Merge pull request #378 from NUM-Forschungsdatenplattform/develop

Release 1.12.0

pom.xml

@@ -7,7 +7,7 @@
 
   <groupId>de.vitagroup.num-portal</groupId>
   <artifactId>num-portal</artifactId>
-  <version>1.11.1</version>
+  <version>1.12.0</version>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
@@ -30,15 +30,19 @@
     <openfeign.version>3.0.3</openfeign.version>
     <commons-csv.version>1.9.0</commons-csv.version>
     <jacoco.version>0.8.7</jacoco.version>
-    <dependency-check.version>6.2.2</dependency-check.version>
+    <dependency-check.version>8.1.2</dependency-check.version>
     <failsafe.version>3.0.0-M5</failsafe.version>
     <surefire.version>3.0.0-M5</surefire.version>
     <ehcache.version>3.10.8</ehcache.version>
-    <git-commit-id-plugin.version>4.9.9</git-commit-id-plugin.version>
+    <git-commit-id-plugin.version>4.9.10</git-commit-id-plugin.version>
     <skip.integration.tests>false</skip.integration.tests>
     <skip.unit.tests>false</skip.unit.tests>
     <skip.dependency.check>false</skip.dependency.check>
-    <postgresql.version>42.5.0</postgresql.version>
+    <postgresql.version>42.5.3</postgresql.version>
+    <hapi.version>5.5.1</hapi.version>
+    <wiremock-standalone.version>3.0.0-beta-2</wiremock-standalone.version>
+    <testcontainers.postgresql.version>1.17.6</testcontainers.postgresql.version>
+    <ossindexAnalyzerEnabled>false</ossindexAnalyzerEnabled>
   </properties>
 
   <repositories>
@@ -115,7 +119,7 @@
     <dependency>
       <groupId>org.testcontainers</groupId>
       <artifactId>postgresql</artifactId>
-      <version>1.16.0</version>
+      <version>${testcontainers.postgresql.version}</version>
       <scope>test</scope>
     </dependency>
     <dependency>
@@ -130,6 +134,10 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-aop</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-configuration-processor</artifactId>
+    </dependency>
     <dependency>
       <groupId>com.github.ehrbase.openEHR_SDK</groupId>
       <artifactId>client</artifactId>
@@ -150,6 +158,11 @@
       <artifactId>modelmapper</artifactId>
       <version>${modelmapper.version}</version>
     </dependency>
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>hapi-fhir-jaxrsserver-base</artifactId>
+      <version>${hapi.version}</version>
+    </dependency>
     <dependency>
       <groupId>org.assertj</groupId>
       <artifactId>assertj-core</artifactId>
@@ -215,9 +228,10 @@
     <dependency>
       <groupId>com.github.tomakehurst</groupId>
       <artifactId>wiremock-standalone</artifactId>
-      <version>2.27.2</version>
+      <version>${wiremock-standalone.version}</version>
       <scope>test</scope>
     </dependency>
+
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-test</artifactId>
@@ -365,6 +379,7 @@
         <configuration>
           <formats>HTML,XML</formats>
           <skip>${skip.dependency.check}</skip>
+          <ossindexAnalyzerEnabled>${ossindexAnalyzerEnabled}</ossindexAnalyzerEnabled>
         </configuration>
         <executions>
           <execution>

src/main/java/de/vitagroup/num/config/FttpClientConfig.java

@@ -0,0 +1,69 @@
+package de.vitagroup.num.config;
+
+import ca.uhn.fhir.context.FhirContext;
+import de.vitagroup.num.properties.FttpProperties;
+import java.security.KeyStore;
+import javax.net.ssl.HostnameVerifier;
+import javax.net.ssl.SSLContext;
+import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.UsernamePasswordCredentials;
+import org.apache.http.conn.ssl.NoopHostnameVerifier;
+import org.apache.http.conn.ssl.SSLConnectionSocketFactory;
+import org.apache.http.impl.client.BasicCredentialsProvider;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.ssl.SSLContextBuilder;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Slf4j
+@Configuration
+@RequiredArgsConstructor
+public class FttpClientConfig {
+
+  private static final String CERTIFICATE_TYPE = "PKCS12";
+
+  private final FttpProperties fttpProperties;
+
+  @Bean
+  public FhirContext fhirContext() {
+    return FhirContext.forR4();
+  }
+
+  @Bean
+  public CloseableHttpClient httpClient() {
+    try {
+      var keyStore = KeyStore.getInstance(CERTIFICATE_TYPE);
+
+      keyStore.load(getClass().getResourceAsStream(fttpProperties.getCertificatePath()),
+          fttpProperties.getCertificateKey().toCharArray());
+
+      SSLContext sslContext =
+          SSLContextBuilder.create().loadKeyMaterial(keyStore, fttpProperties.getCertificateKey().toCharArray()).build();
+
+      HostnameVerifier hostnameVerifier = NoopHostnameVerifier.INSTANCE;
+      SSLConnectionSocketFactory sslFactory =
+          new SSLConnectionSocketFactory(sslContext, hostnameVerifier);
+
+      CloseableHttpClient client;
+
+      if (fttpProperties.isUseBasicAuth()) {
+        var provider = new BasicCredentialsProvider();
+        provider.setCredentials(AuthScope.ANY,
+            new UsernamePasswordCredentials(fttpProperties.getUsername(), fttpProperties.getPassword())
+        );
+
+        client = HttpClients.custom().setSSLSocketFactory(sslFactory).setDefaultCredentialsProvider(provider).build();
+      } else {
+        client = HttpClients.custom().setSSLSocketFactory(sslFactory).build();
+      }
+
+      return client;
+    } catch (Exception e) {
+      log.error("Failed to create http client for fttp communication with cause [{}]", e.getLocalizedMessage());
+    }
+    return null;
+  }
+}

src/main/java/de/vitagroup/num/domain/EntityGroup.java

@@ -0,0 +1,6 @@
+package de.vitagroup.num.domain;
+
+public enum EntityGroup {
+
+    PROJECT_STATUS;
+}

src/main/java/de/vitagroup/num/domain/Project.java

@@ -1,52 +1,34 @@
 package de.vitagroup.num.domain;
 
 import com.fasterxml.jackson.annotation.JsonBackReference;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonManagedReference;
+import de.vitagroup.num.domain.admin.UserDetails;
 import de.vitagroup.num.domain.repository.CategorySetConverter;
 import de.vitagroup.num.domain.repository.MapConverter;
-import de.vitagroup.num.domain.admin.UserDetails;
 import de.vitagroup.num.domain.repository.StringSetConverter;
+import lombok.*;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.ObjectUtils;
+import org.hibernate.annotations.JoinColumnOrFormula;
+import org.hibernate.annotations.NotFound;
+import org.hibernate.annotations.NotFoundAction;
 
+import javax.persistence.*;
 import java.io.Serializable;
 import java.time.LocalDate;
-import java.util.HashSet;
-import java.util.Set;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-
-import lombok.AllArgsConstructor;
-import lombok.Builder;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.NoArgsConstructor;
-
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.CascadeType;
-import javax.persistence.Convert;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
 import java.time.OffsetDateTime;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-
-import lombok.ToString;
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.lang3.ObjectUtils;
+import java.util.Set;
 
 @Entity
 @Data
 @NoArgsConstructor
 @AllArgsConstructor
 @Builder
-@EqualsAndHashCode(exclude = {"cohort", "transitions"})
+@EqualsAndHashCode(exclude = {"cohort", "transitions","translations"})
 public class Project implements Serializable {
 
   @Id
@@ -105,11 +87,25 @@ public class Project implements Serializable {
       inverseJoinColumns = @JoinColumn(name = "user_details_id"))
   private List<UserDetails> researchers;
 
+  @JsonIgnore
+  @ToString.Exclude
+  @OneToMany(fetch = FetchType.LAZY)
+  @JoinColumnOrFormula(column = @JoinColumn(name = "property", referencedColumnName = "status", insertable = false, updatable = false))
+  @NotFound(action = NotFoundAction.IGNORE)
+  private Set<Translation> translations = new HashSet<>();
+
   @ToString.Exclude
   @JsonManagedReference
   @OneToMany(mappedBy = "project", cascade = CascadeType.ALL, orphanRemoval = true)
   private Set<ProjectTransition> transitions = new HashSet<>();
 
+  public Project(Long id, String name, OffsetDateTime createDate, UserDetails coordinator) {
+    this.id = id;
+    this.name = name;
+    this.createDate = createDate;
+    this.coordinator = coordinator;
+  }
+
   public boolean hasEmptyOrDifferentOwner(String userId) {
     return ObjectUtils.isEmpty(coordinator) || !coordinator.getUserId().equals(userId);
   }

src/main/java/de/vitagroup/num/domain/ProjectStatus.java

@@ -110,7 +110,7 @@ public static List<ProjectStatus> getAllProjectStatusToViewAsCoordinator() {
   }
 
   public static List<ProjectStatus> getAllProjectStatusToViewAsResearcher() {
-    return Arrays.asList(ProjectStatus.PUBLISHED, ProjectStatus.CLOSED);
+    return Arrays.asList(ProjectStatus.PUBLISHED);
   }
 
   public static List<ProjectStatus> getAllProjectStatusToViewAsApprover() {

src/main/java/de/vitagroup/num/domain/Translation.java

@@ -0,0 +1,39 @@
+package de.vitagroup.num.domain;
+
+import de.vitagroup.num.domain.dto.Language;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+
+import javax.persistence.*;
+
+@Entity
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+@Cacheable
+@Cache(usage = CacheConcurrencyStrategy.READ_ONLY)
+public class Translation {
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    private Long id;
+
+    @Column(name = "entity_group", nullable = false)
+    @Enumerated(EnumType.STRING)
+    private EntityGroup entityGroup;
+
+    @Column(name = "entity_id")
+    private Long entityId;
+
+    @Column(nullable = false)
+    private String property;
+
+    @Column(nullable = false)
+    private String value;
+
+    @Column(name = "language_code", nullable = false)
+    @Enumerated(EnumType.STRING)
+    private Language language;
+}

src/main/java/de/vitagroup/num/domain/dto/CohortGroupDto.java

@@ -22,7 +22,7 @@
 @NoArgsConstructor
 public class CohortGroupDto {
 
-  @ApiModelProperty(value = "The unique identifier", example = "1")
+  @ApiModelProperty(value = "The unique identifier", example = "1", hidden = true)
   private Long id;
 
   @ApiModelProperty(value = "Cohort group operation to be applied to the children", example = "AND")

src/main/java/de/vitagroup/num/domain/dto/ProjectViewTO.java

@@ -9,6 +9,7 @@
 import lombok.NoArgsConstructor;
 
 import java.time.LocalDate;
+import java.time.OffsetDateTime;
 
 @Data
 @Builder
@@ -29,4 +30,6 @@ public class ProjectViewTO {
 
     private LocalDate endDate;
 
+    private OffsetDateTime createDate;
+
 }

src/main/java/de/vitagroup/num/domain/dto/SearchCriteria.java

@@ -27,6 +27,10 @@ public class SearchCriteria {
     // boolean flag used for users search/filter (optional)
     public static final String FILTER_USER_WITH_ROLES_KEY = "withRoles";
 
+    private static final String AUTHOR_NAME = "author";
+
+    public static final String FILTER_BY_STATUS = "status";
+
     private Map<String, ?> filter;
 
     private String sort;
@@ -44,4 +48,7 @@ public boolean isValid() {
         }
         return true;
     }
+    public boolean isSortByAuthor() {
+        return AUTHOR_NAME.equals(this.getSortBy());
+    }
 }

src/main/java/de/vitagroup/num/domain/repository/ProjectRepository.java

@@ -2,6 +2,7 @@
 
 import de.vitagroup.num.domain.Project;
 import de.vitagroup.num.domain.ProjectStatus;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.stereotype.Repository;
@@ -23,4 +24,9 @@ public interface ProjectRepository extends JpaRepository<Project, Long>, CustomP
       nativeQuery = true)
   List<Project> findLatestProjects(
       int count, String status1, String status2, String status3);
+
+
+  @Query(value = "SELECT new Project(pr.id, pr.name, pr.createDate, pr.coordinator) FROM Project pr " +
+          "WHERE pr.status IN (:statuses) ORDER BY pr.createDate DESC ")
+  List<Project> findByStatusInOrderByCreateDateDesc(List<ProjectStatus> statuses, Pageable pageable);
 }

src/main/java/de/vitagroup/num/domain/repository/ProjectRepositoryImpl.java

@@ -1,5 +1,6 @@
 package de.vitagroup.num.domain.repository;
 
+import de.vitagroup.num.domain.EntityGroup;
 import de.vitagroup.num.domain.Organization;
 import de.vitagroup.num.domain.Project;
 import de.vitagroup.num.domain.admin.UserDetails;
@@ -44,7 +45,7 @@ public Page<Project> findProjects(ProjectSpecification projectSpecification, Pag
         if (projectSpecification.getSortOrder() != null) {
             Sort.Order sortOrder = projectSpecification.getSortOrder();
             Expression<?> orderByExpression = null;
-            if (projectSpecification.getSortOrder().getProperty().equals("organization")) {
+            if (ProjectSpecification.COORDINATOR_ORGANIZATION.equals(projectSpecification.getSortOrder().getProperty())) {
                 Fetch<Project, UserDetails> coordinator = root.fetch("coordinator");
                 Fetch<UserDetails, Organization> organization = coordinator.fetch("organization", JoinType.LEFT);
                 Join<Project, UserDetails> coordinatorJoin = (Join<Project, UserDetails>) coordinator;
@@ -53,7 +54,16 @@ public Page<Project> findProjects(ProjectSpecification projectSpecification, Pag
                 groupByExpressions.add(organizationJoin.get("id"));
                 orderByExpression = organizationJoin.get("name");
             } else {
-                if (!"author".equals(sortOrder.getProperty())) {
+                if (ProjectSpecification.COLUMN_PROJECT_STATUS.equals(projectSpecification.getSortOrder().getProperty())) {
+                    Join<Object, Object> translationJoin = root.join("translations", JoinType.LEFT);
+                    translationJoin.on(cb.and(
+                            cb.equal(translationJoin.get("entityGroup"), EntityGroup.PROJECT_STATUS),
+                            cb.equal(translationJoin.get("language"), projectSpecification.getLanguage()),
+                            cb.equal(translationJoin.get("property"), root.get("status"))
+                    ));
+                    groupByExpressions.add(translationJoin.get("value"));
+                    orderByExpression = translationJoin.get("value");
+                } else if (!"author".equals(sortOrder.getProperty())) {
                     orderByExpression = root.get(sortOrder.getProperty());
                 }
             }