#431

Committed 19 May 2025 02:23PM UTC coverage: 90.418% (+0.2%) from 90.169%

Build # #431

Build Type

Pull #258

github

Committed by

web-flow

Commit Message

Merge 896018de9 into 810d1995c

Pull Request Pull Request #258: Support .ELN-style crates in all zip readers and writers

Run Details

283 of 315 new or added lines in 25 files covered. (89.84%)

1 existing line in 1 file now uncovered.

2010 of 2223 relevant lines covered (90.42%)

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87.14

/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java

package edu.kit.datamanager.ro_crate.writer;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import edu.kit.datamanager.ro_crate.Crate;
import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
import edu.kit.datamanager.ro_crate.preview.CratePreview;
import edu.kit.datamanager.ro_crate.util.FileSystemUtil;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.model.ZipParameters;
import org.apache.commons.io.FileUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.nio.file.Path;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;

/**
 * Implementation of the writing strategy to provide a way of writing crates to
 * a zip archive.
 */
public class WriteZipStrategy implements
        GenericWriterStrategy<String>,
        ElnFormatWriter<String>
{
    private static final Logger logger = LoggerFactory.getLogger(WriteZipStrategy.class);
    public static final String TMP_DIR = "./.tmp/ro-crate-java/writer-zip-strategy/";

    /**
     * Defines if the zip file will directly contain the crate,
     * or if it will contain a subdirectory with the crate.
     */
    protected boolean createRootSubdir = false;

    @Override
    public ElnFormatWriter<String> usingElnStyle() {
        this.createRootSubdir = true;
        return this;
    }

    @Override
    public void save(Crate crate, String destination) throws IOException {
        String innerFolderName = "";
        if (this.createRootSubdir) {
            innerFolderName = FileSystemUtil.filterExtensionsFromFileName(
                    Path.of(destination).getFileName().toString(),
                    Set.of("ELN", "ZIP"));
            innerFolderName = FileSystemUtil.ensureTrailingSlash(innerFolderName);
        }
        try (ZipFile zipFile = new ZipFile(destination)) {
            saveMetadataJson(crate, zipFile, innerFolderName);
            saveDataEntities(crate, zipFile, innerFolderName);
            savePreview(crate, zipFile, innerFolderName);
        }
    }

    private void saveDataEntities(Crate crate, ZipFile zipFile, String prefix) throws IOException {
        for (DataEntity dataEntity : crate.getAllDataEntities()) {
            this.saveToZip(dataEntity, zipFile, prefix);
        }
    }

    private void saveMetadataJson(Crate crate, ZipFile zipFile, String prefix) throws IOException {
        // write the metadata.json file
        ZipParameters zipParameters = new ZipParameters();
        zipParameters.setFileNameInZip(prefix + "ro-crate-metadata.json");
        ObjectMapper objectMapper = MyObjectMapper.getMapper();
        // we create an JsonNode only to have the file written pretty
        JsonNode node = objectMapper.readTree(crate.getJsonMetadata());
        String str = objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(node);
        try (InputStream inputStream = new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8))) {
            // write the ro-crate-metadata
            zipFile.addStream(inputStream, zipParameters);
        }
    }

    private void savePreview(Crate crate, ZipFile zipFile, String prefix) throws IOException {
        Optional<CratePreview> preview = Optional.ofNullable(crate.getPreview());
        if (preview.isEmpty()) {
            return;
        }
        final String ID = UUID.randomUUID().toString();
        File tmpPreviewFolder = Path.of(TMP_DIR)
                .resolve(ID)
                .toFile();
        FileUtils.forceMkdir(tmpPreviewFolder);
        FileUtils.forceDeleteOnExit(tmpPreviewFolder);

        preview.get().generate(crate, tmpPreviewFolder);
        String[] paths = tmpPreviewFolder.list();
        if (paths == null) {
            throw new IOException("No preview files found in temporary folder. Preview generation failed.");
        }
        for (String path : paths) {
            File file = tmpPreviewFolder.toPath().resolve(path).toFile();
            if (file.isDirectory()) {
                ZipParameters parameters = new ZipParameters();
                parameters.setRootFolderNameInZip(prefix + path);
                parameters.setIncludeRootFolder(false);
                zipFile.addFolder(file, parameters);
            } else {
                ZipParameters zipParameters = new ZipParameters();
                zipParameters.setFileNameInZip(prefix + path);
                zipFile.addFile(file, zipParameters);
            }
        }
        try {
            FileUtils.forceDelete(tmpPreviewFolder);
        } catch (IOException e) {
            logger.error("Could not delete temporary preview folder: {}", tmpPreviewFolder);
        }
    }

    private void saveToZip(DataEntity entity, ZipFile zipFile, String prefix) throws IOException {
        if (entity == null || entity.getPath() == null) {
            return;
        }

        boolean isDirectory = entity.getPath().toFile().isDirectory();
        if (isDirectory) {
            ZipParameters parameters = new ZipParameters();
            parameters.setRootFolderNameInZip(prefix + entity.getId());
            parameters.setIncludeRootFolder(false);
            zipFile.addFolder(entity.getPath().toFile(), parameters);
        } else {
            ZipParameters zipParameters = new ZipParameters();
            zipParameters.setFileNameInZip(prefix + entity.getId());
            zipFile.addFile(entity.getPath().toFile(), zipParameters);
        }
    }
}

1	package edu.kit.datamanager.ro_crate.writer;
2
3	import com.fasterxml.jackson.databind.JsonNode;
4	import com.fasterxml.jackson.databind.ObjectMapper;
5	import edu.kit.datamanager.ro_crate.Crate;
6	import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
7	import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
8	import edu.kit.datamanager.ro_crate.preview.CratePreview;
9	import edu.kit.datamanager.ro_crate.util.FileSystemUtil;
10	import net.lingala.zip4j.ZipFile;
11	import net.lingala.zip4j.model.ZipParameters;
12	import org.apache.commons.io.FileUtils;
13	import org.slf4j.Logger;
14	import org.slf4j.LoggerFactory;
15
16	import java.io.ByteArrayInputStream;
17	import java.io.File;
18	import java.io.IOException;
19	import java.io.InputStream;
20	import java.nio.charset.StandardCharsets;
21	import java.nio.file.Path;
22	import java.util.Optional;
23	import java.util.Set;
24	import java.util.UUID;
25
26	/**
27	* Implementation of the writing strategy to provide a way of writing crates to
28	* a zip archive.
29	*/
30	public class WriteZipStrategy implements	1✔
31	GenericWriterStrategy<String>,
32	ElnFormatWriter<String>
33	{
34	private static final Logger logger = LoggerFactory.getLogger(WriteZipStrategy.class);	1✔
35	public static final String TMP_DIR = "./.tmp/ro-crate-java/writer-zip-strategy/";
36
37	/**
38	* Defines if the zip file will directly contain the crate,
39	* or if it will contain a subdirectory with the crate.
40	*/
41	protected boolean createRootSubdir = false;	1✔
42
43	@Override
44	public ElnFormatWriter<String> usingElnStyle() {
45	this.createRootSubdir = true;	1✔
46	return this;	1✔
47	}
48
49	@Override
50	public void save(Crate crate, String destination) throws IOException {
51	String innerFolderName = "";	1✔
52	if (this.createRootSubdir) {	1✔
53	innerFolderName = FileSystemUtil.filterExtensionsFromFileName(	1✔
54	Path.of(destination).getFileName().toString(),	1✔
55	Set.of("ELN", "ZIP"));	1✔
56	innerFolderName = FileSystemUtil.ensureTrailingSlash(innerFolderName);	1✔
57	}
58	try (ZipFile zipFile = new ZipFile(destination)) {	1✔
59	saveMetadataJson(crate, zipFile, innerFolderName);	1✔
60	saveDataEntities(crate, zipFile, innerFolderName);	1✔
61	savePreview(crate, zipFile, innerFolderName);	1✔
62	}
63	}	1✔
64
65	private void saveDataEntities(Crate crate, ZipFile zipFile, String prefix) throws IOException {
66	for (DataEntity dataEntity : crate.getAllDataEntities()) {	1✔
67	this.saveToZip(dataEntity, zipFile, prefix);	1✔
68	}	1✔
69	}	1✔
70
71	private void saveMetadataJson(Crate crate, ZipFile zipFile, String prefix) throws IOException {
72	// write the metadata.json file
73	ZipParameters zipParameters = new ZipParameters();	1✔
74	zipParameters.setFileNameInZip(prefix + "ro-crate-metadata.json");	1✔
75	ObjectMapper objectMapper = MyObjectMapper.getMapper();	1✔
76	// we create an JsonNode only to have the file written pretty
77	JsonNode node = objectMapper.readTree(crate.getJsonMetadata());	1✔
78	String str = objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(node);	1✔
79	try (InputStream inputStream = new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8))) {	1✔
80	// write the ro-crate-metadata
81	zipFile.addStream(inputStream, zipParameters);	1✔
82	}
83	}	1✔
84
85	private void savePreview(Crate crate, ZipFile zipFile, String prefix) throws IOException {
86	Optional<CratePreview> preview = Optional.ofNullable(crate.getPreview());	1✔
87	if (preview.isEmpty()) {	1✔
88	return;	1✔
89	}
90	final String ID = UUID.randomUUID().toString();	1✔
91	File tmpPreviewFolder = Path.of(TMP_DIR)	1✔
92	.resolve(ID)	1✔
93	.toFile();	1✔
94	FileUtils.forceMkdir(tmpPreviewFolder);	1✔
95	FileUtils.forceDeleteOnExit(tmpPreviewFolder);	1✔
96
97	preview.get().generate(crate, tmpPreviewFolder);	1✔
98	String[] paths = tmpPreviewFolder.list();	1✔
99	if (paths == null) {	1✔
NEW 100	throw new IOException("No preview files found in temporary folder. Preview generation failed.");	×
101	}
102	for (String path : paths) {	1✔
103	File file = tmpPreviewFolder.toPath().resolve(path).toFile();	1✔
104	if (file.isDirectory()) {	1✔
NEW 105	ZipParameters parameters = new ZipParameters();	×
NEW 106	parameters.setRootFolderNameInZip(prefix + path);	×
NEW 107	parameters.setIncludeRootFolder(false);	×
NEW 108	zipFile.addFolder(file, parameters);	×
NEW 109	} else {	×
110	ZipParameters zipParameters = new ZipParameters();	1✔
111	zipParameters.setFileNameInZip(prefix + path);	1✔
112	zipFile.addFile(file, zipParameters);	1✔
113	}
114	}
115	try {
116	FileUtils.forceDelete(tmpPreviewFolder);	1✔
NEW 117	} catch (IOException e) {	×
NEW 118	logger.error("Could not delete temporary preview folder: {}", tmpPreviewFolder);	×
119	}	1✔
120	}	1✔
121
122	private void saveToZip(DataEntity entity, ZipFile zipFile, String prefix) throws IOException {
123	if (entity == null \|\| entity.getPath() == null) {	1✔
NEW 124	return;	×
125	}
126
127	boolean isDirectory = entity.getPath().toFile().isDirectory();	1✔
128	if (isDirectory) {	1✔
129	ZipParameters parameters = new ZipParameters();	1✔
130	parameters.setRootFolderNameInZip(prefix + entity.getId());	1✔
131	parameters.setIncludeRootFolder(false);	1✔
132	zipFile.addFolder(entity.getPath().toFile(), parameters);	1✔
133	} else {	1✔
134	ZipParameters zipParameters = new ZipParameters();	1✔
135	zipParameters.setFileNameInZip(prefix + entity.getId());	1✔
136	zipFile.addFile(entity.getPath().toFile(), zipParameters);	1✔
137	}
138	}	1✔
139	}

kit-data-manager / ro-crate-java / #431

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