#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

521 of 659 new or added lines in 18 files covered. (79.06%)

1873 of 2154 relevant lines covered (86.95%)

0.87 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

82.22

/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;

/**
 *
 * @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 create 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) {
                    File extractedFile = new File(folder, localFileHeader.getFileName());
                    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	*
19	* @author jejkal
20	*/
21	public class ZipStreamReader implements StreamReaderStrategy {
22
23	protected final String ID = UUID.randomUUID().toString();	1✔
24	protected Path temporaryFolder = Path.of(String.format("./.tmp/ro-crate-java/zipStreamReader/%s/", ID));	1✔
25	protected boolean isExtracted = false;	1✔
26
27	/**
28	* Crates a ZipStreamReader with the default configuration as described in
29	* the class documentation.
30	*/
31	public ZipStreamReader() {	1✔
32	}	1✔
33
34	/**
35	* Creates a ZipStreamReader which will extract the contents temporary to
36	* the given location instead of the default location.
37	*
38	* @param folderPath the custom directory to extract content to for
39	* temporary access.
40	* @param shallAddUuidSubfolder if true, the reader will extract into
41	* subdirectories of the given directory. These subdirectories will have
42	* UUIDs as their names.
43	*/
44	public ZipStreamReader(Path folderPath, boolean shallAddUuidSubfolder) {	1✔
45	if (shallAddUuidSubfolder) {	1✔
46	this.temporaryFolder = folderPath.resolve(ID);	1✔
47	} else {
48	this.temporaryFolder = folderPath;	1✔
49	}
50	}	1✔
51
52	/**
53	* @return the identifier which may be used as the name for a subfolder in
54	* the temporary directory.
55	*/
56	public String getID() {
57	return ID;	1✔
58	}
59
60	/**
61	* @return the folder (considered temporary) where the zipped crate will be
62	* or has been extracted to.
63	*/
64	public Path getTemporaryFolder() {
65	return temporaryFolder;	1✔
66	}
67
68	/**
69	* @return whether the crate has already been extracted into the temporary
70	* folder.
71	*/
72	public boolean isExtracted() {
73	return isExtracted;	1✔
74	}
75
76	/**Read the create metadata and content from the provided input stream.
77	*
78	* @param stream The input stream.
79	*/
80	private void readCrate(InputStream stream) {
81	try {
82	File folder = temporaryFolder.toFile();	1✔
83	// ensure the directory is clean
84	if (folder.exists()) {	1✔
85	if (folder.isDirectory()) {	1✔
86	FileUtils.cleanDirectory(folder);	1✔
NEW 87	} else if (folder.isFile()) {	×
NEW 88	FileUtils.delete(folder);	×
89	}
90	} else {
91	FileUtils.forceMkdir(folder);	1✔
92	}
93
94	LocalFileHeader localFileHeader;
95	int readLen;
96	byte[] readBuffer = new byte[4096];	1✔
97
98	try (ZipInputStream zipInputStream = new ZipInputStream(stream)) {	1✔
99	while ((localFileHeader = zipInputStream.getNextEntry()) != null) {	1✔
100	File extractedFile = new File(folder, localFileHeader.getFileName());	1✔
101	try (OutputStream outputStream = new FileOutputStream(extractedFile)) {	1✔
102	while ((readLen = zipInputStream.read(readBuffer)) != -1) {	1✔
103	outputStream.write(readBuffer, 0, readLen);	1✔
104	}
105	}
106	}	1✔
107	}
108	this.isExtracted = true;	1✔
109	// register deletion on exit
110	FileUtils.forceDeleteOnExit(folder);	1✔
NEW 111	} catch (IOException ex) {	×
NEW 112	logger.error("Failed to read crate from input stream.", ex);	×
113	}	1✔
114	}	1✔
115
116	@Override
117	public ObjectNode readMetadataJson(InputStream stream) {
118	if (!isExtracted) {	1✔
119	this.readCrate(stream);	1✔
120	}
121
122	ObjectMapper objectMapper = MyObjectMapper.getMapper();	1✔
123	File jsonMetadata = temporaryFolder.resolve("ro-crate-metadata.json").toFile();	1✔
124
125	try {
126	return objectMapper.readTree(jsonMetadata).deepCopy();	1✔
NEW 127	} catch (IOException e) {	×
NEW 128	logger.error("Failed to deserialize crate metadata.", e);	×
NEW 129	return null;	×
130	}
131	}
132
133	@Override
134	public File readContent(InputStream stream) {
135	if (!isExtracted) {	1✔
NEW 136	this.readCrate(stream);	×
137	}
138	return temporaryFolder.toFile();	1✔
139	}
140	}

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

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous