Spring Boot 3x WIP

gsrs-fda-substance-extension/pom.xml

@@ -168,7 +168,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>clinical-trials-api</artifactId>
-            <version>3.1.1-SNAPSHOT</version>
+            <version>3.1-SNAPSHOT</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

gsrs-fda-substance-extension/src/main/java/fda/gsrs/substance/exporters/ProductDTOExporter.java

@@ -10,7 +10,7 @@
 
 import lombok.extern.slf4j.Slf4j;
 
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.Collections;

gsrs-module-substance-example/pom.xml

@@ -14,7 +14,7 @@
     <properties>
         <timestamp>${maven.build.timestamp}</timestamp>
         <maven.build.timestamp.format>yyyy-MM-dd HH:mm:ss</maven.build.timestamp.format>
-        <jackson.version>2.13.4</jackson.version>
+        <jackson.version>2.16.0</jackson.version>
     </properties>
 
     <build>
@@ -31,8 +31,8 @@
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-compiler-plugin</artifactId>
             <configuration>
-                <source>8</source>
-                <target>8</target>
+                <source>${java.version}</source>
+                <target>${java.version}</target>
             </configuration>
         </plugin>
         <!-- Uncomment this for maven public release deployment
@@ -204,7 +204,7 @@
 
         <dependency>
             <groupId>com.h2database</groupId>
-            <artifactId>h2</artifactId>           	
+            <artifactId>h2</artifactId>
         </dependency>
         <dependency>
             <groupId>org.projectlombok</groupId>
@@ -331,7 +331,6 @@
             <groupId>gov.nih.ncats</groupId>
             <artifactId>gsrs-module-substances-data-exchange</artifactId>
             <version>${gsrs.substance.version}</version>
-            <scope>test</scope>
         </dependency>
         <!--dependency>
             <groupId>gov.nih.ncats</groupId>

gsrs-module-substance-example/src/main/java/example/GsrsModuleSubstanceApplication.java

@@ -10,7 +10,6 @@
 import org.springframework.context.annotation.Bean;
 import org.springframework.web.servlet.config.annotation.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
-import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
 
 //import org.springframework.cloud.netflix.eureka.EnableEurekaClient;
 

gsrs-module-substance-example/src/main/resources/application.conf

@@ -2,7 +2,7 @@ include "substances-core.conf"
 
 include "gsrs-h2-local.conf"
 
-include "fda-extension.conf"
+#include "fda-extension.conf"
 gsrs.sessionSecure=false
 #uncomment this setting to change renderer to use USP render settings.
 #substance.renderer.style="USP"

gsrs-module-substance-example/src/test/java/example/structureSearch/BasicLegacyIndexerTest.java

@@ -20,7 +20,7 @@
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.springframework.boot.test.mock.mockito.MockBean;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.io.File;
 import java.io.IOException;
 import static org.junit.jupiter.api.Assertions.*;

gsrs-module-substance-example/src/test/java/example/substance/ChangeSubstanceClassTest.java

@@ -10,7 +10,7 @@
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.security.test.context.support.WithMockUser;
 
-import javax.transaction.Transactional;
+import jakarta.transaction.Transactional;
 import java.io.File;
 import java.io.IOException;
 

gsrs-module-substance-example/src/test/java/example/substance/FlexAndExactSearchFullStackTest.java

@@ -13,7 +13,7 @@
 import java.util.function.Consumer;
 import java.util.function.Supplier;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;

gsrs-module-substance-example/src/test/java/example/substance/RelationshipInvertTest.java

@@ -29,7 +29,7 @@
 import org.springframework.test.context.event.RecordApplicationEvents;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.io.File;
 import java.io.IOException;
 import java.util.Collections;

gsrs-module-substance-example/src/test/java/example/substance/export/AbstractExportSupportingGsrsEntityControllerTest.java

@@ -27,7 +27,7 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.test.context.ActiveProfiles;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.lang.reflect.Field;
 import java.util.*;
 

gsrs-module-substances-api/pom.xml

@@ -12,8 +12,8 @@
     <artifactId>gsrs-module-substances-api</artifactId>
 
     <properties>
-        <maven.compiler.source>8</maven.compiler.source>
-        <maven.compiler.target>8</maven.compiler.target>
+        <maven.compiler.source>${java.version}</maven.compiler.source>
+        <maven.compiler.target>${java.version}</maven.compiler.target>
     </properties>
 
 

gsrs-module-substances-core/pom.xml

@@ -16,8 +16,8 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>8</source>
-                    <target>8</target>
+                    <source>${java.version}</source>
+                    <target>${java.version}</target>
                 </configuration>
             </plugin>
             <!-- Uncomment this for maven public release deployment
@@ -286,12 +286,12 @@
         <dependency>
             <groupId>uk.ac.cam.ch.opsin</groupId>
             <artifactId>opsin-core</artifactId>
-            <version>2.7.0</version>
+            <version>2.8.0</version>
         </dependency>
         <dependency>
             <groupId>org.jsoup</groupId>
             <artifactId>jsoup</artifactId>
-            <version>1.15.3</version>
+            <version>1.17.1</version>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
@@ -307,6 +307,12 @@
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
             <version>4.5.14</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>commons-logging</groupId>
+                    <artifactId>commons-logging</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>net.coobird</groupId>

gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceCoreConfiguration.java

@@ -72,8 +72,8 @@ private static class EmbeddedTomcatCustomizer implements WebServerFactoryCustomi
         @Override
         public void customize(TomcatServletWebServerFactory factory) {
             factory.addConnectorCustomizers((TomcatConnectorCustomizer) connector -> {
-                connector.setAttribute("relaxedPathChars", "<>[\\]^`{|}");
-                connector.setAttribute("relaxedQueryChars", "<>[\\]^`{|}");
+                connector.setProperty("relaxedPathChars", "<>[\\]^`{|}");
+                connector.setProperty("relaxedQueryChars", "<>[\\]^`{|}");
             });
         }
     }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceEntityServiceImpl.java

@@ -41,7 +41,7 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.swing.text.DefaultStyledDocument;
 import java.io.IOException;
 import java.io.UncheckedIOException;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/SubstanceValidatorConfig.java

@@ -4,8 +4,10 @@
 import gsrs.validator.ValidatorConfig;
 import ix.ginas.models.v1.Substance;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 
 @Data
+@EqualsAndHashCode(callSuper=false)
 public class SubstanceValidatorConfig extends DefaultValidatorConfig {
 
     private Substance.SubstanceClass substanceClass;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/LegacyGinasAppController.java

@@ -31,7 +31,7 @@
 import org.springframework.web.servlet.View;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/ReIndexController.java

@@ -13,7 +13,7 @@
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestParam;
 
-import javax.persistence.Id;
+import jakarta.persistence.Id;
 import java.util.Map;
 import java.util.UUID;
 import java.util.concurrent.atomic.AtomicLong;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/StructureOCRController.java

@@ -15,7 +15,7 @@
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.multipart.MultipartFile;
 
-import javax.validation.constraints.NotNull;
+import jakarta.validation.constraints.NotNull;
 import java.io.IOException;
 import java.util.Base64;
 import java.util.Map;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/SubstanceController.java

@@ -25,8 +25,8 @@
 import java.util.stream.Stream;
 
 import javax.imageio.ImageIO;
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.constraints.NotBlank;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.validation.constraints.NotBlank;
 
 import org.freehep.graphicsio.svg.SVGGraphics2D;
 import org.springframework.beans.factory.annotation.Autowired;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/restValidation/StructureFormatValidator.java

@@ -1,7 +1,7 @@
 package gsrs.module.substance.controllers.restValidation;
 
-import javax.validation.ConstraintValidator;
-import javax.validation.ConstraintValidatorContext;
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
 import java.util.HashSet;
 import java.util.Locale;
 import java.util.Set;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/controllers/restValidation/ValidStructureFormat.java

@@ -1,7 +1,7 @@
 package gsrs.module.substance.controllers.restValidation;
 
-import javax.validation.Constraint;
-import javax.validation.Payload;
+import jakarta.validation.Constraint;
+import jakarta.validation.Payload;
 import java.lang.annotation.*;
 
 @Documented

gsrs-module-substances-core/src/main/java/gsrs/module/substance/expanders/basic/BasicRecordExpanderParameters.java

@@ -2,7 +2,7 @@
 
 import java.util.HashMap;
 import java.util.Map;
-import javax.annotation.Generated;
+import jakarta.annotation.Generated;
 import com.fasterxml.jackson.annotation.JsonAnyGetter;
 import com.fasterxml.jackson.annotation.JsonAnySetter;
 import com.fasterxml.jackson.annotation.JsonIgnore;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/importers/importActionFactories/NSRSCustomCodeExtractorActionFactory.java

@@ -11,6 +11,7 @@
 import ix.ginas.modelBuilders.AbstractSubstanceBuilder;
 import ix.ginas.models.v1.Code;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 import lombok.extern.slf4j.Slf4j;
 
 import java.util.ArrayList;
@@ -21,6 +22,7 @@
 
 @Slf4j
 @Data
+@EqualsAndHashCode(callSuper=false)
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class NSRSCustomCodeExtractorActionFactory extends BaseActionFactory {
     private String actionName;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/importers/importActionFactories/ProteinSequenceExtractorActionFactory.java

@@ -9,6 +9,7 @@
 import ix.ginas.modelBuilders.ProteinSubstanceBuilder;
 import ix.ginas.models.v1.Subunit;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 import lombok.extern.slf4j.Slf4j;
 
 import java.util.Map;
@@ -17,6 +18,7 @@
 
 @Slf4j
 @Data
+@EqualsAndHashCode(callSuper=false)
 public class ProteinSequenceExtractorActionFactory extends BaseActionFactory {
 
     private String subunitDelimiter;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/importers/importActionFactories/StructureExtractorActionFactory.java

@@ -13,6 +13,7 @@
 import ix.ginas.models.v1.GinasChemicalStructure;
 import ix.ginas.models.v1.Moiety;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -23,6 +24,7 @@
 import static gsrs.module.substance.importers.SDFImportAdapterFactory.resolveParametersMap;
 
 @Data
+@EqualsAndHashCode(callSuper=false)
 @Slf4j
 public class StructureExtractorActionFactory extends BaseActionFactory {
     private String actionName;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/importers/model/MergeProcessingActionParameters.java

@@ -3,7 +3,7 @@
 
 import java.util.LinkedHashMap;
 import java.util.Map;
-import javax.annotation.Generated;
+import jakarta.annotation.Generated;
 
 import com.fasterxml.jackson.annotation.JsonAnyGetter;
 import com.fasterxml.jackson.annotation.JsonAnySetter;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/processors/TryToCreateInverseRelationshipEvent.java

@@ -32,6 +32,7 @@ public class TryToCreateInverseRelationshipEvent {
     private UUID originatorUUID;
     private UUID relationshipIdToInvert;
 
+    @Builder.Default
     private CreationMode creationMode = CreationMode.CREATE_IF_MISSING_DEEP_CHECK;
 
     private UUID newRelationshipId;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/repository/CodeRepository.java

@@ -26,7 +26,7 @@ public interface CodeRepository extends GsrsVersionedRepository<Code, UUID> {
     Long findMaxCodeByCodeSystemAndCodeLikeAndCodeLessThan(@Param("codesystem") String codeSystem, @Param("codelike") String codeLike, @Param("maxcode") Long maxCode);
 
     //hibernate query will not convert uuid into a string so we have to concatenate it with empty string for this to work.
-    @Query("select s from Name s where CONCAT(s.uuid, '') like ?1%")
+    @Query("select s from Name s where SUBSTRING(s.uuid, 1, 8) = ?1")
     List<Code> findByUuidStartingWith(String partialUUID);
 
     List<Code> findByCodeIgnoreCase(String code);

gsrs-module-substances-core/src/main/java/gsrs/module/substance/repository/NameRepository.java

@@ -23,7 +23,7 @@ public interface NameRepository extends GsrsVersionedRepository<Name, UUID> {
     List<Name> findByNameIgnoreCase(String name);
 
     //hibernate query will not convert uuid into a string so we have to concatenate it with empty string for this to work.
-    @Query("select s from Name s where CONCAT(s.uuid, '') like ?1%")
+    @Query("select s from Name s where SUBSTRING(s.uuid, 1, 8) = ?1")
     List<Name> findByUuidStartingWith(String partialUUID);
 
     @Query("select n.uuid from Name n")

gsrs-module-substances-core/src/main/java/gsrs/module/substance/repository/ReferenceRepository.java

@@ -16,6 +16,6 @@
 public interface ReferenceRepository extends GsrsVersionedRepository<Reference, UUID> {
 
     //hibernate query will not convert uuid into a string so we have to concatenate it with empty string for this to work.
-    @Query("select s from Reference s where CONCAT(s.uuid, '') like ?1%")
+    @Query("select s from Reference s where SUBSTRING(s.uuid, 1, 8) = ?1")
     List<Reference> findByUuidStartingWith(String partialUUID);
 }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/repository/SubstanceRepository.java

@@ -63,7 +63,7 @@ default Substance findBySubstanceReference(SubstanceReference substanceReference
 
     List<SubstanceSummary> findByNames_Name(String name);
 
-    List<SubstanceSummary> findByNames_StdNameIgnoreCase(String stdName);
+    //List<SubstanceSummary> findByNames_StdNameIgnoreCase(String stdName);
 
     List<SubstanceSummary> findByCodes_CodeIgnoreCase(String code);
     List<SubstanceSummary> findByCodes_CodeAndCodes_CodeSystem(String code, String codeSystem);
@@ -99,7 +99,7 @@ default List<Substance> findSubstanceSummaryByMoieties_Structure_Properties_Term
      * @return
      */
     //hibernate query will not convert uuid into a string so we have to concatenate it with empty string for this to work.
-    @Query("select s from Substance s where CONCAT(s.uuid, '') like ?1%")
+    @Query("select s from Substance s where SUBSTRING(s.uuid, 1, 8) = ?1")
     List<Substance> findByUuidStartingWith(String partialUUID);
     @Query("select case when count(s)> 0 then true else false end from Substance s where s.approvalID= ?1")
     boolean existsByApprovalID(String approvalID);
@@ -170,6 +170,6 @@ default SubstanceReference toSubstanceReference(){
     @Query("select s.id from Substance s")
     List<UUID> getAllIds();
 
-    @Query("select s.id from Substance s where dtype='CHE'")
+    @Query("select s.id from ChemicalSubstance s")
     List<UUID> getAllChemicalIds();
 }

gsrs-module-substances-core/src/main/java/gsrs/module/substance/scrubbers/InputScrubberParameters.java

@@ -3,7 +3,7 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import javax.annotation.Generated;
+import jakarta.annotation.Generated;
 
 import com.fasterxml.jackson.annotation.JsonAnyGetter;
 import com.fasterxml.jackson.annotation.JsonAnySetter;

gsrs-module-substances-core/src/main/java/gsrs/module/substance/scrubbers/basic/BasicSubstanceScrubberParameters.java

@@ -4,7 +4,7 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.annotation.Generated;
+import jakarta.annotation.Generated;
 
 import com.fasterxml.jackson.annotation.JsonAnyGetter;
 import com.fasterxml.jackson.annotation.JsonAnySetter;