WIP: springBoot3x

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gsrs-module-invitro-pharmacology</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.2.0-SNAPSHOT</version>
+        <version>3.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -103,17 +103,7 @@
             <version>2.3.0</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>

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/GsrsSpringInvitroPharmacologyApplication.java

@@ -3,19 +3,10 @@
 import gsrs.*;
 
 import org.springframework.boot.SpringApplication;
-import org.springframework.boot.autoconfigure.*;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
-import org.springframework.boot.autoconfigure.jdbc.*;
-import org.springframework.boot.context.properties.*;
-import org.springframework.context.annotation.*;
-import org.springframework.context.annotation.Bean;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.scheduling.annotation.EnableAsync;
-import org.springframework.transaction.annotation.*;
-import org.springframework.web.servlet.config.annotation.CorsRegistry;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
 
 /* June 4, 2021 */
 @SpringBootApplication
@@ -32,25 +23,11 @@
 @EnableGsrsBackup
 @EnableAsync
 
+// SB 3x is the file needed if so make WebMbv config file like in service
+
 public class GsrsSpringInvitroPharmacologyApplication {
 
     public static void main(String[] args) {
         SpringApplication.run(GsrsSpringInvitroPharmacologyApplication.class, args);
     }
-
-    @Bean
-    public WebMvcConfigurer corsConfigurer() {
-        return new WebMvcConfigurerAdapter() {
-            @Override
-            public void addCorsMappings(CorsRegistry registry) {
-                registry.addMapping("/**");
-                        /*
-                        .allowedOrigins("http://localhost:4200")
-                        .allowedMethods("GET", "PUT", "POST", "PATCH", "DELETE", "OPTIONS")
-                        .allowedHeaders("origin", "Content-Type", "Authorization", "Accept", "Accept-Language", "X-Authorization", "X-Requested-With", "auth-username", "auth-password", "auth-token", "auth-key", "auth-token")
-                        .allowCredentials(false).maxAge(300);
-                         */
-            }
-        };
-    }
 }

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/InvitroPharmacologyDataSourceConfig.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-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/autoconfigure/GsrsInvitroPharmacologyAutoConfiguration.java

@@ -6,15 +6,15 @@
 import gsrs.EnableGsrsApi;
 import gsrs.EnableGsrsJpaEntities;
 
-import org.springframework.context.annotation.Configuration;
+import org.springframework.boot.autoconfigure.AutoConfiguration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Bean;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 @EnableGsrsJpaEntities
 @EnableGsrsApi
-@Configuration
+@AutoConfiguration
 @Import({
         SubstanceApiService.class
 })

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/autoconfigure/SubstancesApiConfiguration.java

@@ -15,7 +15,7 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManagerFactory;
+import jakarta.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 @Configuration

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/controllers/InvitroAssayScreeningController.java

@@ -43,17 +43,12 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
-
-import java.io.IOException;
-import java.io.OutputStream;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 import java.security.Principal;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import java.util.stream.Stream;
 
 import net.minidev.json.JSONObject;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/controllers/InvitroPharmacologyController.java

@@ -45,9 +45,9 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.servlet.http.HttpServletRequest;
 
 import java.io.IOException;
 import java.io.OutputStream;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/indexers/InvitroPharmacologyIndexValueMaker.java

@@ -16,9 +16,9 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.Query;
 
 import java.util.function.Consumer;
 import java.util.Optional;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayAnalyte.java

@@ -13,7 +13,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Set;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayInformation.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Date;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayResult.java

@@ -14,7 +14,7 @@
 import lombok.EqualsAndHashCode;
 import lombok.ToString;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.ArrayList;
 import java.util.List;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayResultInformation.java

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

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayScreening.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Date;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssaySet.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Date;
 import java.util.Set;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroControl.java

@@ -13,7 +13,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Set;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroLaboratory.java

@@ -9,7 +9,7 @@
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @SingleParent
 @Data

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroPharmacologyCommanData.java

@@ -15,7 +15,7 @@
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.annotation.LastModifiedDate;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroReference.java

@@ -13,7 +13,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Set;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroSponsor.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Date;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroSponsorReport.java

@@ -10,7 +10,7 @@
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroSponsorSubmitter.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.Date;
 import java.util.ArrayList;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroSummary.java

@@ -14,7 +14,7 @@
 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-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroTestAgent.java

@@ -14,7 +14,7 @@
 import org.hibernate.annotations.LazyCollection;
 import org.hibernate.annotations.LazyCollectionOption;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 import java.util.ArrayList;
 import java.util.List;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/services/InvitroAssayScreeningEntityService.java

@@ -19,7 +19,7 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 
 import java.io.IOException;
 import java.util.List;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/services/InvitroPharmacologyEntityService.java

@@ -20,8 +20,8 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 
 import java.io.IOException;
 import java.util.List;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/validators/AssayInformationUniqueValidator.java

@@ -11,8 +11,8 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 import java.util.Objects;
 
 public class AssayInformationUniqueValidator implements ValidatorPlugin<InvitroAssayInformation> {

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/resources/META-INF/spring.factories

@@ -1,2 +0,0 @@
-org.springframework.boot.autoconfigure.EnableAutoConfiguration=gov.hhs.gsrs.invitropharmacology.autoconfigure.GsrsInvitroPharmacologyAutoConfiguration,\
-gov.hhs.gsrs.invitropharmacology.autoconfigure.SubstancesApiConfiguration

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

@@ -0,0 +1,3 @@
+gov.hhs.gsrs.invitropharmacology.autoconfigure.GsrsInvitroPharmacologyAutoConfiguration
+gov.hhs.gsrs.invitropharmacology.autoconfigure.SubstancesApiConfiguration
+

gsrs-module-invitro-pharmacology-spring-boot-starter/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>gsrs-module-invitro-pharmacology</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.2.0-SNAPSHOT </version>
+        <version>3.2.5-SNAPSHOT </version>
     </parent>
     <modelVersion>4.0.0</modelVersion>