#348

Committed 15 Apr 2025 08:24AM UTC coverage: 86.955%. First build

Build # #348

Build Type

Pull #233

github

Committed by

web-flow

Commit Message

Merge pull request #244 from kit-data-manager/renovate/commons-io-commons-io-2.x

chore(deps): update dependency commons-io:commons-io to v2.19.0

Pull Request Pull Request #233: Version 2.1.0

Run Details

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

        if (graph.isArray()) {

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

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

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

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

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

        ROCratePreviewModel model = new ROCratePreviewModel();
        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.preview.model.ROCratePreviewModel;
6	import edu.kit.datamanager.ro_crate.util.ZipUtil;
7	import freemarker.template.Configuration;
8	import freemarker.template.Template;
9	import freemarker.template.TemplateException;
10	import freemarker.template.TemplateExceptionHandler;
11	import java.io.File;
12	import java.io.FileOutputStream;
13	import java.io.FileWriter;
14	import java.io.IOException;
15	import java.io.OutputStreamWriter;
16	import java.io.Writer;
17	import java.util.ArrayList;
18	import java.util.Collections;
19	import java.util.HashMap;
20	import java.util.LinkedList;
21	import java.util.List;
22	import java.util.Map;
23	import net.lingala.zip4j.ZipFile;
24	import net.lingala.zip4j.exception.ZipException;
25	import net.lingala.zip4j.io.outputstream.ZipOutputStream;
26	import org.apache.commons.io.FileUtils;
27	import org.slf4j.Logger;
28	import org.slf4j.LoggerFactory;
29
30	/**
31	* This class generates a custom preview without requiring external
32	* dependencies, i.e., rochtml. Therefore, the FreeMarker template located under
33	* resources/templates/custom_preview.ftl is used.
34	*
35	* @author jejkal
36	*/
37	public class CustomPreview implements CratePreview {
38
39	private final static Logger logger = LoggerFactory.getLogger(CustomPreview.class);	1✔
40
41	private final Configuration cfg;
42	private Template template = null;	1✔
43
44	public CustomPreview() {	1✔
45	cfg = new Configuration(Configuration.VERSION_2_3_34);	1✔
46	cfg.setClassForTemplateLoading(CustomPreview.class, "/");	1✔
47	cfg.setDefaultEncoding("UTF-8");	1✔
48	cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);	1✔
49	try {
50	template = cfg.getTemplate("templates/custom_preview.ftl");	1✔
NEW 51	} catch (IOException ex) {	×
NEW 52	logger.error("Failed to read template for CustomPreview.", ex);	×
53	}	1✔
54	}	1✔
55
56	private ROCratePreviewModel mapFromJson(String metadata) throws IOException {
57	ObjectMapper mapper = new ObjectMapper();	1✔
58	JsonNode root = (JsonNode) mapper.readValue(metadata, JsonNode.class);	1✔
59	JsonNode graph = root.get("@graph");	1✔
60	ROCratePreviewModel.ROCrate crate = new ROCratePreviewModel.ROCrate();	1✔
61	List<ROCratePreviewModel.Dataset> datasets = new ArrayList<>();	1✔
62	List<ROCratePreviewModel.File> files = new ArrayList<>();	1✔
63
64	if (graph.isArray()) {	1✔
65
66	for (JsonNode node : graph) {	1✔
67	String id = node.get("@id").asText();	1✔
68	List<String> types = new LinkedList<>();	1✔
69	if (node.get("@type").isArray()) {	1✔
70
NEW 71	Collections.addAll(types, (String[]) mapper.convertValue(node.get("@type"), String[].class));	×
72	} else {
73	types.add(node.get("@type").asText());	1✔
74	}
75
76	if (types.contains("Dataset") && "./".equals(id)) {	1✔
77	crate.name = node.get("name").asText();	1✔
78	crate.description = node.get("description") == null ? null : node.get("description").asText();	1✔
79	crate.type = "Dataset";	1✔
80	if (node.get("license") != null) {	1✔
81	crate.license = node.get("license").isObject() ? node.get("license").get("@id").asText() : node.get("license").asText();	1✔
82	}
83	crate.datePublished = node.get("datePublished") == null ? null : node.get("datePublished").asText();	1✔
84	crate.hasPart = new ArrayList<>();	1✔
85
86	if (node.has("hasPart")) {	1✔
87	for (JsonNode part : node.get("hasPart")) {	1✔
88	ROCratePreviewModel.Part p = new ROCratePreviewModel.Part();	1✔
89	if (part.isObject()) {	1✔
90	p.id = part.get("@id").asText();	1✔
91	p.name = part.get("@id").asText(); // Name will be replaced later	1✔
92	} else {
93	p.id = part.asText();	1✔
94	}
95
96	crate.hasPart.add(p);	1✔
97	}	1✔
98	}
99	} else if (types.contains("Dataset")) {	1✔
100	ROCratePreviewModel.Dataset dataset = new ROCratePreviewModel.Dataset();	1✔
101	dataset.id = id;	1✔
102	dataset.name = node.get("name").asText();	1✔
103	dataset.description = node.get("description").asText();	1✔
104	datasets.add(dataset);	1✔
105	} else if (types.contains("File")) {	1✔
106	ROCratePreviewModel.File file = new ROCratePreviewModel.File();	1✔
107	file.id = id;	1✔
108	file.name = node.get("name") == null ? null : node.get("name").asText();	1✔
109	file.description = node.get("description") == null ? null : node.get("description").asText();	1✔
110	file.contentSize = node.get("contentSize") == null ? null : node.get("contentSize").asText();	1✔
111	file.encodingFormat = node.get("encodingFormat") == null ? null : node.get("encodingFormat").asText();	1✔
112	files.add(file);	1✔
113	}
114	}	1✔
115	}
116
117	// Update Part names using dataset and file lists
118	if (crate.hasPart != null) {	1✔
119	for (ROCratePreviewModel.Part part : crate.hasPart) {	1✔
120	for (ROCratePreviewModel.Dataset dataset : datasets) {	1✔
121	if (dataset.id.equals(part.id) && dataset.name != null) {	1✔
122	part.name = dataset.name;	1✔
123	}
124	}	1✔
125	for (ROCratePreviewModel.File file : files) {	1✔
126	if (file.id.equals(part.id) && file.name != null) {	1✔
127	part.name = file.name;	1✔
128	}
129	}	1✔
130	}	1✔
131	}
132
133	ROCratePreviewModel model = new ROCratePreviewModel();	1✔
134	model.crate = crate;	1✔
135	model.datasets = datasets;	1✔
136	model.files = files;	1✔
137	return model;	1✔
138	}
139
140	@Override
141	public void saveAllToZip(ZipFile zipFile) throws IOException {
142	if (template == null) {	1✔
NEW 143	throw new IOException("Preview template did not load. Unable to proceed.");	×
144	}
145	if (zipFile == null) {	1✔
NEW 146	throw new IOException("Argument zipFile must not be null.");	×
147	}
148	try {
149	zipFile.extractFile("ro-crate-metadata.json", "temp");	1✔
150	} catch (ZipException ex) {	1✔
151	throw new IOException("ro-crate-metadata.json not found in provided ZIP.", ex);	1✔
152	}	1✔
153
154	String metadata = FileUtils.readFileToString(new File("temp/ro-crate-metadata.json"), "UTF-8");	1✔
155	try {
156	Map<String, Object> dataModel = new HashMap<>();	1✔
157	dataModel.put("crateModel", mapFromJson(metadata));	1✔
158
159	try (Writer out = new OutputStreamWriter(new FileOutputStream("temp/ro-crate-preview.html"))) {	1✔
160	template.process(dataModel, out);	1✔
161	out.flush();	1✔
162	}
163	zipFile.addFile("temp/ro-crate-preview.html");	1✔
NEW 164	} catch (TemplateException ex) {	×
NEW 165	throw new IOException("Failed to generate preview.", ex);	×
166	} finally {
167	try {
168	FileUtils.deleteDirectory(new File("temp"));	1✔
NEW 169	} catch (IOException ex) {	×
170	//ignore
171	}	1✔
172	}
173	}	1✔
174
175	@Override
176	public void saveAllToFolder(File folder) throws IOException {
177	if (template == null) {	1✔
NEW 178	throw new IOException("Preview template did not load. Unable to proceed.");	×
179	}
180	if (folder == null \|\| !folder.exists()) {	1✔
181	throw new IOException("Preview target folder " + folder + " does not exist.");	1✔
182	}
183	String metadata = FileUtils.readFileToString(new File(folder, "ro-crate-metadata.json"), "UTF-8");	1✔
184	try {
185	Map<String, Object> dataModel = new HashMap<>();	1✔
186	dataModel.put("crateModel", mapFromJson(metadata));	1✔
187	try (Writer out = new OutputStreamWriter(new FileOutputStream(new File(folder, "ro-crate-preview.html")))) {	1✔
188	template.process(dataModel, out);	1✔
189	out.flush();	1✔
190	}
NEW 191	} catch (TemplateException ex) {	×
NEW 192	throw new IOException("Failed to generate preview.", ex);	×
193	}	1✔
194	}	1✔
195
196	@Override
197	public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException {
198	if (template == null) {	1✔
NEW 199	throw new IOException("Preview template did not load. Unable to proceed.");	×
200	}
201	try {
202	//prepare metadata for template
203	Map<String, Object> dataModel = new HashMap<>();	1✔
204	dataModel.put("crateModel", mapFromJson(metadata));	1✔
205
206	//prepare output folder and writer
207	FileUtils.forceMkdir(new File("temp"));	1✔
208	//load and process template
209	try (FileWriter writer = new FileWriter(new File("temp/ro-crate-preview.html"))) {	1✔
210	//load and process template
211	template.process(dataModel, writer);	1✔
212	writer.flush();	1✔
213	}
214
215	ZipUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html");	1✔
NEW 216	} catch (TemplateException ex) {	×
NEW 217	throw new IOException("Failed to generate preview.", ex);	×
218	} finally {
219	try {
220	FileUtils.deleteDirectory(new File("temp"));	1✔
NEW 221	} catch (IOException ex) {	×
222	//ignore
223	}	1✔
224	}
225	}	1✔
226
227	}

kit-data-manager / ro-crate-java / #348

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