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Rel 5 6 1 mergeback (#3228) 

* 3138 externalized binary packages (#3139)

* Add test and impl

* Add changelog

* Fix test

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml

* add beans to test configs

* Typo

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java

Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>

* 3131 - Added support for the lookup operation in the Remote Terminology code (#3134)

* Remove leading underscores from identifiers (#3146)

* Version bump

* License files

* version.yaml

* Add executeRawSql() method to Migrator (#3183)

* Add implementation, add test

* Add javadoc

* Add another helper function

* Bump version

* 3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155)

* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add backport info

* Avoid creating ResourcePersistentId for placeholder resources with null ID (#3158)

* Add check before mapping storage ID to resource ID in TransactionDetails.

* Add change log.

* Changed to instead prevent creation of ResourcePersistentId with null ID value.

* Changed to instead prevent ResourcePersistentId being created with null resource ID.

Co-authored-by: ianmarshall <ian@simpatico.ai>

* Fix bug loading packages in non-database mode (#3199)

* Add implementation

* Add changelog

* Add backports

* 3164 updating code review points (#3165)

* 3164 updating code review points

* 3164 updating code review points

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* Add executeRawSqlStub (#3203)

Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>

* Add new version

* begin with failing test

* fix bug

* change log

* change log

* Add backport informationm

* begin with failing test

* fix issue

* change log

* code review

* Add backport info. Add folder

* fixed

* Add test

* Update test

* Add backport info

* Add 5.5.4

* Remove jpaconstants

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>
Co-authored-by: michaelabuckley <michaelabuckley@gmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: IanMMarshall <49525404+IanMMarshall@users.noreply.github.com>
Co-authored-by: ianmarshall <ian@simpatico.ai>
Co-authored-by: Joanne Mendoza <joannemmendoza@gmail.com>
Co-authored-by: Joanne Mendoza <joanne@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: katie_smilecdr <katie@smilecdr.com>
This commit is contained in:
Tadgh 2021-12-09 13:14:48 -08:00 committed by GitHub
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commit 9593b6b0b8
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10 changed files with 114 additions and 2 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
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@ -78,7 +78,9 @@ public enum VersionEnum {
V5_5_1,
V5_5_2,
V5_5_3,
V5_5_4,
V5_6_0,
V5_6_1,
V5_7_0
;

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_1/version.yaml Normal file
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@ -0,0 +1,3 @@
---
release-date: "2021-12-03"
codename: "Raccoon"

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3153-updating-unknowncodesystem-to-allow-warnings-to-be-registered-as-warnings.yaml
View File

@ -1,6 +1,7 @@
---
type: fix
issue: 3153
backport: 5.6.1
jira: SMILE-3289
title: "Updated UnknownCodeSystemWarningValidationSupport to allow the throwing of warnings if
configured to do so."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3158-creation-of-versioned-placeholders.yaml
View File

@ -1,5 +1,6 @@
---
type: fix
issue: 3158
backport: 5.6.1
title: "Resource links were previously not being consistently created in cases where references were versioned and
pointing to recently auto-created placeholder resources."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3198-package-loading-woes.yaml
View File

@ -2,4 +2,5 @@
type: change
issue: 3198
jira: SMILE-3452
backport: 5.6.1
title: "Fixed a regression where packages would fail to load if HAPI-FHIR was operating in DATABASE binary storage mode."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3211-reindex-performance.yaml
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@ -1,4 +1,5 @@
---
type: fix
backport: 5.6.1
jira: SMILE-3472
title: "Fixed a serious performance issue with the `$reindex` operation."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3215-nextURL-does-not-work-for-a-certain-offset-with-everything.yaml
View File

@ -1,4 +1,5 @@
---
type: fix
issue: 3215
backport: 5.6.1
title: "$everything operation returns a 500 error when querying for a page when _getpagesoffset is greater than or equal to 300. This has been corrected."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3216-mdm-possible-match-to-match.yaml
View File

@ -1,3 +1,4 @@
---
type: fix
backport: 5.6.1
title: "MDM was throwing a NullPointerException when upgrading a match from POSSIBLE_MATCH to MATCH. This has been corrected."

52
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/Builder.java
View File

@ -46,7 +46,10 @@ import org.apache.commons.lang3.Validate;
import org.intellij.lang.annotations.Language;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
@ -73,11 +76,21 @@ public class Builder {
}
public BuilderCompleteTask executeRawSql(String theVersion, @Language("SQL") String theSql) {
ExecuteRawSqlTask task = new ExecuteRawSqlTask(myRelease, theVersion).addSql(theSql);
mySink.addTask(task);
ExecuteRawSqlTask task = executeRawSqlOptional(false, theVersion, theSql);
return new BuilderCompleteTask(task);
}
public void executeRawSqlStub(String theVersion, @Language("SQL") String theSql) {
executeRawSqlOptional(true, theVersion, theSql);
}
private ExecuteRawSqlTask executeRawSqlOptional(boolean theDoNothing, String theVersion, @Language("SQL") String theSql) {
ExecuteRawSqlTask task = new ExecuteRawSqlTask(myRelease, theVersion).addSql(theSql);
task.setDoNothing(theDoNothing);
mySink.addTask(task);
return task;
}
public Builder initializeSchema(String theVersion, ISchemaInitializationProvider theSchemaInitializationProvider) {
mySink.addTask(new InitializeSchemaTask(myRelease, theVersion, theSchemaInitializationProvider));
return this;
@ -96,6 +109,41 @@ public class Builder {
return this;
}
/**
* Builder method to define a raw SQL execution migration that needs to take place against multiple database types,
* and the SQL they need to use is not equal. Provide a map of driver types to SQL statements.
*
* @param theVersion The version of the migration.
* @param theDriverToSql Map of driver types to SQL statements.
* @return
*/
public Builder executeRawSql(String theVersion, Map<DriverTypeEnum, String> theDriverToSql) {
Map<DriverTypeEnum, List<String>> singleSqlStatementMap = new HashMap<>();
theDriverToSql.entrySet().stream()
.forEach(entry -> {
singleSqlStatementMap.put(entry.getKey(), Collections.singletonList(entry.getValue()));
});
return executeRawSqls(theVersion, singleSqlStatementMap);
}
/**
* Builder method to define a raw SQL execution migration that needs to take place against multiple database types,
* and the SQL they need to use is not equal, and there are multiple sql commands for a given database.
* Provide a map of driver types to list of SQL statements.
*
* @param theVersion The version of the migration.
* @param theDriverToSqls Map of driver types to list of SQL statements.
* @return
*/
public Builder executeRawSqls(String theVersion, Map<DriverTypeEnum, List<String>> theDriverToSqls) {
ExecuteRawSqlTask executeRawSqlTask = new ExecuteRawSqlTask(myRelease, theVersion);
theDriverToSqls.entrySet().stream()
.forEach(entry -> {
entry.getValue().forEach(sql -> executeRawSqlTask.addSql(entry.getKey(), sql));
});
mySink.addTask(executeRawSqlTask);
return this;
}
// Flyway doesn't support these kinds of migrations
@Deprecated

53
hapi-fhir-sql-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ExecuteRawSqlTaskTest.java
View File

@ -6,6 +6,7 @@ import ca.uhn.fhir.util.VersionEnum;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.MethodSource;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Supplier;
@ -81,5 +82,57 @@ public class ExecuteRawSqlTaskTest extends BaseTest {
}
}
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void testDriverTypeBasedRawSqlExecution(Supplier<TestDatabaseDetails> theTestDatabaseDetails) {
//Given
before(theTestDatabaseDetails);
executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
BaseMigrationTasks<VersionEnum> tasks = new BaseMigrationTasks<>();
Map<DriverTypeEnum, String> driverToSql = new HashMap<>();
//When
driverToSql.put(DriverTypeEnum.H2_EMBEDDED, "INSERT INTO SOMETABLE (PID, TEXTCOL) VALUES (123, 'abc')");
driverToSql.put(DriverTypeEnum.DERBY_EMBEDDED, "INSERT INTO SOMETABLE (PID, TEXTCOL) VALUES (456, 'def')");
tasks
.forVersion(VersionEnum.V4_0_0)
.executeRawSql("2001.01", driverToSql);
getMigrator().addTasks(tasks.getTasks(VersionEnum.V0_1, VersionEnum.V4_0_0));
getMigrator().migrate();
List<Map<String, Object>> output = executeQuery("SELECT PID,TEXTCOL FROM SOMETABLE");
//Then
if (theTestDatabaseDetails.get().getDriverType() == DriverTypeEnum.H2_EMBEDDED) {
assertEquals(1, output.size());
assertEquals(123L, output.get(0).get("PID"));
assertEquals("abc", output.get(0).get("TEXTCOL"));
} else if (theTestDatabaseDetails.get().getDriverType() == DriverTypeEnum.DERBY_EMBEDDED) {
assertEquals(1, output.size());
assertEquals(456L, output.get(0).get("PID"));
assertEquals("def", output.get(0).get("TEXTCOL"));
} else {
assertEquals(0, output.size());
}
}
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void testExecuteRawSqlStub(Supplier<TestDatabaseDetails> theTestDatabaseDetails) {
//Given
before(theTestDatabaseDetails);
executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255))");
BaseMigrationTasks<VersionEnum> tasks = new BaseMigrationTasks<>();
tasks.forVersion(VersionEnum.V4_0_0)
.executeRawSqlStub("2001.01", "INSERT INTO SOMETABLE (PID, TEXTCOL) VALUES (123, 'abc')");
getMigrator().addTasks(tasks.getTasks(VersionEnum.V0_1, VersionEnum.V4_0_0));
getMigrator().migrate();
List<Map<String, Object>> output = executeQuery("SELECT PID,TEXTCOL FROM SOMETABLE");
assertEquals(0, output.size());
}
}