Merge 5b50545a50 into 3f6d1eb29b

#5768 Upgrade to latest simple-java-mail (#6261 )
attribution and pom change (#6309 )
2024-09-26 02:08:11 +00:00 · 2024-09-26 02:07:27 +00:00 · 2024-09-25 20:38:22 +00:00 · 2024-09-24 09:44:00 -04:00 · 2024-09-13 11:15:39 -04:00
14 changed files with 740 additions and 58 deletions
--- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6290-mssql-migration-trim-fix.yaml
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6290-mssql-migration-trim-fix.yaml
@ -0,0 +1,5 @@
+---
+type: fix
+issue: 6290
+title: "Previously, a specific migration task was using the `TRIM()` function, which does not exist in MSSQL 2012. This was causing migrations targeting MSSQL 2012 to fail. 
+This has been corrected and replaced with usage of a combination of LTRIM() and RTRIM(). Thanks to Primož Delopst at Better for the contribution!"
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
@ -436,7 +436,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc, IHas
 		return retVal;
 	}

-	private boolean isJobsExecuting() {
+	public boolean isJobsExecuting() {
 		cleanseEndedJobs();

 		return !myJobExecutions.isEmpty();
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
@ -78,6 +78,8 @@ public interface ITermDeferredStorageSvc {

 	void logQueueForUnitTest();

+	boolean isJobsExecuting();
+
 	/**
 	 * Only to be used from tests - Disallow test timeouts on deferred tasks
 	 */
--- a/hapi-fhir-jpaserver-subscription/pom.xml
+++ b/hapi-fhir-jpaserver-subscription/pom.xml
@ -70,6 +70,11 @@
 			<artifactId>jakarta.servlet-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
+		<dependency>
+			<groupId>jakarta.mail</groupId>
+			<artifactId>jakarta.mail-api</artifactId>
+			<optional>true</optional>
+		</dependency>

 		<!-- test dependencies -->
 		<dependency>
--- a/hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java
+++ b/hapi-fhir-jpaserver-test-dstu2/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java
@ -28,8 +28,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;

-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
--- a/hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java
+++ b/hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java
@ -17,8 +17,8 @@ import org.junit.jupiter.api.extension.RegisterExtension;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.Arrays;

 import static org.assertj.core.api.Assertions.assertThat;
--- a/hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java
+++ b/hapi-fhir-jpaserver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java
@ -26,8 +26,8 @@ import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.RegisterExtension;
 import org.springframework.beans.factory.annotation.Autowired;

-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
--- a/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java
+++ b/hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java
@ -1,5 +1,9 @@
 package ca.uhn.fhir.jpa.term;

+import ca.uhn.fhir.batch2.api.IJobCoordinator;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
+import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.support.ConceptValidationOptions;
@ -9,6 +13,7 @@ import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
+import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
 import ca.uhn.fhir.jpa.entity.TermCodeSystem;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
@ -25,9 +30,13 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
 import ca.uhn.fhir.jpa.util.SqlQuery;
 import ca.uhn.fhir.jpa.util.ValueSetTestUtil;
+import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.BundleBuilder;
 import com.google.common.collect.Lists;
 import jakarta.annotation.Nonnull;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@ -45,16 +54,22 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Pageable;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;

 import java.io.IOException;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Optional;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;

+import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
+import static ca.uhn.fhir.batch2.jobs.termcodesystem.TermCodeSystemJobConfig.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
 import static ca.uhn.fhir.util.HapiExtensions.EXT_VALUESET_EXPANSION_MESSAGE;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.awaitility.Awaitility.await;
@ -2081,7 +2096,662 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test implements IValueSet
 		outcome = myValueSetDao.validateCode(vs.getUrlElement(), null, new StringType("A"), cs.getUrlElement(), null, null, null, mySrd);
 		assertEquals(false, outcome.isOk());
 		assertThat(outcome.getMessage()).contains("Code validation occurred using a ValueSet expansion that was pre-calculated");
-
 	}

+	@Test
+	public void expandValuesetAfterReindex() {
+		// setup
+		IParser parser = myFhirContext.newJsonParser();
+		CodeSystem cs;
+		ValueSet vs;
+		String csStr;
+		{
+			String vsStr = """
+					{
+					    "resourceType": "ValueSet",
+					    "id": "0447bffa-01fa-4405-828a-96192e74a5d8",
+					    "meta": {
+					        "versionId": "2",
+					        "lastUpdated": "2024-04-09T15:06:24.025+00:00",
+					        "source": "#f4491e490a6a2900"
+					    },
+					    "url": "https://health.gov.on.ca/idms/fhir/ValueSet/IDMS-Submission-Types",
+					    "version": "1.0.0",
+					    "name": "IDMS-SUBMISSION-TYPES",
+					    "title": "IDMS Submission Types",
+					    "status": "active",
+					    "experimental": false,
+					    "date": "2023-09-28",
+					    "publisher": "IDMS",
+					    "description": "List of Submission Types",
+					    "compose": {
+					        "include": [
+					            {
+					                "system": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types"
+					            }
+					        ]
+					    }
+					}
+				""";
+			vs = parser.parseResource(ValueSet.class, vsStr);
+			csStr = """
+				{
+					        "resourceType": "CodeSystem",
+					        "id": "d9acd5b8-9533-4fa1-bb70-b4380957a8c3",
+					        "meta": {
+					            "versionId": "14",
+					            "lastUpdated": "2024-06-03T17:49:56.580+00:00",
+					            "source": "#261a82258b0978a8"
+					        },
+					        "url": "https://health.gov.on.ca/idms/fhir/CodeSystem/Internal-Submission-Types",
+					        "version": "1.0.0",
+					        "name": "IDMS-Internal-Submission-Types",
+					        "status": "active",
+					        "date": "2023-09-07",
+					        "publisher": "IDMS",
+					        "description": "This contains a lists of codes Submission Type Codes.",
+					        "content": "complete",
+					        "concept": [
+					            {
+					                "code": "SUB-BRAND-PRODUCT",
+					                "display": "New Brand Product (Non-New Chemical Entity)"
+					            },
+					            {
+					                "code": "SUB-CLASSIFICATION",
+					                "display": "Classification Change"
+					            },
+					            {
+					                "code": "SUB-CLINICIAN-LED-SUBMISSIONS",
+					                "display": "Clinician-Led Submissions"
+					            },
+					            {
+					                "code": "SUB-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-DIN-CHANGE",
+					                "display": "Drug Identification Number (DIN) Change"
+					            },
+					            {
+					                "code": "SUB-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-DRUG-PRODUCT-NAME",
+					                "display": "Drug Product Name Change"
+					            },
+					            {
+					                "code": "SUB-FORMULATION",
+					                "display": "Formulation Change"
+					            },
+					            {
+					                "code": "SUB-GENERIC-LINE",
+					                "display": "Generic Line Extension"
+					            },
+					            {
+					                "code": "SUB-GENERIC-PRODUCT",
+					                "display": "New Generic Product"
+					            },
+					            {
+					                "code": "SUB-LINE-EXTENSION",
+					                "display": "Line Extension"
+					            },
+					            {
+					                "code": "SUB-NEW-INDICATION",
+					                "display": "New Indication"
+					            },
+					            {
+					                "code": "SUB-NEW-NATURAL",
+					                "display": "New Natural Health Product"
+					            },
+					            {
+					                "code": "SUB-NEW-OVER-COUNTER",
+					                "display": "New Over the Counter (OTC) Product"
+					            },
+					            {
+					                "code": "SUB-NEW-CHEMICAL",
+					                "display": "New Chemical Entity"
+					            },
+					            {
+					                "code": "SUB-NEW-NUTRITIONAL",
+					                "display": "New Nutrition Product"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-LINE",
+					                "display": "Line Extension"
+					            },
+					            {
+					                "code": "SUB-NEW-BIOSIMILAR",
+					                "display": "New Biosimilar"
+					            },
+					            {
+					                "code": "SUB-BIOSIMILAR-LINE",
+					                "display": "Line Extension"
+					            },
+					            {
+					                "code": "SUB-NEW-DIABETIC",
+					                "display": "New Diabetic Testing Agent (DTA)"
+					            },
+					            {
+					                "code": "SUB-NEW-GLUCOUSE",
+					                "display": "New Flash Glucose Monitoring (FGM) Product"
+					            },
+					            {
+					                "code": "SUB-NON-FORMULARY-SINGLE",
+					                "display": "Non-Formulary Single Source"
+					            },
+					            {
+					                "code": "SUB-NON-FORMULARY-MULTIPLE",
+					                "display": "Non-Formulary Multiple Source "
+					            },
+					            {
+					                "code": "SUB-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-PRODUCT-MONOGRAPH",
+					                "display": "Product Monograph Change"
+					            },
+					            {
+					                "code": "SUB-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-SPECIAL-PROJECTS",
+					                "display": "Special Projects"
+					            },
+					            {
+					                "code": "SUB-TEMPORARY-BENEFITS",
+					                "display": "Temporary Benefits"
+					            },
+					            {
+					                "code": "SUB-VALVED",
+					                "display": "New Valved Holding Chamber (VHC)"
+					            },
+					            {
+					                "code": "SUB-REDESIGNATION-BENEFITS",
+					                "display": "Re-Designation of Benefits"
+					            },
+					            {
+					                "code": "SUB-MANUFACTURER-INQUIRIES",
+					                "display": "Manufacturer Inquiries"
+					            },
+					            {
+					                "code": "SUB-CHALLENGES",
+					                "display": "Challenges"
+					            },
+					            {
+					                "code": "SUB-NEW-LINE",
+					                "display": "Line Extension"
+					            },
+					            {
+					                "code": "SUB-MULTI-DIN-CHANGE",
+					                "display": "Drug Identification Number (DIN) Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-DRUG-PRODUCT-NAME",
+					                "display": "Drug Product Name Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-PRODUCT-MONOGRAPH",
+					                "display": "Product Monograph Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-FORMULATION",
+					                "display": "Formulation Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-MULTI-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-MULTI-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-MULTI-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-BIO-DIN-CHANGE",
+					                "display": "Drug Identification Number (DIN) Change"
+					            },
+					            {
+					                "code": "SUB-BIO-DRUG-PRODUCT-NAME",
+					                "display": "Drug Product Name Change"
+					            },
+					            {
+					                "code": "SUB-BIO-PRODUCT-MONOGRAPH",
+					                "display": "Product Monograph Change"
+					            },
+					            {
+					                "code": "SUB-BIO-FORMULATION",
+					                "display": "Formulation Change"
+					            },
+					            {
+					                "code": "SUB-BIO-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-BIO-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-BIO-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-BIO-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-BIO-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-BIO-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-BIO-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-OTC-DIN-CHANGE",
+					                "display": "Drug Identification Number (DIN) Change"
+					            },
+					            {
+					                "code": "SUB-OTC-DRUG-PRODUCT-NAME",
+					                "display": "Drug Product Name Change"
+					            },
+					            {
+					                "code": "SUB-OTC-PRODUCT-MONOGRAPH",
+					                "display": "Product Monograph Change"
+					            },
+					            {
+					                "code": "SUB-OTC-FORMULATION",
+					                "display": "Formulation Change"
+					            },
+					            {
+					                "code": "SUB-OTC-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-OTC-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-OTC-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-OTC-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-OTC-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-OTC-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-OTC-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-DIABETIC-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-GLUCOSE-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-VALVED-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-VALVED-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-VALVED-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-VALVED-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-NATURAL-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-NATURAL-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-NATURAL-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-NATURAL-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-OTHER-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-PRODUCT-CHANGE",
+					                "display": "Product Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-OTHER-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-OTHER-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-OTHER-OTHER-TYPE-IN",
+					                "display": "Other"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-PRODUCT-NAME",
+					                "display": "Product Name Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-FORMULATION",
+					                "display": "Formulation Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-DRUG-REGULATION",
+					                "display": "Change in Food and Drug Regulation Classification"
+					            },
+					            {
+					                "code": "SUB-ADVERTISING-POLICY",
+					                "display": "Change in Advertising Policy"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-OWNERSHIP",
+					                "display": "Ownership Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-DISTRIBUTOR",
+					                "display": "Distributor Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-ORG-NAME",
+					                "display": "Organization Name Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-PRODUCT-DISCONTINUE",
+					                "display": "Product Discontinuation"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-DELISTING",
+					                "display": "Delisting"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-PRICE-CHANGE",
+					                "display": "Price Change"
+					            },
+					            {
+					                "code": "SUB-NUTRITIONAL-OTHER-TYPE-IN",
+					                "display": "Other"
+					            }
+					        ]
+					    }
+				""";
+			cs = parser.parseResource(CodeSystem.class, csStr);
+		}
+
+		RequestDetails rq = new SystemRequestDetails();
+		int csToCreate = 1;
+
+		// create a bunch of code systems
+		myValueSetDao.update(vs, rq);
+		String csUrl = cs.getUrl();
+		BundleBuilder builder = new BundleBuilder(myFhirContext);
+//		while (cs.getConcept().size() > 90) {
+//			cs.getConcept().remove(1);
+//		}
+		for (int i = 0; i < csToCreate; i++) {
+			if (i > 0) {
+				cs = parser.parseResource(CodeSystem.class, csStr);
+				cs.setId("cs" + i);
+				cs.setUrl(csUrl + "-" + i);
+			}
+			builder.addTransactionUpdateEntry(cs);
+//			myCodeSystemDao.update(cs, rq);
+		}
+		builder.setType("transaction");
+		Bundle bundle = (Bundle) builder.getBundle();
+		mySystemDao.transaction(rq, bundle);
+
+		System.out.println("XXXX " + myDeferredStorageSvc.isStorageQueueEmpty());
+		myDeferredStorageSvc.logQueueForUnitTest();
+
+
+		AtomicInteger counter = new AtomicInteger();
+		await()
+			.atMost(10, TimeUnit.SECONDS)
+			.pollDelay(500, TimeUnit.MILLISECONDS)
+				.until(() -> {
+					boolean isQueueEmpty = myDeferredStorageSvc.isStorageQueueEmpty(false);
+					if (!isQueueEmpty) {
+						myDeferredStorageSvc.saveAllDeferred();
+					}
+					return isQueueEmpty;
+				});
+		if (myDeferredStorageSvc.isJobsExecuting()) {
+			System.out.println("running jobs");
+			myDeferredStorageSvc.saveAllDeferred();
+			myBatch2JobHelper.awaitJobCompletion(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
+			myBatch2JobHelper.awaitJobCompletion(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
+
+		}
+		System.out.println("XXX " + myDeferredStorageSvc.isStorageQueueEmpty() + " " + counter.get());
+		myDeferredStorageSvc.logQueueForUnitTest();
+		myDeferredStorageSvc.toString();
+
+//		myDeferredStorageSvc.saveAllDeferred();
+
+		// perform the reindex
+		ReindexJobParameters params = new ReindexJobParameters();
+		params.addUrl("CodeSystem?");
+		JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
+		startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
+		startRequest.setParameters(params);
+		System.out.println("xxxx starting reindex");
+		Batch2JobStartResponse response = myJobCoordinator.startInstance(rq, startRequest);
+		myBatch2JobHelper.awaitJobCompletion(response);
+		System.out.println("XXXX reindex done " + myDeferredStorageSvc.isStorageQueueEmpty());
+
+		// get the codes
+		SearchParameterMap spMap = new SearchParameterMap();
+		spMap.setLoadSynchronous(true);
+		IBundleProvider bp = myCodeSystemDao.search(spMap, rq);
+
+		// do value expansion
+		ValueSetExpansionOptions options = new ValueSetExpansionOptions();
+		options.setCount(200);
+		ValueSet expanded = myValueSetDao.expand(vs, options);
+		assertNotNull(expanded);
+		HashSet<String> all = new HashSet<>();
+		for (CodeSystem.ConceptDefinitionComponent set : cs.getConcept()) {
+			all.add(set.getCode());
+		}
+		for (ValueSet.ValueSetExpansionContainsComponent v : expanded.getExpansion().getContains()) {
+			all.remove(v.getCode());
+		}
+		assertTrue(all.isEmpty(), String.join(", ", all));
+		assertEquals(cs.getConcept().size(), expanded.getExpansion().getTotal());
+	}
+
+	@Autowired
+	private IJobCoordinator myJobCoordinator;
+
+	@Autowired
+	private ITermDeferredStorageSvc myDeferredStorageSvc;
 }
--- a/hapi-fhir-server-cds-hooks/pom.xml
+++ b/hapi-fhir-server-cds-hooks/pom.xml
@ -79,25 +79,11 @@
 		<dependency>
 			<groupId>org.simplejavamail</groupId>
 			<artifactId>simple-java-mail</artifactId>
-			<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
-			<exclusions>
-				<exclusion>
-					<groupId>com.sun.activation</groupId>
-					<artifactId>jakarta.activation</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>com.icegreen</groupId>
 			<artifactId>greenmail</artifactId>
 			<scope>compile</scope>
-			<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
-			<exclusions>
-				<exclusion>
-					<groupId>com.sun.activation</groupId>
-					<artifactId>jakarta.activation</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 	</dependencies>

--- a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/IMailSvc.java
+++ b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/IMailSvc.java
@ -21,9 +21,9 @@ package ca.uhn.fhir.rest.server.mail;

 import jakarta.annotation.Nonnull;
 import org.simplejavamail.api.email.Email;
-import org.simplejavamail.api.mailer.AsyncResponse;

 import java.util.List;
+import java.util.function.Consumer;

 public interface IMailSvc {
 	void sendMail(@Nonnull List<Email> theEmails);
@ -31,7 +31,5 @@ public interface IMailSvc {
 	void sendMail(@Nonnull Email theEmail);

 	void sendMail(
-			@Nonnull Email theEmail,
-			@Nonnull Runnable theOnSuccess,
-			@Nonnull AsyncResponse.ExceptionConsumer theErrorHandler);
+			@Nonnull Email theEmail, @Nonnull Runnable theOnSuccess, @Nonnull Consumer<Throwable> theErrorHandler);
 }
--- a/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/MailSvc.java
+++ b/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/mail/MailSvc.java
@ -20,12 +20,9 @@
 package ca.uhn.fhir.rest.server.mail;

 import jakarta.annotation.Nonnull;
-import org.apache.commons.lang3.Validate;
 import org.simplejavamail.MailException;
 import org.simplejavamail.api.email.Email;
 import org.simplejavamail.api.email.Recipient;
-import org.simplejavamail.api.mailer.AsyncResponse;
-import org.simplejavamail.api.mailer.AsyncResponse.ExceptionConsumer;
 import org.simplejavamail.api.mailer.Mailer;
 import org.simplejavamail.api.mailer.config.TransportStrategy;
 import org.simplejavamail.mailer.MailerBuilder;
@ -33,6 +30,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

 import java.util.List;
+import java.util.Objects;
+import java.util.function.Consumer;
 import java.util.stream.Collectors;

 public class MailSvc implements IMailSvc {
@ -42,14 +41,14 @@ public class MailSvc implements IMailSvc {
 	private final Mailer myMailer;

 	public MailSvc(@Nonnull MailConfig theMailConfig) {
-		Validate.notNull(theMailConfig);
+		Objects.requireNonNull(theMailConfig);
 		myMailConfig = theMailConfig;
 		myMailer = makeMailer(myMailConfig);
 	}

 	@Override
 	public void sendMail(@Nonnull List<Email> theEmails) {
-		Validate.notNull(theEmails);
+		Objects.requireNonNull(theEmails);
 		theEmails.forEach(theEmail -> send(theEmail, new OnSuccess(theEmail), new ErrorHandler(theEmail)));
 	}

@ -60,21 +59,23 @@ public class MailSvc implements IMailSvc {

 	@Override
 	public void sendMail(
-			@Nonnull Email theEmail, @Nonnull Runnable theOnSuccess, @Nonnull ExceptionConsumer theErrorHandler) {
+			@Nonnull Email theEmail, @Nonnull Runnable theOnSuccess, @Nonnull Consumer<Throwable> theErrorHandler) {
 		send(theEmail, theOnSuccess, theErrorHandler);
 	}

 	private void send(
-			@Nonnull Email theEmail, @Nonnull Runnable theOnSuccess, @Nonnull ExceptionConsumer theErrorHandler) {
-		Validate.notNull(theEmail);
-		Validate.notNull(theOnSuccess);
-		Validate.notNull(theErrorHandler);
+			@Nonnull Email theEmail, @Nonnull Runnable theOnSuccess, @Nonnull Consumer<Throwable> theErrorHandler) {
+		Objects.requireNonNull(theEmail);
+		Objects.requireNonNull(theOnSuccess);
+		Objects.requireNonNull(theErrorHandler);
 		try {
-			final AsyncResponse asyncResponse = myMailer.sendMail(theEmail, true);
-			if (asyncResponse != null) {
-				asyncResponse.onSuccess(theOnSuccess);
-				asyncResponse.onException(theErrorHandler);
+			myMailer.sendMail(theEmail, true).whenComplete((result, ex) -> {
+				if (ex != null) {
+					theErrorHandler.accept(ex);
+				} else {
+					theOnSuccess.run();
 				}
+			});
 		} catch (MailException e) {
 			theErrorHandler.accept(e);
 		}
@ -117,7 +118,7 @@ public class MailSvc implements IMailSvc {
 		}
 	}

-	private class ErrorHandler implements ExceptionConsumer {
+	private class ErrorHandler implements Consumer<Throwable> {
 		private final Email myEmail;

 		private ErrorHandler(@Nonnull Email theEmail) {
@ -125,7 +126,7 @@ public class MailSvc implements IMailSvc {
 		}

 		@Override
-		public void accept(Exception t) {
+		public void accept(Throwable t) {
 			ourLog.error("Email not sent" + makeMessage(myEmail), t);
 		}
 	}
--- a/hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailSvcIT.java
+++ b/hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/mail/MailSvcIT.java
@ -4,6 +4,7 @@ import com.icegreen.greenmail.junit5.GreenMailExtension;
 import com.icegreen.greenmail.util.GreenMailUtil;
 import com.icegreen.greenmail.util.ServerSetupTest;
 import jakarta.annotation.Nonnull;
+import jakarta.mail.internet.MimeMessage;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.RegisterExtension;
@ -11,7 +12,6 @@ import org.simplejavamail.MailException;
 import org.simplejavamail.api.email.Email;
 import org.simplejavamail.email.EmailBuilder;

-import javax.mail.internet.MimeMessage;
 import java.util.Arrays;
 import java.util.List;

@ -86,13 +86,14 @@ public class MailSvcIT {
 	@Test
 	public void testSendMailWithInvalidToAddressExpectErrorHandler() {
 		// setup
-		final Email email = withEmail("xyz");
+		String invalidEmailAdress = "xyz";
+		final Email email = withEmail(invalidEmailAdress);
 		// execute
 		fixture.sendMail(email,
 			() -> fail("Should not execute on Success"),
 			(e) -> {
 				assertTrue(e instanceof MailException);
-				assertEquals("Invalid TO address: " + email, e.getMessage());
+				assertEquals("Invalid TO address: " + invalidEmailAdress, e.getMessage());
 			});
 		// validate
 		assertTrue(ourGreenMail.waitForIncomingEmail(1000, 0));
--- a/hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexAppCtx.java
+++ b/hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexAppCtx.java
@ -59,7 +59,9 @@ public class ReindexAppCtx {
 						"Load IDs of resources to reindex",
 						ResourceIdListWorkChunkJson.class,
 						reindexLoadIdsStep(theBatch2DaoSvc))
-				.addLastStep("reindex", "Perform the resource reindex", reindexStep())
+				.addLastStep("reindex",
+					"Perform the resource reindex",
+					reindexStep())
 				.build();
 	}

--- a/pom.xml
+++ b/pom.xml
@ -869,6 +869,7 @@
 		<developer>
 			<id>delopst</id>
 			<name>Primož Delopst</name>
+			<organization>Better</organization>
 		</developer>
 		<developer>
 			<id>Zach Smith</id>
@ -1160,27 +1161,38 @@
 			<dependency>
 				<groupId>org.simplejavamail</groupId>
 				<artifactId>simple-java-mail</artifactId>
-				<version>6.6.1</version>
+				<version>8.11.2</version>
 				<exclusions>
 					<exclusion>
-						<groupId>com.sun.activation</groupId>
-						<artifactId>jakarta.activation-api</artifactId>
+						<groupId>com.github.bbottema</groupId>
+						<artifactId>jetbrains-runtime-annotations</artifactId>
 					</exclusion>
 					<exclusion>
-						<groupId>com.sun.activation</groupId>
-						<artifactId>jakarta.activation</artifactId>
+						<groupId>jakarta.mail</groupId>
+						<artifactId>jakarta.mail-api</artifactId>
+					</exclusion>
+				</exclusions>
+			</dependency>
+			<dependency>
+				<groupId>jakarta.mail</groupId>
+				<artifactId>jakarta.mail-api</artifactId>
+				<version>2.1.3</version>
+			</dependency>
+			<dependency>
+				<groupId>com.icegreen</groupId>
+				<artifactId>greenmail</artifactId>
+				<version>2.1.0-rc-1</version>
+				<exclusions>
+					<exclusion>
+						<groupId>jakarta.mail</groupId>
+						<artifactId>jakarta.mail-api</artifactId>
 					</exclusion>
 				</exclusions>
 			</dependency>
-			<dependency>
-				<groupId>com.icegreen</groupId>
-				<artifactId>greenmail</artifactId>
-				<version>1.6.4</version>
-			</dependency>
 			<dependency>
 				<groupId>com.icegreen</groupId>
 				<artifactId>greenmail-junit5</artifactId>
-				<version>1.6.4</version>
+				<version>2.1.0-rc-1</version>
 				<scope>compile</scope>
 			</dependency>
 			<!-- mail end -->
Author	SHA1	Message	Date
TipzCM	877aa14c4e	Merge `5b50545a50` into `3f6d1eb29b`	2024-09-26 02:08:11 +00:00
Thomas Papke	3f6d1eb29b	#5768 Upgrade to latest simple-java-mail (#6261 )	2024-09-26 02:07:27 +00:00
Tadgh	377e44b6ca	attribution and pom change (#6309 )	2024-09-25 20:38:22 +00:00
leif stawnyczy	5b50545a50	Merge branch 'master' into 6285-value-set-expansion-issues	2024-09-24 09:44:00 -04:00
leif stawnyczy	dd9dcfd501	Shelfving	2024-09-13 11:15:39 -04:00