Select contacts (#464)

* add selection component to project edit form * Fix ontology column size and type * Fix ontology column size and type * provide prefill for add project as well complicated setup of add project made this difficult. further refactoring might be needed. * Fix stepper * introduce HasBinder interface * fix dialog validation and scope Co-authored-by: steffengreiner <[email protected]> * Add JavaDoc * Use HasBinderValidation for AutocompleteContactField * add javadoc * Fix field title * Remove unused methods * "Fix" column names. These should be adapted in the future. Using the plural for singular column is not good IMHO. * Adjust terms used to fit the database * Improve JavaDoc Co-authored-by: steffengreiner <[email protected]> * Add placeholder Co-authored-by: steffengreiner <[email protected]> * do not require the view object to contain data * remove hard-coded 100 width and height * remove unused annotation * add error message to requireNonNull * move page size to css * Fix wrong mapping Co-authored-by: steffengreiner <[email protected]> --------- Co-authored-by: Tobias Koch <[email protected]> Co-authored-by: steffengreiner <[email protected]>
qbicsoftware · Jan 25, 2024 · 8bab447 · 8bab447
1 parent 18691f5
commit 8bab447
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diff --git a/...n/java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermJpaRepository.java b/...n/java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermJpaRepository.java
@@ -41,14 +41,15 @@ public List<OntologyClassEntity> query(int offset, int limit) {
   private String buildSearchTerm(String searchString) {
     StringBuilder searchTermBuilder = new StringBuilder();
     for(String word : searchString.split(" ")) {
-      searchTermBuilder.append(" +" + word);
+      searchTermBuilder.append(" +").append(word);
     }
     searchTermBuilder.append("*");
     return searchTermBuilder.toString().trim();
   }
 
   @Override
-  public List<OntologyClassEntity> query(String searchString, List<String> ontologyAbbreviations,
+  public List<OntologyClassEntity> query(String searchString,
+      List<String> ontologyAbbreviations,
       int offset,
       int limit, List<SortOrder> sortOrders) {
     List<Order> orders = sortOrders.stream().map(it -> {

diff --git a/...main/java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermRepository.java b/...main/java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermRepository.java
@@ -19,9 +19,5 @@ public interface OntologyTermRepository extends
       countQuery = "SELECT count(*) FROM ontology_classes WHERE MATCH(label) AGAINST(?1 IN BOOLEAN MODE) AND ontology in (?2);",
       nativeQuery = true)
   Page<OntologyClassEntity> findByLabelFulltextMatching(
-      String termFilter, List<String> ontology, Pageable pageable);
-
-  Page<OntologyClassEntity> findByLabelNotNullAndOntologyIn(List<String> ontologies, Pageable pageable);
-
-  Page<OntologyClassEntity> findByLabelStartingWithIgnoreCaseAndOntologyIn(String filter, List<String> ontology, Pageable pageable);
+      String termFilter, List<String> ontologyAbbreviations, Pageable pageable);
 }
diff --git a/.../java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermRepositoryImpl.java b/.../java/life/qbic/projectmanagement/infrastructure/ontology/OntologyTermRepositoryImpl.java
@@ -38,7 +38,7 @@ public OntologyTermRepositoryImpl(QbicOntologyTermRepo ontologyTermRepo) {
 
   @Override
   public List<OntologyClassEntity> find(String name) {
-    return ontologyTermRepo.findOntologyTermByName(name);
+    return ontologyTermRepo.findOntologyClassEntitiesByClassName(name);
   }
 
   @Override

diff --git a/...c/main/java/life/qbic/projectmanagement/infrastructure/ontology/QbicOntologyTermRepo.java b/...c/main/java/life/qbic/projectmanagement/infrastructure/ontology/QbicOntologyTermRepo.java
@@ -17,5 +17,5 @@
  */
 public interface QbicOntologyTermRepo extends CrudRepository<OntologyClassEntity, Long> {
 
-  List<OntologyClassEntity> findOntologyTermByName(String name);
+  List<OntologyClassEntity> findOntologyClassEntitiesByClassName(String name);
 }
diff --git a/...t-management/src/main/java/life/qbic/projectmanagement/application/ContactRepository.java b/...t-management/src/main/java/life/qbic/projectmanagement/application/ContactRepository.java
@@ -0,0 +1,29 @@
+package life.qbic.projectmanagement.application;
+
+import java.util.List;
+import life.qbic.projectmanagement.domain.model.project.Contact;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ContactRepository {
+
+  public List<Contact> findAll() {
+    //TODO implement
+    return dummyContacts();
+  }
+
+  private static List<Contact> dummyContacts() {
+    return List.of(
+        new Contact("Max Mustermann", "[email protected]"),
+        new Contact("David Müller", "[email protected]"),
+        new Contact("John Koch", "[email protected]"),
+        new Contact("Trevor Noah", "[email protected]"),
+        new Contact("Sarah Connor", "[email protected]"),
+        new Contact("Anna Bell", "[email protected]"),
+        new Contact("Sophia Turner", "[email protected]"),
+        new Contact("Tylor Smith", "[email protected]")
+    );
+  }
+
+
+}
diff --git a/...management/src/main/java/life/qbic/projectmanagement/application/OntologyClassEntity.java b/...management/src/main/java/life/qbic/projectmanagement/application/OntologyClassEntity.java
@@ -1,5 +1,6 @@
 package life.qbic.projectmanagement.application;
 
+import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
 import jakarta.persistence.GeneratedValue;
 import jakarta.persistence.Id;
@@ -10,18 +11,19 @@
 @Table(name = "ontology_classes")
 public class OntologyClassEntity {
 
-  String ontology;
-
+  @Column(name = "ontology")
+  String ontologyAbbreviation;
+  @Column(name = "ontologyVersion")
   String ontologyVersion;
-
+  @Column(name = "ontologyIri")
   String ontologyIri;
-
-  String label;
-
-  String name;
-
+  @Column(name = "label")
+  String classLabel;
+  @Column(name = "name")
+  String className;
+  @Column(name = "description", length = 2000)
   String description;
-
+  @Column(name = "classIri")
   String classIri;
 
   @Id
@@ -31,23 +33,24 @@ public class OntologyClassEntity {
   public OntologyClassEntity() {
   }
 
-  public OntologyClassEntity(String ontology, String ontologyVersion, String ontologyIri,
-      String label, String name, String description, String classIri) {
-    this.ontology = ontology;
+  public OntologyClassEntity(String ontologyAbbreviation, String ontologyVersion,
+      String ontologyIri,
+      String classLabel, String className, String description, String classIri) {
+    this.ontologyAbbreviation = ontologyAbbreviation;
     this.ontologyVersion = ontologyVersion;
     this.ontologyIri = ontologyIri;
-    this.label = label;
-    this.name = name;
+    this.classLabel = classLabel;
+    this.className = className;
     this.description = description;
     this.classIri = classIri;
   }
 
-  public String getOntology() {
-    return ontology;
+  public String getOntologyAbbreviation() {
+    return ontologyAbbreviation;
   }
 
-  public void setOntology(String ontology) {
-    this.ontology = ontology;
+  public void setOntologyAbbreviation(String ontology) {
+    this.ontologyAbbreviation = ontology;
   }
 
   public String getOntologyVersion() {
@@ -66,20 +69,20 @@ public void setOntologyIri(String ontologyIri) {
     this.ontologyIri = ontologyIri;
   }
 
-  public String getLabel() {
-    return label;
+  public String getClassLabel() {
+    return classLabel;
   }
 
-  public void setLabel(String label) {
-    this.label = label;
+  public void setClassLabel(String label) {
+    this.classLabel = label;
   }
 
-  public String getName() {
-    return name;
+  public String getClassName() {
+    return className;
   }
 
-  public void setName(String name) {
-    this.name = name;
+  public void setClassName(String name) {
+    this.className = name;
   }
 
   public String getDescription() {
@@ -107,16 +110,17 @@ public boolean equals(Object o) {
       return false;
     }
     OntologyClassEntity that = (OntologyClassEntity) o;
-    return Objects.equals(ontology, that.ontology) && Objects.equals(
+    return Objects.equals(ontologyAbbreviation, that.ontologyAbbreviation) && Objects.equals(
         ontologyVersion, that.ontologyVersion) && Objects.equals(ontologyIri,
-        that.ontologyIri) && Objects.equals(label, that.label) && Objects.equals(
-        name, that.name) && Objects.equals(description, that.description)
+        that.ontologyIri) && Objects.equals(classLabel, that.classLabel) && Objects.equals(
+        className, that.className) && Objects.equals(description, that.description)
         && Objects.equals(classIri, that.classIri);
   }
 
   @Override
   public int hashCode() {
-    return Objects.hash(ontology, ontologyVersion, ontologyIri, label, name, description, classIri);
+    return Objects.hash(ontologyAbbreviation, ontologyVersion, ontologyIri, classLabel, className,
+        description, classIri);
   }
 
   public Long getId() {
@@ -126,4 +130,4 @@ public Long getId() {
   public void setId(Long id) {
     this.id = id;
   }
-}
+}
diff --git a/...src/main/java/life/qbic/projectmanagement/application/OntologyTermInformationService.java b/...src/main/java/life/qbic/projectmanagement/application/OntologyTermInformationService.java
@@ -45,7 +45,7 @@ public List<OntologyClassEntity> queryOntologyTerm(String termFilter, List<Strin
       int offset, int limit, List<SortOrder> sortOrders) {
     // returned by JPA -> UnmodifiableRandomAccessList
     List<OntologyClassEntity> termList = ontologyTermLookup.query(termFilter, ontologyAbbreviations, offset,
-        50, sortOrders);
+        limit, sortOrders);
     // the list must be modifiable for spring security to filter it
     return new ArrayList<>(termList);
   }

diff --git a/...anagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java b/...anagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java
@@ -3,21 +3,18 @@
 import jakarta.persistence.AttributeOverride;
 import jakarta.persistence.CascadeType;
 import jakarta.persistence.Column;
-import jakarta.persistence.Convert;
 import jakarta.persistence.Embedded;
 import jakarta.persistence.EmbeddedId;
 import jakarta.persistence.Entity;
 import jakarta.persistence.JoinColumn;
 import jakarta.persistence.OneToOne;
 import jakarta.persistence.Table;
 import java.util.Objects;
-import life.qbic.projectmanagement.domain.model.Ontology;
 import life.qbic.projectmanagement.domain.model.batch.Batch;
 import life.qbic.projectmanagement.domain.model.experiment.BiologicalReplicate;
 import life.qbic.projectmanagement.domain.model.experiment.Experiment;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentId;
 import life.qbic.projectmanagement.domain.model.experiment.ExperimentalGroup;
-import life.qbic.projectmanagement.domain.model.experiment.repository.jpa.OntologyClassAttributeConverter;
 import life.qbic.projectmanagement.domain.model.experiment.vocabulary.OntologyClassDTO;
 import life.qbic.projectmanagement.domain.model.sample.Sample;
 import life.qbic.projectmanagement.domain.model.sample.SampleCode;
@@ -54,11 +51,8 @@ public class SamplePreview {
   @OneToOne(cascade = CascadeType.ALL)
   @JoinColumn(name = "experimentalGroupId")
   private ExperimentalGroup experimentalGroup;
-  @Convert(converter = OntologyClassAttributeConverter.class)
   private OntologyClassDTO species;
-  @Convert(converter = OntologyClassAttributeConverter.class)
   private OntologyClassDTO specimen;
-  @Convert(converter = OntologyClassAttributeConverter.class)
   private OntologyClassDTO analyte;
 
   protected SamplePreview() {

diff --git a/...agement/src/main/java/life/qbic/projectmanagement/domain/model/experiment/Experiment.java b/...agement/src/main/java/life/qbic/projectmanagement/domain/model/experiment/Experiment.java
@@ -1,7 +1,6 @@
 package life.qbic.projectmanagement.domain.model.experiment;
 
 import jakarta.persistence.Column;
-import jakarta.persistence.Convert;
 import jakarta.persistence.ElementCollection;
 import jakarta.persistence.Embedded;
 import jakarta.persistence.EmbeddedId;
@@ -18,7 +17,6 @@
 import life.qbic.projectmanagement.domain.model.experiment.exception.ConditionExistsException;
 import life.qbic.projectmanagement.domain.model.experiment.exception.ExperimentalVariableExistsException;
 import life.qbic.projectmanagement.domain.model.experiment.exception.ExperimentalVariableNotDefinedException;
-import life.qbic.projectmanagement.domain.model.experiment.repository.jpa.OntologyClassAttributeConverter;
 import life.qbic.projectmanagement.domain.model.experiment.vocabulary.OntologyClassDTO;
 
 
@@ -43,13 +41,15 @@ public class Experiment {
   private ExperimentalDesign experimentalDesign;
 
   @ElementCollection(targetClass = OntologyClassDTO.class)
-  @Convert(converter = OntologyClassAttributeConverter.class)
+  @Column(name = "analytes", columnDefinition = "longtext CHECK (json_valid(`analyte`))")
+  //FIXME should be `analyte`in the database and here
   private List<OntologyClassDTO> analytes = new ArrayList<>();
   @ElementCollection(targetClass = OntologyClassDTO.class)
-  @Convert(converter = OntologyClassAttributeConverter.class)
+  @Column(name = "species", columnDefinition = "longtext CHECK (json_valid(`species`))")
   private List<OntologyClassDTO> species = new ArrayList<>();
   @ElementCollection(targetClass = OntologyClassDTO.class)
-  @Convert(converter = OntologyClassAttributeConverter.class)
+  @Column(name = "specimens", columnDefinition = "longtext CHECK (json_valid(`specimen`))")
+  //FIXME should be `specimen`in the database and here
   private List<OntologyClassDTO> specimens = new ArrayList<>();
 
 

diff --git a/...ectmanagement/domain/model/experiment/repository/jpa/OntologyClassAttributeConverter.java b/...ectmanagement/domain/model/experiment/repository/jpa/OntologyClassAttributeConverter.java
@@ -6,9 +6,10 @@
 import jakarta.persistence.Converter;
 import life.qbic.projectmanagement.domain.model.experiment.vocabulary.OntologyClassDTO;
 
-@Converter()
-public class OntologyClassAttributeConverter implements AttributeConverter<OntologyClassDTO,
-    String> {
+@Converter(autoApply = true)
+
+public class OntologyClassAttributeConverter implements
+    AttributeConverter<OntologyClassDTO, String> {
 
   private static final ObjectMapper objectMapper = new ObjectMapper();
 
@@ -23,11 +24,11 @@ public String convertToDatabaseColumn(OntologyClassDTO attribute) {
 
   @Override
   public OntologyClassDTO convertToEntityAttribute(String dbData) {
-      try {
-        return objectMapper.readValue(dbData, OntologyClassDTO.class);
-      } catch (JsonProcessingException e) {
-        throw new RuntimeException(e);
-      }
+    try {
+      return objectMapper.readValue(dbData, OntologyClassDTO.class);
+    } catch (JsonProcessingException e) {
+      throw new RuntimeException(e);
+    }
   }
 
 }