#578

Committed 11 Nov 2025 01:46AM UTC coverage: 91.327% (-0.1%) from 91.45%

Build # #578

Build Type

Pull #303

github

Committed by

web-flow

Commit Message

Merge 48b203e5a into 6a21367d1

Pull Request Pull Request #303: chore(deps): update plugin io.freefair.maven-publish-java to v9.1.0

Run Details

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94.0

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

package edu.kit.datamanager.ro_crate.externalproviders.dataentities;

import com.apicatalog.jsonld.JsonLd;
import com.apicatalog.jsonld.JsonLdError;
import com.apicatalog.jsonld.document.JsonDocument;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;

import edu.kit.datamanager.ro_crate.Crate;
import edu.kit.datamanager.ro_crate.RoCrate;
import edu.kit.datamanager.ro_crate.RoCrate.RoCrateBuilder;
import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;

import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Optional;

import org.apache.http.HttpHeaders;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;

/**
 * Class providing functionality for importing a resource from zenodo.
 */
public class ImportFromZenodo {

  /**
   * Class has only static methods, therefore forbid instance creation.
   */
  private ImportFromZenodo() {}

  /**
   * Creating a crate and adding the zenodo resource to it.
   *
   * @param url           the url of the zenodo resource.
   * @param name          the name of the crate created.
   * @param description   the description of the crate created.
   * @param datePublished the published date of the crate.
   * @param licenseId     the license identifier of the crate.
   * @return the created crate.
   */
  public static Crate createCrateWithItem(
      String url,
      Optional<String> name,
      Optional<String> description,
      Optional<String> datePublished,
      Optional<String> licenseId) {

    RoCrateBuilder builder = new RoCrate.RoCrateBuilder();
    name.ifPresent(builder::addName);
    description.ifPresent(builder::addDescription);
    datePublished.ifPresent(builder::addDatePublishedWithExceptions);
    licenseId.ifPresent(builder::setLicense);

    Crate crate = builder.build();
    addToCrateFromZotero(url, crate);
    return crate;
  }

  public static void addZenodoToCrate(String ulr, Crate crate) {
    addToCrateFromZotero(ulr, crate);
  }

  private static void addToCrateFromZotero(String url, Crate crate) {
    ObjectMapper objectMapper = MyObjectMapper.getMapper();
    CloseableHttpClient httpClient = HttpClients.createDefault();
    HttpGet requestZenodo = new HttpGet(url);

    // HttpGet requestSchema= new HttpGet("https://www.researchobject.org/ro-crate/1.1/context.jsonld");
    HttpGet requestSchema = new HttpGet("https://schema.org/docs/jsonldcontext.json");
    requestZenodo.addHeader(HttpHeaders.ACCEPT, "application/ld+json");
    ObjectNode jsonNode;
    String mainId;
    try {
      CloseableHttpResponse response = httpClient.execute(requestZenodo);
      var stream = response.getEntity().getContent();

      // get the item of the main entity
      jsonNode = (ObjectNode) objectMapper.readTree(stream);
      mainId = jsonNode.get("@id").asText();

      final var el = JsonLd.flatten(JsonDocument.of(
              new ByteArrayInputStream(
                  jsonNode.toString().getBytes(StandardCharsets.UTF_8)))).get();

      CloseableHttpResponse schema = httpClient.execute(requestSchema);
      ObjectNode doc = (ObjectNode) objectMapper.readTree(schema.getEntity().getContent());
      var con = (ObjectNode) doc.get("@context");
      con.remove("type");
      con.remove("id");
      doc.set("@context", con);
      var finalVersion = JsonLd.compact(
          JsonDocument.of(el),
          JsonDocument.of(new ByteArrayInputStream(
              doc.toString().getBytes(StandardCharsets.UTF_8)))).get();


      jsonNode = (ObjectNode) objectMapper.readTree(finalVersion.toString());
    } catch (IOException | JsonLdError e) {
      e.printStackTrace();
      return;
    }
    // we don't need this context since we are going to add it to a crate which allready has one
    jsonNode.remove("@context");
    var graph = jsonNode.get("@graph");
    if (graph != null) {
      for (var entity : graph) {
        if (entity.get("@id").asText().equals(mainId)) {
          var dataEntity = new DataEntity.DataEntityBuilder()
              .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()
              .setAllUnsafe((ObjectNode) entity).build();
          crate.addContextualEntity(contextualEntity);
        }
      }
    }
  }
}

1	package edu.kit.datamanager.ro_crate.externalproviders.dataentities;
2
3	import com.apicatalog.jsonld.JsonLd;
4	import com.apicatalog.jsonld.JsonLdError;
5	import com.apicatalog.jsonld.document.JsonDocument;
6	import com.fasterxml.jackson.databind.ObjectMapper;
7	import com.fasterxml.jackson.databind.node.ObjectNode;
8
9	import edu.kit.datamanager.ro_crate.Crate;
10	import edu.kit.datamanager.ro_crate.RoCrate;
11	import edu.kit.datamanager.ro_crate.RoCrate.RoCrateBuilder;
12	import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
13	import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
14	import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
15
16	import java.io.ByteArrayInputStream;
17	import java.io.IOException;
18	import java.nio.charset.StandardCharsets;
19	import java.util.Optional;
20
21	import org.apache.http.HttpHeaders;
22	import org.apache.http.client.methods.CloseableHttpResponse;
23	import org.apache.http.client.methods.HttpGet;
24	import org.apache.http.impl.client.CloseableHttpClient;
25	import org.apache.http.impl.client.HttpClients;
26
27	/**
28	* Class providing functionality for importing a resource from zenodo.
29	*/
30	public class ImportFromZenodo {
31
32	/**
33	* Class has only static methods, therefore forbid instance creation.
34	*/
35	private ImportFromZenodo() {}
36
37	/**
38	* Creating a crate and adding the zenodo resource to it.
39	*
40	* @param url the url of the zenodo resource.
41	* @param name the name of the crate created.
42	* @param description the description of the crate created.
43	* @param datePublished the published date of the crate.
44	* @param licenseId the license identifier of the crate.
45	* @return the created crate.
46	*/
47	public static Crate createCrateWithItem(
48	String url,
49	Optional<String> name,
50	Optional<String> description,
51	Optional<String> datePublished,
52	Optional<String> licenseId) {
53
54	RoCrateBuilder builder = new RoCrate.RoCrateBuilder();	1✔
55	name.ifPresent(builder::addName);	1✔
56	description.ifPresent(builder::addDescription);	1✔
57	datePublished.ifPresent(builder::addDatePublishedWithExceptions);	1✔
58	licenseId.ifPresent(builder::setLicense);	1✔
59
60	Crate crate = builder.build();	1✔
61	addToCrateFromZotero(url, crate);	1✔
62	return crate;	1✔
63	}
64
65	public static void addZenodoToCrate(String ulr, Crate crate) {
66	addToCrateFromZotero(ulr, crate);	1✔
67	}	1✔
68
69	private static void addToCrateFromZotero(String url, Crate crate) {
70	ObjectMapper objectMapper = MyObjectMapper.getMapper();	1✔
71	CloseableHttpClient httpClient = HttpClients.createDefault();	1✔
72	HttpGet requestZenodo = new HttpGet(url);	1✔
73
74	// HttpGet requestSchema= new HttpGet("https://www.researchobject.org/ro-crate/1.1/context.jsonld");
75	HttpGet requestSchema = new HttpGet("https://schema.org/docs/jsonldcontext.json");	1✔
76	requestZenodo.addHeader(HttpHeaders.ACCEPT, "application/ld+json");	1✔
77	ObjectNode jsonNode;
78	String mainId;
79	try {
80	CloseableHttpResponse response = httpClient.execute(requestZenodo);	1✔
81	var stream = response.getEntity().getContent();	1✔
82
83	// get the item of the main entity
84	jsonNode = (ObjectNode) objectMapper.readTree(stream);	1✔
85	mainId = jsonNode.get("@id").asText();	1✔
86
87	final var el = JsonLd.flatten(JsonDocument.of(	1✔
88	new ByteArrayInputStream(
89	jsonNode.toString().getBytes(StandardCharsets.UTF_8)))).get();	1✔
90
91	CloseableHttpResponse schema = httpClient.execute(requestSchema);	1✔
92	ObjectNode doc = (ObjectNode) objectMapper.readTree(schema.getEntity().getContent());	1✔
93	var con = (ObjectNode) doc.get("@context");	1✔
94	con.remove("type");	1✔
95	con.remove("id");	1✔
96	doc.set("@context", con);	1✔
97	var finalVersion = JsonLd.compact(	1✔
98	JsonDocument.of(el),	1✔
99	JsonDocument.of(new ByteArrayInputStream(	1✔
100	doc.toString().getBytes(StandardCharsets.UTF_8)))).get();	1✔
101
102
103	jsonNode = (ObjectNode) objectMapper.readTree(finalVersion.toString());	1✔
104	} catch (IOException \| JsonLdError e) {	×
105	e.printStackTrace();	×
106	return;	×
107	}	1✔
108	// we don't need this context since we are going to add it to a crate which allready has one
109	jsonNode.remove("@context");	1✔
110	var graph = jsonNode.get("@graph");	1✔
111	if (graph != null) {	1✔
112	for (var entity : graph) {	1✔
113	if (entity.get("@id").asText().equals(mainId)) {	1✔
114	var dataEntity = new DataEntity.DataEntityBuilder()	1✔
115	.setAllUnsafe((ObjectNode) entity).build();	1✔
116	crate.addDataEntity(dataEntity);	1✔
117	} else {	1✔
118	// here we have to think of a way to differentiate between data and contextual entities.
119	var contextualEntity = new ContextualEntity.ContextualEntityBuilder()	1✔
120	.setAllUnsafe((ObjectNode) entity).build();	1✔
121	crate.addContextualEntity(contextualEntity);	1✔
122	}
123	}	1✔
124	}
125	}	1✔
126	}

kit-data-manager / ro-crate-java / #578

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