Merge pull request #93 from fscheel/MigrateToSpringBoot2

Migrate to spring boot2
nmdp-bioinformatics · Feb 18, 2019 · da7e7de · da7e7de
2 parents 3fe038d + ee4c16f
commit da7e7de
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Showing 24 changed files with 190 additions and 625 deletions.
diff --git a/pom.xml b/pom.xml
@@ -10,12 +10,12 @@
         <java.version>1.8</java.version>
         <maven.compiler.source>${java.version}</maven.compiler.source>
         <maven.compiler.target>${java.version}</maven.compiler.target>
-        <springfox-version>2.7.0</springfox-version>
+        <springfox-version>2.9.2</springfox-version>
     </properties>
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>1.3.5.RELEASE</version>
+        <version>2.1.0.RELEASE</version>
         <relativePath/>
     </parent>
 
@@ -37,6 +37,10 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-actuator</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.flywaydb</groupId>
             <artifactId>flyway-core</artifactId>
@@ -57,11 +61,10 @@
             <groupId>com.fasterxml.jackson.datatype</groupId>
             <artifactId>jackson-datatype-jsr310</artifactId>
         </dependency>
-        <!-- Bean Validation API support -->
         <dependency>
-            <groupId>javax.validation</groupId>
-            <artifactId>validation-api</artifactId>
-            <version>1.1.0.Final</version>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.4</version>
             <scope>provided</scope>
         </dependency>
     </dependencies>

diff --git a/src/main/java/org/nmdp/hfcus/controller/CohortApiController.java b/src/main/java/org/nmdp/hfcus/controller/CohortApiController.java
@@ -38,7 +38,7 @@ public ResponseEntity<CohortData> createCohort(@ApiParam(value = "Cohort Request
 
     @Override
     public ResponseEntity<CohortData> getCohortForId(@ApiParam(value = "Cohort ID",required=true ) @PathVariable("cohortId") Long cohortId) {
-        Cohort cohort = cohortRepository.findOne(cohortId);
+        Cohort cohort = cohortRepository.findById(cohortId).orElse(null);
         ResponseEntity<CohortData> responseEntity;
         if (cohort != null) {
             responseEntity = ResponseEntity.ok(cohort.toSwaggerObject());

diff --git a/src/main/java/org/nmdp/hfcus/controller/HFCurationApiController.java b/src/main/java/org/nmdp/hfcus/controller/HFCurationApiController.java
@@ -61,7 +61,7 @@ private <ModelType, ResponseType> ResponseEntity<ResponseType> RetrieveSubdataFr
             Function<ModelType, ResponseType> converter
     ) {
         ResponseEntity<ResponseType> responseEntity;
-        HFCuration curation = repositoryContainer.getCurationRepository().findOne(submissionId);
+        HFCuration curation = repositoryContainer.getCurationRepository().findById(submissionId).orElse(null);
         if (curation != null) {
             ModelType dataModel = getDataItem.apply(curation);
             if (dataModel != null) {
@@ -138,7 +138,7 @@ public ResponseEntity<LabelResponse> hfcLabelGet() {
     public ResponseEntity<PopulationSubmissionResponse> hfcPopulationPopulationIdGet(
             @ApiParam(value = "The populationId id", required = true) @PathVariable("populationId") Long populationId
     ) {
-        Population population = repositoryContainer.getPopulationRepository().findOne(populationId);
+        Population population = repositoryContainer.getPopulationRepository().findById(populationId).orElse(null);
         ResponseEntity<PopulationSubmissionResponse> responseEntity;
         if (population != null) {
             PopulationSubmissionData pop = new PopulationSubmissionData();
@@ -177,13 +177,13 @@ public ResponseEntity<HFCurationResponse> hfcSubmissionIdGet(
     public ResponseEntity<Void> hfcSubmissionIdDelete(
             @ApiParam(value = "", required = true) @PathVariable("submissionId") Long submissionId
     ) {
-        HFCuration curation = repositoryContainer.getCurationRepository().findOne(submissionId);
+        HFCuration curation = repositoryContainer.getCurationRepository().findById(submissionId).orElse(null);
         if (curation != null) {
             curation.setPopulationData(null);
             repositoryContainer.getCurationRepository().delete(curation);
-            return new ResponseEntity<Void>(HttpStatus.NO_CONTENT);
+            return new ResponseEntity<>(HttpStatus.NO_CONTENT);
         } else {
-            return new ResponseEntity<Void>(HttpStatus.NOT_FOUND);
+            return new ResponseEntity<>(HttpStatus.NOT_FOUND);
         }
     }
 

diff --git a/src/main/java/org/nmdp/hfcus/controller/PopulationApiController.java b/src/main/java/org/nmdp/hfcus/controller/PopulationApiController.java
@@ -37,7 +37,7 @@ public ResponseEntity<PopulationData> createPopulation(@ApiParam(value = "Popula
 
     @Override
     public ResponseEntity<PopulationData> getPopulationForId(@ApiParam(value = "Population ID",required=true ) @PathVariable("populationId") Long populationId) {
-        Population population = populationRepository.findOne(populationId);
+        Population population = populationRepository.findById(populationId).orElse(null);
         ResponseEntity<PopulationData> responseEntity;
         if (population != null) {
             responseEntity = ResponseEntity.ok(population.toSwaggerObject());

diff --git a/src/main/java/org/nmdp/hfcus/model/Access.java b/src/main/java/org/nmdp/hfcus/model/Access.java
@@ -1,6 +1,8 @@
 package org.nmdp.hfcus.model;
 
 import io.swagger.model.AccessData;
+import lombok.Data;
+import lombok.NoArgsConstructor;
 import org.nmdp.hfcus.model.exceptions.RequiredFieldInvalidException;
 
 import javax.persistence.Entity;
@@ -9,39 +11,22 @@
 import javax.persistence.Id;
 
 @Entity
+@Data
+@NoArgsConstructor
 public class Access implements ICurationDataModel<AccessData> {
-    public Access(){
-        //intentionally left empty
-    }
 
-    public Access(AccessData swaggerObject) {
+    Access(AccessData swaggerObject) {
         typeOfAccess = swaggerObject.getTypeOfAccess();
         if (typeOfAccess == null){
             throw new RequiredFieldInvalidException("Requires type of access");
         }
     }
 
     @Id
-    @GeneratedValue(strategy = GenerationType.AUTO)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;
     private String typeOfAccess;
 
-    public Long getId() {
-        return id;
-    }
-
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    public String getTypeOfAccess() {
-        return typeOfAccess;
-    }
-
-    public void setTypeOfAccess(String typeOfAccess) {
-        this.typeOfAccess = typeOfAccess;
-    }
-
     @Override
     public  AccessData toSwaggerObject(){
         AccessData data = new AccessData();

diff --git a/src/main/java/org/nmdp/hfcus/model/Cohort.java b/src/main/java/org/nmdp/hfcus/model/Cohort.java
@@ -2,24 +2,24 @@
 
 
 import io.swagger.model.CohortData;
+import lombok.Data;
+import lombok.NoArgsConstructor;
 import org.nmdp.hfcus.model.exceptions.RequiredFieldInvalidException;
 
 import javax.persistence.*;
 
 @Entity
+@Data
+@NoArgsConstructor
 public class Cohort implements ICurationDataModel<CohortData> {
 
     @Id
-    @GeneratedValue(strategy = GenerationType.AUTO)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;
     @OneToOne(cascade = CascadeType.ALL)
     private GenotypeList genotypeList;
     private String name;
 
-    public Cohort(){
-        //intentionally left empty
-    }
-
     public Cohort(CohortData swaggerObject){
         if (swaggerObject.getGenotypeList() != null) {
             genotypeList = new GenotypeList(swaggerObject.getGenotypeList());
@@ -34,28 +34,6 @@ public Cohort(CohortData swaggerObject){
         }
     }
 
-    public Long getId() { return id; }
-
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    public GenotypeList getGenotypeList() {
-        return genotypeList;
-    }
-
-    public void setGenotypeList(GenotypeList genotypeList) {
-        this.genotypeList = genotypeList;
-    }
-
-    public String getName() {
-    	return name;
-    }
-
-    public void setName(String name) {
-    	this.name = name;
-    }
-
     @Override
     public CohortData toSwaggerObject(){
         CohortData data = new CohortData();

diff --git a/src/main/java/org/nmdp/hfcus/model/FrequencyError.java b/src/main/java/org/nmdp/hfcus/model/FrequencyError.java
@@ -1,51 +1,29 @@
 package org.nmdp.hfcus.model;
 
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
 
 @Entity
+@Data
+@NoArgsConstructor
 public class FrequencyError implements ICurationDataModel<io.swagger.model.FrequencyError> {
-    public FrequencyError(){
-        //intentionally left empty
-    }
 
     public FrequencyError(io.swagger.model.FrequencyError error) {
         value = error.getValue();
         typeOfError = error.getTypeOfError();
     }
 
     @Id
-    @GeneratedValue(strategy = GenerationType.AUTO)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;
     private Double value;
     private String typeOfError;
 
-    public Long getId() {
-        return id;
-    }
-
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    public Double getValue() {
-        return value;
-    }
-
-    public void setValue(Double value) {
-        this.value = value;
-    }
-
-    public String getTypeOfError() {
-        return typeOfError;
-    }
-
-    public void setTypeOfError(String typeOfError) {
-        this.typeOfError = typeOfError;
-    }
-
     @Override
     public io.swagger.model.FrequencyError toSwaggerObject(){
         io.swagger.model.FrequencyError data = new io.swagger.model.FrequencyError();

diff --git a/src/main/java/org/nmdp/hfcus/model/Genotype.java b/src/main/java/org/nmdp/hfcus/model/Genotype.java
@@ -1,25 +1,25 @@
 package org.nmdp.hfcus.model;
 
+import lombok.Data;
+import lombok.NoArgsConstructor;
 import org.nmdp.hfcus.model.exceptions.RequiredFieldInvalidException;
 
 import javax.persistence.*;
 import java.util.ArrayList;
 import java.util.List;
 
 @Entity
+@Data
+@NoArgsConstructor
 public class Genotype implements ICurationDataModel<io.swagger.model.Genotype> {
 
     @Id
-    @GeneratedValue(strategy = GenerationType.AUTO)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long genotypeId;
     private String genotypeString;
     @OneToMany(cascade = CascadeType.ALL)
     private List<GenotypeMethod> genotypingMethods;
 
-    public Genotype(){
-        //intentionally left empty
-    }
-
     public Genotype(io.swagger.model.Genotype swaggerObject){
         genotypeString = swaggerObject.getGenotypeString();
         if (genotypeString == null){
@@ -33,30 +33,6 @@ public Genotype(io.swagger.model.Genotype swaggerObject){
         }
     }
 
-    public Long getGenotypeId() {
-        return genotypeId;
-    }
-
-    public void setGenotypeId(Long genotypeId) {
-        this.genotypeId = genotypeId;
-    }
-
-    public String getGenotypeString() {
-        return genotypeString;
-    }
-
-    public void setGenotypeString(String genotypeString) {
-        this.genotypeString = genotypeString;
-    }
-
-    public List<GenotypeMethod> getGenotypingMethods() {
-        return genotypingMethods;
-    }
-
-    public void setGenotypingMethods(List<GenotypeMethod> genotypingMethods) {
-        this.genotypingMethods = genotypingMethods;
-    }
-
     @Override
     public io.swagger.model.Genotype toSwaggerObject(){
         io.swagger.model.Genotype data = new io.swagger.model.Genotype();

diff --git a/src/main/java/org/nmdp/hfcus/model/GenotypeList.java b/src/main/java/org/nmdp/hfcus/model/GenotypeList.java
@@ -1,26 +1,26 @@
 package org.nmdp.hfcus.model;
 
 import io.swagger.model.License;
+import lombok.Data;
+import lombok.NoArgsConstructor;
 
 import javax.persistence.*;
 import java.util.ArrayList;
 import java.util.List;
 
 @Entity
+@Data
+@NoArgsConstructor
 public class GenotypeList implements ICurationDataModel<io.swagger.model.GenotypeList> {
 
     @Id
-    @GeneratedValue(strategy = GenerationType.AUTO)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;
     @Enumerated(EnumType.STRING)
     private License.TypeOfLicenseEnum license;
     @OneToMany(cascade = CascadeType.ALL)
     private List<Genotype> genotypeList;
 
-    public GenotypeList(){
-        //intentionallyLeftEmpty
-    }
-
     public GenotypeList(io.swagger.model.GenotypeList swaggerObject){
         if (swaggerObject.getLicense() != null) {
             license = swaggerObject.getLicense().getTypeOfLicense();
@@ -33,30 +33,6 @@ public GenotypeList(io.swagger.model.GenotypeList swaggerObject){
         }
     }
 
-    public Long getId() {
-        return id;
-    }
-
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    public License.TypeOfLicenseEnum getLicense() {
-        return license;
-    }
-
-    public void setLicense(License.TypeOfLicenseEnum license) {
-        this.license = license;
-    }
-
-    public List<Genotype> getGenotypeList() {
-        return genotypeList;
-    }
-
-    public void setGenotypeList(List<Genotype> genotypeList) {
-        this.genotypeList = genotypeList;
-    }
-
     @Override
     public io.swagger.model.GenotypeList toSwaggerObject(){
         io.swagger.model.GenotypeList data = new io.swagger.model.GenotypeList();