#334

Committed 10 Apr 2025 09:06AM UTC coverage: 85.3%. First build

Build # #334

Build Type

Pull #233

github

Committed by

ThomasJejkal

Commit Message

Fixed issues with stale writers

Pull Request Pull Request #233: Version 2.1.0

Run Details

280 of 440 new or added lines in 15 files covered. (63.64%)

1764 of 2068 relevant lines covered (85.3%)

0.85 hits per line

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57.14

/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;

/**
 * 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 Configuration cfg;

    public CustomPreview() {
        cfg = new Configuration(Configuration.VERSION_2_3_34);
        cfg.setClassForTemplateLoading(CustomPreview.class, "/");
        cfg.setDefaultEncoding("UTF-8");
        cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);

    }

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

kit-data-manager / ro-crate-java / #334

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