6_4 mergeback (#4547)

* One more fix for #4467 * Enabling massIngestionMode causes incomplete resource deletion (#4476) * Adding initial test. * Adding fix and subsequent test. * Adding changelog. --------- Co-authored-by: peartree <[email protected]> * Provide the capability to request that the name of the subscription matching channel be unqualified (#4464) * Adding initial test. * Adding initial solution implementation. * Adding change log and code clean up. * addressing comments from 1st code review. --------- Co-authored-by: peartree <[email protected]> * Change visibility of migration method (#4471) * change migration visibility * add empty migration method for 640 --------- Co-authored-by: nathaniel.doef <[email protected]> * Fix subscription validation not to validate partition ID when invoked from an update pointcut (#4484) * First commit: Make SubscriptionValidatingInterceptor aware of which Pointcut is being called. In validatePermissions(), skip determinePartition() if the Pointcut is STORAGE_PRESTORAGE_RESOURCE_UPDATED. Fix resulting compile errors in various unit tests. * Fix/enhance unit tests. Mark methods as deprecated instead of deleting them. Add proper error code. Complete changelog. * Remove erroneous TODOs and tweak the validation logic. * Enhance unit tests and fix changelog. * Reindex batch job fails when processing deleted resources. (#4482) * adding changelog. * Providing solution and adding changelog. * Adding new test. --------- Co-authored-by: peartree <[email protected]> * cleaning up checkstyle files (#4470) * cleaning up checkstyle files * One more fix for #4467 (#4469) * added exlusions for files at base project level so checkstyle doesn't error out * duplicate error code from merge * changing lifecycle goal for all module checkstyle check * moving checkstyle to base pom file, changing exectution phase on base check, cleaning dependency, resolving duplicate error code * wip * trying to figure out why pipeline cannot copy files * removing modules that don't actually need to be built. * I messed up the version --------- Co-authored-by: James Agnew <[email protected]> * Bump core to 5.6.881 (#4496) * Bump core to 5.6.881-SNAPSHOT * Work on fixing tests * Work on fixing tests 2 * Bump to core release --------- Co-authored-by: dotasek <[email protected]> * Issue 4486 mdm inconsistent possible match score values (#4487) * Extract method for readability * Save always normalized score values in POSSIBLE_MATCH links. * Avoid setting properties to null values. Adjust test. * Simplify fix * Fix test. Add RangeTestHelper. --------- Co-authored-by: juan.marchionatto <[email protected]> * Revert "cleaning up checkstyle files (#4470)" This reverts commit efae3b5. * core version fix * Loosen rules for id helper * License * fix batch2 reduction step (#4499) * fix bug where FINALIZE jobs are not cancellable * moved reduction step to message hander * moving reduction step to queue * addingchangelog * cleaning up * review fixes * review fix' --------- Co-authored-by: leif stawnyczy <[email protected]> * Scheduled batch 2 bulk export job and binary delete (#4492) * First commit: Scheduled batch 2 bulk export job delete and binary, incomplete mock-based unit test, and a mess of TODOs and code that needs to be deleted. * Refine solution and add a concrete unit test but still work to do. * Comment out code in cancelAndPurgeAllJobs() and see if it breaks the pipeline. * Unit tests complete. New Msg code for new IJobPersistence.fetchInstances() method. Cleanup TODOs and add others. * Finish final touches on implementation. * Add changelog. * Various cleanup. * Code review feedback. * Small tweak to changelog. * Last code review tweak. * Address more code review comments. * Reverse changes to consider work chunks. Add a constant for write-to-binary. * Change bulk import test for valueUri type (#4503) * change tests * suggested test change * CVE resolutions (#4513) * Bump Postgres for CVE * Bump jetty * Verison bump * Remove comments * Revrt bump * Add check in scanner (#4518) * 4516 create hapi fhir cli command to clear stale lock entries (#4517) * Initial implementation * better tests * Add changelog and docs * Forgotten files * Code review comments * Fix checkstyle * Unable to Expunge CodeSystem (#4507) * changes for GL-3943 * changes for GL-3943 --------- Co-authored-by: isaacwen <[email protected]> * New line:: * Update to documentation regarding narrative generation; (#4521) Providing changelog; Co-authored-by: peartree <[email protected]> * changed what score is set for mdmlinks that created new golden resource (#4514) * changed what score is set for mdmlinks that created new golden resource * fix test --------- Co-authored-by: Long Ma <[email protected]> * REVERT: change to operationoutcome.html * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNo… (#4527) * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * added change log --------- Co-authored-by: leif stawnyczy <[email protected]> * fix build (#4530) * Making narrative_generation.md reference an html snippet (#4531) Co-authored-by: peartree <[email protected]> * fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524) * fix + test * minor fix * Addressing suggestion * Minor changes * 4441 rel 6 4 bad references creation bug (#4519) * adding a test * fail in the case of ref enforce on type and on write and autocreate are all true * update to code * removing a line * cleanup * removing check on urn * changing just to trigger a build * adding a comment to the pom * updating test for better information --------- Co-authored-by: leif stawnyczy <[email protected]> * fixed channel import null pointer exception from null header (#4534) * retryCount 0 on null header + test + changelog * suggested changes * Revert "fixed the issue of meta.source field inconsistently populated in subscription messages for different requests (#4524)" (#4535) This reverts commit 53252b8. * Better error handling for when channel type is not supported (#4538) Co-authored-by: kylejule <[email protected]> * Avoid logging message payloads that contain sensitive data (#4537) Don't log payloads - they may contain sensitive data. * Bulk Export Bug With Many Resources and Low Max File Size (#4506) * failing test * fix + changelog * tweak * add method to IJobPersistence to use a Stream * tweak * tweak * decrease test time * clean up * code review comments * version bump * Increase timeout limit to match BulkExportUseCaseTest * shorten test * maintenance pass * add logging * Revert "add logging" This reverts commit b0453fd. * Revert "maintenance pass" This reverts commit bbc7418. * test * trying to fix BulkDataExportTest testGroupBulkExportNotInGroup_DoesNotShowUp * shorten tests * logging * move test location * fixes a regression caused my change in hapi-fhir * timeout * Revert "fixes a regression caused my change in hapi-fhir" This reverts commit 4b58013. * testing * Revert "testing" This reverts commit aafc95c. --------- Co-authored-by: leif stawnyczy <[email protected]> * bump ver * License updates' * Remove checkstyle * Verison bump * Move migrations * semicolon --------- Co-authored-by: James Agnew <[email protected]> Co-authored-by: Etienne Poirier <[email protected]> Co-authored-by: peartree <[email protected]> Co-authored-by: Nathan Doef <[email protected]> Co-authored-by: nathaniel.doef <[email protected]> Co-authored-by: Luke deGruchy <[email protected]> Co-authored-by: Mark Iantorno <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: dotasek <[email protected]> Co-authored-by: jmarchionatto <[email protected]> Co-authored-by: juan.marchionatto <[email protected]> Co-authored-by: Tadgh <[email protected]> Co-authored-by: TipzCM <[email protected]> Co-authored-by: leif stawnyczy <[email protected]> Co-authored-by: samguntersmilecdr <[email protected]> Co-authored-by: Isaac Wen <[email protected]> Co-authored-by: isaacwen <[email protected]> Co-authored-by: longma1 <[email protected]> Co-authored-by: Long Ma <[email protected]> Co-authored-by: Qingyixia <[email protected]> Co-authored-by: KGJ-software <[email protected]> Co-authored-by: kylejule <[email protected]> Co-authored-by: michaelabuckley <[email protected]> Co-authored-by: Ken Stevens <[email protected]>
hapifhir · Feb 13, 2023 · 794e451 · 794e451
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diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,14 +4,14 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir-bom</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-fhir</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.5.0-SNAPSHOT</version>
+ <version>6.5.1-SNAPSHOT</version>
  <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
 

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java
@@ -186,6 +186,7 @@ protected List<BaseCommand> provideCommands() {
  commands.add(new ExportConceptMapToCsvCommand());
  commands.add(new ImportCsvToConceptMapCommand());
  commands.add(new HapiFlywayMigrateDatabaseCommand());
+ commands.add(new HapiClearMigrationLockCommand());
  commands.add(new CreatePackageCommand());
  commands.add(new BulkImportCommand());
  commands.add(new ReindexTerminologyCommand());

diff --git a/...ir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseClearMigrationLockCommand.java b/...ir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseClearMigrationLockCommand.java
@@ -0,0 +1,92 @@
+package ca.uhn.fhir.cli;
+
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - API
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * 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:https://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.i18n.Msg;
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.HapiMigrator;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import java.util.Arrays;
+import java.util.stream.Collectors;
+
+/**
+ *
+ */
+public abstract class BaseClearMigrationLockCommand extends BaseCommand {
+
+ public static final String CLEAR_LOCK = "clear-migration-lock";
+ private String myMigrationTableName;
+
+ @Override
+ public String getCommandDescription() {
+ return "This command clears a database migration lock";
+ }
+
+
+ @Override
+ public String getCommandName() {
+ return CLEAR_LOCK;
+ }
+
+ @Override
+ public Options getOptions() {
+ Options retVal = new Options();
+ addRequiredOption(retVal, "u", "url", "URL", "The JDBC database URL");
+ addRequiredOption(retVal, "n", "username", "Username", "The JDBC database username");
+ addRequiredOption(retVal, "p", "password", "Password", "The JDBC database password");
+ addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")");
+ addRequiredOption(retVal, "l", "lock-uuid", "Lock UUID", "The UUID value of the lock held in the database.");
+ return retVal;
+ }
+
+ private String driverOptions() {
+ return Arrays.stream(DriverTypeEnum.values()).map(Enum::name).collect(Collectors.joining(", "));
+ }
+
+ @Override
+ public void run(CommandLine theCommandLine) throws ParseException {
+
+ String url = theCommandLine.getOptionValue("u");
+ String username = theCommandLine.getOptionValue("n");
+ String password = theCommandLine.getOptionValue("p");
+ String lockUUID = theCommandLine.getOptionValue("l");
+ DriverTypeEnum driverType;
+ String driverTypeString = theCommandLine.getOptionValue("d");
+ try {
+ driverType = DriverTypeEnum.valueOf(driverTypeString);
+ } catch (Exception e) {
+ throw new ParseException(Msg.code(2774) + "Invalid driver type \"" + driverTypeString + "\". Valid values are: " + driverOptions());
+ }
+
+
+ DriverTypeEnum.ConnectionProperties connectionProperties = driverType.newConnectionProperties(url, username, password);
+ HapiMigrator migrator = new HapiMigrator(myMigrationTableName, connectionProperties.getDataSource(), driverType);
+ migrator.clearMigrationLockWithUUID(lockUUID);
+ }
+
+
+ protected void setMigrationTableName(String theMigrationTableName) {
+ myMigrationTableName = theMigrationTableName;
+ }
+}
diff --git a/...ir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiClearMigrationLockCommand.java b/...ir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/HapiClearMigrationLockCommand.java
@@ -0,0 +1,33 @@
+package ca.uhn.fhir.cli;
+
+/*-
+ * #%L
+ * HAPI FHIR - Command Line Client - API
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * 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:https://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.migrate.SchemaMigrator;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.ParseException;
+
+public class HapiClearMigrationLockCommand extends BaseClearMigrationLockCommand {
+ @Override
+ public void run(CommandLine theCommandLine) throws ParseException {
+ setMigrationTableName(SchemaMigrator.HAPI_FHIR_MIGRATION_TABLENAME);
+ super.run(theCommandLine);
+ }
+}
diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BaseAppTest.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BaseAppTest.java
diff --git a/...r-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ConsoleOutputCapturingBaseTest.java b/...r-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ConsoleOutputCapturingBaseTest.java
@@ -0,0 +1,32 @@
+package ca.uhn.fhir.cli;
+
+import org.apache.commons.io.output.TeeOutputStream;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+
+/**
+ * This class splits output stream to both STDOUT, and a capturing byte array output stream, which can later be inspected.
+ */
+public class ConsoleOutputCapturingBaseTest {
+
+ protected final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
+ protected final TeeOutputStream myTeeOutputStream = new TeeOutputStream(System.out, outputStreamCaptor);
+
+ @BeforeEach
+ public void setUp() {
+ System.setOut(new PrintStream(myTeeOutputStream));
+ }
+
+ @AfterEach
+ public void tearDown() {
+ outputStreamCaptor.reset();
+ System.setOut(System.out);
+ }
+ protected String getConsoleOutput() {
+ return outputStreamCaptor.toString().trim();
+ }
+
+}