Merge pull request #183 from kit-data-manager/review-api-lists

Avoid the use of lists in APIs and replace them with appropriate interfaces.

Author: Pfeil

src/main/java/edu/kit/datamanager/ro_crate/Crate.java

@@ -2,8 +2,8 @@
 
 import java.io.File;
 import java.util.Collection;
-import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 
 import edu.kit.datamanager.ro_crate.context.CrateMetadataContext;
 import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
@@ -25,13 +25,13 @@ public interface Crate {
    * Read version from the crate descriptor and return it as a class
    * representation.
    * 
-   * NOTE: If there is not version in the crate, it does not comply with the
+   * NOTE: If there is no version in the crate, it does not comply with the
    * specification.
    * 
    * @return the class representation indication the version of this crate, if
    *         available.
    */
-  public Optional<CrateVersion> getVersion();
+  Optional<CrateVersion> getVersion();
 
   /**
    * Returns strings indicating the conformance of a crate with other
@@ -45,7 +45,7 @@ public interface Crate {
    * @return a collection of the profiles or specifications this crate conforms
    *         to.
    */
-  public Collection<String> getProfiles();
+  Collection<String> getProfiles();
 
   CratePreview getPreview();
 
@@ -63,11 +63,11 @@ public interface Crate {
 
   DataEntity getDataEntityById(java.lang.String id);
 
-  List<DataEntity> getAllDataEntities();
+  Set<DataEntity> getAllDataEntities();
 
   ContextualEntity getContextualEntityById(java.lang.String id);
 
-  List<ContextualEntity> getAllContextualEntities();
+  Set<ContextualEntity> getAllContextualEntities();
 
   AbstractEntity getEntityById(java.lang.String id);
 
@@ -77,15 +77,15 @@ public interface Crate {
 
   void deleteEntityById(String entityId);
 
-  void setUntrackedFiles(List<File> files);
+  void setUntrackedFiles(Collection<File> files);
 
   void addFromCollection(Collection<AbstractEntity> entities);
 
   void addItemFromDataCite(String locationUrl);
 
-  public void deleteValuePairFromContext(String key);
+  void deleteValuePairFromContext(String key);
 
-  public void deleteUrlFromContext(String url);
+  void deleteUrlFromContext(String url);
 
-  List<File> getUntrackedFiles();
+  Collection<File> getUntrackedFiles();
 }

src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java

@@ -24,11 +24,7 @@
 
 import java.io.File;
 import java.net.URI;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
 
@@ -50,7 +46,7 @@ public class RoCrate implements Crate {
     private RootDataEntity rootDataEntity;
     private ContextualEntity jsonDescriptor;
 
-    private List<File> untrackedFiles;
+    private Collection<File> untrackedFiles;
 
     @Override
     public CratePreview getPreview() {
@@ -86,7 +82,7 @@ public void setRootDataEntity(RootDataEntity rootDataEntity) {
      */
     public RoCrate() {
         this.roCratePayload = new RoCratePayload();
-        this.untrackedFiles = new ArrayList<>();
+        this.untrackedFiles = new HashSet<>();
         this.metadataContext = new RoCrateMetadataContext();
         rootDataEntity = new RootDataEntity.RootDataEntityBuilder()
                 .build();
@@ -135,7 +131,6 @@ public Collection<String> getProfiles() {
             return StreamSupport.stream(conformsTo.spliterator(), false)
                     .filter(TreeNode::isObject)
                     .map(obj -> obj.path("@id").asText())
-                    .filter(txt -> !CrateVersion.fromSpecUri(txt).isPresent())
                     .collect(Collectors.toSet());
         } else {
             return Collections.emptySet();
@@ -167,8 +162,8 @@ public DataEntity getDataEntityById(java.lang.String id) {
     }
 
     @Override
-    public List<DataEntity> getAllDataEntities() {
-        return this.roCratePayload.getAllDataEntities();
+    public Set<DataEntity> getAllDataEntities() {
+        return new HashSet<>(this.roCratePayload.getAllDataEntities());
     }
 
     @Override
@@ -177,8 +172,8 @@ public ContextualEntity getContextualEntityById(String id) {
     }
 
     @Override
-    public List<ContextualEntity> getAllContextualEntities() {
-        return this.roCratePayload.getAllContextualEntities();
+    public Set<ContextualEntity> getAllContextualEntities() {
+        return new HashSet<>(this.roCratePayload.getAllContextualEntities());
     }
 
     @Override
@@ -213,7 +208,7 @@ public void deleteEntityById(String entityId) {
     }
 
     @Override
-    public void setUntrackedFiles(List<File> files) {
+    public void setUntrackedFiles(Collection<File> files) {
         this.untrackedFiles = files;
     }
 
@@ -238,7 +233,7 @@ public void addItemFromDataCite(String locationUrl) {
     }
 
     @Override
-    public List<File> getUntrackedFiles() {
+    public Collection<File> getUntrackedFiles() {
         return this.untrackedFiles;
     }
 
@@ -254,7 +249,7 @@ public static class RoCrateBuilder {
         CrateMetadataContext metadataContext;
         ContextualEntity license;
         RootDataEntity rootDataEntity;
-        List<File> untrackedFiles;
+        Collection<File> untrackedFiles = new HashSet<>();
 
         JsonDescriptor.Builder descriptorBuilder = new JsonDescriptor.Builder();
 
@@ -268,7 +263,6 @@ public static class RoCrateBuilder {
          */
         public RoCrateBuilder(String name, String description, String datePublished, String licenseId) {
             this.payload = new RoCratePayload();
-            this.untrackedFiles = new ArrayList<>();
             this.metadataContext = new RoCrateMetadataContext();
             this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder()
                     .addProperty("name", name)
@@ -288,7 +282,6 @@ public RoCrateBuilder(String name, String description, String datePublished, Str
          */
         public RoCrateBuilder(String name, String description, String datePublished, ContextualEntity license) {
             this.payload = new RoCratePayload();
-            this.untrackedFiles = new ArrayList<>();
             this.metadataContext = new RoCrateMetadataContext();
             this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder()
                     .addProperty("name", name)
@@ -304,7 +297,6 @@ public RoCrateBuilder(String name, String description, String datePublished, Con
          */
         public RoCrateBuilder() {
             this.payload = new RoCratePayload();
-            this.untrackedFiles = new ArrayList<>();
             this.metadataContext = new RoCrateMetadataContext();
             rootDataEntity = new RootDataEntity.RootDataEntityBuilder()
                     .build();

src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java

@@ -12,7 +12,7 @@
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
-import java.util.List;
+import java.util.Collection;
 import java.util.Map;
 import java.util.Set;
 import java.util.function.Consumer;
@@ -49,12 +49,10 @@ public RoCrateMetadataContext() {
   /**
    * Constructor for creating the context from a list of url.
    *
-   * @param url the url list with different context.
+   * @param urls the url list with different context.
    */
-  public RoCrateMetadataContext(List<String> url) {
-    for (String e : url) {
-      this.addToContextFromUrl(e);
-    }
+  public RoCrateMetadataContext(Collection<String> urls) {
+    urls.forEach(this::addToContextFromUrl);
   }
 
   /**

src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java

@@ -16,12 +16,7 @@
 import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions;
 import edu.kit.datamanager.ro_crate.special.IdentifierUtils;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.UUID;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -57,16 +52,14 @@ public class AbstractEntity {
     private final Set<String> linkedTo;
 
     @JsonIgnore
-    private final List<Observer> observers;
+    private final Set<Observer> observers;
 
     public void addObserver(Observer observer) {
         this.observers.add(observer);
     }
 
     private void notifyObservers() {
-        for (var obs : this.observers) {
-            obs.update(this.getId());
-        }
+        this.observers.forEach(observer -> observer.update(this.getId()));
     }
 
     /**
@@ -78,7 +71,7 @@ public AbstractEntity(AbstractEntityBuilder<?> entityBuilder) {
         this.types = entityBuilder.types;
         this.properties = entityBuilder.properties;
         this.linkedTo = entityBuilder.relatedItems;
-        this.observers = new ArrayList<>();
+        this.observers = new HashSet<>();
         if (this.properties.get("@id") == null) {
             if (entityBuilder.id == null) {
                 this.properties.put("@id", UUID.randomUUID().toString());
@@ -154,12 +147,12 @@ public void removeProperty(String key) {
     }
 
     /**
-     * removes a list of properties from an entity.
+     * Removes a collection of properties from an entity.
      *
-     * @param keyList list of keys, which will be removed.
+     * @param keys collection of keys, which will be removed.
      */
-    public void removeProperties(List<String> keyList) {
-        this.getProperties().remove(keyList);
+    public void removeProperties(Collection<String> keys) {
+        this.getProperties().remove(keys);
         this.notifyObservers();
     }
 
@@ -265,12 +258,12 @@ private static JsonNode addToIdProperty(String name, String id, JsonNode propert
     }
 
     /**
-     * Adds everything from the stringList to the property "name" as id.
+     * Adds everything from the properties to the property "name" as id.
      *
      * @param name the key of the property.
-     * @param stringList List containing all the id as String.
+     * @param properties a collection containing all the id as String.
      */
-    public void addIdListProperties(String name, Collection<String> stringList) {
+    public void addIdListProperties(String name, Collection<String> properties) {
         ObjectMapper objectMapper = MyObjectMapper.getMapper();
         ArrayNode node = objectMapper.createArrayNode();
         if (this.properties.get(name) == null) {
@@ -280,7 +273,7 @@ public void addIdListProperties(String name, Collection<String> stringList) {
                 node.add(this.properties.get(name));
             }
         }
-        for (String s : stringList) {
+        for (String s : properties) {
             this.linkedTo.add(s);
             node.add(objectMapper.createObjectNode().put("@id", s));
         }
@@ -395,12 +388,12 @@ public T addType(String type) {
         }
 
         /**
-         * Adding multiple types as list.
+         * Adds multiple types in one call.
          *
-         * @param types the types in a String List.
+         * @param types the types to add.
          * @return the generic builder.
          */
-        public T addTypes(List<String> types) {
+        public T addTypes(Collection<String> types) {
             if (this.types == null) {
                 this.types = new HashSet<>();
             }

src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java

@@ -2,25 +2,23 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 
 /**
  * A helping class for the creation of workflow data entities.
  */
 public class WorkflowEntity extends FileEntity {
 
-  private static final List<String> TYPES = List.of(
-      new String[]{"SoftwareSourceCode", "ComputationalWorkflow"});
+  private static final Set<String> TYPES = Set.of("SoftwareSourceCode", "ComputationalWorkflow");
 
   /**
    * Constructor for creating the workflow entity from a builder.
    *
    * @param entityBuilder the builder from which the entity should be created.
    */
-  public WorkflowEntity(AbstractWorkflowEntityBuilder<?> entityBuilder) {
+  private WorkflowEntity(AbstractWorkflowEntityBuilder<?> entityBuilder) {
     super(entityBuilder);
-    for (String str : TYPES) {
-      this.addType(str);
-    }
+    TYPES.forEach(this::addType);
     this.addIdListProperties("input", entityBuilder.input);
     this.addIdListProperties("output", entityBuilder.output);
   }

src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java

@@ -7,7 +7,7 @@
 import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
 
 import java.util.Collection;
-import java.util.List;
+import java.util.Set;
 
 /**
  * Interface for the ROCrate payload.
@@ -32,11 +32,11 @@ public interface CratePayload {
 
   void addEntities(Collection<AbstractEntity> entity);
 
-  List<AbstractEntity> getAllEntities();
+  Set<AbstractEntity> getAllEntities();
 
-  List<DataEntity> getAllDataEntities();
+  Set<DataEntity> getAllDataEntities();
 
-  List<ContextualEntity> getAllContextualEntities();
+  Set<ContextualEntity> getAllContextualEntities();
 
   ArrayNode getEntitiesMetadata();