#368

Committed 23 Apr 2025 02:53PM UTC coverage: 86.477% (+0.5%) from 85.989%

Build # #368

Build Type

Pull #247

github

Committed by

web-flow

Commit Message

Merge 71e7caa5e into 0ab3f3ca9

Pull Request Pull Request #247: Generalize reading and writing crates

Run Details

251 of 278 new or added lines in 16 files covered. (90.29%)

21 existing lines in 5 files now uncovered.

1880 of 2174 relevant lines covered (86.48%)

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91.67

/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 edu.kit.datamanager.ro_crate.util.ZipUtil;

import java.io.File;
import java.io.IOException;
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) {
            ZipUtil.addFileToZipStream(zipStream, this.path.toFile(), this.getId());
        }
    }

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

kit-data-manager / ro-crate-java / #368

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