Support .ELN-style crates in all zip readers and writers

build.gradle

@@ -71,6 +71,11 @@ dependencies {
     implementation("org.freemarker:freemarker:2.3.34")
 }
 
+// enable -Xlint:deprecation
+tasks.withType(JavaCompile).configureEach {
+    options.compilerArgs << "-Xlint:deprecation"
+}
+
 logging.captureStandardOutput LogLevel.INFO
 
 def signingTasks = tasks.withType(Sign)

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

@@ -113,9 +113,10 @@ public boolean checkEntity(AbstractEntity entity) {
     node.remove("@id");
     node.remove("@type");
 
-    Set<String> types = objectMapper.convertValue(entity.getProperties().get("@type"),
-        new TypeReference<>() {
-        });
+    Set<String> types = objectMapper.convertValue(
+            entity.getProperties().path("@type"),
+            new TypeReference<>() {}
+    );
     // check if the items in the array of types are present in the context
     for (String s : types) {
       // special cases:
@@ -174,15 +175,14 @@ public void addToContextFromUrl(String url) {
       }
     }
     if (jsonNode == null) {
-      CloseableHttpClient httpclient = HttpClients.createDefault();
       HttpGet httpGet = new HttpGet(url);
       CloseableHttpResponse response;
-      try {
+      try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
         response = httpclient.execute(httpGet);
         jsonNode = objectMapper.readValue(response.getEntity().getContent(),
             JsonNode.class);
       } catch (IOException e) {
-        System.err.println(String.format("Cannot get context from url %s", url));
+        System.err.printf("Cannot get context from url %s%n", url);
         return;
       }
       if (url.equals(DEFAULT_CONTEXT)) {

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

@@ -558,20 +558,62 @@ public T addIdFromCollectionOfEntities(String name, Collection<AbstractEntity> e
         }
 
         /**
-         * This sets everything from a json object to the property. Can be
-         * useful when the entity is already available somewhere.
+         * Deprecated. Equivalent to {@link #setAllIfValid(ObjectNode)}.
          *
          * @param properties the Json representing all the properties.
-         * @return the generic builder.
+         * @return the generic builder, either including all given properties
+         *          * or unchanged.
+         *
+         * @deprecated To enforce the user know what this method does,
+         *   we want the user to use one of the more explicitly named
+         *   methods {@link #setAllIfValid(ObjectNode)} or
+         *   {@link #setAllIfValid(ObjectNode)}.
+         * @see #setAllIfValid(ObjectNode)
          */
+        @Deprecated(since = "2.1.0", forRemoval = true)
         public T setAll(ObjectNode properties) {
+            return setAllIfValid(properties);
+        }
+
+        /**
+         * This sets everything from a json object to the property,
+         * <b>if the result is valid</b>. Otherwise, it will do <b>nothing</b>.
+         * <p>
+         * Valid means here that the json object needs to be flat as specified
+         * in the RO-Crate specification. In principle, this means that
+         * primitives and objects referencing an ID are allowed,
+         * as well as arrays of these.
+         *
+         * @param properties the Json representing all the properties.
+         * @return the generic builder, either including all given properties
+         * or unchanged.
+         */
+        public T setAllIfValid(ObjectNode properties) {
             if (AbstractEntity.entityValidation.entityValidation(properties)) {
                 this.properties = properties;
                 this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties));
             }
             return self();
         }
 
+        /**
+         * This sets everything from a json object to the property. Can be
+         * useful when the entity is already available somewhere.
+         * <p>
+         * Errors on validation are printed, but everything will be added.
+         * For more about validation, see {@link #setAllIfValid(ObjectNode)}.
+         *
+         * @param properties the Json representing all the properties.
+         * @return the generic builder with all properties added.
+         */
+        public T setAllUnsafe(ObjectNode properties) {
+            // This will currently only print errors.
+            AbstractEntity.entityValidation.entityValidation(properties);
+            this.properties = properties;
+            this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties));
+            return self();
+        }
+
         public abstract T self();
 
         public abstract AbstractEntity build();

src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java

@@ -13,8 +13,8 @@
 
 public class JsonDescriptor extends ContextualEntity {
 
-    private static final String CONFORMS_TO = "conformsTo";
-    protected static final String ID = "ro-crate-metadata.json";
+    protected static final String CONFORMS_TO = "conformsTo";
+    public static final String ID = "ro-crate-metadata.json";
 
     /**
      * Returns a JsonDescriptor with the conformsTo value set to the latest stable
@@ -39,7 +39,7 @@ private JsonDescriptor(ContextualEntityBuilder builder) {
 
     /**
      * Builder for the JsonDescriptor.
-     * 
+     * <p>
      * Defaults to the latest stable crate version and no other conformsTo values.
      */
     public static final class Builder {

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

@@ -5,19 +5,11 @@
 import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
 import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
 import static edu.kit.datamanager.ro_crate.special.IdentifierUtils.isUrl;
-import edu.kit.datamanager.ro_crate.util.ZipUtil;
 
-import java.io.File;
-import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
-import net.lingala.zip4j.ZipFile;
-import net.lingala.zip4j.exception.ZipException;
-import net.lingala.zip4j.io.outputstream.ZipOutputStream;
-import net.lingala.zip4j.model.ZipParameters;
-import org.apache.commons.io.FileUtils;
 
 /**
  * The base class of every data entity.
@@ -56,54 +48,6 @@ public void addAuthorId(String id) {
         this.addIdProperty("author", id);
     }
 
-    /**
-     * If the data entity contains a physical file. This method will write it
-     * when the crate is being written to a zip archive.
-     *
-     * @param zipFile the zipFile where it should be written.
-     * @throws ZipException when something goes wrong with the writing to the
-     * zip file.
-     */
-    public void saveToZip(ZipFile zipFile) throws ZipException {
-        if (this.path != null) {
-            ZipParameters zipParameters = new ZipParameters();
-            zipParameters.setFileNameInZip(this.getId());
-            zipFile.addFile(this.path.toFile(), zipParameters);
-        }
-    }
-
-    /**
-     * If the data entity contains a physical file. This method will write it
-     * when the crate is being written to a zip archive.
-     *
-     * @param zipStream The zip output stream where it should be written.
-     * @throws ZipException when something goes wrong with the writing to the
-     * zip file.
-     * @throws IOException If opening the file input stream fails.
-     */
-    public void saveToStream(ZipOutputStream zipStream) throws ZipException, IOException {
-        if (this.path != null) {
-            ZipUtil.addFileToZipStream(zipStream, this.path.toFile(), this.getId());
-        }
-    }
-
-    /**
-     * If the data entity contains a physical file. This method will write it
-     * when the crate is being written to a folder.
-     *
-     * @param file the folder location where the entity should be written.
-     * @throws IOException if something goes wrong with the writing.
-     */
-    public void savetoFile(File file) throws IOException {
-        if (this.getPath() != null) {
-            if (this.getPath().toFile().isDirectory()) {
-                FileUtils.copyDirectory(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());
-            } else {
-                FileUtils.copyFile(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());
-            }
-        }
-    }
-
     @JsonIgnore
     public Path getPath() {
         return path;

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

@@ -4,15 +4,9 @@
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 import edu.kit.datamanager.ro_crate.entities.serializers.HasPartSerializer;
-import edu.kit.datamanager.ro_crate.util.ZipUtil;
-import java.io.IOException;
 
 import java.util.HashSet;
 import java.util.Set;
-import net.lingala.zip4j.ZipFile;
-import net.lingala.zip4j.exception.ZipException;
-import net.lingala.zip4j.io.outputstream.ZipOutputStream;
-import net.lingala.zip4j.model.ZipParameters;
 
 /**
  * A helping class for the creating of Data entities of type Dataset.
@@ -43,26 +37,6 @@ public void removeFromHasPart(String str) {
         this.hasPart.remove(str);
     }
 
-    @Override
-    public void saveToZip(ZipFile zipFile) throws ZipException {
-        if (this.getPath() != null) {
-            ZipParameters parameters = new ZipParameters();
-            parameters.setRootFolderNameInZip(this.getId());
-            parameters.setIncludeRootFolder(false);
-            zipFile.addFolder(this.getPath().toFile(), parameters);
-        }
-    }
-
-    @Override
-    public void saveToStream(ZipOutputStream zipOutputStream) throws IOException {
-        if (this.getPath() != null) {
-            ZipUtil.addFolderToZipStream(
-                    zipOutputStream,
-                    this.getPath().toAbsolutePath().toString(),
-                    this.getId());
-        }
-    }
-
     public void addToHasPart(String id) {
         this.hasPart.add(id);
     }

src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java

@@ -60,6 +60,7 @@ public boolean validateEntity(JsonNode entity) {
     Set<ValidationMessage> errors = this.entitySchema.validate(entity);
     if (errors.size() != 0) {
       System.err.println("This entity does not comply to the basic RO-Crate entity structure.");
+      errors.forEach(error -> System.err.println(error.getMessage()));
       return false;
     }
     return true;

src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java

@@ -112,12 +112,12 @@ private static void addToCrateFromZotero(String url, Crate crate) {
       for (var entity : graph) {
         if (entity.get("@id").asText().equals(mainId)) {
           var dataEntity = new DataEntity.DataEntityBuilder()
-              .setAll((ObjectNode) entity).build();
+              .setAllUnsafe((ObjectNode) entity).build();
           crate.addDataEntity(dataEntity);
         } else {
           // here we have to think of a way to differentiate between data and contextual entities.
           var contextualEntity = new ContextualEntity.ContextualEntityBuilder()
-              .setAll((ObjectNode) entity).build();
+              .setAllUnsafe((ObjectNode) entity).build();
           crate.addContextualEntity(contextualEntity);
         }
       }

src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java

@@ -72,7 +72,7 @@ public static PersonEntity getPerson(String url) {
           node.set(element.getKey(), element.getValue());
         }
       }
-      return new PersonEntity.PersonEntityBuilder().setAll(node).build();
+      return new PersonEntity.PersonEntityBuilder().setAllUnsafe(node).build();
     } catch (IOException e) {
       String errorMessage = String.format("IO error: %s", e.getMessage());
       logger.error(errorMessage);

src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java

@@ -1,6 +1,6 @@
 package edu.kit.datamanager.ro_crate.preview;
 
-import edu.kit.datamanager.ro_crate.util.ZipUtil;
+import edu.kit.datamanager.ro_crate.util.ZipStreamUtil;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
@@ -10,9 +10,9 @@
 import org.apache.commons.io.FileUtils;
 
 /**
- * The default preview should use the rochtml tool
- * (https://www.npmjs.com/package/ro-crate-html-js) for creating a simple
- * preview file.
+ * The default preview should use the
+ * <a href="https://www.npmjs.com/package/ro-crate-html-js">rochtml tool</a>
+ * for creating a simple preview file.
  *
  * @author Nikola Tzotchev on 6.2.2022 г.
  * @version 1
@@ -66,13 +66,13 @@ public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOEx
         if (PreviewGenerator.isRochtmlAvailable()) {
             try {
                 FileUtils.forceMkdir(new File("temp"));
-                try (FileWriter writer = new FileWriter(new File("temp/ro-crate-metadata.json"))) {
+                try (FileWriter writer = new FileWriter("temp/ro-crate-metadata.json")) {
                     writer.write(metadata);
                     writer.flush();
                 }
                 if (PreviewGenerator.isRochtmlAvailable()) {
                     PreviewGenerator.generatePreview("temp");
-                    ZipUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html");
+                    ZipStreamUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html");
                 }
             } finally {
                 try {