#359

Committed 16 Apr 2025 04:37PM UTC coverage: 85.989%. First build

Build # #359

Build Type

Pull #233

github

Committed by

Pfeil

Commit Message

fix: add null and existence checks for JSON-LD file in JsonLdExpander

Pull Request Pull Request #233: Version 2.1.0

Run Details

532 of 694 new or added lines in 19 files covered. (76.66%)

1878 of 2184 relevant lines covered (85.99%)

0.86 hits per line

Source File
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81.25

/src/main/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReader.java

package edu.kit.datamanager.ro_crate.reader;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Path;
import java.util.UUID;
import net.lingala.zip4j.io.inputstream.ZipInputStream;
import net.lingala.zip4j.model.LocalFileHeader;
import org.apache.commons.io.FileUtils;

/**
 * A ZIP file reader implementation of the StreamReaderStrategy interface.
 * This class handles reading and extraction of RO-Crate content from ZIP archives
 * into a temporary directory structure, which allows for accessing the contained files.
 *
 * @author jejkal
 */
public class ZipStreamReader implements StreamReaderStrategy {

    protected final String ID = UUID.randomUUID().toString();
    protected Path temporaryFolder = Path.of(String.format("./.tmp/ro-crate-java/zipStreamReader/%s/", ID));
    protected boolean isExtracted = false;

    /**
     * Crates a ZipStreamReader with the default configuration as described in
     * the class documentation.
     */
    public ZipStreamReader() {
    }

    /**
     * Creates a ZipStreamReader which will extract the contents temporary to
     * the given location instead of the default location.
     *
     * @param folderPath the custom directory to extract content to for
     * temporary access.
     * @param shallAddUuidSubfolder if true, the reader will extract into
     * subdirectories of the given directory. These subdirectories will have
     * UUIDs as their names.
     */
    public ZipStreamReader(Path folderPath, boolean shallAddUuidSubfolder) {
        if (shallAddUuidSubfolder) {
            this.temporaryFolder = folderPath.resolve(ID);
        } else {
            this.temporaryFolder = folderPath;
        }
    }

    /**
     * @return the identifier which may be used as the name for a subfolder in
     * the temporary directory.
     */
    public String getID() {
        return ID;
    }

    /**
     * @return the folder (considered temporary) where the zipped crate will be
     * or has been extracted to.
     */
    public Path getTemporaryFolder() {
        return temporaryFolder;
    }

    /**
     * @return whether the crate has already been extracted into the temporary
     * folder.
     */
    public boolean isExtracted() {
        return isExtracted;
    }

    /**Read the crate metadata and content from the provided input stream.
     * 
     * @param stream The input stream.
     */
    private void readCrate(InputStream stream) {
        try {
            File folder = temporaryFolder.toFile();
            // ensure the directory is clean
            if (folder.exists()) {
                if (folder.isDirectory()) {
                    FileUtils.cleanDirectory(folder);
                } else if (folder.isFile()) {
                    FileUtils.delete(folder);
                }
            } else {
                FileUtils.forceMkdir(folder);
            }

            LocalFileHeader localFileHeader;
            int readLen;
            byte[] readBuffer = new byte[4096];

            try (ZipInputStream zipInputStream = new ZipInputStream(stream)) {
                while ((localFileHeader = zipInputStream.getNextEntry()) != null) {
                    String fileName = localFileHeader.getFileName();
                    File extractedFile = new File(folder, fileName).getCanonicalFile();
                    if (!extractedFile.toPath().startsWith(folder.getCanonicalPath())) {
                        throw new IOException("Entry is outside of target directory: " + fileName);
                    }
                    try (OutputStream outputStream = new FileOutputStream(extractedFile)) {
                        while ((readLen = zipInputStream.read(readBuffer)) != -1) {
                            outputStream.write(readBuffer, 0, readLen);
                        }
                    }
                }
            }
            this.isExtracted = true;
            // register deletion on exit
            FileUtils.forceDeleteOnExit(folder);
        } catch (IOException ex) {
            logger.error("Failed to read crate from input stream.", ex);
        }
    }

    @Override
    public ObjectNode readMetadataJson(InputStream stream) {
        if (!isExtracted) {
            this.readCrate(stream);
        }

        ObjectMapper objectMapper = MyObjectMapper.getMapper();
        File jsonMetadata = temporaryFolder.resolve("ro-crate-metadata.json").toFile();

        try {
            return objectMapper.readTree(jsonMetadata).deepCopy();
        } catch (IOException e) {
            logger.error("Failed to deserialize crate metadata.", e);
            return null;
        }
    }

    @Override
    public File readContent(InputStream stream) {
        if (!isExtracted) {
            this.readCrate(stream);
        }
        return temporaryFolder.toFile();
    }
}

1	package edu.kit.datamanager.ro_crate.reader;
2
3	import com.fasterxml.jackson.databind.ObjectMapper;
4	import com.fasterxml.jackson.databind.node.ObjectNode;
5	import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
6	import java.io.File;
7	import java.io.FileOutputStream;
8	import java.io.IOException;
9	import java.io.InputStream;
10	import java.io.OutputStream;
11	import java.nio.file.Path;
12	import java.util.UUID;
13	import net.lingala.zip4j.io.inputstream.ZipInputStream;
14	import net.lingala.zip4j.model.LocalFileHeader;
15	import org.apache.commons.io.FileUtils;
16
17	/**
18	* A ZIP file reader implementation of the StreamReaderStrategy interface.
19	* This class handles reading and extraction of RO-Crate content from ZIP archives
20	* into a temporary directory structure, which allows for accessing the contained files.
21	*
22	* @author jejkal
23	*/
24	public class ZipStreamReader implements StreamReaderStrategy {
25
26	protected final String ID = UUID.randomUUID().toString();	1✔
27	protected Path temporaryFolder = Path.of(String.format("./.tmp/ro-crate-java/zipStreamReader/%s/", ID));	1✔
28	protected boolean isExtracted = false;	1✔
29
30	/**
31	* Crates a ZipStreamReader with the default configuration as described in
32	* the class documentation.
33	*/
34	public ZipStreamReader() {	1✔
35	}	1✔
36
37	/**
38	* Creates a ZipStreamReader which will extract the contents temporary to
39	* the given location instead of the default location.
40	*
41	* @param folderPath the custom directory to extract content to for
42	* temporary access.
43	* @param shallAddUuidSubfolder if true, the reader will extract into
44	* subdirectories of the given directory. These subdirectories will have
45	* UUIDs as their names.
46	*/
47	public ZipStreamReader(Path folderPath, boolean shallAddUuidSubfolder) {	1✔
48	if (shallAddUuidSubfolder) {	1✔
49	this.temporaryFolder = folderPath.resolve(ID);	1✔
50	} else {
51	this.temporaryFolder = folderPath;	1✔
52	}
53	}	1✔
54
55	/**
56	* @return the identifier which may be used as the name for a subfolder in
57	* the temporary directory.
58	*/
59	public String getID() {
60	return ID;	1✔
61	}
62
63	/**
64	* @return the folder (considered temporary) where the zipped crate will be
65	* or has been extracted to.
66	*/
67	public Path getTemporaryFolder() {
68	return temporaryFolder;	1✔
69	}
70
71	/**
72	* @return whether the crate has already been extracted into the temporary
73	* folder.
74	*/
75	public boolean isExtracted() {
76	return isExtracted;	1✔
77	}
78
79	/**Read the crate metadata and content from the provided input stream.
80	*
81	* @param stream The input stream.
82	*/
83	private void readCrate(InputStream stream) {
84	try {
85	File folder = temporaryFolder.toFile();	1✔
86	// ensure the directory is clean
87	if (folder.exists()) {	1✔
88	if (folder.isDirectory()) {	1✔
89	FileUtils.cleanDirectory(folder);	1✔
NEW 90	} else if (folder.isFile()) {	×
NEW 91	FileUtils.delete(folder);	×
92	}
93	} else {
94	FileUtils.forceMkdir(folder);	1✔
95	}
96
97	LocalFileHeader localFileHeader;
98	int readLen;
99	byte[] readBuffer = new byte[4096];	1✔
100
101	try (ZipInputStream zipInputStream = new ZipInputStream(stream)) {	1✔
102	while ((localFileHeader = zipInputStream.getNextEntry()) != null) {	1✔
103	String fileName = localFileHeader.getFileName();	1✔
104	File extractedFile = new File(folder, fileName).getCanonicalFile();	1✔
105	if (!extractedFile.toPath().startsWith(folder.getCanonicalPath())) {	1✔
NEW 106	throw new IOException("Entry is outside of target directory: " + fileName);	×
107	}
108	try (OutputStream outputStream = new FileOutputStream(extractedFile)) {	1✔
109	while ((readLen = zipInputStream.read(readBuffer)) != -1) {	1✔
110	outputStream.write(readBuffer, 0, readLen);	1✔
111	}
112	}
113	}	1✔
114	}
115	this.isExtracted = true;	1✔
116	// register deletion on exit
117	FileUtils.forceDeleteOnExit(folder);	1✔
NEW 118	} catch (IOException ex) {	×
NEW 119	logger.error("Failed to read crate from input stream.", ex);	×
120	}	1✔
121	}	1✔
122
123	@Override
124	public ObjectNode readMetadataJson(InputStream stream) {
125	if (!isExtracted) {	1✔
126	this.readCrate(stream);	1✔
127	}
128
129	ObjectMapper objectMapper = MyObjectMapper.getMapper();	1✔
130	File jsonMetadata = temporaryFolder.resolve("ro-crate-metadata.json").toFile();	1✔
131
132	try {
133	return objectMapper.readTree(jsonMetadata).deepCopy();	1✔
NEW 134	} catch (IOException e) {	×
NEW 135	logger.error("Failed to deserialize crate metadata.", e);	×
NEW 136	return null;	×
137	}
138	}
139
140	@Override
141	public File readContent(InputStream stream) {
142	if (!isExtracted) {	1✔
NEW 143	this.readCrate(stream);	×
144	}
145	return temporaryFolder.toFile();	1✔
146	}
147	}

kit-data-manager / ro-crate-java / #359

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