+ * This is useful e.g. to assign e.g. a DOI to this crate. + * @param identifier the identifier to add. + * @return this builder. + */ + public RoCrateBuilder addIdentifier(String identifier) { + this.rootDataEntity.addProperty("identifier", identifier.strip()); + return this; + } + public RoCrateBuilder addDescription(String description) { this.rootDataEntity.addProperty(PROPERTY_DESCRIPTION, description); return this; diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java index 580e625b..8699fd5b 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java +++ b/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java @@ -239,33 +239,60 @@ private static boolean addProperty(ObjectNode whereToAdd, String key, JsonNode v * @param id the "id" of the property. */ public void addIdProperty(String name, String id) { - JsonNode jsonNode = addToIdProperty(name, id, this.properties.get(name)); - if (jsonNode != null) { - this.linkedTo.add(id); - this.properties.set(name, jsonNode); - this.notifyObservers(); - } + mergeIdIntoValue(id, this.properties.get(name)) + .ifPresent(newValue -> { + this.linkedTo.add(id); + this.properties.set(name, newValue); + this.notifyObservers(); + }); } - private static JsonNode addToIdProperty(String name, String id, JsonNode property) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - if (name != null && id != null) { - if (property == null) { - return objectMapper.createObjectNode().put("@id", id); - } else { - if (property.isArray()) { - ArrayNode ns = (ArrayNode) property; - ns.add(objectMapper.createObjectNode().put("@id", id)); - return ns; - } else { - ArrayNode newNodes = objectMapper.createArrayNode(); - newNodes.add(property); - newNodes.add(objectMapper.createObjectNode().put("@id", id)); - return newNodes; - } - } + /** + * Merges the given id into the current value, + * using this representation: {"@id" : "id"}. + *
+ * The current value can be null without errors. + * Only the id will be considered in this case. + *
+ * If the id is null-ish, it will not be added, similar to a null-ish value.
+ * If the id is already present, nothing will be done.
+ * If it is not an array and the id is not present, an array will be applied.
+ *
+ * @param id the id to add.
+ * @param currentValue the current value of the property.
+ * @return The updated value of the property.
+ * Empty if value does not change!
+ */
+ private static Optional
+ * NOTE: IDs are not just names! The ID may have effects
+ * on parts of your crate! For example: If the entity represents a
+ * file which will be copied into the crate, writers must use the
+ * ID as filename.
*
* @param id the String representing the id.
* @return the generic builder.
@@ -486,11 +518,11 @@ public T addProperty(String key, boolean value) {
* @return the generic builder
*/
public T addIdProperty(String name, String id) {
- JsonNode jsonNode = AbstractEntity.addToIdProperty(name, id, this.properties.get(name));
- if (jsonNode != null) {
- this.properties.set(name, jsonNode);
- this.relatedItems.add(id);
- }
+ AbstractEntity.mergeIdIntoValue(id, this.properties.get(name))
+ .ifPresent(newValue -> {
+ this.properties.set(name, newValue);
+ this.relatedItems.add(id);
+ });
return self();
}
diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java
index 398615c1..5a627e17 100644
--- a/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java
+++ b/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java
@@ -3,7 +3,6 @@
import edu.kit.datamanager.ro_crate.util.ZipUtil;
import java.io.File;
import java.io.IOException;
-import java.util.Optional;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.io.outputstream.ZipOutputStream;
@@ -13,7 +12,7 @@
/**
* This class adds a static preview to the crate, which consists of a
* metadataHtml file and a folder containing other files required to render
- * metadataHtml. If will be put unchanged to the writer output, i.e., a zip
+ * metadataHtml. It will be put unchanged to the writer output, i.e., a zip
* file, folder, or stream.
*
* @author jejkal
diff --git a/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java b/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java
index 8f32213f..2c733d3e 100644
--- a/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java
+++ b/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java
@@ -4,6 +4,7 @@
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions;
@@ -11,6 +12,7 @@
import org.apache.commons.io.FileUtils;
import io.json.compare.JSONCompare;
import io.json.compare.JsonComparator;
+import org.opentest4j.AssertionFailedError;
import java.io.File;
import java.io.IOException;
@@ -34,8 +36,7 @@ public static void compareEntityWithFile(AbstractEntity entity, String string) t
public static void compare(JsonNode node1, JsonNode node2, Boolean equals) {
var comparator = new JsonComparator() {
- public boolean compareValues(Object expected, Object actual) {
-
+ public boolean compareValues(Object expected, Object actual) {
return expected.equals(actual);
}
@@ -43,6 +44,7 @@ public boolean compareFields(String expected, String actual) {
return expected.equals(actual);
}
};
+
if (equals) {
JSONCompare.assertMatches(node1, node2, comparator);
} else {
@@ -73,6 +75,32 @@ public static void compareTwoCrateJson(Crate crate1, Crate crate2) throws JsonPr
compare(node1, node2, true);
}
+ public static void prettyPrintJsonString(String minimalJsonMetadata) {
+ try {
+ ObjectMapper objectMapper = new ObjectMapper();
+ JsonNode jsonNode = objectMapper.readTree(minimalJsonMetadata);
+ // Enable pretty printing
+ String prettyJson = objectMapper
+ .enable(SerializationFeature.INDENT_OUTPUT)
+ .writeValueAsString(jsonNode);
+ // Print the pretty JSON
+ System.out.println(prettyJson);
+ } catch (JsonProcessingException e) {
+ throw new AssertionFailedError("Not able to process string as JSON!", e);
+ }
+ }
+
+ public static void printAndAssertEquals(RoCrate crate, String pathToResource) {
+ // So you get something to see
+ prettyPrintJsonString(crate.getJsonMetadata());
+ // Compare with the example from the specification
+ try {
+ HelpFunctions.compareCrateJsonToFileInResources(crate, pathToResource);
+ } catch (IOException e) {
+ throw new AssertionFailedError("Missing resources file!", e);
+ }
+ }
+
public static void compareCrateJsonToFileInResources(File file1, File file2) throws IOException {
ObjectMapper objectMapper = MyObjectMapper.getMapper();
JsonNode node1 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file1));
@@ -80,6 +108,13 @@ public static void compareCrateJsonToFileInResources(File file1, File file2) thr
compare(node1, node2, true);
}
+ /**
+ * Compares the JSON metadata of a Crate object with a JSON file in the resources directory.
+ *
+ * @param crate1 The Crate object to compare.
+ * @param jsonFileString The path to the JSON file in the resources directory.
+ * @throws IOException If an error occurs while reading the JSON file.
+ */
public static void compareCrateJsonToFileInResources(Crate crate1, String jsonFileString) throws IOException {
InputStream inputStream = HelpFunctions.class.getResourceAsStream(
jsonFileString);
diff --git a/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java b/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java
new file mode 100644
index 00000000..d699eeae
--- /dev/null
+++ b/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java
@@ -0,0 +1,407 @@
+package edu.kit.datamanager.ro_crate.examples;
+
+import edu.kit.datamanager.ro_crate.RoCrate;
+import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.PersonEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.PlaceEntity;
+import edu.kit.datamanager.ro_crate.entities.data.*;
+
+import edu.kit.datamanager.ro_crate.writer.CrateWriter;
+import org.junit.jupiter.api.Test;
+
+import java.net.URI;
+import java.nio.file.Paths;
+
+import static edu.kit.datamanager.ro_crate.HelpFunctions.printAndAssertEquals;
+
+/**
+ * This class contains examples of the RO-Crate specification version 1.1.
+ *
+ * This is supposed to serve both as a user guide and as a test for the implementation.
+ * Executing a test may also print some interesting information to the console.
+ */
+public class ExamplesOfSpecificationV1p1Test {
+
+ /**
+ * From:
+ * Minimal Example
+ * (location in repo)
+ *
+ * This example produces a minimal crate with a
+ * name, description, date, license and identifier.
+ *
+ * This example produces the same result as
+ * {@link #testMinimalCrateWithoutCrateBuilder()}, but using more convenient APIs.
+ */
+ @Test
+ void testMinimalCrateConvenient() {
+ String licenseID = "https://creativecommons.org/licenses/by-nc-sa/3.0/au/";
+ RoCrate minimal = new RoCrate.RoCrateBuilder(
+ "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...",
+ "Palliative care planning for nursing home residents with advanced dementia ...",
+ "2017",
+ licenseID
+ )
+ // We already had to set the license ID in the builder,
+ // but we can override it with more details to fit the example:
+ .setLicense( new ContextualEntity.ContextualEntityBuilder()
+ .addType("CreativeWork")
+ .setId(licenseID)
+ .addProperty("description", "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
+ .addProperty("identifier", licenseID)
+ .addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
+ .build()
+ )
+ .addIdentifier("https://doi.org/10.4225/59/59672c09f4a4b")
+ .build();
+
+ printAndAssertEquals(minimal, "/spec-v1.1-example-json-files/minimal.json");
+ }
+
+ /**
+ * From:
+ * Minimal Example
+ * (location in repo)
+ *
+ * In this example, the minimal crate is created without the builder.
+ * This should only be done if necessary: Use the builder if possible.
+ * This example produces the same result as {@link #testMinimalCrateConvenient()}.
+ */
+ @Test
+ void testMinimalCrateWithoutCrateBuilder() {
+ RoCrate minimal = new RoCrate();
+
+ ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
+ .addType("CreativeWork")
+ .setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
+ .addProperty("description", "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
+ .addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
+ .addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
+ .build();
+
+ minimal.setRootDataEntity(new RootDataEntity.RootDataEntityBuilder()
+ .addProperty("identifier", "https://doi.org/10.4225/59/59672c09f4a4b")
+ .addProperty("datePublished", "2017")
+ .addProperty("name", "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...")
+ .addProperty("description", "Palliative care planning for nursing home residents with advanced dementia ...")
+ .setLicense(license)
+ .build());
+
+ // This is pretty low-level. We are considering hiding/replacing this detailed API in major versions,
+ // so tell us (for example, open an issue) if you have a use case for it!
+ minimal.setJsonDescriptor(new ContextualEntity.ContextualEntityBuilder()
+ .setId("ro-crate-metadata.json")
+ .addType("CreativeWork")
+ .addIdProperty("about", "./")
+ .addIdProperty("conformsTo", "https://w3id.org/ro/crate/1.1")
+ .build()
+ );
+ minimal.addContextualEntity(license);
+
+ printAndAssertEquals(minimal, "/spec-v1.1-example-json-files/minimal.json");
+ }
+
+ // https://www.researchobject.org/ro-crate/specification/1.1/data-entities.html#example-linking-to-a-file-and-folders
+
+ /**
+ * From:
+ * "Example linking to a file and folders"
+ * (location in repo)
+ *
+ * This example adds a File(Entity) and a DataSet(Entity) to the crate.
+ * The file and the folder are referenced by their location. This way
+ * they will be copied to the crate when writing it using a
+ * {@link CrateWriter}.
+ * The name of the file and the folder will be implicitly set to the
+ * ID of the respective entity in order to conform to the specification.
+ *
+ * Here we use the inner builder classes for the construction of the
+ * crate. In contrast to {@link #testMinimalCrateWithoutCrateBuilder()},
+ * we do not have to care about specification details.
+ */
+ @Test
+ void testLinkingToFileAndFolders() {
+ RoCrate crate = new RoCrate.RoCrateBuilder()
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ // This will tell us where the file is located. It will be copied to the crate.
+ .setLocation(Paths.get("path to file"))
+ // If no ID is given explicitly, the ID will be set to the filename.
+ // Changing the ID means also to set the file name within the crate!
+ .setId("cp7glop.ai")
+ .addProperty("name", "Diagram showing trend to increase")
+ .addProperty("contentSize", "383766")
+ .addProperty("description", "Illustrator file for Glop Pot")
+ .setEncodingFormat("application/pdf")
+ .build()
+ )
+ .addDataEntity(
+ new DataSetEntity.DataSetBuilder()
+ .setLocation(Paths.get("path_to_files"))
+ .setId("lots_of_little_files/")
+ .addProperty("name", "Too many files")
+ .addProperty("description", "This directory contains many small files, that we're not going to describe in detail.")
+ .build()
+ )
+ .build();
+
+ printAndAssertEquals(crate, "/spec-v1.1-example-json-files/files-and-folders.json");
+ }
+
+ /**
+ * From:
+ * Example with web-based data entities
+ * (location in repo)
+ *
+ * This example adds twp FileEntities to the crate.
+ * One is a local file, the other one is located in the web
+ * and will not be copied to the crate.
+ */
+ @Test
+ void testWebBasedDataEntities() {
+ RoCrate crate = new RoCrate.RoCrateBuilder()
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ .setLocation(Paths.get("README.md"))
+ .setId("survey-responses-2019.csv")
+ .addProperty("name", "Survey responses")
+ .addProperty("contentSize", "26452")
+ .setEncodingFormat("text/csv")
+ .build()
+ )
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ .setLocation(URI.create("https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf"))
+ .addProperty("name", "RO-Crate specification")
+ .addProperty("contentSize", "310691")
+ .addProperty("description", "RO-Crate specification")
+ .setEncodingFormat("application/pdf")
+ .build()
+ )
+ .build();
+
+ printAndAssertEquals(crate, "/spec-v1.1-example-json-files/web-based-data-entities.json");
+ }
+
+ /**
+ * From:
+ * Example with file, author, and location
+ * (location in repo)
+ *
+ * This example shows how to connect entities. If there is no specific method like
+ * {@link DataEntity.DataEntityBuilder#addAuthor(String)} for referencing other
+ * entities, one can use the more generic
+ * {@link AbstractEntity.AbstractEntityBuilder#addIdProperty(String, AbstractEntity)}
+ * or {@link AbstractEntity.AbstractEntityBuilder#addIdProperty(String, String)}.
+ *
+ * Important Note! If you connect entities, make sure all entities are being
+ * added to the crate. We currently can't enforce this properly yet.
+ */
+ @Test
+ void testWithFileAuthorLocation() {
+ // These two entities will be connected to others later on. Therefore, we make
+ // them easier referencable. Referencing can be done using the whole entity or
+ // its ID.
+ final PersonEntity alice = new PersonEntity.PersonEntityBuilder()
+ .setId("#alice")
+ .addProperty("name", "Alice")
+ .addProperty("description", "One of hopefully many Contextual Entities")
+ .build();
+ final PlaceEntity park = new PlaceEntity.PlaceEntityBuilder()
+ .setId(URI.create("http://sws.geonames.org/8152662/").toString())
+ .addProperty("name", "Catalina Park")
+ .build();
+ final String licenseId = "https://spdx.org/licenses/CC-BY-NC-SA-4.0";
+
+ final RoCrate crate = new RoCrate.RoCrateBuilder(
+ "Example RO-Crate",
+ "The RO-Crate Root Data Entity",
+ "2020",
+ licenseId
+ )
+ .addContextualEntity(park)
+ .addContextualEntity(alice)
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ .setLocation(Paths.get("......."))
+ .setId("data2.txt")
+ .build()
+ )
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ .setLocation(Paths.get("......."))
+ .setId("data1.txt")
+ .addProperty("description", "One of hopefully many Data Entities")
+ // ↓ This is the specific way to add an author
+ .addAuthor(alice.getId())
+ // ↓ This is the generic way to add a location or other relations
+ .addIdProperty("contentLocation", park)
+ .build()
+ )
+ .build();
+
+ /*
+ The builder enforces to provide a license and a publishing date,
+ but the example does not have them. So we have to remove them below:
+ */
+
+ // **Note**: When you add a license, even if only by a string, the crate will
+ // implicitly also get a small ContextEntity for this license. When we remove
+ // this (any) entity, all references to it will be removed as well to ensure
+ // consistency within the crate. Therefore, there will be no trace left of
+ // the license.
+ crate.deleteEntityById(licenseId);
+
+ // The datePublished property is a simple property and simple to remove without
+ // any further internal checks.
+ crate.getRootDataEntity().removeProperty("datePublished");
+
+ printAndAssertEquals(crate, "/spec-v1.1-example-json-files/file-author-location.json");
+ }
+
+ /**
+ * From:
+ * Example with complete workflow
+ * (location in repo)
+ *
+ * This example shows how to connect entities. If there is no specific method like
+ * {@link DataEntity.DataEntityBuilder#addAuthor(String)} for referencing other
+ * entities, one can use the more generic
+ * {@link AbstractEntity.AbstractEntityBuilder#addIdProperty(String, AbstractEntity)}
+ * or {@link AbstractEntity.AbstractEntityBuilder#addIdProperty(String, String)}.
+ *
+ * Important Note! If you connect entities, make sure all entities are being
+ * added to the crate. We currently can't enforce this properly yet.
+ */
+ @Test
+ void testCompleteWorkflowExample() {
+ final String licenseId = "https://spdx.org/licenses/CC-BY-NC-SA-4.0";
+ ContextualEntity license = new ContextualEntity.ContextualEntityBuilder()
+ .addType("CreativeWork")
+ .setId(licenseId)
+ .addProperty("name", "Creative Commons Attribution Non Commercial Share Alike 4.0 International")
+ .addProperty("alternateName", "CC-BY-NC-SA-4.0")
+ .build();
+ ContextualEntity knime = new ContextualEntity.ContextualEntityBuilder()
+ .setId("#knime")
+ .addType("ComputerLanguage")
+ .addProperty("name", "KNIME Analytics Platform")
+ .addProperty("alternateName", "KNIME")
+ .addProperty("url", "https://www.knime.com/whats-new-in-knime-41")
+ .addProperty("version", "4.1.3")
+ .build();
+ OrganizationEntity workflowHub = new OrganizationEntity.OrganizationEntityBuilder()
+ .setId("#workflow-hub")
+ .addProperty("name", "Example Workflow Hub")
+ .addProperty("url", "http://example.com/workflows/")
+ .build();
+ ContextualEntity fasta = new ContextualEntity.ContextualEntityBuilder()
+ .setId("http://edamontology.org/format_1929")
+ .addType("Thing")
+ .addProperty("name", "FASTA sequence format")
+ .build();
+ ContextualEntity clustalW = new ContextualEntity.ContextualEntityBuilder()
+ .setId("http://edamontology.org/format_1982")
+ .addType("Thing")
+ .addProperty("name", "ClustalW alignment format")
+ .build();
+ ContextualEntity ban = new ContextualEntity.ContextualEntityBuilder()
+ .setId("http://edamontology.org/format_2572")
+ .addType("Thing")
+ .addProperty("name", "BAM format")
+ .build();
+ ContextualEntity nucSec = new ContextualEntity.ContextualEntityBuilder()
+ .setId("http://edamontology.org/data_2977")
+ .addType("Thing")
+ .addProperty("name", "Nucleic acid sequence")
+ .build();
+ ContextualEntity nucAlign = new ContextualEntity.ContextualEntityBuilder()
+ .setId("http://edamontology.org/data_1383")
+ .addType("Thing")
+ .addProperty("name", "Nucleic acid sequence alignment")
+ .build();
+ PersonEntity alice = new PersonEntity.PersonEntityBuilder()
+ .setId("#alice")
+ .addProperty("name", "Alice Brown")
+ .build();
+ ContextualEntity requiredParam = new ContextualEntity.ContextualEntityBuilder()
+ .addType("FormalParameter")
+ .setId("#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b")
+ .addProperty("name", "genome_sequence")
+ .addProperty("valueRequired", true)
+ .addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
+ .addIdProperty("additionalType", nucSec)
+ .addIdProperty("format", fasta)
+ .build();
+ ContextualEntity clnParam = new ContextualEntity.ContextualEntityBuilder()
+ .addType("FormalParameter")
+ .setId("#6c703fee-6af7-4fdb-a57d-9e8bc4486044")
+ .addProperty("name", "cleaned_sequence")
+ .addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
+ .addIdProperty("additionalType", nucSec)
+ .addIdProperty("encodingFormat", ban)
+ .build();
+ ContextualEntity alignParam = new ContextualEntity.ContextualEntityBuilder()
+ .addType("FormalParameter")
+ .setId("#2f32b861-e43c-401f-8c42-04fd84273bdf")
+ .addProperty("name", "sequence_alignment")
+ .addIdProperty("conformsTo", "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/")
+ .addIdProperty("additionalType", nucAlign)
+ .addIdProperty("encodingFormat", clustalW)
+ .build();
+
+ RoCrate crate = new RoCrate.RoCrateBuilder(
+ "Example RO-Crate",
+ "The RO-Crate Root Data Entity",
+ "2020",
+ licenseId
+ )
+ .setLicense(license)
+ .addContextualEntity(knime)
+ .addContextualEntity(workflowHub)
+ .addContextualEntity(fasta)
+ .addContextualEntity(clustalW)
+ .addContextualEntity(ban)
+ .addContextualEntity(nucSec)
+ .addContextualEntity(nucAlign)
+ .addContextualEntity(alice)
+ .addContextualEntity(requiredParam)
+ .addContextualEntity(clnParam)
+ .addContextualEntity(alignParam)
+ .addDataEntity(
+ new WorkflowEntity.WorkflowEntityBuilder()
+ .setId("workflow/alignment.knime")
+ .setLocation(Paths.get("src"))
+ .addIdProperty("conformsTo", "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/")
+ .addProperty("name", "Sequence alignment workflow")
+ .addIdProperty("programmingLanguage", "#knime")
+ // This example does not use the term "author"...
+ //.addAuthor("#alice")
+ // instead, it uses "creator":
+ .addIdProperty("creator", "#alice")
+ .addProperty("dateCreated", "2020-05-23")
+ .setLicense(licenseId)
+ .addInput("#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b")
+ .addOutput("#6c703fee-6af7-4fdb-a57d-9e8bc4486044")
+ .addOutput("#2f32b861-e43c-401f-8c42-04fd84273bdf")
+ .addProperty("url", "http://example.com/workflows/alignment")
+ .addProperty("version", "0.5.0")
+ .addIdProperty("sdPublisher", "#workflow-hub")
+ .build()
+ )
+ .build();
+
+ // Similar to the previous example, this example from the specification
+ // spared out some details we now need to remove.
+ // Here we do not want to remove the license, only the reference to our root data entity.
+ // This is because (the way we constructed the crate) other entities use the license as well.
+ crate.getRootDataEntity().removeProperty("license");
+ crate.getRootDataEntity().removeProperty("datePublished");
+ crate.getRootDataEntity().removeProperty("name");
+ crate.getRootDataEntity().removeProperty("description");
+
+ printAndAssertEquals(crate, "/spec-v1.1-example-json-files/complete-workflow-example.json");
+ }
+}
diff --git a/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java b/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java
new file mode 100644
index 00000000..aab61632
--- /dev/null
+++ b/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java
@@ -0,0 +1,417 @@
+package edu.kit.datamanager.ro_crate.examples;
+
+import edu.kit.datamanager.ro_crate.HelpFunctions;
+import edu.kit.datamanager.ro_crate.RoCrate;
+import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity;
+import edu.kit.datamanager.ro_crate.entities.contextual.PersonEntity;
+import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
+import edu.kit.datamanager.ro_crate.entities.data.FileEntity;
+import edu.kit.datamanager.ro_crate.externalproviders.organizationprovider.RorProvider;
+import edu.kit.datamanager.ro_crate.externalproviders.personprovider.OrcidProvider;
+import edu.kit.datamanager.ro_crate.preview.AutomaticPreview;
+import edu.kit.datamanager.ro_crate.preview.StaticPreview;
+import edu.kit.datamanager.ro_crate.reader.CrateReader;
+import edu.kit.datamanager.ro_crate.reader.GenericReaderStrategy;
+import edu.kit.datamanager.ro_crate.reader.Readers;
+import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation;
+import edu.kit.datamanager.ro_crate.validation.Validator;
+import edu.kit.datamanager.ro_crate.writer.CrateWriter;
+import edu.kit.datamanager.ro_crate.writer.FolderStrategy;
+import edu.kit.datamanager.ro_crate.writer.GenericWriterStrategy;
+import edu.kit.datamanager.ro_crate.writer.Writers;
+import org.apache.commons.io.FileUtils;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import java.io.*;
+import java.net.URI;
+import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Objects;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+/**
+ * This class is meant to be a small example-driven introduction to the ro-crate-java library.
+ * It is meant to be read from top to bottom.
+ */
+public class LearnByExampleTest {
+
+ /**
+ * This creates a valid, empty RO-Crate builder.
+ */
+ static final RoCrate.RoCrateBuilder STARTER_CRATE = new RoCrate.RoCrateBuilder(
+ "name",
+ "description",
+ "2025",
+ "licenseIdentifier"
+ );
+
+ /**
+ * Calling the `build()` method on the builder creates a valid RO-Crate.
+ * Run this test to view the STARTER_CRATE JSON in the console.
+ */
+ @Test
+ void aSimpleCrate() {
+ RoCrate almostEmptyCrate = STARTER_CRATE.build();
+ assertNotNull(almostEmptyCrate);
+ HelpFunctions.prettyPrintJsonString(almostEmptyCrate.getJsonMetadata());
+ }
+
+ /**
+ * This is how we can add things to a crate.
+ *
+ * Note that methods starting with `add` can be used multiple times to add more.
+ * For example, we can add multiple files or multiple contexts.
+ *
+ * On the other hand, methods starting with `set` will override previous calls.
+ *
+ * There may be inconsistencies yet, which are tracked here: Issue #242
+ */
+ @Test
+ void addingYourFirstEntity() {
+ RoCrate myFirstCrate = STARTER_CRATE
+ // We can add new terms to our crate. The terms we can use are called "context".
+ .addValuePairToContext("Station", "www.station.com")
+ // We can also add whole contexts to our crate.
+ .addUrlToContext("contextUrl")
+ // Let's add a file to our crate.
+ .addDataEntity(
+ new FileEntity.FileEntityBuilder()
+ // For files (or folders, which are DataSetEntities),
+ // the ID determines the file name in the crate.
+ .setId("survey-responses-2019.csv")
+ // This is where we get the file from. The path will not be part of the metadata.
+ .setLocation(Paths.get("copy/from/this/file-and-rename-it.csv"))
+ // And now, the remaining metadata.
+ // Note that "name", "contentSize", and "encodingFormat"
+ // are already defined in our default context.
+ .addProperty("name", "Survey responses")
+ .addProperty("contentSize", "26452")
+ .addProperty("encodingFormat", "text/csv")
+ .build()
+ )
+ // We could add more, but let's keep it simple for now.
+ //.addDataEntity(...)
+ //.addContextualEntity(...)
+ //...
+ .build();
+
+ assertNotNull(myFirstCrate);
+ HelpFunctions.prettyPrintJsonString(myFirstCrate.getJsonMetadata());
+ }
+
+ /**
+ * The library currently comes with three specialized DataEntities:
+ *
+ * 1. `DataSetEntity`
+ * 2. `FileEntity` (used in the example above)
+ * 3. `WorkflowEntity`
+ *
+ * If another type of `DataEntity` is required,
+ * the base class `DataEntity` can be used. Example:
+ */
+ @Test
+ void specializingYourFirstEntity() {
+ RoCrate crate = STARTER_CRATE
+ .addDataEntity(
+ // Let's do something custom:
+ new DataEntity.DataEntityBuilder()
+ // You need to add the type of your `DataEntity`
+ // because for DataEntity, there is no default.
+ .addType("CreativeWork")
+ .setId("myEntityInstance")
+ // Now that we are a CreativeWork instance,
+ // it is fine to use some of its properties.
+ .addProperty("https://schema.org/award", "Wow-award")
+ .build()
+ )
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+ }
+
+ /**
+ * A `DataEntity` and its subclasses can have a file located on the web.
+ * In this case, it does not need to reside in a crate's folder.
+ * This can be useful for large, publicly available files,
+ * or in order to reuse or share files.
+ *
+ * Note: Technically, an entity pointing to a file on the web is just an entity
+ * that uses the URL as an ID.
+ */
+ @Test
+ void referencingFilesOnTheWeb() {
+ // Let's say this is the file we would like to point at with an entity.
+ String lovelyFile = "https://github.com/kit-data-manager/ro-crate-java/issues/5";
+
+ RoCrate crate = STARTER_CRATE
+ .addDataEntity(
+ // Build our entity to point to the file:
+ new FileEntity.FileEntityBuilder()
+ // Make it point to an external file.
+ .setLocation(URI.create(lovelyFile))
+ // This would do the same:
+ .setId(lovelyFile)
+ // don't forget to add metadata!
+ .addProperty("description", "my new file that I added")
+ .build()
+ )
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+ }
+
+ /**
+ * A `DataEntity` and its subclasses can have a local file associated with them,
+ * instead of one located on the web.
+ *
+ * @param tempDir We'll use this to create a temporary folder for our crate.
+ * @throws IOException If the file cannot be created or written to.
+ */
+ @Test
+ void includingFilesIntoTheCrateFolder(@TempDir Path tempDir) throws IOException {
+ // Let's say this is the file we would like to point at with an entity.
+ String lovelyFile = tempDir.resolve("my/experiment.csv").toString();
+ {
+ // (Let's quickly create a dummy file, but the rest will not make use of this knowledge.)
+ File lovelyFilePointer = new File(lovelyFile);
+ FileUtils.touch(lovelyFilePointer);
+ FileUtils.write(lovelyFilePointer, "My great experiment 001", "UTF-8");
+ }
+
+ // But in the crate we want it to be
+ String seriousExperimentFile = "fantastic-experiment/2025-01-01.csv";
+
+ RoCrate crate = STARTER_CRATE
+ .addDataEntity(
+ // Build our entity to point to the file:
+ new FileEntity.FileEntityBuilder()
+ // Let's tell the library where to find and copy the file from.
+ .setLocation(Paths.get(lovelyFile))
+ // Let's tell it to adjust the file name and path in the crate.
+ .setId(seriousExperimentFile)
+ .addProperty("description", "my new local file that I added")
+ .build()
+ )
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+
+ // Let's write it to disk and see if the file is there!
+ // (We'll discuss writing and reading crates later on.)
+ Path crateFolder = tempDir.resolve("myCrate");
+ Writers.newFolderWriter().save(crate, crateFolder.toString());
+ assertTrue(crateFolder.resolve(seriousExperimentFile).toFile().exists());
+ }
+
+ /**
+ * Contextual entities cannot be associated with a file: they are pure metadata
+ * To add a contextual entity to a crate you use the function
+ * {@link RoCrate.RoCrateBuilder#addContextualEntity(ContextualEntity)}.
+ *
+ * Some types of derived/specializes entities are:
+ *
+ * 1. `OrganizationEntity`
+ * 2. `PersonEntity`
+ * 3. `PlaceEntity`
+ *
+ * If you need another type of contextual entity, use the base class
+ * {@link ContextualEntity}, similar to how we did it in
+ * {@link #specializingYourFirstEntity()}.
+ *
+ * The library provides a way to automatically create contextual entities from
+ * external providers. Currently, support for [ORCID](https://orcid.org/) and
+ * [ROR](https://ror.org/) is implemented.
+ * Check the module {@link edu.kit.datamanager.ro_crate.externalproviders} for
+ * more implementations.
+ */
+ @Test
+ void addingContextualEntities() {
+ PersonEntity person = OrcidProvider.getPerson("https://orcid.org/0000-0001-6575-1022");
+ OrganizationEntity organization = RorProvider.getOrganization("https://ror.org/04t3en479");
+
+ RoCrate crate = STARTER_CRATE
+ .addContextualEntity(person)
+ .addContextualEntity(organization)
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+ }
+
+ /**
+ * RO-Crates are file based, but in your application you may want to create a crate
+ * on the fly and directly send it somewhere else without storing it on disk.
+ * This is why we can't only write to a folder or a zip file, but also to a stream
+ * (containing the zip file).
+ *
+ * There is a generic interface to implement Writers (and Readers), so even more
+ * exotic use cases should be possible. The readers work the same way.
+ *
+ * - {@link GenericWriterStrategy}
+ * - {@link GenericReaderStrategy}
+ */
+ @Test
+ void writingAndReadingCrates(@TempDir Path tempDir) throws IOException {
+ // Ok lets make a small, but not fully boring crate.
+ PersonEntity person = OrcidProvider.getPerson("https://orcid.org/0000-0001-6575-1022");
+ OrganizationEntity organization = RorProvider.getOrganization("https://ror.org/04t3en479");
+
+ RoCrate crate = STARTER_CRATE
+ .addContextualEntity(person)
+ .addContextualEntity(organization)
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+
+ {
+ // Now, let's write it to a folder.
+ Path folder = tempDir.resolve("folderCrate");
+ Writers.newFolderWriter()
+ .save(crate, folder.toString());
+ // and read it back.
+ RoCrate read = Readers.newFolderReader()
+ .readCrate(folder.toAbsolutePath().toString());
+
+ HelpFunctions.compareTwoCrateJson(crate, read);
+ }
+
+ {
+ // Now, let's write it to a zip file.
+ Path zipFile = tempDir.resolve("zipCrate.zip");
+ Writers.newZipPathWriter()
+ .save(crate, zipFile.toString());
+ // and read it back.
+ RoCrate read = Readers.newZipPathReader()
+ .readCrate(zipFile.toAbsolutePath().toString());
+
+ HelpFunctions.compareTwoCrateJson(crate, read);
+ }
+
+ {
+ // Now, let's write it to a zip stream.
+ Path zipStreamFile = tempDir.resolve("zipStreamCrate.zip");
+ try (OutputStream outputStream = new FileOutputStream(zipStreamFile.toFile())) {
+ Writers.newZipStreamWriter().save(crate, outputStream);
+ }
+ // and read it back.
+ try (InputStream inputStream = new FileInputStream(zipStreamFile.toFile())) {
+ RoCrate read = Readers.newZipStreamReader()
+ .readCrate(inputStream);
+
+ HelpFunctions.compareTwoCrateJson(crate, read);
+ }
+ }
+ }
+
+ /**
+ * In {@link #writingAndReadingCrates(Path)} we already saw how to write or read
+ * a crate. We used the Readers and Writers classes to get the available options.
+ * But what if you want to write your own reader or writer strategy?
+ *
+ * Let's see how you can make a reader or writer, manually configuring the strategy.
+ */
+ @Test
+ void writingAndReadingStrategies(@TempDir Path tempDir) throws IOException {
+ // Ok lets make a small, but not fully boring crate.
+ PersonEntity person = OrcidProvider.getPerson("https://orcid.org/0000-0001-6575-1022");
+ OrganizationEntity organization = RorProvider.getOrganization("https://ror.org/04t3en479");
+
+ RoCrate crate = STARTER_CRATE
+ .addContextualEntity(person)
+ .addContextualEntity(organization)
+ .build();
+
+ assertNotNull(crate);
+ HelpFunctions.prettyPrintJsonString(crate.getJsonMetadata());
+
+ // Now, let's write it to a folder. Note the used strategy could be replaced with your own.
+ Path folder = tempDir.resolve("folderCrate");
+ new CrateWriter<>(new FolderStrategy())
+ .save(crate, folder.toString());
+ // and read it back.
+ RoCrate read = new CrateReader<>(
+ // Note: There are two FolderStrategy implementations, one for reading and one for writing.
+ // Java is a bit bad with imports, so we use the fully qualified name here.
+ new edu.kit.datamanager.ro_crate.reader.FolderStrategy()
+ )
+ .readCrate(folder.toAbsolutePath().toString());
+
+ HelpFunctions.compareTwoCrateJson(crate, read);
+ }
+
+ /**
+ * RO-Crate specified there should be a human-readable preview of the crate.
+ * This is a HTML file that can be opened in a browser.
+ * ro-crate-java offers three different ways to create this file:
+ *
+ * - AutomaticPreview: Uses third-party library
+ * ro-crate-html-js,
+ * which must be installed separately via `npm install --global ro-crate-html-js`.
+ *
+ * - CustomPreview: Pure Java-based preview using an included template processed by
+ * the FreeMarker template engine. At the same time, CustomPreview is the fallback
+ * for AutomaticPreview if ro-crate-html-js is not installed.
+ *
+ * - StaticPreview: Allows to provide a static HTML page (including additional
+ * dependencies, e.g., CSS, JS) which is then shipped with the RO-Crate.
+ *
+ * When creating a new RO-Crate using the builder, the default setting is to use
+ * CustomPreview. This example shows you how to change it.
+ */
+ @Test
+ void humanReadableContent() {
+ RoCrate crate = STARTER_CRATE
+ .setPreview(new AutomaticPreview())
+ .build();
+
+ assertNotNull(crate);
+ }
+
+ /**
+ * A static preview means you'll just add your own HTML file to the crate.
+ * Therefore, the constructor is a bit more complicated.
+ */
+ @Test
+ void staticPreview(@TempDir Path tempDir) {
+ File mainPreviewHtml = tempDir.resolve("mainPreview.html").toFile();
+ File additionalFilesDirectory = tempDir.resolve("additionalFiles").toFile();
+
+ RoCrate crate = STARTER_CRATE
+ .setPreview(new StaticPreview(mainPreviewHtml, additionalFilesDirectory))
+ .build();
+
+ assertNotNull(crate);
+ }
+
+ /**
+ * Crates can be validated.
+ * Right now, the only implemented way of validating a RO-crate is to use a
+ * [JSON-Schema](https://json-schema.org/) that the crate's metadata JSON file should
+ * match. JSON-Schema is an established standard and therefore a good choice for a
+ * crate profile. This example shows how to use it.
+ *
+ * Note: If you happen to implement your own validator anyway, please consider
+ * contributing your code!
+ */
+ @Test
+ void validation() {
+ // Let's find a schema file in the resources folder.
+ URL schemaUrl = Objects.requireNonNull(this.getClass().getResource("/crates/validation/workflowschema.json"));
+ String schemaPath = schemaUrl.getPath();
+
+ // This crate for sure is not a workflow, so validation will fail.
+ RoCrate crate = STARTER_CRATE.build();
+
+ // And now do the validation.
+ Validator validator = new Validator(new JsonSchemaValidation(schemaPath));
+ assertFalse(validator.validate(crate));
+ }
+}
diff --git a/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json b/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json
new file mode 100644
index 00000000..011258f6
--- /dev/null
+++ b/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json
@@ -0,0 +1,113 @@
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@type": "CreativeWork",
+ "@id": "ro-crate-metadata.json",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"}
+ },
+ {
+ "@id": "./",
+ "@type": "Dataset",
+ "hasPart": [
+ { "@id": "workflow/alignment.knime" }
+ ]
+ },
+ {
+ "@id": "workflow/alignment.knime",
+ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+ "conformsTo":
+ {"@id": "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/"},
+ "name": "Sequence alignment workflow",
+ "programmingLanguage": {"@id": "#knime"},
+ "creator": {"@id": "#alice"},
+ "dateCreated": "2020-05-23",
+ "license": { "@id": "https://spdx.org/licenses/CC-BY-NC-SA-4.0"},
+ "input": [
+ { "@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b"}
+ ],
+ "output": [
+ { "@id": "#6c703fee-6af7-4fdb-a57d-9e8bc4486044"},
+ { "@id": "#2f32b861-e43c-401f-8c42-04fd84273bdf"}
+ ],
+ "sdPublisher": {"@id": "#workflow-hub"},
+ "url": "http://example.com/workflows/alignment",
+ "version": "0.5.0"
+ },
+ {
+ "@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b",
+ "@type": "FormalParameter",
+ "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
+ "name": "genome_sequence",
+ "valueRequired": true,
+ "additionalType": {"@id": "http://edamontology.org/data_2977"},
+ "format": {"@id": "http://edamontology.org/format_1929"}
+ },
+ {
+ "@id": "#6c703fee-6af7-4fdb-a57d-9e8bc4486044",
+ "@type": "FormalParameter",
+ "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
+ "name": "cleaned_sequence",
+ "additionalType": {"@id": "http://edamontology.org/data_2977"},
+ "encodingFormat": {"@id": "http://edamontology.org/format_2572"}
+ },
+ {
+ "@id": "#2f32b861-e43c-401f-8c42-04fd84273bdf",
+ "@type": "FormalParameter",
+ "conformsTo": {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
+ "name": "sequence_alignment",
+ "additionalType": {"@id": "http://edamontology.org/data_1383"},
+ "encodingFormat": {"@id": "http://edamontology.org/format_1982"}
+ },
+ {
+ "@id": "https://spdx.org/licenses/CC-BY-NC-SA-4.0",
+ "@type": "CreativeWork",
+ "name": "Creative Commons Attribution Non Commercial Share Alike 4.0 International",
+ "alternateName": "CC-BY-NC-SA-4.0"
+ },
+ {
+ "@id": "#knime",
+ "@type": "ComputerLanguage",
+ "name": "KNIME Analytics Platform",
+ "alternateName": "KNIME",
+ "url": "https://www.knime.com/whats-new-in-knime-41",
+ "version": "4.1.3"
+ },
+ {
+ "@id": "#alice",
+ "@type": "Person",
+ "name": "Alice Brown"
+ },
+ {
+ "@id": "#workflow-hub",
+ "@type": "Organization",
+ "name": "Example Workflow Hub",
+ "url":"http://example.com/workflows/"
+ },
+ {
+ "@id": "http://edamontology.org/format_1929",
+ "@type": "Thing",
+ "name": "FASTA sequence format"
+ },
+ {
+ "@id": "http://edamontology.org/format_1982",
+ "@type": "Thing",
+ "name": "ClustalW alignment format"
+ },
+ {
+ "@id": "http://edamontology.org/format_2572",
+ "@type": "Thing",
+ "name": "BAM format"
+ },
+ {
+ "@id": "http://edamontology.org/data_2977",
+ "@type": "Thing",
+ "name": "Nucleic acid sequence"
+ },
+ {
+ "@id": "http://edamontology.org/data_1383",
+ "@type": "Thing",
+ "name": "Nucleic acid sequence alignment"
+ }
+ ]
+}
diff --git a/src/test/resources/spec-v1.1-example-json-files/file-author-location.json b/src/test/resources/spec-v1.1-example-json-files/file-author-location.json
new file mode 100644
index 00000000..6bd83070
--- /dev/null
+++ b/src/test/resources/spec-v1.1-example-json-files/file-author-location.json
@@ -0,0 +1,47 @@
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+
+ {
+ "@type": "CreativeWork",
+ "@id": "ro-crate-metadata.json",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"},
+ "description": "RO-Crate Metadata File Descriptor (this file)"
+ },
+ {
+ "@id": "./",
+ "@type": "Dataset",
+ "name": "Example RO-Crate",
+ "description": "The RO-Crate Root Data Entity",
+ "hasPart": [
+ {"@id": "data1.txt"},
+ {"@id": "data2.txt"}
+ ]
+ },
+
+
+ {
+ "@id": "data1.txt",
+ "@type": "File",
+ "description": "One of hopefully many Data Entities",
+ "author": {"@id": "#alice"},
+ "contentLocation": {"@id": "http://sws.geonames.org/8152662/"}
+ },
+ {
+ "@id": "data2.txt",
+ "@type": "File"
+ },
+
+ {
+ "@id": "#alice",
+ "@type": "Person",
+ "name": "Alice",
+ "description": "One of hopefully many Contextual Entities"
+ },
+ {
+ "@id": "http://sws.geonames.org/8152662/",
+ "@type": "Place",
+ "name": "Catalina Park"
+ }
+ ]
+}
diff --git a/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json b/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json
new file mode 100644
index 00000000..e8bb2ab0
--- /dev/null
+++ b/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json
@@ -0,0 +1,38 @@
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@type": "CreativeWork",
+ "@id": "ro-crate-metadata.json",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"}
+ },
+ {
+ "@id": "./",
+ "@type": [
+ "Dataset"
+ ],
+ "hasPart": [
+ {
+ "@id": "cp7glop.ai"
+ },
+ {
+ "@id": "lots_of_little_files/"
+ }
+ ]
+ },
+ {
+ "@id": "cp7glop.ai",
+ "@type": "File",
+ "name": "Diagram showing trend to increase",
+ "contentSize": "383766",
+ "description": "Illustrator file for Glop Pot",
+ "encodingFormat": "application/pdf"
+ },
+ {
+ "@id": "lots_of_little_files/",
+ "@type": "Dataset",
+ "name": "Too many files",
+ "description": "This directory contains many small files, that we're not going to describe in detail."
+ }
+ ]
+}
diff --git a/src/test/resources/spec-v1.1-example-json-files/minimal.json b/src/test/resources/spec-v1.1-example-json-files/minimal.json
new file mode 100644
index 00000000..3aee3b8c
--- /dev/null
+++ b/src/test/resources/spec-v1.1-example-json-files/minimal.json
@@ -0,0 +1,27 @@
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+
+ {
+ "@type": "CreativeWork",
+ "@id": "ro-crate-metadata.json",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"}
+ },
+ {
+ "@id": "./",
+ "identifier": "https://doi.org/10.4225/59/59672c09f4a4b",
+ "@type": "Dataset",
+ "datePublished": "2017",
+ "name": "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...",
+ "description": "Palliative care planning for nursing home residents with advanced dementia ...",
+ "license": {"@id": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/"}
+ },
+ {
+ "@id": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/",
+ "@type": "CreativeWork",
+ "description": "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.",
+ "identifier": "https://creativecommons.org/licenses/by-nc-sa/3.0/au/",
+ "name": "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json b/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json
new file mode 100644
index 00000000..d5245907
--- /dev/null
+++ b/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json
@@ -0,0 +1,39 @@
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@type": "CreativeWork",
+ "@id": "ro-crate-metadata.json",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"}
+ },
+ {
+ "@id": "./",
+ "@type": [
+ "Dataset"
+ ],
+ "hasPart": [
+ {
+ "@id": "survey-responses-2019.csv"
+ },
+ {
+ "@id": "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf"
+ }
+ ]
+ },
+ {
+ "@id": "survey-responses-2019.csv",
+ "@type": "File",
+ "name": "Survey responses",
+ "contentSize": "26452",
+ "encodingFormat": "text/csv"
+ },
+ {
+ "@id": "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf",
+ "@type": "File",
+ "name": "RO-Crate specification",
+ "contentSize": "310691",
+ "description": "RO-Crate specification",
+ "encodingFormat": "application/pdf"
+ }
+ ]
+}