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Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler

This commit is contained in:
Ken Stevens 2019-12-05 13:06:44 -05:00
parent a939dab894 f2b3a39abb
commit 66cc83464f
11 changed files with 579 additions and 101 deletions
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19
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java
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@ -20,8 +20,11 @@ package ca.uhn.fhir.cli;
* #L% * #L%
*/ */
import ca.uhn.fhir.jpa.migrate.BaseMigrator;
import ca.uhn.fhir.jpa.migrate.BruteForceMigrator;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum; import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.FlywayMigrator; import ca.uhn.fhir.jpa.migrate.FlywayMigrator;
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options; import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException; import org.apache.commons.cli.ParseException;
@ -35,10 +38,14 @@ import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.defaultString;
/**
* NB since 2019-12-05: This class is kind of weirdly named now, since it can either use Flyway or not use Flyway
*/
public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends BaseCommand { public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends BaseCommand {
public static final String MIGRATE_DATABASE = "migrate-database"; public static final String MIGRATE_DATABASE = "migrate-database";
public static final String DONT_USE_FLYWAY = "dont-use-flyway";
private Set<String> myFlags; private Set<String> myFlags;
private String myMigrationTableName; private String myMigrationTableName;
@ -78,6 +85,7 @@ public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends B
addRequiredOption(retVal, "p", "password", "Password", "The JDBC database password"); addRequiredOption(retVal, "p", "password", "Password", "The JDBC database password");
addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")"); 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)"); addOptionalOption(retVal, "x", "flags", "Flags", "A comma-separated list of any specific migration flags (these flags are version specific, see migrator documentation for details)");
addOptionalOption(retVal, null, DONT_USE_FLYWAY,false, "If this option is set, the migrator will not use FlywayDB for migration. This setting should only be used if you are trying to migrate a legacy database platform that is not supported by FlywayDB.");
addOptionalOption(retVal, null, "no-column-shrink", false, "If this flag is set, the system will not attempt to reduce the length of columns. This is useful in environments with a lot of existing data, where shrinking a column can take a very long time."); addOptionalOption(retVal, null, "no-column-shrink", false, "If this flag is set, the system will not attempt to reduce the length of columns. This is useful in environments with a lot of existing data, where shrinking a column can take a very long time.");
return retVal; return retVal;
@ -110,7 +118,14 @@ public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends B
.filter(StringUtils::isNotBlank) .filter(StringUtils::isNotBlank)
.collect(Collectors.toSet()); .collect(Collectors.toSet());
FlywayMigrator migrator = new FlywayMigrator(myMigrationTableName); boolean dontUseFlyway = theCommandLine.hasOption("dont-use-flyway");
BaseMigrator migrator;
if (dontUseFlyway) {
migrator = new BruteForceMigrator();
} else {
migrator = new FlywayMigrator(myMigrationTableName);
}
migrator.setConnectionUrl(url); migrator.setConnectionUrl(url);
migrator.setDriverType(driverType); migrator.setDriverType(driverType);
migrator.setUsername(username); migrator.setUsername(username);
@ -121,7 +136,7 @@ public abstract class BaseFlywayMigrateDatabaseCommand<T extends Enum> extends B
migrator.migrate(); migrator.migrate();
} }
protected abstract void addTasks(FlywayMigrator theMigrator); protected abstract void addTasks(BaseMigrator theMigrator);
public void setMigrationTableName(String theMigrationTableName) { public void setMigrationTableName(String theMigrationTableName) {
myMigrationTableName = theMigrationTableName; myMigrationTableName = theMigrationTableName;

3
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommand.java
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@ -20,6 +20,7 @@ package ca.uhn.fhir.cli;
* #L% * #L%
*/ */
import ca.uhn.fhir.jpa.migrate.BaseMigrator;
import ca.uhn.fhir.jpa.migrate.FlywayMigrator; import ca.uhn.fhir.jpa.migrate.FlywayMigrator;
import ca.uhn.fhir.jpa.migrate.SchemaMigrator; import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask; import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
@ -44,7 +45,7 @@ public class HapiFlywayMigrateDatabaseCommand extends BaseFlywayMigrateDatabaseC
} }
@Override @Override
protected void addTasks(FlywayMigrator theMigrator) { protected void addTasks(BaseMigrator theMigrator) {
List<BaseTask<?>> tasks = new HapiFhirJpaMigrationTasks(getFlags()).getAllTasks(VersionEnum.values()); List<BaseTask<?>> tasks = new HapiFhirJpaMigrationTasks(getFlags()).getAllTasks(VersionEnum.values());
theMigrator.addTasks(tasks); theMigrator.addTasks(tasks);
} }

41
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java
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@ -77,6 +77,47 @@ public class HapiFlywayMigrateDatabaseCommandTest {
}); });
} }
@Test
public void testMigrateFrom340_NoFlyway() throws IOException, SQLException {
File location = getLocation("migrator_h2_test_340_current");
String url = "jdbc:h2:" + location.getAbsolutePath() + ";create=true";
DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "", "");
String initSql = "/persistence_create_h2_340.sql";
executeSqlStatements(connectionProperties, initSql);
seedDatabase340(connectionProperties);
ourLog.info("**********************************************");
ourLog.info("Done Setup, Starting Migration...");
ourLog.info("**********************************************");
String[] args = new String[]{
BaseFlywayMigrateDatabaseCommand.MIGRATE_DATABASE,
"-d", "H2_EMBEDDED",
"-u", url,
"-n", "",
"-p", "",
"--" + BaseFlywayMigrateDatabaseCommand.DONT_USE_FLYWAY
};
assertFalse(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_RES_REINDEX_JOB"));
App.main(args);
assertTrue(JdbcUtils.getTableNames(connectionProperties).contains("HFJ_RES_REINDEX_JOB"));
connectionProperties.getTxTemplate().execute(t -> {
JdbcTemplate jdbcTemplate = connectionProperties.newJdbcTemplate();
List<Map<String, Object>> 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 @Test
public void testMigrateFromEmptySchema() throws IOException, SQLException { public void testMigrateFromEmptySchema() throws IOException, SQLException {

280
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/atlas/points.json Normal file
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@ -0,0 +1,280 @@
{
"comment": [
"This is the HAPI FHIR Global Atlas data file. Please feel free to file a pull request",
"if you would like to add or update your project or organization. Any elements named",
"comment (such as this one) will be ignored because lousy JSON has no comments."
],
"points": [
{
"title": "OKDC - FHIR Manager",
"description": "Post orders, get results from federal laboratory system",
"lat": 47.223040,
"lon": 39.721380,
"city": "Rostov-On-Don",
"added": "2019-08-19"
},
{
"title": "Care Connect Reference Implementation",
"description": "UK/England NHS Reference FHIR Implementation",
"company": "Mayfield IS",
"contactName": "Kevin Mayfield",
"contactEmail": "Kevin.mayfield@mayfield-is.co.uk",
"link": "https://data.developer.nhs.uk/ccri/exp",
"lat": 55.378052,
"lon": -3.435973,
"added": "2019-08-19"
},
{
"title": "clinFHIR",
"contactName": "David Hay",
"contactEmail": "davidhay@gmail.com",
"link": "http://clinfhir.com",
"lat": -42.651737,
"lon": 171.926909,
"added": "2019-08-18"
},
{
"title": "EDS AP-HP",
"description": "Health Datawarehouse",
"lat": 48.8647,
"lon": 2.349014,
"city": "Paris",
"added": "2019-09-02"
},
{
"title": "eHealth Innovation",
"description": "eHealth Innovation uses HAPI FHIR to power patient apps for managing chronic conditions",
"link": "http://ehealthinnovation.org",
"lat": 43.741667,
"lon": -79.373333,
"city": "Toronto",
"added": "2019-11-20"
},
{
"title": "CSIRO OntoServer",
"description": "Australia's national terminology server. FHIR-native, fast, and comprehensive support for FHIR DSTU2.1, STU3, and R4",
"link": "https://ontoserver.csiro.au",
"contactName": "Michael Lawley",
"contactEmail": "ontoserver-support@csiro.au",
"city": "Brisbane",
"lat": -27.469770,
"lon": 153.025131
},
{
"title": "MOLIT Institut: VITU, HUB, EQU",
"description": "Virtual tumorboard based on FHIR, Management Frontend to import Patients from HIS and assign Questionnaire Tasks, Electronic Questionnaire based on FHIR Questionnaire",
"link": "https://demo.molit.eu",
"contactName": "Patrick Werner",
"contactEmail": "pa.f.werner@gmail.com",
"city": "Germany",
"lat": 50.1188,
"lon": 8.6843,
"added": "2019-08-18"
},
{
"title": "Altarum Institute",
"description": null,
"link": "https://demo.molit.eu",
"contactName": "Altarum Institute",
"contactEmail": "ray.humphrys@altarum.org",
"city": "Michigan",
"lat": 42.2807,
"lon": -83.7801,
"added": "2019-08-18"
},
{
"title": "Audacious Inquiry",
"description": "HIE Services",
"link": null,
"contactName": "Keith Boone",
"contactEmail": "kboone@ainq.com",
"city": "Maryland",
"lat": 39.4756,
"lon": -76.2420,
"added": "2019-08-18"
},
{
"title": "InfoClinic",
"description": "InfoClinic HAPI FHIR R4 Testing Server",
"link": "http://fhir.infoclinic.co",
"contactName": null,
"contactEmail": null,
"city": "Seoul, South Korea",
"lat": 37.5339,
"lon": 126.9775,
"added": "2019-08-18"
},
{
"title": "PGD FHIR",
"description": "Apothesource",
"link": null,
"contactName": null,
"contactEmail": null,
"city": "South Carolina, USA",
"lat": 34.2296,
"lon": -80.7147,
"added": "2019-08-19"
},
{
"title": "Drummond Group: Interoperability Hub",
"description": "Certified EHR FHIR Surveillance App",
"link": "http://www.interophub.com",
"contactName": null,
"contactEmail": null,
"city": "USA",
"lat": 35.3961,
"lon": -81.6303,
"added": "2019-08-19"
},
{
"title": "United States Digital Service/CMS",
"description": "Data at the Point of Care: FHIR API for enabling providers to retrieve CMS claims data in a bulk manner.",
"link": "http://dpc.cms.gov",
"contactName": null,
"contactEmail": null,
"city": "Washington DC, USA",
"lat": 38.8939,
"lon": -77.0365,
"added": "2019-08-20"
},
{
"title": "AHDIS AG",
"description": "Matchbox: Validation and conversion services",
"link": "http://dpc.cms.gov",
"contactName": "Oliver Egger",
"contactEmail": "oliver.egger@ahdis.ch",
"city": "Switzerland",
"lat": 47.2569,
"lon": 8.6989,
"added": "2019-08-20"
},
{
"title": "Trifork",
"description": "National Telemedicine Project",
"link": "https://ehealth-documentation.s3-eu-west-1.amazonaws.com/latest/ig/index.html",
"contactName": "Jens Villadsen",
"contactEmail": "jvi@trifork.com",
"city": "Aarhus, Denmark",
"lat": 56.1534,
"lon": 10.2255,
"added": "2019-08-20"
},
{
"title": "VietTel",
"description": "VEHR-HL7",
"link": null,
"contactName": null,
"contactEmail": null,
"city": "Vietnam",
"lat": 10.8142,
"lon": 106.6438,
"added": "2019-08-20"
},
{
"title": "ISKRA Solutions Inc.",
"description": "Automatic reconciliation of FHIR messages: Highly scalable FHIR based microservice that uses rules engine to automatically match/reconcile FHIR submissions based on externalized configurable set of business defined criteria.",
"link": null,
"contactName": null,
"contactEmail": null,
"city": "Toronto, Canada",
"lat": 43.741667,
"lon": -79.373333,
"added": "2019-08-20"
},
{
"title": "Insiel S.p.a.",
"description": null,
"link": null,
"contactName": "Ivano Tomainu",
"contactEmail": "ivano.tomainu@insiel.it",
"city": "Italy",
"lat": 38.1193,
"lon": 13.3675,
"added": "2019-08-20"
},
{
"title": "Insiel S.p.a.",
"description": "PathLab.Tech",
"link": null,
"contactName": "Prateek Patil",
"contactEmail": "prateek@pathlab.tech",
"city": "Santa Clara, California",
"lat": 37.3526,
"lon": -121.9541,
"added": "2019-09-13"
},
{
"title": "Telemedis",
"description": "tisFHIR: Telemedicine Information System",
"link": null,
"contactName": "Władysław Węglarz",
"contactEmail": "wladyslaw.weglarz@telemedis.pl",
"city": "Warsaw, Poland",
"lat": 52.2500,
"lon": 21.0000,
"added": "2019-09-13"
},
{
"title": "CINVESTAV",
"description": "Estudio de algoritmos criptograficos ligeros para la seguridad de expedientes clínicos electrónicos",
"link": null,
"contactName": null,
"contactEmail": null,
"city": null,
"lat": 40.4172,
"lon": -3.6840,
"added": "2019-09-29"
},
{
"title": "ResMed",
"description": "Digital Health Technologies: The largest tele-monitored device fleet in the world. Focus on various respiratory diseases from Sleep Disordered breathing (sleep apnea) to COPD.",
"link": null,
"contactName": null,
"contactEmail": null,
"city": "San Diego, California",
"lat": 32.8246,
"lon": -117.1971,
"added": "2019-09-29"
},
{
"title": "Highmark",
"description": "FHIR-based Provider Directory Message Model: Using R4 FHIR we created a standard provider directory message model that captures all practitioners, practitioner roles, vendors, vendor roles, locations, healthcare services, affiliated directory networks and tiered insurance plans. We supply this FHIR-based extract to a well-known transparency vendor whom processes our FHIR message model extract and loads the data to be consumed and accessed on a web-based provider search application. Members can then access this provider search app to search for practitioners whom participate in their products and networks.",
"link": "https://highmark.sapphirecareselect.com",
"contactName": "Wayne Williams",
"contactEmail": "Wayne.Williams@hmhs.com",
"city": "Pittsburgh, PA",
"lat": 40.4562,
"lon": -79.8163,
"added": "2019-09-29"
},
{
"title": "ePHealth: ACS Health Care",
"description": "With the ACS App, Community Health Agents (CHA) work gets faster and faster, and they can take better care of their community. Best of all, it is 100% free to the Health Agent.",
"link": "http://ephealth.com.br/?lang=en",
"contactName": "Alan Lescano",
"contactEmail": "alan@ephealth.com.br",
"city": "Sao Paulo, Brazil",
"lat": -6.6167,
"lon": -38.1500,
"added": "2019-09-29"
},
{
"title": "CENS",
"description": "Centro Nacional en Sistemas de Información en Salud - CENS operates a national testing infrastructure based on HAPI FHIR.",
"link": "http://cens.cl",
"city": "Santiago, Chile",
"lat": -33.4000,
"lon": -70.6000,
"added": "2019-11-25"
},
{
"title": "Software Interoperability Lab for Asia",
"description": "",
"link": "",
"city": "Manila, Philippines",
"lat": 14.6914,
"lon": 120.9686,
"added": "2019-11-25"
}
]
}

72
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BaseMigrator.java Normal file
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@ -0,0 +1,72 @@
package ca.uhn.fhir.jpa.migrate;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
import org.flywaydb.core.api.MigrationInfoService;
import java.util.List;
import java.util.Optional;
public abstract class BaseMigrator {
private boolean myDryRun;
private boolean myNoColumnShrink;
private DriverTypeEnum myDriverType;
private String myConnectionUrl;
private String myUsername;
private String myPassword;
public abstract void migrate();
public boolean isDryRun() {
return myDryRun;
}
public void setDryRun(boolean theDryRun) {
myDryRun = theDryRun;
}
public boolean isNoColumnShrink() {
return myNoColumnShrink;
}
public void setNoColumnShrink(boolean theNoColumnShrink) {
myNoColumnShrink = theNoColumnShrink;
}
public abstract Optional<MigrationInfoService> getMigrationInfo();
public abstract void addTasks(List<BaseTask<?>> theMigrationTasks);
public DriverTypeEnum getDriverType() {
return myDriverType;
}
public void setDriverType(DriverTypeEnum theDriverType) {
myDriverType = theDriverType;
}
public String getConnectionUrl() {
return myConnectionUrl;
}
public void setConnectionUrl(String theConnectionUrl) {
myConnectionUrl = theConnectionUrl;
}
public String getUsername() {
return myUsername;
}
public void setUsername(String theUsername) {
myUsername = theUsername;
}
public String getPassword() {
return myPassword;
}
public void setPassword(String thePassword) {
myPassword = thePassword;
}
}

50
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BruteForceMigrator.java Normal file
View File

@ -0,0 +1,50 @@
package ca.uhn.fhir.jpa.migrate;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.flywaydb.core.api.MigrationInfoService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
/**
* This class is an alternative to {@link FlywayMigrator). It doesn't use Flyway, but instead just
* executes all tasks.
*/
public class BruteForceMigrator extends BaseMigrator {
private static final Logger ourLog = LoggerFactory.getLogger(BruteForceMigrator.class);
private List<BaseTask<?>> myTasks = new ArrayList<>();
@Override
public void migrate() {
for (BaseTask<?> next : myTasks) {
next.setDriverType(getDriverType());
next.setDryRun(isDryRun());
next.setNoColumnShrink(isNoColumnShrink());
DriverTypeEnum.ConnectionProperties connectionProperties = getDriverType().newConnectionProperties(getConnectionUrl(), getUsername(), getPassword());
next.setConnectionProperties(connectionProperties);
try {
ourLog.info("Executing task of type: {}", next.getClass().getSimpleName());
next.execute();
} catch (SQLException e) {
throw new InternalErrorException(e);
}
}
}
@Override
public Optional<MigrationInfoService> getMigrationInfo() {
return Optional.empty();
}
@Override
public void addTasks(List<BaseTask<?>> theMigrationTasks) {
myTasks.addAll(theMigrationTasks);
}
}

85
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/FlywayMigrator.java
View File

@ -31,34 +31,30 @@ import org.slf4j.LoggerFactory;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Optional;
public class FlywayMigrator { public class FlywayMigrator extends BaseMigrator {
private static final Logger ourLog = LoggerFactory.getLogger(FlywayMigrator.class); private static final Logger ourLog = LoggerFactory.getLogger(FlywayMigrator.class);
private DriverTypeEnum myDriverType;
private final String myMigrationTableName; private final String myMigrationTableName;
private String myConnectionUrl;
private String myUsername;
private String myPassword;
private List<FlywayMigration> myTasks = new ArrayList<>(); private List<FlywayMigration> myTasks = new ArrayList<>();
private boolean myDryRun;
private boolean myNoColumnShrink;
public FlywayMigrator(String theMigrationTableName, BasicDataSource theDataSource) { public FlywayMigrator(String theMigrationTableName, BasicDataSource theDataSource) {
this(theMigrationTableName); this(theMigrationTableName);
myConnectionUrl = theDataSource.getUrl(); setConnectionUrl(theDataSource.getUrl());
myUsername = theDataSource.getUsername(); setUsername(theDataSource.getUsername());
myPassword = theDataSource.getPassword(); setPassword(theDataSource.getPassword());
String driverClassName = theDataSource.getDriverClassName(); String driverClassName = theDataSource.getDriverClassName();
if (driverClassName == null) { if (driverClassName == null) {
ourLog.error(this.getClass().getSimpleName() + " constructed without a database driver"); ourLog.error(this.getClass().getSimpleName() + " constructed without a database driver");
} else { } else {
myDriverType = DriverTypeEnum.fromDriverClassName(driverClassName); DriverTypeEnum driverType = DriverTypeEnum.fromDriverClassName(driverClassName);
if (myDriverType == null) { if (driverType == null) {
ourLog.error("Unknown driver class " + driverClassName); ourLog.error("Unknown driver class " + driverClassName);
} }
setDriverType(driverType);
} }
} }
@ -66,32 +62,13 @@ public class FlywayMigrator {
myMigrationTableName = theMigrationTableName; myMigrationTableName = theMigrationTableName;
} }
public void setDriverType(DriverTypeEnum theDriverType) {
myDriverType = theDriverType;
}
public void setConnectionUrl(String theConnectionUrl) {
myConnectionUrl = theConnectionUrl;
}
public void setUsername(String theUsername) {
myUsername = theUsername;
}
public void setPassword(String thePassword) {
myPassword = thePassword;
}
public void addTask(BaseTask<?> theTask) { public void addTask(BaseTask<?> theTask) {
myTasks.add(new FlywayMigration(theTask, this)); myTasks.add(new FlywayMigration(theTask, this));
} }
public void setDryRun(boolean theDryRun) { @Override
myDryRun = theDryRun;
}
public void migrate() { public void migrate() {
try (DriverTypeEnum.ConnectionProperties connectionProperties = myDriverType.newConnectionProperties(myConnectionUrl, myUsername, myPassword)) { try (DriverTypeEnum.ConnectionProperties connectionProperties = getDriverType().newConnectionProperties(getConnectionUrl(), getUsername(), getPassword())) {
Flyway flyway = initFlyway(connectionProperties); Flyway flyway = initFlyway(connectionProperties);
flyway.migrate(); flyway.migrate();
} catch (Exception e) { } catch (Exception e) {
@ -103,7 +80,7 @@ public class FlywayMigrator {
// TODO KHS Is there a way we can use datasource instead of url, username, password here // TODO KHS Is there a way we can use datasource instead of url, username, password here
Flyway flyway = Flyway.configure() Flyway flyway = Flyway.configure()
.table(myMigrationTableName) .table(myMigrationTableName)
.dataSource(myConnectionUrl, myUsername, myPassword) .dataSource(getConnectionUrl(), getUsername(), getPassword())
.baselineOnMigrate(true) .baselineOnMigrate(true)
.javaMigrations(myTasks.toArray(new JavaMigration[0])) .javaMigrations(myTasks.toArray(new JavaMigration[0]))
.load(); .load();
@ -113,45 +90,19 @@ public class FlywayMigrator {
return flyway; return flyway;
} }
@Override
public void addTasks(List<BaseTask<?>> theTasks) { public void addTasks(List<BaseTask<?>> theTasks) {
theTasks.forEach(this::addTask); theTasks.forEach(this::addTask);
} }
public void setNoColumnShrink(boolean theNoColumnShrink) { @Override
myNoColumnShrink = theNoColumnShrink; public Optional<MigrationInfoService> getMigrationInfo() {
} if (getDriverType() == null) {
return Optional.empty();
public DriverTypeEnum getDriverType() {
return myDriverType;
}
public String getConnectionUrl() {
return myConnectionUrl;
}
public String getUsername() {
return myUsername;
}
public String getPassword() {
return myPassword;
}
public boolean isDryRun() {
return myDryRun;
}
public boolean isNoColumnShrink() {
return myNoColumnShrink;
}
public MigrationInfoService getMigrationInfo() {
if (myDriverType == null) {
return null;
} }
try (DriverTypeEnum.ConnectionProperties connectionProperties = myDriverType.newConnectionProperties(myConnectionUrl, myUsername, myPassword)) { try (DriverTypeEnum.ConnectionProperties connectionProperties = getDriverType().newConnectionProperties(getConnectionUrl(), getUsername(), getPassword())) {
Flyway flyway = initFlyway(connectionProperties); Flyway flyway = initFlyway(connectionProperties);
return flyway.info(); return Optional.of(flyway.info());
} }
} }

56
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/SchemaMigrator.java
View File

@ -32,25 +32,36 @@ import org.slf4j.LoggerFactory;
import java.sql.Connection; import java.sql.Connection;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.Properties; import java.util.Properties;
public class SchemaMigrator { public class SchemaMigrator {
private static final Logger ourLog = LoggerFactory.getLogger(SchemaMigrator.class);
public static final String HAPI_FHIR_MIGRATION_TABLENAME = "FLY_HFJ_MIGRATION"; public static final String HAPI_FHIR_MIGRATION_TABLENAME = "FLY_HFJ_MIGRATION";
private static final Logger ourLog = LoggerFactory.getLogger(SchemaMigrator.class);
private final BasicDataSource myDataSource; private final BasicDataSource myDataSource;
private final FlywayMigrator myMigrator;
private final boolean mySkipValidation; private final boolean mySkipValidation;
private final String myMigrationTableName;
private final List<BaseTask<?>> myMigrationTasks;
private boolean myDontUseFlyway;
private DriverTypeEnum myDriverType;
/**
* Constructor
*/
public SchemaMigrator(String theMigrationTableName, BasicDataSource theDataSource, Properties jpaProperties, List<BaseTask<?>> theMigrationTasks) { public SchemaMigrator(String theMigrationTableName, BasicDataSource theDataSource, Properties jpaProperties, List<BaseTask<?>> theMigrationTasks) {
myDataSource = theDataSource; myDataSource = theDataSource;
myMigrationTableName = theMigrationTableName;
myMigrationTasks = theMigrationTasks;
if (jpaProperties.containsKey(AvailableSettings.HBM2DDL_AUTO) && "update".equals(jpaProperties.getProperty(AvailableSettings.HBM2DDL_AUTO))) { if (jpaProperties.containsKey(AvailableSettings.HBM2DDL_AUTO) && "update".equals(jpaProperties.getProperty(AvailableSettings.HBM2DDL_AUTO))) {
mySkipValidation = true; mySkipValidation = true;
} else { } else {
mySkipValidation = false; mySkipValidation = false;
} }
myMigrator = new FlywayMigrator(theMigrationTableName, theDataSource); }
myMigrator.addTasks(theMigrationTasks);
public void setDontUseFlyway(boolean theDontUseFlyway) {
myDontUseFlyway = theDontUseFlyway;
} }
public void validate() { public void validate() {
@ -59,13 +70,15 @@ public class SchemaMigrator {
return; return;
} }
try (Connection connection = myDataSource.getConnection()) { try (Connection connection = myDataSource.getConnection()) {
MigrationInfoService migrationInfo = myMigrator.getMigrationInfo(); Optional<MigrationInfoService> migrationInfo = newMigrator().getMigrationInfo();
if (migrationInfo.pending().length > 0) { if (migrationInfo.isPresent()) {
throw new ConfigurationException("The database schema for " + myDataSource.getUrl() + " is out of date. " + if (migrationInfo.get().pending().length > 0) {
"Current database schema version is " + getCurrentVersion(migrationInfo) + ". Schema version required by application is " + throw new ConfigurationException("The database schema for " + myDataSource.getUrl() + " is out of date. " +
getLastVersion(migrationInfo) + ". Please run the database migrator."); "Current database schema version is " + getCurrentVersion(migrationInfo.get()) + ". Schema version required by application is " +
getLastVersion(migrationInfo.get()) + ". Please run the database migrator.");
}
ourLog.info("Database schema confirmed at expected version " + getCurrentVersion(migrationInfo.get()));
} }
ourLog.info("Database schema confirmed at expected version " + getCurrentVersion(migrationInfo));
} catch (SQLException e) { } catch (SQLException e) {
throw new ConfigurationException("Unable to connect to " + myDataSource.toString(), e); throw new ConfigurationException("Unable to connect to " + myDataSource.toString(), e);
} }
@ -76,7 +89,22 @@ public class SchemaMigrator {
ourLog.warn("Database running in hibernate auto-update mode. Skipping schema migration."); ourLog.warn("Database running in hibernate auto-update mode. Skipping schema migration.");
return; return;
} }
myMigrator.migrate(); newMigrator().migrate();
}
private BaseMigrator newMigrator() {
BaseMigrator migrator;
if (myDontUseFlyway) {
migrator = new BruteForceMigrator();
migrator.setDriverType(myDriverType);
migrator.setConnectionUrl(myDataSource.getUrl());
migrator.setUsername(myDataSource.getUsername());
migrator.setPassword(myDataSource.getPassword());
} else {
migrator = new FlywayMigrator(myMigrationTableName, myDataSource);
}
migrator.addTasks(myMigrationTasks);
return migrator;
} }
private String getCurrentVersion(MigrationInfoService theMigrationInfo) { private String getCurrentVersion(MigrationInfoService theMigrationInfo) {
@ -94,4 +122,8 @@ public class SchemaMigrator {
} }
return "unknown"; return "unknown";
} }
public void setDriverType(DriverTypeEnum theDriverType) {
myDriverType = theDriverType;
}
} }

27
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -357,23 +357,24 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
version.onTable("HFJ_SEARCH_PARM").dropThisTable("20190814.8"); version.onTable("HFJ_SEARCH_PARM").dropThisTable("20190814.8");
version.onTable("HFJ_SPIDX_COORDS").modifyColumn("20190814.9", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); // Make some columns non-nullable that were previously nullable - These are marked as failure allowed, since
version.onTable("HFJ_SPIDX_DATE").modifyColumn("20190814.10", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); // SQL Server won't let us change nullability on columns with indexes pointing to them
version.onTable("HFJ_SPIDX_STRING").modifyColumn("20190814.11", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_COORDS").modifyColumn("20190814.9", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_DATE").modifyColumn("20190814.10", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_STRING").modifyColumn("20190814.11", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_STRING").addColumn("20190814.12", "HASH_IDENTITY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG); version.onTable("HFJ_SPIDX_STRING").addColumn("20190814.12", "HASH_IDENTITY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_STRING").addIndex("20190814.13", "IDX_SP_STRING_HASH_IDENT").unique(false).withColumns("HASH_IDENTITY"); version.onTable("HFJ_SPIDX_STRING").addIndex("20190814.13", "IDX_SP_STRING_HASH_IDENT").unique(false).withColumns("HASH_IDENTITY");
version.onTable("HFJ_SPIDX_COORDS").modifyColumn("20190814.14", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_COORDS").modifyColumn("20190814.14", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_QUANTITY").modifyColumn("20190814.15", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_QUANTITY").modifyColumn("20190814.15", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("20190814.16", "HASH_UNITS_AND_VALPREFIX"); version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("20190814.16", "HASH_UNITS_AND_VALPREFIX");
version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("20190814.17", "HASH_VALPREFIX"); version.onTable("HFJ_SPIDX_QUANTITY").dropColumn("20190814.17", "HASH_VALPREFIX");
version.onTable("HFJ_SPIDX_NUMBER").modifyColumn("20190814.18", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_NUMBER").modifyColumn("20190814.18", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_TOKEN").modifyColumn("20190814.19", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_TOKEN").modifyColumn("20190814.19", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_URI").modifyColumn("20190814.20", "RES_TYPE").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100); version.onTable("HFJ_SPIDX_URI").modifyColumn("20190814.20", "RES_TYPE").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 100);
version.onTable("HFJ_SPIDX_URI").modifyColumn("20190814.21", "SP_URI").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 254); version.onTable("HFJ_SPIDX_URI").modifyColumn("20190814.21", "SP_URI").nullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 254);
version.onTable("TRM_CODESYSTEM").modifyColumn("20190814.22", "CODE_SYSTEM_URI").nonNullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CODESYSTEM").modifyColumn("20190814.22", "CODE_SYSTEM_URI").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200); version.onTable("TRM_CODESYSTEM").modifyColumn("20190814.23", "CS_NAME").nullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CODESYSTEM").modifyColumn("20190814.23", "CS_NAME").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200); version.onTable("TRM_CODESYSTEM_VER").modifyColumn("20190814.24", "CS_VERSION_ID").nullable().failureAllowed().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
version.onTable("TRM_CODESYSTEM_VER").modifyColumn("20190814.24", "CS_VERSION_ID").nullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 200);
} }

43
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/SchemaMigratorTest.java
View File

@ -3,24 +3,32 @@ package ca.uhn.fhir.jpa.migrate;
import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.migrate.taskdef.AddTableRawSqlTask; import ca.uhn.fhir.jpa.migrate.taskdef.AddTableRawSqlTask;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTest; import ca.uhn.fhir.jpa.migrate.taskdef.BaseTest;
import com.google.common.collect.ImmutableList;
import org.hamcrest.Matchers;
import org.junit.Assert;
import org.junit.Test; import org.junit.Test;
import org.mockito.ArgumentMatchers;
import java.sql.SQLException;
import java.util.Collections; import java.util.Collections;
import java.util.Properties; import java.util.Properties;
import java.util.Set;
import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail; import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.contains;
public class SchemaMigratorTest extends BaseTest { public class SchemaMigratorTest extends BaseTest {
@Test @Test
public void migrationRequired() { public void testMigrationRequired() {
AddTableRawSqlTask task = new AddTableRawSqlTask("1", "1"); AddTableRawSqlTask task = new AddTableRawSqlTask("1", "1");
task.setTableName("SOMETABLE"); task.setTableName("SOMETABLE");
task.addSql(DriverTypeEnum.H2_EMBEDDED, "create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))"); task.addSql(DriverTypeEnum.H2_EMBEDDED, "create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
getMigrator().addTask(task);
SchemaMigrator schemaMigrator = new SchemaMigrator(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME, getDataSource(), new Properties(), Collections.singletonList(task)); SchemaMigrator schemaMigrator = new SchemaMigrator(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME, getDataSource(), new Properties(), ImmutableList.of(task));
schemaMigrator.setDriverType(DriverTypeEnum.H2_EMBEDDED);
try { try {
schemaMigrator.validate(); schemaMigrator.validate();
@ -28,7 +36,34 @@ public class SchemaMigratorTest extends BaseTest {
} catch (ConfigurationException e) { } catch (ConfigurationException e) {
assertEquals("The database schema for " + getUrl() + " is out of date. Current database schema version is unknown. Schema version required by application is " + task.getFlywayVersion() + ". Please run the database migrator.", e.getMessage()); assertEquals("The database schema for " + getUrl() + " is out of date. Current database schema version is unknown. Schema version required by application is " + task.getFlywayVersion() + ". Please run the database migrator.", e.getMessage());
} }
getMigrator().migrate();
schemaMigrator.migrate();
schemaMigrator.validate(); schemaMigrator.validate();
} }
@Test
public void testMigrationRequiredNoFlyway() throws SQLException {
AddTableRawSqlTask task = new AddTableRawSqlTask("1", "1");
task.setTableName("SOMETABLE");
task.addSql(DriverTypeEnum.H2_EMBEDDED, "create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
SchemaMigrator schemaMigrator = new SchemaMigrator(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME, getDataSource(), new Properties(), ImmutableList.of(task));
schemaMigrator.setDriverType(DriverTypeEnum.H2_EMBEDDED);
schemaMigrator.setDontUseFlyway(true);
// Validate shouldn't fail if we aren't using Flyway
schemaMigrator.validate();
schemaMigrator.migrate();
schemaMigrator.validate();
DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(getDataSource().getUrl(), getDataSource().getUsername(), getDataSource().getPassword());
Set<String> tableNames = JdbcUtils.getTableNames(connectionProperties);
assertThat(tableNames, Matchers.contains("SOMETABLE"));
}
} }

4
hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/DropTableTest.java
View File

@ -67,9 +67,9 @@ public class DropTableTest extends BaseTest {
assertThat(JdbcUtils.getTableNames(getConnectionProperties()), (hasItems("SOMETABLE"))); assertThat(JdbcUtils.getTableNames(getConnectionProperties()), (hasItems("SOMETABLE")));
assertThat(getMigrator().getMigrationInfo().pending().length, greaterThan(0)); assertThat(getMigrator().getMigrationInfo().get().pending().length, greaterThan(0));
getMigrator().migrate(); getMigrator().migrate();
assertThat(getMigrator().getMigrationInfo().pending().length, equalTo(0)); assertThat(getMigrator().getMigrationInfo().get().pending().length, equalTo(0));
assertThat(JdbcUtils.getTableNames(getConnectionProperties()), not(hasItems("SOMETABLE"))); assertThat(JdbcUtils.getTableNames(getConnectionProperties()), not(hasItems("SOMETABLE")));
} }