatedTimes = new long[]{ + 10 * DateUtils.MILLIS_PER_DAY, + 20 * DateUtils.MILLIS_PER_DAY, + 40 * DateUtils.MILLIS_PER_DAY, + 30 * DateUtils.MILLIS_PER_DAY, + }; + String[] resourceTypes = new String[]{ + "Patient", + "Patient", + "Observation", + "Observation" + }; + List resources = Arrays.asList( + new Patient().setId("Patient/0"), + new Patient().setId("Patient/1"), + new Observation().setId("Observation/2"), + new Observation().setId("Observation/3") + ); + mockWhenResourceTableFindById(updatedTimes, resourceTypes); + when(myDaoRegistry.getResourceDao(eq("Patient"))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq(Patient.class))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq("Observation"))).thenReturn(myResourceDao); + when(myDaoRegistry.getResourceDao(eq(Observation.class))).thenReturn(myResourceDao); + when(myResourceDao.toResource(any(), anyBoolean())).thenAnswer(t -> { + ResourceTable table = (ResourceTable) t.getArguments()[0]; + Long id = table.getId(); + return resources.get(id.intValue()); + }); + } + + private void mockFourResourcesNeedReindexing() { + // Mock resource fetch + List values = Arrays.asList(0L, 1L, 2L, 3L); + when(myResourceTableDao.findIdsOfResourcesWithinUpdatedRangeOrderedFromOldest(myPageRequestCaptor.capture(), myLowCaptor.capture(), myHighCaptor.capture())).thenReturn(new SliceImpl<>(values)); + } + + private void mockSingleReindexingJob(String theResourceType) { + // Mock the reindexing job + mySingleJob = new ResourceReindexJobEntity(); + mySingleJob.setIdForUnitTest(123L); + mySingleJob.setThresholdHigh(DateUtils.addMinutes(new Date(), 1)); + mySingleJob.setResourceType(theResourceType); + when(myReindexJobDao.findAll(any(), eq(false))).thenReturn(Arrays.asList(mySingleJob)); + } + + private void mockNothingToExpunge() { + // Nothing to expunge + when(myReindexJobDao.findAll(any(), eq(true))).thenReturn(new ArrayList<>()); + } +} diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java index 86908943ce1..f46a7001a8f 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java @@ -550,14 +550,6 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test { assertEquals("D1V", concept.getDesignation().get(0).getValue()); } - @Test - public void testReindexTerminology() { - IIdType id = createCodeSystem(); - - assertThat(mySystemDao.markAllResourcesForReindexing(), greaterThan(0)); - - assertThat(mySystemDao.performReindexingPass(100), greaterThan(0)); - } @Test public void testStoreCodeSystemInvalidCyclicLoop() { diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java index 98e4cd3a5b7..d15e4bc6027 100644 --- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java +++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java @@ -77,7 +77,7 @@ public enum DriverTypeEnum { BasicDataSource dataSource = new BasicDataSource(){ @Override public Connection getConnection() throws SQLException { - ourLog.info("Creating new DB connection"); + ourLog.debug("Creating new DB connection"); return super.getConnection(); } }; diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java index c12d773dfa7..60792b73811 100644 --- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java +++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java @@ -92,4 +92,5 @@ public class Migrator { ourLog.info("Finished migration of {} tasks", myTasks.size()); } + } diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java index ef93f2e8f02..d25f3c496f5 100644 --- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java +++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java @@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.tasks; * 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. @@ -30,13 +30,26 @@ import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask; import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks; import ca.uhn.fhir.util.VersionEnum; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + @SuppressWarnings({"UnstableApiUsage", "SqlNoDataSourceInspection", "SpellCheckingInspection"}) public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { + private final Set myFlags; + /** * Constructor */ - public HapiFhirJpaMigrationTasks() { + public HapiFhirJpaMigrationTasks(Set theFlags) { + myFlags = theFlags + .stream() + .map(FlagEnum::fromCommandLineValue) + .collect(Collectors.toSet()); + init340(); init350(); init360(); @@ -60,6 +73,15 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { .addColumn("OPTLOCK_VERSION") .nullable() .type(BaseTableColumnTypeTask.ColumnTypeEnum.INT); + + version.addTable("HFJ_RES_REINDEX_JOB") + .addSql(DriverTypeEnum.MSSQL_2012, "create table HFJ_RES_REINDEX_JOB (PID bigint not null, JOB_DELETED bit not null, RES_TYPE varchar(255), SUSPENDED_UNTIL datetime2, UPDATE_THRESHOLD_HIGH datetime2 not null, UPDATE_THRESHOLD_LOW datetime2, primary key (PID))") + .addSql(DriverTypeEnum.DERBY_EMBEDDED, "create table HFJ_RES_REINDEX_JOB (PID bigint not null, JOB_DELETED boolean not null, RES_TYPE varchar(255), SUSPENDED_UNTIL timestamp, UPDATE_THRESHOLD_HIGH timestamp not null, UPDATE_THRESHOLD_LOW timestamp, primary key (PID))") + .addSql(DriverTypeEnum.MARIADB_10_1, "create table HFJ_RES_REINDEX_JOB (PID bigint not null, JOB_DELETED bit not null, RES_TYPE varchar(255), SUSPENDED_UNTIL datetime(6), UPDATE_THRESHOLD_HIGH datetime(6) not null, UPDATE_THRESHOLD_LOW datetime(6), primary key (PID))") + .addSql(DriverTypeEnum.POSTGRES_9_4, "persistence_create_postgres94.sql:create table HFJ_RES_REINDEX_JOB (PID int8 not null, JOB_DELETED boolean not null, RES_TYPE varchar(255), SUSPENDED_UNTIL timestamp, UPDATE_THRESHOLD_HIGH timestamp not null, UPDATE_THRESHOLD_LOW timestamp, primary key (PID))") + .addSql(DriverTypeEnum.MYSQL_5_7, " create table HFJ_RES_REINDEX_JOB (PID bigint not null, JOB_DELETED bit not null, RES_TYPE varchar(255), SUSPENDED_UNTIL datetime(6), UPDATE_THRESHOLD_HIGH datetime(6) not null, UPDATE_THRESHOLD_LOW datetime(6), primary key (PID))") + .addSql(DriverTypeEnum.ORACLE_12C, "create table HFJ_RES_REINDEX_JOB (PID number(19,0) not null, JOB_DELETED number(1,0) not null, RES_TYPE varchar2(255 char), SUSPENDED_UNTIL timestamp, UPDATE_THRESHOLD_HIGH timestamp not null, UPDATE_THRESHOLD_LOW timestamp, primary key (PID))"); + } private void init350() { @@ -80,65 +102,69 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { // Indexes - Coords Builder.BuilderWithTableName spidxCoords = version.onTable("HFJ_SPIDX_COORDS"); version.startSectionWithMessage("Starting work on table: " + spidxCoords.getTableName()); - spidxCoords - .dropIndex("IDX_SP_COORDS"); spidxCoords .addColumn("HASH_IDENTITY") .nullable() .type(AddColumnTask.ColumnTypeEnum.LONG); - spidxCoords - .addIndex("IDX_SP_COORDS_HASH") - .unique(false) - .withColumns("HASH_IDENTITY", "SP_LATITUDE", "SP_LONGITUDE"); - spidxCoords - .addTask(new CalculateHashesTask() - .setColumnName("HASH_IDENTITY") - .addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxCoords + .dropIndex("IDX_SP_COORDS"); + spidxCoords + .addIndex("IDX_SP_COORDS_HASH") + .unique(false) + .withColumns("HASH_IDENTITY", "SP_LATITUDE", "SP_LONGITUDE"); + spidxCoords + .addTask(new CalculateHashesTask() + .setColumnName("HASH_IDENTITY") + .addCalculator("HASH_IDENTITY", t -> BaseResourceIndexedSearchParam.calculateHashIdentity(t.getResourceType(), t.getString("SP_NAME"))) + ); + } // Indexes - Date Builder.BuilderWithTableName spidxDate = version.onTable("HFJ_SPIDX_DATE"); version.startSectionWithMessage("Starting work on table: " + spidxDate.getTableName()); - 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"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxDate + .dropIndex("IDX_SP_TOKEN"); + 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 = version.onTable("HFJ_SPIDX_NUMBER"); version.startSectionWithMessage("Starting work on table: " + spidxNumber.getTableName()); - 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"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxNumber + .dropIndex("IDX_SP_NUMBER"); + 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 = version.onTable("HFJ_SPIDX_QUANTITY"); version.startSectionWithMessage("Starting work on table: " + spidxQuantity.getTableName()); - spidxQuantity - .dropIndex("IDX_SP_QUANTITY"); spidxQuantity .addColumn("HASH_IDENTITY") .nullable() @@ -151,61 +177,63 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { .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"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxQuantity + .dropIndex("IDX_SP_QUANTITY"); + 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 = version.onTable("HFJ_SPIDX_STRING"); version.startSectionWithMessage("Starting work on table: " + spidxString.getTableName()); - spidxString - .dropIndex("IDX_SP_STRING"); spidxString .addColumn("HASH_NORM_PREFIX") .nullable() .type(AddColumnTask.ColumnTypeEnum.LONG); - spidxString - .addIndex("IDX_SP_STRING_HASH_NRM") - .unique(false) - .withColumns("HASH_NORM_PREFIX", "SP_VALUE_NORMALIZED"); - spidxString - .addColumn("HASH_EXACT") - .nullable() - .type(AddColumnTask.ColumnTypeEnum.LONG); - spidxString - .addIndex("IDX_SP_STRING_HASH_EXCT") - .unique(false) - .withColumns("HASH_EXACT"); - spidxString - .addTask(new CalculateHashesTask() - .setColumnName("HASH_NORM_PREFIX") - .addCalculator("HASH_NORM_PREFIX", t -> ResourceIndexedSearchParamString.calculateHashNormalized(new DaoConfig(), t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_VALUE_NORMALIZED"))) - .addCalculator("HASH_EXACT", t -> ResourceIndexedSearchParamString.calculateHashExact(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE_EXACT"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxString + .dropIndex("IDX_SP_STRING"); + spidxString + .addIndex("IDX_SP_STRING_HASH_NRM") + .unique(false) + .withColumns("HASH_NORM_PREFIX", "SP_VALUE_NORMALIZED"); + spidxString + .addColumn("HASH_EXACT") + .nullable() + .type(AddColumnTask.ColumnTypeEnum.LONG); + spidxString + .addIndex("IDX_SP_STRING_HASH_EXCT") + .unique(false) + .withColumns("HASH_EXACT"); + spidxString + .addTask(new CalculateHashesTask() + .setColumnName("HASH_NORM_PREFIX") + .addCalculator("HASH_NORM_PREFIX", t -> ResourceIndexedSearchParamString.calculateHashNormalized(new DaoConfig(), t.getResourceType(), t.getString("SP_NAME"), t.getString("SP_VALUE_NORMALIZED"))) + .addCalculator("HASH_EXACT", t -> ResourceIndexedSearchParamString.calculateHashExact(t.getResourceType(), t.getParamName(), t.getString("SP_VALUE_EXACT"))) + ); + } // Indexes - Token Builder.BuilderWithTableName spidxToken = version.onTable("HFJ_SPIDX_TOKEN"); version.startSectionWithMessage("Starting work on table: " + spidxToken.getTableName()); - spidxToken - .dropIndex("IDX_SP_TOKEN"); - spidxToken - .dropIndex("IDX_SP_TOKEN_UNQUAL"); spidxToken .addColumn("HASH_IDENTITY") .nullable() @@ -222,30 +250,36 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { .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"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxToken + .dropIndex("IDX_SP_TOKEN"); + spidxToken + .dropIndex("IDX_SP_TOKEN_UNQUAL"); + 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 = version.onTable("HFJ_SPIDX_URI"); @@ -254,24 +288,26 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { .addColumn("HASH_IDENTITY") .nullable() .type(AddColumnTask.ColumnTypeEnum.LONG); - spidxUri - .addIndex("IDX_SP_URI_HASH_IDENTITY") - .unique(false) - .withColumns("HASH_IDENTITY", "SP_URI"); - spidxUri - .addColumn("HASH_URI") - .nullable() - .type(AddColumnTask.ColumnTypeEnum.LONG); - 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"))) - ); + if (!myFlags.contains(FlagEnum.NO_MIGRATE_HASHES)) { + spidxUri + .addIndex("IDX_SP_URI_HASH_IDENTITY") + .unique(false) + .withColumns("HASH_IDENTITY", "SP_URI"); + spidxUri + .addColumn("HASH_URI") + .nullable() + .type(AddColumnTask.ColumnTypeEnum.LONG); + 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 = version.onTable("HFJ_RES_PARAM_PRESENT"); @@ -492,5 +528,27 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks { } + public enum FlagEnum { + NO_MIGRATE_HASHES("no-migrate-350-hashes"); + + private final String myCommandLineValue; + + FlagEnum(String theCommandLineValue) { + myCommandLineValue = theCommandLineValue; + } + + public String getCommandLineValue() { + return myCommandLineValue; + } + + public static FlagEnum fromCommandLineValue(String theCommandLineValue) { + Optional retVal = Arrays.stream(values()).filter(t -> t.myCommandLineValue.equals(theCommandLineValue)).findFirst(); + return retVal.orElseThrow(() -> { + List validValues = Arrays.stream(values()).map(t -> t.myCommandLineValue).sorted().collect(Collectors.toList()); + return new IllegalArgumentException("Invalid flag \"" + theCommandLineValue + "\". Valid values: " + validValues); + }); + } + } + } diff --git a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java b/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java index 4ff02d95a2d..4d29e9588a1 100644 --- a/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java +++ b/hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java @@ -2,11 +2,13 @@ package ca.uhn.fhir.jpa.migrate.tasks; import org.junit.Test; +import java.util.Collections; + public class HapiFhirJpaMigrationTasksTest { @Test public void testCreate() { - new HapiFhirJpaMigrationTasks(); + new HapiFhirJpaMigrationTasks(Collections.emptySet()); } diff --git a/pom.xml b/pom.xml index d5ff60b05fb..fcb53fa4161 100644 --- a/pom.xml +++ b/pom.xml @@ -2066,7 +2066,7 @@ org.apache.maven.plugins maven-project-info-reports-plugin - 2.8.1 + 3.0.0 false diff --git a/src/site/xdoc/doc_cli.xml b/src/site/xdoc/doc_cli.xml index 8f65b8732d8..5598f02a7fa 100644 --- a/src/site/xdoc/doc_cli.xml +++ b/src/site/xdoc/doc_cli.xml @@ -142,42 +142,16 @@ Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)]]>

- When upgrading the JPA server from one version of HAPI FHIR to a newer version, - often there will be changes to the database schema. The Migrate Database - command can be used to perform a migration from one version to the next. -

-

- Note that this feature was added in HAPI FHIR 3.5.0. It is not able to migrate - from versions prior to HAPI FHIR 3.4.0. Please make a backup of your - database before running this command! -

-

- The following example shows how to use the migrator utility to migrate between two versions. -

- 
./hapi-fhir-cli migrate-database -d DERBY_EMBEDDED -u "jdbc:derby:directory:target/jpaserver_derby_files;create=true" -n "" -p "" -f V3_4_0 -t V3_5_0
- -

- You may use the following command to get detailed help on the options: -

- 
./hapi-fhir-cli help migrate-database
- -

- Note the arguments: -

    -
  • -d [dialect] - This indicates the database dialect to use. See the detailed help for a list of options
    • -
  • -f [version] - The version to migrate from
    • -
  • -t [version] - The version to migrate to
    • -
+ The migrate-database command may be used to Migrate a database + schema when upgrading a + HAPI FHIR JPA project from one version of HAPI + FHIR to another version.

- -

- Note that the Oracle JDBC drivers are not distributed in the Maven Central repository, - so they are not included in HAPI FHIR. In order to use this command with an Oracle database, - you will need to invoke the CLI as follows: -

- 
java -cp hapi-fhir-cli.jar ca.uhn.fhir.cli.App migrate-database -d ORACLE_12C -u "[url]" -n "[username]" -p "[password]" -f V3_4_0 -t V3_5_0
- +

+ See Upgrading HAPI FHIR JPA + for information on how to use this command. +

diff --git a/src/site/xdoc/doc_jpa.xml b/src/site/xdoc/doc_jpa.xml index a79c2d83689..7719d4c592a 100644 --- a/src/site/xdoc/doc_jpa.xml +++ b/src/site/xdoc/doc_jpa.xml @@ -366,7 +366,143 @@ delete from hfj_res_ver where res_id in (select res_id from hfj_resource where s --> - + + +
+ +

+ HAPI FHIR JPA is a constantly evolving product, with new features being added to each + new version of the library. As a result, it is generally necessary to execute a database + migration as a part of an upgrade to HAPI FHIR. +

+ +

+ When upgrading the JPA server from one version of HAPI FHIR to a newer version, + often there will be changes to the database schema. The Migrate Database + command can be used to perform a migration from one version to the next. +

+ +

+ Note that this feature was added in HAPI FHIR 3.5.0. It is not able to migrate + from versions prior to HAPI FHIR 3.4.0. Please make a backup of your + database before running this command! +

+

+ The following example shows how to use the migrator utility to migrate between two versions. +

+ 
./hapi-fhir-cli migrate-database -d DERBY_EMBEDDED -u "jdbc:derby:directory:target/jpaserver_derby_files;create=true" -n "" -p "" -f V3_4_0 -t V3_5_0
+ +

+ You may use the following command to get detailed help on the options: +

+ 
./hapi-fhir-cli help migrate-database
+ +

+ Note the arguments: +

    +
  • -d [dialect] - This indicates the database dialect to use. See the detailed help for a list of options
    • +
  • -f [version] - The version to migrate from
    • +
  • -t [version] - The version to migrate to
    • +
+

+ + +

+ Note that the Oracle JDBC drivers are not distributed in the Maven Central repository, + so they are not included in HAPI FHIR. In order to use this command with an Oracle database, + you will need to invoke the CLI as follows: +

+ 
java -cp hapi-fhir-cli.jar ca.uhn.fhir.cli.App migrate-database -d ORACLE_12C -u "[url]" -n "[username]" -p "[password]" -f V3_4_0 -t V3_5_0
+ + + +

+ As of HAPI FHIR 3.5.0 a new mechanism for creating the JPA index tables (HFJ_SPIDX_xxx) + has been implemented. This new mechanism uses hashes in place of large multi-column + indexes. This improves both lookup times as well as required storage space. This change + also paves the way for future ability to provide efficient multi-tenant searches (which + is not yet implemented but is planned as an incremental improvement). +

+

+ This change is not a lightweight change however, as it requires a rebuild of the + index tables in order to generate the hashes. This can take a long time on databases + that already have a large amount of data. +

+

+ As a result, in HAPI FHIR JPA 3.6.0, an efficient way of upgrading existing databases + was added. Under this new scheme, columns for the hashes are added but values are not + calculated initially, database indexes are not modified on the HFJ_SPIDX_xxx tables, + and the previous columns are still used for searching as was the case in HAPI FHIR + JPA 3.4.0. +

+

+ In order to perform a migration using this functionality, the following steps should + be followed: +

+
    +
  • + Stop your running HAPI FHIR JPA instance (and remember to make a backup of your + database before proceeding with any changes!) +
    • +
  • + Modify your DaoConfig to specify that hash-based searches should not be used, using + the following setting:
    + 
    myDaoConfig.setDisableHashBasedSearches(true);
    +
    • +
  • + Make sure that you have your JPA settings configured to not automatically + create database indexes and columns using the following setting + in your JPA Properties:
    + 
    extraProperties.put("hibernate.hbm2ddl.auto", "none");
    +
    • +
  • + Run the database migrator command, including the entry -x no-migrate-350-hashes + on the command line. For example:
    + 
    ./hapi-fhir-cli migrate-database -d DERBY_EMBEDDED -u "jdbc:derby:directory:target/jpaserver_derby_files;create=true" -n "" -p "" -f V3_4_0 -t V3_6_0 -x no-migrate-350-hashes
    +
    • +
  • + Rebuild and start your HAPI FHIR JPA server. At this point you should have a working + HAPI FHIR JPA 3.6.0 server that is is still using HAPI FHIR 3.4.0 search indexes. Search hashes + will be generated for any newly created or updated data but existing data will have null + hashes. +
    • +
  • + With the system running, request a complete reindex of the data in the database using + an HTTP request such as the following:
    + 
    GET /$mark-all-resources-for-reindexing
    + Note that this is a custom operation built into the HAPI FHIR JPA server. It should + be secured in a real deployment, so Authentication is likely required for this + call. +
    • +
  • + You can track the reindexing process by watching your server logs, + but also by using the following SQL executed directly against your database: +
    + 
    SELECT * FROM HFJ_RES_REINDEX_JOB
    + When this query no longer returns any rows, the reindexing process is complete. +
    • +
  • + At this time, HAPI FHIR should be stopped once again in order to convert it + to using the hash based indexes. +
    • +
  • + Modify your DaoConfig to specify that hash-based searches are used, using + the following setting (this is the default setting, so it could also simply + be omitted):
    + 
    myDaoConfig.setDisableHashBasedSearches(false);
    +
    • +
  • + Execute the migrator tool again, this time omitting the flag option, e.g.
    + 
    ./hapi-fhir-cli migrate-database -d DERBY_EMBEDDED -u "jdbc:derby:directory:target/jpaserver_derby_files;create=true" -n "" -p "" -f V3_4_0 -t V3_6_0
    +
    • +
  • + Rebuild, and start HAPI FHIR JPA again. +
    • +
+ + +
+