#323

Committed 01 Apr 2025 01:45PM UTC coverage: 88.589%. First build

Build # #323

Build Type

Pull #233

github

Committed by

ThomasJejkal

Commit Message

Added zip stream writer, minor cleanup

Pull Request Pull Request #233: CI trigger adjustments

Run Details

34 of 82 new or added lines in 4 files covered. (41.46%)

1607 of 1814 relevant lines covered (88.59%)

0.89 hits per line

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74.55

/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java

package edu.kit.datamanager.ro_crate.entities.data;

import com.fasterxml.jackson.annotation.JsonIgnore;

import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
import static edu.kit.datamanager.ro_crate.special.IdentifierUtils.isUrl;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import net.lingala.zip4j.ZipFile;
import net.lingala.zip4j.exception.ZipException;
import net.lingala.zip4j.io.outputstream.ZipOutputStream;
import net.lingala.zip4j.model.ZipParameters;
import org.apache.commons.io.FileUtils;

/**
 * The base class of every data entity.
 *
 * @author Nikola Tzotchev on 4.2.2022 г.
 * @version 1
 */
public class DataEntity extends AbstractEntity {

    @JsonIgnore
    private Path path;

    /**
     * The constructor that takes an DataEntity builder and instantiates the
     * entity.
     *
     * @param entityBuilder the builder passed as argument.
     */
    public DataEntity(AbstractDataEntityBuilder<?> entityBuilder) {
        super(entityBuilder);
        if (!entityBuilder.authors.isEmpty()) {
            this.addIdListProperties("author", entityBuilder.authors);
        }
        this.path = entityBuilder.location;
    }

    /**
     * Adds an author ID to the entity.
     *
     * Calling this multiple times will add multiple author IDs.
     *
     * @param id the identifier of the author.
     */
    public void addAuthorId(String id) {
        this.addIdProperty("author", id);
    }

    /**
     * If the data entity contains a physical file. This method will write it
     * when the crate is being written to a zip archive.
     *
     * @param zipFile the zipFile where it should be written.
     * @throws ZipException when something goes wrong with the writing to the
     * zip file.
     */
    public void saveToZip(ZipFile zipFile) throws ZipException {
        if (this.path != null) {
            ZipParameters zipParameters = new ZipParameters();
            zipParameters.setFileNameInZip(this.getId());
            zipFile.addFile(this.path.toFile(), zipParameters);
        }
    }

    /**
     * If the data entity contains a physical file. This method will write it
     * when the crate is being written to a zip archive.
     *
     * @param zipStream The zip output stream where it should be written.
     * @throws ZipException when something goes wrong with the writing to the
     * zip file.
     * @throws IOException If opening the file input stream fails.
     */
    public void saveToStream(ZipOutputStream zipStream) throws ZipException, IOException {
        if (this.path != null) {
            byte[] buff = new byte[4096];
            int readLen;
            ZipParameters zipParameters = new ZipParameters();
            zipParameters.setFileNameInZip(this.getId());
            zipStream.putNextEntry(zipParameters);
            try (InputStream inputStream = new FileInputStream(this.path.toFile())) {
                while ((readLen = inputStream.read(buff)) != -1) {
                    zipStream.write(buff, 0, readLen);
                }
            }
            zipStream.closeEntry();
        }
    }

    /**
     * If the data entity contains a physical file. This method will write it
     * when the crate is being written to a folder.
     *
     * @param file the folder location where the entity should be written.
     * @throws IOException if something goes wrong with the writing.
     */
    public void savetoFile(File file) throws IOException {
        if (this.getPath() != null) {
            if (this.getPath().toFile().isDirectory()) {
                FileUtils.copyDirectory(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());
            } else {
                FileUtils.copyFile(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());
            }
        }
    }

    @JsonIgnore
    public Path getPath() {
        return path;
    }

    abstract static class AbstractDataEntityBuilder<T extends AbstractDataEntityBuilder<T>> extends
            AbstractEntityBuilder<T> {

        private Path location;
        private List<String> authors = new ArrayList<>();

        /**
         * Sets the location of the data entity.
         *
         * If the ID has not been set manually in beforehand, it will be derived
         * from the path. Use {@link #setId(String)} to override it or set it in
         * beforehand. Note that another call of {@link #setLocation(Path)} will
         * not override the ID as it has been set by the previous call!
         *
         * @param path the location of the data. May be null, in which case
         * nothing happens.
         * @return this builder
         */
        public T setLocation(Path path) {
            if (path != null) {
                if (this.getId() == null) {
                    this.setId(path.getFileName().toString());
                }
                this.location = path;
            }
            return self();
        }

        /**
         * A variant of {@link #setLocation(Path)} which may throw exceptions.
         *
         * @param path the location of the data
         * @return this builder
         * @throws IllegalArgumentException if path is null
         */
        public T setLocationWithExceptions(Path path) throws IllegalArgumentException {
            if (path == null) {
                throw new IllegalArgumentException("The given path should not be null.");
            }
            return setLocation(path);
        }

        /**
         * Same as {@link #setLocation(Path)} but instead of associating this
         * entity with a file, it will point to some place on the internet.
         *
         * Via the specification, this means the uri will be set as the ID. This
         * call is therefore equivalent to {@link #setId(String)}.
         *
         * @param uri the URI, should point at the data reachable on the
         * internet.
         * @return this builder
         */
        public T setLocation(URI uri) {
            if (uri != null && this.getId() == null) {
                this.setId(uri.toString());
            }
            return self();
        }

        /**
         * A variant of {@link #setLocation(URI)} which may throw exceptions.
         *
         * @param uri the given uri
         * @return this builder
         * @throws IllegalArgumentException if uri is null or not a valid URL
         */
        public T setLocationWithExceptions(URI uri) throws IllegalArgumentException {
            if (!isUrl(uri.toString())) {
                throw new IllegalArgumentException("This Data Entity remote ID does not resolve to a valid URL.");
            }
            return setLocation(uri);
        }

        public T setLicense(String id) {
            this.addIdProperty("license", id);
            return self();
        }

        public T setLicense(ContextualEntity license) {
            this.addIdProperty("license", license.getId());
            return self();
        }

        public T addAuthor(String id) {
            this.authors.add(id);
            return self();
        }

        public T setContentLocation(String id) {
            this.addIdProperty("contentLocation", id);
            return self();
        }

        @Override
        public abstract DataEntity build();
    }

    /**
     * Data Entity builder class that allows for easier data entity creation.
     *
     * If not explicitly mentioned, all methods avoid Exceptions and will
     * silently ignore null-parameters, in which case nothing will happen. Use
     * the available *WithExceptions-methods in case you need them.
     */
    public static final class DataEntityBuilder extends AbstractDataEntityBuilder<DataEntityBuilder> {

        @Override
        public DataEntityBuilder self() {
            return this;
        }

        @Override
        public DataEntity build() {
            return new DataEntity(this);
        }
    }
}

1	package edu.kit.datamanager.ro_crate.entities.data;
2
3	import com.fasterxml.jackson.annotation.JsonIgnore;
4
5	import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
6	import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
7	import static edu.kit.datamanager.ro_crate.special.IdentifierUtils.isUrl;
8
9	import java.io.File;
10	import java.io.FileInputStream;
11	import java.io.IOException;
12	import java.io.InputStream;
13	import java.net.URI;
14	import java.nio.file.Path;
15	import java.util.ArrayList;
16	import java.util.List;
17	import net.lingala.zip4j.ZipFile;
18	import net.lingala.zip4j.exception.ZipException;
19	import net.lingala.zip4j.io.outputstream.ZipOutputStream;
20	import net.lingala.zip4j.model.ZipParameters;
21	import org.apache.commons.io.FileUtils;
22
23	/**
24	* The base class of every data entity.
25	*
26	* @author Nikola Tzotchev on 4.2.2022 г.
27	* @version 1
28	*/
29	public class DataEntity extends AbstractEntity {
30
31	@JsonIgnore
32	private Path path;
33
34	/**
35	* The constructor that takes an DataEntity builder and instantiates the
36	* entity.
37	*
38	* @param entityBuilder the builder passed as argument.
39	*/
40	public DataEntity(AbstractDataEntityBuilder<?> entityBuilder) {
41	super(entityBuilder);	1✔
42	if (!entityBuilder.authors.isEmpty()) {	1✔
43	this.addIdListProperties("author", entityBuilder.authors);	1✔
44	}
45	this.path = entityBuilder.location;	1✔
46	}	1✔
47
48	/**
49	* Adds an author ID to the entity.
50	*
51	* Calling this multiple times will add multiple author IDs.
52	*
53	* @param id the identifier of the author.
54	*/
55	public void addAuthorId(String id) {
56	this.addIdProperty("author", id);	×
57	}	×
58
59	/**
60	* If the data entity contains a physical file. This method will write it
61	* when the crate is being written to a zip archive.
62	*
63	* @param zipFile the zipFile where it should be written.
64	* @throws ZipException when something goes wrong with the writing to the
65	* zip file.
66	*/
67	public void saveToZip(ZipFile zipFile) throws ZipException {
68	if (this.path != null) {	1✔
69	ZipParameters zipParameters = new ZipParameters();	1✔
70	zipParameters.setFileNameInZip(this.getId());	1✔
71	zipFile.addFile(this.path.toFile(), zipParameters);	1✔
72	}
73	}	1✔
74
75	/**
76	* If the data entity contains a physical file. This method will write it
77	* when the crate is being written to a zip archive.
78	*
79	* @param zipStream The zip output stream where it should be written.
80	* @throws ZipException when something goes wrong with the writing to the
81	* zip file.
82	* @throws IOException If opening the file input stream fails.
83	*/
84	public void saveToStream(ZipOutputStream zipStream) throws ZipException, IOException {
NEW 85	if (this.path != null) {	×
NEW 86	byte[] buff = new byte[4096];	×
87	int readLen;
NEW 88	ZipParameters zipParameters = new ZipParameters();	×
NEW 89	zipParameters.setFileNameInZip(this.getId());	×
NEW 90	zipStream.putNextEntry(zipParameters);	×
NEW 91	try (InputStream inputStream = new FileInputStream(this.path.toFile())) {	×
NEW 92	while ((readLen = inputStream.read(buff)) != -1) {	×
NEW 93	zipStream.write(buff, 0, readLen);	×
94	}
95	}
NEW 96	zipStream.closeEntry();	×
97	}
NEW 98	}	×
99
100	/**
101	* If the data entity contains a physical file. This method will write it
102	* when the crate is being written to a folder.
103	*
104	* @param file the folder location where the entity should be written.
105	* @throws IOException if something goes wrong with the writing.
106	*/
107	public void savetoFile(File file) throws IOException {
108	if (this.getPath() != null) {	1✔
109	if (this.getPath().toFile().isDirectory()) {	1✔
110	FileUtils.copyDirectory(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());	1✔
111	} else {
112	FileUtils.copyFile(this.getPath().toFile(), file.toPath().resolve(this.getId()).toFile());	1✔
113	}
114	}
115	}	1✔
116
117	@JsonIgnore
118	public Path getPath() {
119	return path;	1✔
120	}
121
122	abstract static class AbstractDataEntityBuilder<T extends AbstractDataEntityBuilder<T>> extends	1✔
123	AbstractEntityBuilder<T> {
124
125	private Path location;
126	private List<String> authors = new ArrayList<>();	1✔
127
128	/**
129	* Sets the location of the data entity.
130	*
131	* If the ID has not been set manually in beforehand, it will be derived
132	* from the path. Use {@link #setId(String)} to override it or set it in
133	* beforehand. Note that another call of {@link #setLocation(Path)} will
134	* not override the ID as it has been set by the previous call!
135	*
136	* @param path the location of the data. May be null, in which case
137	* nothing happens.
138	* @return this builder
139	*/
140	public T setLocation(Path path) {
141	if (path != null) {	1✔
142	if (this.getId() == null) {	1✔
143	this.setId(path.getFileName().toString());	1✔
144	}
145	this.location = path;	1✔
146	}
147	return self();	1✔
148	}
149
150	/**
151	* A variant of {@link #setLocation(Path)} which may throw exceptions.
152	*
153	* @param path the location of the data
154	* @return this builder
155	* @throws IllegalArgumentException if path is null
156	*/
157	public T setLocationWithExceptions(Path path) throws IllegalArgumentException {
158	if (path == null) {	1✔
159	throw new IllegalArgumentException("The given path should not be null.");	×
160	}
161	return setLocation(path);	1✔
162	}
163
164	/**
165	* Same as {@link #setLocation(Path)} but instead of associating this
166	* entity with a file, it will point to some place on the internet.
167	*
168	* Via the specification, this means the uri will be set as the ID. This
169	* call is therefore equivalent to {@link #setId(String)}.
170	*
171	* @param uri the URI, should point at the data reachable on the
172	* internet.
173	* @return this builder
174	*/
175	public T setLocation(URI uri) {
176	if (uri != null && this.getId() == null) {	1✔
177	this.setId(uri.toString());	1✔
178	}
179	return self();	1✔
180	}
181
182	/**
183	* A variant of {@link #setLocation(URI)} which may throw exceptions.
184	*
185	* @param uri the given uri
186	* @return this builder
187	* @throws IllegalArgumentException if uri is null or not a valid URL
188	*/
189	public T setLocationWithExceptions(URI uri) throws IllegalArgumentException {
190	if (!isUrl(uri.toString())) {	1✔
191	throw new IllegalArgumentException("This Data Entity remote ID does not resolve to a valid URL.");	1✔
192	}
193	return setLocation(uri);	×
194	}
195
196	public T setLicense(String id) {
197	this.addIdProperty("license", id);	1✔
198	return self();	1✔
199	}
200
201	public T setLicense(ContextualEntity license) {
202	this.addIdProperty("license", license.getId());	1✔
203	return self();	1✔
204	}
205
206	public T addAuthor(String id) {
207	this.authors.add(id);	1✔
208	return self();	1✔
209	}
210
211	public T setContentLocation(String id) {
212	this.addIdProperty("contentLocation", id);	1✔
213	return self();	1✔
214	}
215
216	@Override
217	public abstract DataEntity build();
218	}
219
220	/**
221	* Data Entity builder class that allows for easier data entity creation.
222	*
223	* If not explicitly mentioned, all methods avoid Exceptions and will
224	* silently ignore null-parameters, in which case nothing will happen. Use
225	* the available *WithExceptions-methods in case you need them.
226	*/
227	public static final class DataEntityBuilder extends AbstractDataEntityBuilder<DataEntityBuilder> {	1✔
228
229	@Override
230	public DataEntityBuilder self() {
231	return this;	1✔
232	}
233
234	@Override
235	public DataEntity build() {
236	return new DataEntity(this);	1✔
237	}
238	}
239	}

kit-data-manager / ro-crate-java / #323

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