WIP: SpringBoot3x

clinical-trials-api/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gsrs-module-clinical-trials</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.2.5-SNAPSHOT</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -24,7 +24,7 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-test</artifactId>
-            <version>2.7.18</version>
+            <version>3.5.7</version>
             <scope>test</scope>
         </dependency>
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gsrs-module-clinical-trials</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -109,42 +109,12 @@
             <version>2.3.0</version>
         </dependency>
 
-        <!-- TO BE REMOVED -->
-        <!-- dependency>
-            <groupId>gov.nih.ncats</groupId>
-            <artifactId>gsrs-module-substances-spring-boot-starter</artifactId>
-            <version>${gsrs.substance.version}</version>
-        </dependency -->
-
-        <!-- DATABASE Dependencies  TO BE MOVED TO GSRS-CI? -->
-        <dependency>
-            <groupId>com.oracle.database.jdbc</groupId>
-            <artifactId>ojdbc8</artifactId>
-            <version>19.6.0.0</version>
-        </dependency>
-        <dependency>
-            <groupId>org.postgresql</groupId>
-            <artifactId>postgresql</artifactId>
-            <scope>runtime</scope>
-        </dependency>
+        <!-- DATABASE Dependencies -->
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
             <scope>runtime</scope>
         </dependency>
-
-        <!--
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-jdbc</artifactId>
-        </dependency>
-        <dependency>
-        <groupId>org.springframework.boot</groupId>
-        <artifactId>spring-boot-devtools</artifactId>
-        <scope>runtime</scope>
-        <optional>true</optional>
-       </dependency>
-        -->
     </dependencies>
 
 </project>

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/ClinicalTrialDataSourceConfig.java

@@ -4,7 +4,7 @@
 import java.util.Map;
 import java.util.Optional;
 
-import javax.persistence.EntityManagerFactory;
+import jakarta.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import org.springframework.beans.factory.annotation.Autowired;

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/autoconfigure/GsrsClinicalTrialsAutoConfiguration.java

@@ -5,14 +5,13 @@
 import gsrs.EnableGsrsJpaEntities;
 import gsrs.api.substances.SubstanceRestApi;
 import ix.core.search.bulk.EnableBulkSearch;
+import org.springframework.boot.autoconfigure.AutoConfiguration;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
 
 @EnableGsrsJpaEntities
 @EnableGsrsApi
 @EnableBulkSearch
-@Configuration
-// @Import({})
+@AutoConfiguration
 public class GsrsClinicalTrialsAutoConfiguration {
 
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/autoconfigure/SubstancesApiConfiguration.java

@@ -1,26 +1,14 @@
 package gov.hhs.gsrs.clinicaltrial.autoconfigure;
 
 import gsrs.api.AbstractGsrsRestApiConfiguration;
-import gsrs.GSRSDataSourceConfig;
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties;
 import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.orm.jpa.EntityManagerFactoryBuilder;
-import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
-import org.springframework.orm.jpa.JpaTransactionManager;
-import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
-
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
 
 @Configuration
 @Slf4j
 @ConfigurationProperties("gsrs.microservice.substances.api")
 public class SubstancesApiConfiguration extends AbstractGsrsRestApiConfiguration {
-
 }
 
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/base/models/ClinicalTrialBase.java

@@ -11,8 +11,8 @@
 import lombok.experimental.SuperBuilder;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import javax.persistence.*;
-import javax.persistence.InheritanceType;
+import jakarta.persistence.*;
+import jakarta.persistence.InheritanceType;
 
 
 @Data

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/common/ClinicalTrialOnStartup.java

@@ -3,18 +3,22 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import gsrs.cv.api.ControlledVocabularyApi;
 import gsrs.cv.api.ControlledVocabularyRestApi;
+import gsrs.indexer.ConfigBasedIndexValueMakerConfiguration;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.web.client.RestTemplateBuilder;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.security.core.annotation.AuthenticationPrincipal;
 import org.springframework.web.WebApplicationInitializer;
 
-import javax.servlet.ServletContext;
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletContext;
+import jakarta.servlet.ServletException;
 
 @Configuration
 public class ClinicalTrialOnStartup implements WebApplicationInitializer {
 
+
     @Value("${mygsrs.clinicaltrial.cvUrl}")
     private String cvUrl;
 
@@ -27,4 +31,5 @@ public void onStartup(ServletContext servletContext) throws ServletException {
     public ControlledVocabularyApi controlledVocabularyApi(RestTemplateBuilder restTemplateBuilder) {
         return new ControlledVocabularyRestApi(restTemplateBuilder, cvUrl, new ObjectMapper());
     }
+
 }

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/models/ClinicalTrialEurope.java

@@ -17,7 +17,7 @@
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.annotation.LastModifiedDate;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.*;
 @Data
 @Entity

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/models/ClinicalTrialEuropeDrug.java

@@ -10,7 +10,7 @@
 import lombok.EqualsAndHashCode;
 import lombok.experimental.SuperBuilder;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Data
 @Entity

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/models/ClinicalTrialEuropeMeddra.java

@@ -12,7 +12,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Data
 @Entity

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/models/ClinicalTrialEuropeMedical.java

@@ -11,7 +11,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Data
 @Entity

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/models/ClinicalTrialEuropeProduct.java

@@ -12,7 +12,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.List;
 import java.util.ArrayList;
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/europe/services/ClinicalTrialEuropeExportService.java

@@ -5,7 +5,7 @@
 import gov.hhs.gsrs.clinicaltrial.europe.repositories.ClinicalTrialEuropeRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
-import javax.servlet.ServletContext;
+import jakarta.servlet.ServletContext;
 import java.io.*;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Path;

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/controllers/ClinicalTrialUSController.java

@@ -19,8 +19,8 @@
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.PathVariable;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.stream.Stream;

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/models/ClinicalTrialUS.java

@@ -16,7 +16,7 @@
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.annotation.LastModifiedDate;
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.*;
 
 @Data

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/models/ClinicalTrialUSDrug.java

@@ -10,7 +10,7 @@
 import org.hibernate.annotations.LazyCollectionOption;
 import org.springframework.beans.factory.annotation.Value;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.ArrayList;
 import java.util.List;
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/models/OutcomeResultNote.java

@@ -8,7 +8,7 @@
 import lombok.Data;
 import org.apache.commons.lang3.builder.ReflectionToStringBuilder;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Data
 @Entity

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/models/SubstanceRole.java

@@ -9,7 +9,7 @@
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 import org.apache.commons.lang3.builder.ReflectionToStringBuilder;
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 
 @Data

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/repositories/ClinicalTrialUSRepository.java

@@ -6,7 +6,7 @@
 import org.springframework.stereotype.Repository;
 import org.springframework.stereotype.Service;
 
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.PersistenceContext;
 import org.springframework.transaction.annotation.Transactional;
 
 @Repository

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/services/ClinicalTrialUSEntityService.java

@@ -23,7 +23,7 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.io.IOException;
 import java.util.List;
 import java.util.Optional;

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/services/SubstanceAPIService.java

@@ -101,7 +101,7 @@ public Boolean substanceExists(String uuid) {
         }
         if(response == null) return null;
 
-        HttpStatus statusCode = response.getStatusCode();
+        HttpStatus statusCode = (HttpStatus) response.getStatusCode();
         if (statusCode == null)  return null;
 
         if (statusCode.equals(HttpStatus.valueOf(404))) {
@@ -155,7 +155,7 @@ public ResponseEntity<List<QuickResult>> getQuickResultMatchesByUuids() {
             if (response == null) {
                 continue;
             }
-            statusCode = response.getStatusCode();
+            statusCode = (HttpStatus) response.getStatusCode();
             if (statusCode.equals(HttpStatus.valueOf(404))) {
                 qr.hasResponseError = true;
             }

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/utils/importmapper/SourceToTargetFieldsMapper.java

@@ -2,7 +2,7 @@
 
 import gov.hhs.gsrs.clinicaltrial.us.models.ClinicalTrialUS;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
 import java.lang.reflect.Field;
 import java.util.ArrayList;
 import java.util.Arrays;

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/resources/META-INF/spring.factories

@@ -1 +0,0 @@
-org.springframework.boot.autoconfigure.EnableAutoConfiguration=gov.hhs.gsrs.clinicaltrial.autoconfigure.GsrsClinicalTrialsAutoConfiguration

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports

@@ -0,0 +1 @@
+gov.hhs.gsrs.clinicaltrial.autoconfigure.GsrsClinicalTrialsAutoConfiguration

gsrs-module-clinical-trials-spring-boot-starter-tests/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gsrs-module-clinical-trials</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

gsrs-module-clinical-trials-spring-boot-starter/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>gsrs-module-clinical-trials</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -30,7 +30,7 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter</artifactId>
-            <version>2.7.18</version>
+            <version>${spring-boot.version}</version>
         </dependency>
     </dependencies>