#378

Committed 29 Apr 2025 01:00PM UTC coverage: 86.311%. First build

Build # #378

Build Type

Pull #233

github

Committed by

web-flow

Commit Message

Merge pull request #253 from kit-data-manager/fix-renaming-of-data-set-entities

Fix renaming of data set entities

Pull Request Pull Request #233: Version 2.1.0

Run Details

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1879 of 2177 relevant lines covered (86.31%)

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80.83

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

package edu.kit.datamanager.ro_crate.preview;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import edu.kit.datamanager.ro_crate.util.ZipUtil;
import freemarker.template.Configuration;
import freemarker.template.Template;
import freemarker.template.TemplateException;
import freemarker.template.TemplateExceptionHandler;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.exception.ZipException;
import net.lingala.zip4j.io.outputstream.ZipOutputStream;
import org.apache.commons.io.FileUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This class generates a custom preview without requiring external
 * dependencies, i.e., rochtml. Therefore, the FreeMarker template located under
 * resources/templates/custom_preview.ftl is used.
 *
 * @author jejkal
 */
public class CustomPreview implements CratePreview {

    private final static Logger logger = LoggerFactory.getLogger(CustomPreview.class);

    private final Configuration cfg;
    private Template template = null;

    public CustomPreview() {
        cfg = new Configuration(Configuration.VERSION_2_3_34);
        cfg.setClassForTemplateLoading(CustomPreview.class, "/");
        cfg.setDefaultEncoding("UTF-8");
        cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);
        try {
            template = cfg.getTemplate("templates/custom_preview.ftl");
        } catch (IOException ex) {
            logger.error("Failed to read template for CustomPreview.", ex);
        }
    }

    private CustomPreviewModel mapFromJson(String metadata) throws IOException {
        ObjectMapper mapper = new ObjectMapper();
        JsonNode root = (JsonNode) mapper.readValue(metadata, JsonNode.class);
        JsonNode graph = root.get("@graph");
        CustomPreviewModel.ROCrate crate = new CustomPreviewModel.ROCrate();
        List<CustomPreviewModel.Dataset> datasets = new ArrayList<>();
        List<CustomPreviewModel.File> files = new ArrayList<>();

        if (graph.isArray()) {

            for (JsonNode node : graph) {
                String id = node.path("@id").asText();
                List<String> types = new LinkedList<>();
                if (node.path("@type").isArray()) {

                    Collections.addAll(types, mapper.convertValue(node.path("@type"), String[].class));
                } else {
                    types.add(node.path("@type").asText());
                }

                if (types.contains("Dataset") && "./".equals(id)) {
                    crate.name = node.path("name").asText();
                    crate.description = node.path("description").asText(null);
                    crate.type = "Dataset";
                    crate.license = node.path("license").path("@id").asText(node.path("license").asText(null));
                    crate.datePublished = node.path("datePublished").asText(null);
                    crate.hasPart = new ArrayList<>();

                    for (JsonNode part : node.path("hasPart")) {
                        CustomPreviewModel.Part p = new CustomPreviewModel.Part();
                        String tmpId = part.path("@id").asText(part.asText());
                        p.id = tmpId;
                        p.name = tmpId; // Name will be replaced later
                        crate.hasPart.add(p);
                    }
                } else if (types.contains("Dataset")) {
                    CustomPreviewModel.Dataset dataset = new CustomPreviewModel.Dataset();
                    dataset.id = id;
                    dataset.name = node.path("name").asText();
                    dataset.description = node.path("description").asText();
                    datasets.add(dataset);
                } else if (types.contains("File")) {
                    CustomPreviewModel.File file = new CustomPreviewModel.File();
                    file.id = id;
                    file.name = node.path("name").asText(null);
                    file.description = node.path("description").asText(null);
                    file.contentSize = node.path("contentSize").asText(null);
                    file.encodingFormat = node.path("encodingFormat").asText(null);
                    files.add(file);
                }
            }
        }

        // Update Part names using dataset and file lists
        if (crate.hasPart != null) {
            for (CustomPreviewModel.Part part : crate.hasPart) {
                for (CustomPreviewModel.Dataset dataset : datasets) {
                    if (dataset.id.equals(part.id) && dataset.name != null) {
                        part.name = dataset.name;
                    }
                }
                for (CustomPreviewModel.File file : files) {
                    if (file.id.equals(part.id) && file.name != null) {
                        part.name = file.name;
                    }
                }
            }
        }

        CustomPreviewModel model = new CustomPreviewModel();
        model.crate = crate;
        model.datasets = datasets;
        model.files = files;
        return model;
    }

    @Override
    public void saveAllToZip(ZipFile zipFile) throws IOException {
        if (template == null) {
            throw new IOException("Preview template did not load. Unable to proceed.");
        }
        if (zipFile == null) {
            throw new IOException("Argument zipFile must not be null.");
        }
        try {
            zipFile.extractFile("ro-crate-metadata.json", "temp");
        } catch (ZipException ex) {
            throw new IOException("ro-crate-metadata.json not found in provided ZIP.", ex);
        }

        String metadata = FileUtils.readFileToString(new File("temp/ro-crate-metadata.json"), "UTF-8");
        try {
            Map<String, Object> dataModel = new HashMap<>();
            dataModel.put("crateModel", mapFromJson(metadata));

            try (Writer out = new OutputStreamWriter(new FileOutputStream("temp/ro-crate-preview.html"))) {
                template.process(dataModel, out);
                out.flush();
            }
            zipFile.addFile("temp/ro-crate-preview.html");
        } catch (TemplateException ex) {
            throw new IOException("Failed to generate preview.", ex);
        } finally {
            try {
                FileUtils.deleteDirectory(new File("temp"));
            } catch (IOException ex) {
                //ignore
            }
        }
    }

    @Override
    public void saveAllToFolder(File folder) throws IOException {
        if (template == null) {
            throw new IOException("Preview template did not load. Unable to proceed.");
        }
        if (folder == null || !folder.exists()) {
            throw new IOException("Preview target folder " + folder + " does not exist.");
        }
        String metadata = FileUtils.readFileToString(new File(folder, "ro-crate-metadata.json"), "UTF-8");
        try {
            Map<String, Object> dataModel = new HashMap<>();
            dataModel.put("crateModel", mapFromJson(metadata));
            try (Writer out = new OutputStreamWriter(new FileOutputStream(new File(folder, "ro-crate-preview.html")))) {
                template.process(dataModel, out);
                out.flush();
            }
        } catch (TemplateException ex) {
            throw new IOException("Failed to generate preview.", ex);
        }
    }

    @Override
    public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException {
        if (template == null) {
            throw new IOException("Preview template did not load. Unable to proceed.");
        }
        try {
            //prepare metadata for template
            Map<String, Object> dataModel = new HashMap<>();
            dataModel.put("crateModel", mapFromJson(metadata));

            //prepare output folder and writer
            FileUtils.forceMkdir(new File("temp"));
            //load and process template
            try (FileWriter writer = new FileWriter(new File("temp/ro-crate-preview.html"))) {
                //load and process template
                template.process(dataModel, writer);
                writer.flush();
            }

            ZipUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html");
        } catch (TemplateException ex) {
            throw new IOException("Failed to generate preview.", ex);
        } finally {
            try {
                FileUtils.deleteDirectory(new File("temp"));
            } catch (IOException ex) {
                //ignore
            }
        }
    }

}

1	package edu.kit.datamanager.ro_crate.preview;
2
3	import com.fasterxml.jackson.databind.JsonNode;
4	import com.fasterxml.jackson.databind.ObjectMapper;
5	import edu.kit.datamanager.ro_crate.util.ZipUtil;
6	import freemarker.template.Configuration;
7	import freemarker.template.Template;
8	import freemarker.template.TemplateException;
9	import freemarker.template.TemplateExceptionHandler;
10	import java.io.File;
11	import java.io.FileOutputStream;
12	import java.io.FileWriter;
13	import java.io.IOException;
14	import java.io.OutputStreamWriter;
15	import java.io.Writer;
16	import java.util.ArrayList;
17	import java.util.Collections;
18	import java.util.HashMap;
19	import java.util.LinkedList;
20	import java.util.List;
21	import java.util.Map;
22	import net.lingala.zip4j.ZipFile;
23	import net.lingala.zip4j.exception.ZipException;
24	import net.lingala.zip4j.io.outputstream.ZipOutputStream;
25	import org.apache.commons.io.FileUtils;
26	import org.slf4j.Logger;
27	import org.slf4j.LoggerFactory;
28
29	/**
30	* This class generates a custom preview without requiring external
31	* dependencies, i.e., rochtml. Therefore, the FreeMarker template located under
32	* resources/templates/custom_preview.ftl is used.
33	*
34	* @author jejkal
35	*/
36	public class CustomPreview implements CratePreview {
37
38	private final static Logger logger = LoggerFactory.getLogger(CustomPreview.class);	1✔
39
40	private final Configuration cfg;
41	private Template template = null;	1✔
42
43	public CustomPreview() {	1✔
44	cfg = new Configuration(Configuration.VERSION_2_3_34);	1✔
45	cfg.setClassForTemplateLoading(CustomPreview.class, "/");	1✔
46	cfg.setDefaultEncoding("UTF-8");	1✔
47	cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);	1✔
48	try {
49	template = cfg.getTemplate("templates/custom_preview.ftl");	1✔
NEW 50	} catch (IOException ex) {	×
NEW 51	logger.error("Failed to read template for CustomPreview.", ex);	×
52	}	1✔
53	}	1✔
54
55	private CustomPreviewModel mapFromJson(String metadata) throws IOException {
56	ObjectMapper mapper = new ObjectMapper();	1✔
57	JsonNode root = (JsonNode) mapper.readValue(metadata, JsonNode.class);	1✔
58	JsonNode graph = root.get("@graph");	1✔
59	CustomPreviewModel.ROCrate crate = new CustomPreviewModel.ROCrate();	1✔
60	List<CustomPreviewModel.Dataset> datasets = new ArrayList<>();	1✔
61	List<CustomPreviewModel.File> files = new ArrayList<>();	1✔
62
63	if (graph.isArray()) {	1✔
64
65	for (JsonNode node : graph) {	1✔
66	String id = node.path("@id").asText();	1✔
67	List<String> types = new LinkedList<>();	1✔
68	if (node.path("@type").isArray()) {	1✔
69
NEW 70	Collections.addAll(types, mapper.convertValue(node.path("@type"), String[].class));	×
71	} else {
72	types.add(node.path("@type").asText());	1✔
73	}
74
75	if (types.contains("Dataset") && "./".equals(id)) {	1✔
76	crate.name = node.path("name").asText();	1✔
77	crate.description = node.path("description").asText(null);	1✔
78	crate.type = "Dataset";	1✔
79	crate.license = node.path("license").path("@id").asText(node.path("license").asText(null));	1✔
80	crate.datePublished = node.path("datePublished").asText(null);	1✔
81	crate.hasPart = new ArrayList<>();	1✔
82
83	for (JsonNode part : node.path("hasPart")) {	1✔
84	CustomPreviewModel.Part p = new CustomPreviewModel.Part();	1✔
85	String tmpId = part.path("@id").asText(part.asText());	1✔
86	p.id = tmpId;	1✔
87	p.name = tmpId; // Name will be replaced later	1✔
88	crate.hasPart.add(p);	1✔
89	}	1✔
90	} else if (types.contains("Dataset")) {	1✔
NEW 91	CustomPreviewModel.Dataset dataset = new CustomPreviewModel.Dataset();	×
NEW 92	dataset.id = id;	×
NEW 93	dataset.name = node.path("name").asText();	×
NEW 94	dataset.description = node.path("description").asText();	×
NEW 95	datasets.add(dataset);	×
96	} else if (types.contains("File")) {	1✔
97	CustomPreviewModel.File file = new CustomPreviewModel.File();	1✔
98	file.id = id;	1✔
99	file.name = node.path("name").asText(null);	1✔
100	file.description = node.path("description").asText(null);	1✔
101	file.contentSize = node.path("contentSize").asText(null);	1✔
102	file.encodingFormat = node.path("encodingFormat").asText(null);	1✔
103	files.add(file);	1✔
104	}
105	}	1✔
106	}
107
108	// Update Part names using dataset and file lists
109	if (crate.hasPart != null) {	1✔
110	for (CustomPreviewModel.Part part : crate.hasPart) {	1✔
111	for (CustomPreviewModel.Dataset dataset : datasets) {	1✔
NEW 112	if (dataset.id.equals(part.id) && dataset.name != null) {	×
NEW 113	part.name = dataset.name;	×
114	}
NEW 115	}	×
116	for (CustomPreviewModel.File file : files) {	1✔
117	if (file.id.equals(part.id) && file.name != null) {	1✔
118	part.name = file.name;	1✔
119	}
120	}	1✔
121	}	1✔
122	}
123
124	CustomPreviewModel model = new CustomPreviewModel();	1✔
125	model.crate = crate;	1✔
126	model.datasets = datasets;	1✔
127	model.files = files;	1✔
128	return model;	1✔
129	}
130
131	@Override
132	public void saveAllToZip(ZipFile zipFile) throws IOException {
133	if (template == null) {	1✔
NEW 134	throw new IOException("Preview template did not load. Unable to proceed.");	×
135	}
136	if (zipFile == null) {	1✔
NEW 137	throw new IOException("Argument zipFile must not be null.");	×
138	}
139	try {
140	zipFile.extractFile("ro-crate-metadata.json", "temp");	1✔
141	} catch (ZipException ex) {	1✔
142	throw new IOException("ro-crate-metadata.json not found in provided ZIP.", ex);	1✔
143	}	1✔
144
145	String metadata = FileUtils.readFileToString(new File("temp/ro-crate-metadata.json"), "UTF-8");	1✔
146	try {
147	Map<String, Object> dataModel = new HashMap<>();	1✔
148	dataModel.put("crateModel", mapFromJson(metadata));	1✔
149
150	try (Writer out = new OutputStreamWriter(new FileOutputStream("temp/ro-crate-preview.html"))) {	1✔
151	template.process(dataModel, out);	1✔
152	out.flush();	1✔
153	}
154	zipFile.addFile("temp/ro-crate-preview.html");	1✔
NEW 155	} catch (TemplateException ex) {	×
NEW 156	throw new IOException("Failed to generate preview.", ex);	×
157	} finally {
158	try {
159	FileUtils.deleteDirectory(new File("temp"));	1✔
NEW 160	} catch (IOException ex) {	×
161	//ignore
162	}	1✔
163	}
164	}	1✔
165
166	@Override
167	public void saveAllToFolder(File folder) throws IOException {
168	if (template == null) {	1✔
NEW 169	throw new IOException("Preview template did not load. Unable to proceed.");	×
170	}
171	if (folder == null \|\| !folder.exists()) {	1✔
172	throw new IOException("Preview target folder " + folder + " does not exist.");	1✔
173	}
174	String metadata = FileUtils.readFileToString(new File(folder, "ro-crate-metadata.json"), "UTF-8");	1✔
175	try {
176	Map<String, Object> dataModel = new HashMap<>();	1✔
177	dataModel.put("crateModel", mapFromJson(metadata));	1✔
178	try (Writer out = new OutputStreamWriter(new FileOutputStream(new File(folder, "ro-crate-preview.html")))) {	1✔
179	template.process(dataModel, out);	1✔
180	out.flush();	1✔
181	}
NEW 182	} catch (TemplateException ex) {	×
NEW 183	throw new IOException("Failed to generate preview.", ex);	×
184	}	1✔
185	}	1✔
186
187	@Override
188	public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException {
189	if (template == null) {	1✔
NEW 190	throw new IOException("Preview template did not load. Unable to proceed.");	×
191	}
192	try {
193	//prepare metadata for template
194	Map<String, Object> dataModel = new HashMap<>();	1✔
195	dataModel.put("crateModel", mapFromJson(metadata));	1✔
196
197	//prepare output folder and writer
198	FileUtils.forceMkdir(new File("temp"));	1✔
199	//load and process template
200	try (FileWriter writer = new FileWriter(new File("temp/ro-crate-preview.html"))) {	1✔
201	//load and process template
202	template.process(dataModel, writer);	1✔
203	writer.flush();	1✔
204	}
205
206	ZipUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html");	1✔
NEW 207	} catch (TemplateException ex) {	×
NEW 208	throw new IOException("Failed to generate preview.", ex);	×
209	} finally {
210	try {
211	FileUtils.deleteDirectory(new File("temp"));	1✔
NEW 212	} catch (IOException ex) {	×
213	//ignore
214	}	1✔
215	}
216	}	1✔
217
218	}

kit-data-manager / ro-crate-java / #378

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